Starting phenix.real_space_refine on Fri Mar 6 03:39:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7cn8_30418/03_2026/7cn8_30418_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7cn8_30418/03_2026/7cn8_30418.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7cn8_30418/03_2026/7cn8_30418.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7cn8_30418/03_2026/7cn8_30418.map" model { file = "/net/cci-nas-00/data/ceres_data/7cn8_30418/03_2026/7cn8_30418_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7cn8_30418/03_2026/7cn8_30418_neut.cif" } resolution = 2.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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 123 5.16 5 C 17586 2.51 5 N 4491 2.21 5 O 5475 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 61 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 27675 Number of models: 1 Model: "" Number of chains: 39 Chain: "A" Number of atoms: 8771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1125, 8771 Classifications: {'peptide': 1125} Link IDs: {'PTRANS': 54, 'TRANS': 1070} Chain: "B" Number of atoms: 8771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1125, 8771 Classifications: {'peptide': 1125} Link IDs: {'PTRANS': 54, 'TRANS': 1070} Chain: "C" Number of atoms: 8771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1125, 8771 Classifications: {'peptide': 1125} Link IDs: {'PTRANS': 54, 'TRANS': 1070} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: "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: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "h" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "i" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: "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: "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: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 146 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 146 Unusual residues: {'EIC': 1, 'NAG': 9} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "B" Number of atoms: 146 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 146 Unusual residues: {'EIC': 1, 'NAG': 9} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "C" Number of atoms: 146 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 146 Unusual residues: {'EIC': 1, 'NAG': 9} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Time building chain proxies: 5.59, per 1000 atoms: 0.20 Number of scatterers: 27675 At special positions: 0 Unit cell: (153.715, 141.807, 173.2, 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 123 16.00 O 5475 8.00 N 4491 7.00 C 17586 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 134 " distance=2.03 Simple disulfide: pdb=" SG CYS A 129 " - pdb=" SG CYS A 164 " distance=2.03 Simple disulfide: pdb=" SG CYS A 289 " - pdb=" SG CYS A 299 " distance=2.03 Simple disulfide: pdb=" SG CYS A 334 " - pdb=" SG CYS A 359 " distance=2.03 Simple disulfide: pdb=" SG CYS A 377 " - pdb=" SG CYS A 430 " distance=2.03 Simple disulfide: pdb=" SG CYS A 389 " - pdb=" SG CYS A 523 " distance=2.03 Simple disulfide: pdb=" SG CYS A 478 " - pdb=" SG CYS A 486 " distance=2.06 Simple disulfide: pdb=" SG CYS A 536 " - pdb=" SG CYS A 588 " distance=2.02 Simple disulfide: pdb=" SG CYS A 615 " - pdb=" SG CYS A 647 " distance=2.04 Simple disulfide: pdb=" SG CYS A 660 " - pdb=" SG CYS A 669 " distance=2.03 Simple disulfide: pdb=" SG CYS A 732 " - pdb=" SG CYS A 754 " distance=2.04 Simple disulfide: pdb=" SG CYS A 737 " - pdb=" SG CYS A 743 " distance=2.03 Simple disulfide: pdb=" SG CYS A 834 " - pdb=" SG CYS A 845 " distance=2.03 Simple disulfide: pdb=" SG CYS A1026 " - pdb=" SG CYS A1037 " distance=2.03 Simple disulfide: pdb=" SG CYS A1076 " - pdb=" SG CYS A1120 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 134 " distance=2.03 Simple disulfide: pdb=" SG CYS B 129 " - pdb=" SG CYS B 164 " distance=2.04 Simple disulfide: pdb=" SG CYS B 289 " - pdb=" SG CYS B 299 " distance=2.03 Simple disulfide: pdb=" SG CYS B 334 " - pdb=" SG CYS B 359 " distance=2.03 Simple disulfide: pdb=" SG CYS B 377 " - pdb=" SG CYS B 430 " distance=2.03 Simple disulfide: pdb=" SG CYS B 389 " - pdb=" SG CYS B 523 " distance=2.03 Simple disulfide: pdb=" SG CYS B 478 " - pdb=" SG CYS B 486 " distance=2.07 Simple disulfide: pdb=" SG CYS B 536 " - pdb=" SG CYS B 588 " distance=2.02 Simple disulfide: pdb=" SG CYS B 615 " - pdb=" SG CYS B 647 " distance=2.04 Simple disulfide: pdb=" SG CYS B 660 " - pdb=" SG CYS B 669 " distance=2.03 Simple disulfide: pdb=" SG CYS B 732 " - pdb=" SG CYS B 754 " distance=2.04 Simple disulfide: pdb=" SG CYS B 737 " - pdb=" SG CYS B 743 " distance=2.03 Simple disulfide: pdb=" SG CYS B 834 " - pdb=" SG CYS B 845 " distance=2.03 Simple disulfide: pdb=" SG CYS B1026 " - pdb=" SG CYS B1037 " distance=2.03 Simple disulfide: pdb=" SG CYS B1076 " - pdb=" SG CYS B1120 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 134 " distance=2.03 Simple disulfide: pdb=" SG CYS C 129 " - pdb=" SG CYS C 164 " distance=2.05 Simple disulfide: pdb=" SG CYS C 289 " - pdb=" SG CYS C 299 " distance=2.03 Simple disulfide: pdb=" SG CYS C 334 " - pdb=" SG CYS C 359 " distance=2.03 Simple disulfide: pdb=" SG CYS C 377 " - pdb=" SG CYS C 430 " distance=2.03 Simple disulfide: pdb=" SG CYS C 389 " - pdb=" SG CYS C 523 " distance=2.03 Simple disulfide: pdb=" SG CYS C 478 " - pdb=" SG CYS C 486 " distance=2.03 Simple disulfide: pdb=" SG CYS C 536 " - pdb=" SG CYS C 588 " distance=2.02 Simple disulfide: pdb=" SG CYS C 615 " - pdb=" SG CYS C 647 " distance=2.04 Simple disulfide: pdb=" SG CYS C 660 " - pdb=" SG CYS C 669 " distance=2.03 Simple disulfide: pdb=" SG CYS C 732 " - pdb=" SG CYS C 754 " distance=2.04 Simple disulfide: pdb=" SG CYS C 737 " - pdb=" SG CYS C 743 " distance=2.03 Simple disulfide: pdb=" SG CYS C 834 " - pdb=" SG CYS C 845 " distance=2.03 Simple disulfide: pdb=" SG CYS C1026 " - pdb=" SG CYS C1037 " distance=2.03 Simple disulfide: pdb=" SG CYS C1076 " - pdb=" SG CYS C1120 " 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=2, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG k 1 " - " NAG k 2 " " NAG l 1 " - " NAG l 2 " " NAG m 1 " - " NAG m 2 " NAG-ASN " NAG A1301 " - " ASN A 280 " " NAG A1302 " - " ASN A 341 " " NAG A1303 " - " ASN A 655 " " NAG A1304 " - " ASN A 703 " " NAG A1305 " - " ASN A 601 " " NAG A1306 " - " ASN A 120 " " NAG A1307 " - " ASN A 61 " " NAG A1308 " - " ASN A 614 " " NAG A1309 " - " ASN A 329 " " NAG B1301 " - " ASN B 280 " " NAG B1302 " - " ASN B 341 " " NAG B1303 " - " ASN B 655 " " NAG B1304 " - " ASN B 703 " " NAG B1305 " - " ASN B 601 " " NAG B1306 " - " ASN B 120 " " NAG B1307 " - " ASN B 61 " " NAG B1308 " - " ASN B 614 " " NAG B1309 " - " ASN B 329 " " NAG C1301 " - " ASN C 280 " " NAG C1302 " - " ASN C 341 " " NAG C1303 " - " ASN C 655 " " NAG C1304 " - " ASN C 703 " " NAG C1305 " - " ASN C 601 " " NAG C1306 " - " ASN C 120 " " NAG C1307 " - " ASN C 61 " " NAG C1308 " - " ASN C 614 " " NAG C1309 " - " ASN C 329 " " NAG D 1 " - " ASN A 17 " " NAG E 1 " - " ASN A 232 " " NAG F 1 " - " ASN A 368 " " NAG G 1 " - " ASN A 711 " " NAG H 1 " - " ASN A 795 " " NAG I 1 " - " ASN A1068 " " NAG J 1 " - " ASN A1092 " " NAG K 1 " - " ASN A 163 " " NAG L 1 " - " ASN A 30 " " NAG M 1 " - " ASN A 147 " " NAG N 1 " - " ASN B 17 " " NAG O 1 " - " ASN B 795 " " NAG P 1 " - " ASN B 232 " " NAG Q 1 " - " ASN B 368 " " NAG R 1 " - " ASN B1092 " " NAG S 1 " - " ASN B1068 " " NAG T 1 " - " ASN B1128 " " NAG U 1 " - " ASN C 17 " " NAG V 1 " - " ASN B 163 " " NAG W 1 " - " ASN B 30 " " NAG X 1 " - " ASN B 147 " " NAG Y 1 " - " ASN C 795 " " NAG Z 1 " - " ASN C1068 " " NAG a 1 " - " ASN C 232 " " NAG b 1 " - " ASN C 368 " " NAG e 1 " - " ASN C1128 " " NAG f 1 " - " ASN C1092 " " NAG g 1 " - " ASN C 163 " " NAG h 1 " - " ASN C 30 " " NAG i 1 " - " ASN C 147 " " NAG k 1 " - " ASN A1128 " " NAG l 1 " - " ASN B 711 " " NAG m 1 " - " ASN C 711 " Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.32 Conformation dependent library (CDL) restraints added in 1.2 seconds 6738 Ramachandran restraints generated. 3369 Oldfield, 0 Emsley, 3369 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6288 Finding SS restraints... Secondary structure from input PDB file: 81 helices and 48 sheets defined 26.5% alpha, 24.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.93 Creating SS restraints... Processing helix chain 'A' and resid 292 through 302 Processing helix chain 'A' and resid 335 through 341 Processing helix chain 'A' and resid 365 through 370 removed outlier: 4.239A pdb=" N SER A 369 " --> pdb=" O VAL A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 387 removed outlier: 4.108A pdb=" N ASN A 386 " --> pdb=" O THR A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 405 No H-bonds generated for 'chain 'A' and resid 403 through 405' Processing helix chain 'A' and resid 414 through 420 Processing helix chain 'A' and resid 436 through 441 Processing helix chain 'A' and resid 500 through 503 Processing helix chain 'A' and resid 614 through 616 No H-bonds generated for 'chain 'A' and resid 614 through 616' Processing helix chain 'A' and resid 617 through 623 Processing helix chain 'A' and resid 624 through 627 Processing helix chain 'A' and resid 628 through 636 removed outlier: 3.559A pdb=" N TYR A 634 " --> pdb=" O ALA A 630 " (cutoff:3.500A) Processing helix chain 'A' and resid 676 through 680 removed outlier: 3.589A pdb=" N ARG A 679 " --> pdb=" O SER A 676 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N SER A 680 " --> pdb=" O SER A 677 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 676 through 680' Processing helix chain 'A' and resid 731 through 738 Processing helix chain 'A' and resid 746 through 777 removed outlier: 4.382A pdb=" N TYR A 750 " --> pdb=" O LEU A 746 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N SER A 752 " --> pdb=" O LEU A 748 " (cutoff:3.500A) removed outlier: 5.180A pdb=" N PHE A 753 " --> pdb=" O GLN A 749 " (cutoff:3.500A) Processing helix chain 'A' and resid 810 through 820 Processing helix chain 'A' and resid 830 through 837 Processing helix chain 'A' and resid 842 through 850 removed outlier: 3.518A pdb=" N ALA A 846 " --> pdb=" O ASP A 842 " (cutoff:3.500A) Processing helix chain 'A' and resid 860 through 879 Processing helix chain 'A' and resid 880 through 883 Processing helix chain 'A' and resid 891 through 903 Processing helix chain 'A' and resid 906 through 913 removed outlier: 3.923A pdb=" N LEU A 910 " --> pdb=" O THR A 906 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 935 Processing helix chain 'A' and resid 939 through 960 removed outlier: 3.579A pdb=" N LEU A 960 " --> pdb=" O LEU A 956 " (cutoff:3.500A) Processing helix chain 'A' and resid 970 through 978 Processing helix chain 'A' and resid 979 through 1027 removed outlier: 3.795A pdb=" N VAL A 985 " --> pdb=" O PRO A 981 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLN A 986 " --> pdb=" O GLU A 982 " (cutoff:3.500A) Processing helix chain 'A' and resid 1121 through 1123 No H-bonds generated for 'chain 'A' and resid 1121 through 1123' Processing helix chain 'B' and resid 292 through 302 Processing helix chain 'B' and resid 335 through 341 Processing helix chain 'B' and resid 365 through 370 removed outlier: 4.239A pdb=" N SER B 369 " --> pdb=" O VAL B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 387 removed outlier: 4.109A pdb=" N ASN B 386 " --> pdb=" O THR B 383 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 405 No H-bonds generated for 'chain 'B' and resid 403 through 405' Processing helix chain 'B' and resid 414 through 420 Processing helix chain 'B' and resid 436 through 441 Processing helix chain 'B' and resid 500 through 503 Processing helix chain 'B' and resid 614 through 616 No H-bonds generated for 'chain 'B' and resid 614 through 616' Processing helix chain 'B' and resid 617 through 623 Processing helix chain 'B' and resid 624 through 627 Processing helix chain 'B' and resid 628 through 636 removed outlier: 3.559A pdb=" N TYR B 634 " --> pdb=" O ALA B 630 " (cutoff:3.500A) Processing helix chain 'B' and resid 676 through 680 removed outlier: 3.590A pdb=" N ARG B 679 " --> pdb=" O SER B 676 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N SER B 680 " --> pdb=" O SER B 677 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 676 through 680' Processing helix chain 'B' and resid 731 through 738 Processing helix chain 'B' and resid 746 through 777 removed outlier: 4.382A pdb=" N TYR B 750 " --> pdb=" O LEU B 746 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N SER B 752 " --> pdb=" O LEU B 748 " (cutoff:3.500A) removed outlier: 5.180A pdb=" N PHE B 753 " --> pdb=" O GLN B 749 " (cutoff:3.500A) Processing helix chain 'B' and resid 810 through 820 Processing helix chain 'B' and resid 830 through 837 Processing helix chain 'B' and resid 842 through 850 removed outlier: 3.518A pdb=" N ALA B 846 " --> pdb=" O ASP B 842 " (cutoff:3.500A) Processing helix chain 'B' and resid 860 through 879 Processing helix chain 'B' and resid 880 through 883 Processing helix chain 'B' and resid 891 through 903 Processing helix chain 'B' and resid 906 through 913 removed outlier: 3.923A pdb=" N LEU B 910 " --> pdb=" O THR B 906 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 935 Processing helix chain 'B' and resid 939 through 960 removed outlier: 3.579A pdb=" N LEU B 960 " --> pdb=" O LEU B 956 " (cutoff:3.500A) Processing helix chain 'B' and resid 970 through 978 Processing helix chain 'B' and resid 979 through 1027 removed outlier: 3.795A pdb=" N VAL B 985 " --> pdb=" O PRO B 981 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLN B 986 " --> pdb=" O GLU B 982 " (cutoff:3.500A) Processing helix chain 'B' and resid 1121 through 1123 No H-bonds generated for 'chain 'B' and resid 1121 through 1123' Processing helix chain 'C' and resid 292 through 302 Processing helix chain 'C' and resid 335 through 341 Processing helix chain 'C' and resid 365 through 370 removed outlier: 4.239A pdb=" N SER C 369 " --> pdb=" O VAL C 365 " (cutoff:3.500A) Processing helix chain 'C' and resid 381 through 387 removed outlier: 4.108A pdb=" N ASN C 386 " --> pdb=" O THR C 383 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 405 No H-bonds generated for 'chain 'C' and resid 403 through 405' Processing helix chain 'C' and resid 414 through 420 Processing helix chain 'C' and resid 436 through 441 Processing helix chain 'C' and resid 500 through 503 Processing helix chain 'C' and resid 614 through 616 No H-bonds generated for 'chain 'C' and resid 614 through 616' Processing helix chain 'C' and resid 617 through 623 Processing helix chain 'C' and resid 624 through 627 Processing helix chain 'C' and resid 628 through 636 removed outlier: 3.559A pdb=" N TYR C 634 " --> pdb=" O ALA C 630 " (cutoff:3.500A) Processing helix chain 'C' and resid 676 through 680 removed outlier: 3.589A pdb=" N ARG C 679 " --> pdb=" O SER C 676 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N SER C 680 " --> pdb=" O SER C 677 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 676 through 680' Processing helix chain 'C' and resid 731 through 738 Processing helix chain 'C' and resid 746 through 777 removed outlier: 4.382A pdb=" N TYR C 750 " --> pdb=" O LEU C 746 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N SER C 752 " --> pdb=" O LEU C 748 " (cutoff:3.500A) removed outlier: 5.180A pdb=" N PHE C 753 " --> pdb=" O GLN C 749 " (cutoff:3.500A) Processing helix chain 'C' and resid 810 through 820 Processing helix chain 'C' and resid 830 through 837 Processing helix chain 'C' and resid 842 through 850 removed outlier: 3.519A pdb=" N ALA C 846 " --> pdb=" O ASP C 842 " (cutoff:3.500A) Processing helix chain 'C' and resid 860 through 879 Processing helix chain 'C' and resid 880 through 883 Processing helix chain 'C' and resid 891 through 903 Processing helix chain 'C' and resid 906 through 913 removed outlier: 3.923A pdb=" N LEU C 910 " --> pdb=" O THR C 906 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 935 Processing helix chain 'C' and resid 939 through 960 removed outlier: 3.579A pdb=" N LEU C 960 " --> pdb=" O LEU C 956 " (cutoff:3.500A) Processing helix chain 'C' and resid 970 through 978 Processing helix chain 'C' and resid 979 through 1027 removed outlier: 3.795A pdb=" N VAL C 985 " --> pdb=" O PRO C 981 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLN C 986 " --> pdb=" O GLU C 982 " (cutoff:3.500A) Processing helix chain 'C' and resid 1121 through 1123 No H-bonds generated for 'chain 'C' and resid 1121 through 1123' Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 31 removed outlier: 4.165A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N ASN A 61 " --> pdb=" O TYR A 267 " (cutoff:3.500A) removed outlier: 5.127A pdb=" N TYR A 267 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N VAL A 225 " --> pdb=" O ILE A 201 " (cutoff:3.500A) removed outlier: 5.775A pdb=" N SER A 203 " --> pdb=" O PRO A 223 " (cutoff:3.500A) removed outlier: 9.079A pdb=" N HIS A 205 " --> pdb=" O LEU A 221 " (cutoff:3.500A) removed outlier: 9.477A pdb=" N LEU A 221 " --> pdb=" O HIS A 205 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N VAL A 36 " --> pdb=" O LEU A 221 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.948A pdb=" N ASP A 285 " --> pdb=" O SER A 276 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 81 through 83 removed outlier: 12.550A pdb=" N PHE A 133 " --> pdb=" O PHE A 236 " (cutoff:3.500A) removed outlier: 12.333A pdb=" N THR A 238 " --> pdb=" O PHE A 133 " (cutoff:3.500A) removed outlier: 11.359A pdb=" N THR A 135 " --> pdb=" O THR A 238 " (cutoff:3.500A) removed outlier: 10.181A pdb=" N LEU A 240 " --> pdb=" O THR A 135 " (cutoff:3.500A) removed outlier: 8.656A pdb=" N LEU A 242 " --> pdb=" O PRO A 137 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N LEU A 139 " --> pdb=" O LEU A 242 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N ARG A 244 " --> pdb=" O LEU A 139 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N VAL A 141 " --> pdb=" O ARG A 244 " (cutoff:3.500A) removed outlier: 9.043A pdb=" N ASP A 136 " --> pdb=" O TYR A 158 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N TYR A 158 " --> pdb=" O ASP A 136 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 149 through 150 removed outlier: 3.580A pdb=" N THR A 149 " --> pdb=" O HIS A 144 " (cutoff:3.500A) removed outlier: 12.550A pdb=" N PHE A 133 " --> pdb=" O PHE A 236 " (cutoff:3.500A) removed outlier: 12.333A pdb=" N THR A 238 " --> pdb=" O PHE A 133 " (cutoff:3.500A) removed outlier: 11.359A pdb=" N THR A 135 " --> pdb=" O THR A 238 " (cutoff:3.500A) removed outlier: 10.181A pdb=" N LEU A 240 " --> pdb=" O THR A 135 " (cutoff:3.500A) removed outlier: 8.656A pdb=" N LEU A 242 " --> pdb=" O PRO A 137 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N LEU A 139 " --> pdb=" O LEU A 242 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N ARG A 244 " --> pdb=" O LEU A 139 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N VAL A 141 " --> pdb=" O ARG A 244 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLY A 101 " --> pdb=" O LEU A 239 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N ALA A 241 " --> pdb=" O ILE A 99 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N ILE A 99 " --> pdb=" O ALA A 241 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N ARG A 100 " --> pdb=" O ASN A 119 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 322 through 326 removed outlier: 4.813A pdb=" N ILE A 322 " --> pdb=" O CYS A 536 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 352 through 356 removed outlier: 4.337A pdb=" N VAL A 393 " --> pdb=" O ILE A 356 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 359 through 360 removed outlier: 6.737A pdb=" N CYS A 359 " --> pdb=" O CYS A 523 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N VAL A 522 " --> pdb=" O PHE A 390 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 450 through 452 Processing sheet with id=AA9, first strand: chain 'A' and resid 471 through 472 Processing sheet with id=AB1, first strand: chain 'A' and resid 594 through 596 Processing sheet with id=AB2, first strand: chain 'A' and resid 652 through 653 removed outlier: 6.440A pdb=" N ILE A 668 " --> pdb=" O VAL A 664 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 696 through 697 Processing sheet with id=AB4, first strand: chain 'A' and resid 705 through 709 removed outlier: 3.699A pdb=" N ALA A1072 " --> pdb=" O PHE A1089 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N PHE A1089 " --> pdb=" O ALA A1072 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 712 through 722 removed outlier: 5.895A pdb=" N TYR A1061 " --> pdb=" O HIS A1042 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N HIS A1042 " --> pdb=" O TYR A1061 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 727 through 730 removed outlier: 4.306A pdb=" N LYS A 727 " --> pdb=" O LEU A 855 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 782 through 784 Processing sheet with id=AB8, first strand: chain 'A' and resid 1114 through 1119 removed outlier: 4.213A pdb=" N ALA A1081 " --> pdb=" O SER A1117 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 27 through 31 removed outlier: 4.165A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N ASN B 61 " --> pdb=" O TYR B 267 " (cutoff:3.500A) removed outlier: 5.127A pdb=" N TYR B 267 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N VAL B 225 " --> pdb=" O ILE B 201 " (cutoff:3.500A) removed outlier: 5.775A pdb=" N SER B 203 " --> pdb=" O PRO B 223 " (cutoff:3.500A) removed outlier: 9.079A pdb=" N HIS B 205 " --> pdb=" O LEU B 221 " (cutoff:3.500A) removed outlier: 9.477A pdb=" N LEU B 221 " --> pdb=" O HIS B 205 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N VAL B 36 " --> pdb=" O LEU B 221 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.948A pdb=" N ASP B 285 " --> pdb=" O SER B 276 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 81 through 83 removed outlier: 12.590A pdb=" N PHE B 133 " --> pdb=" O PHE B 236 " (cutoff:3.500A) removed outlier: 12.329A pdb=" N THR B 238 " --> pdb=" O PHE B 133 " (cutoff:3.500A) removed outlier: 11.631A pdb=" N THR B 135 " --> pdb=" O THR B 238 " (cutoff:3.500A) removed outlier: 10.440A pdb=" N LEU B 240 " --> pdb=" O THR B 135 " (cutoff:3.500A) removed outlier: 8.602A pdb=" N LEU B 242 " --> pdb=" O PRO B 137 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N LEU B 139 " --> pdb=" O LEU B 242 " (cutoff:3.500A) removed outlier: 7.667A pdb=" N ARG B 244 " --> pdb=" O LEU B 139 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N VAL B 141 " --> pdb=" O ARG B 244 " (cutoff:3.500A) removed outlier: 9.191A pdb=" N ASP B 136 " --> pdb=" O TYR B 158 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N TYR B 158 " --> pdb=" O ASP B 136 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 149 through 150 removed outlier: 3.574A pdb=" N THR B 149 " --> pdb=" O HIS B 144 " (cutoff:3.500A) removed outlier: 12.590A pdb=" N PHE B 133 " --> pdb=" O PHE B 236 " (cutoff:3.500A) removed outlier: 12.329A pdb=" N THR B 238 " --> pdb=" O PHE B 133 " (cutoff:3.500A) removed outlier: 11.631A pdb=" N THR B 135 " --> pdb=" O THR B 238 " (cutoff:3.500A) removed outlier: 10.440A pdb=" N LEU B 240 " --> pdb=" O THR B 135 " (cutoff:3.500A) removed outlier: 8.602A pdb=" N LEU B 242 " --> pdb=" O PRO B 137 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N LEU B 139 " --> pdb=" O LEU B 242 " (cutoff:3.500A) removed outlier: 7.667A pdb=" N ARG B 244 " --> pdb=" O LEU B 139 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N VAL B 141 " --> pdb=" O ARG B 244 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLY B 101 " --> pdb=" O LEU B 239 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N ALA B 241 " --> pdb=" O ILE B 99 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N ILE B 99 " --> pdb=" O ALA B 241 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N ARG B 100 " --> pdb=" O ASN B 119 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 322 through 326 removed outlier: 4.813A pdb=" N ILE B 322 " --> pdb=" O CYS B 536 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 352 through 356 removed outlier: 4.337A pdb=" N VAL B 393 " --> pdb=" O ILE B 356 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 359 through 360 removed outlier: 6.737A pdb=" N CYS B 359 " --> pdb=" O CYS B 523 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N VAL B 522 " --> pdb=" O PHE B 390 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 450 through 452 Processing sheet with id=AC8, first strand: chain 'B' and resid 471 through 472 Processing sheet with id=AC9, first strand: chain 'B' and resid 594 through 596 Processing sheet with id=AD1, first strand: chain 'B' and resid 652 through 653 removed outlier: 6.440A pdb=" N ILE B 668 " --> pdb=" O VAL B 664 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 696 through 698 removed outlier: 7.168A pdb=" N ASN B 697 " --> pdb=" O LYS C 784 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'B' and resid 705 through 709 removed outlier: 3.699A pdb=" N ALA B1072 " --> pdb=" O PHE B1089 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N PHE B1089 " --> pdb=" O ALA B1072 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 712 through 722 removed outlier: 5.895A pdb=" N TYR B1061 " --> pdb=" O HIS B1042 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N HIS B1042 " --> pdb=" O TYR B1061 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 727 through 730 removed outlier: 4.305A pdb=" N LYS B 727 " --> pdb=" O LEU B 855 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 1114 through 1119 removed outlier: 4.212A pdb=" N ALA B1081 " --> pdb=" O SER B1117 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 27 through 31 removed outlier: 4.166A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N ASN C 61 " --> pdb=" O TYR C 267 " (cutoff:3.500A) removed outlier: 5.127A pdb=" N TYR C 267 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL C 225 " --> pdb=" O ILE C 201 " (cutoff:3.500A) removed outlier: 5.775A pdb=" N SER C 203 " --> pdb=" O PRO C 223 " (cutoff:3.500A) removed outlier: 9.079A pdb=" N HIS C 205 " --> pdb=" O LEU C 221 " (cutoff:3.500A) removed outlier: 9.478A pdb=" N LEU C 221 " --> pdb=" O HIS C 205 " (cutoff:3.500A) removed outlier: 7.400A pdb=" N VAL C 36 " --> pdb=" O LEU C 221 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.948A pdb=" N ASP C 285 " --> pdb=" O SER C 276 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 81 through 83 removed outlier: 12.657A pdb=" N PHE C 133 " --> pdb=" O PHE C 236 " (cutoff:3.500A) removed outlier: 12.526A pdb=" N THR C 238 " --> pdb=" O PHE C 133 " (cutoff:3.500A) removed outlier: 11.352A pdb=" N THR C 135 " --> pdb=" O THR C 238 " (cutoff:3.500A) removed outlier: 10.316A pdb=" N LEU C 240 " --> pdb=" O THR C 135 " (cutoff:3.500A) removed outlier: 8.673A pdb=" N LEU C 242 " --> pdb=" O PRO C 137 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N LEU C 139 " --> pdb=" O LEU C 242 " (cutoff:3.500A) removed outlier: 7.697A pdb=" N ARG C 244 " --> pdb=" O LEU C 139 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N VAL C 141 " --> pdb=" O ARG C 244 " (cutoff:3.500A) removed outlier: 9.280A pdb=" N ASP C 136 " --> pdb=" O TYR C 158 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N TYR C 158 " --> pdb=" O ASP C 136 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 149 through 150 removed outlier: 3.570A pdb=" N THR C 149 " --> pdb=" O HIS C 144 " (cutoff:3.500A) removed outlier: 12.657A pdb=" N PHE C 133 " --> pdb=" O PHE C 236 " (cutoff:3.500A) removed outlier: 12.526A pdb=" N THR C 238 " --> pdb=" O PHE C 133 " (cutoff:3.500A) removed outlier: 11.352A pdb=" N THR C 135 " --> pdb=" O THR C 238 " (cutoff:3.500A) removed outlier: 10.316A pdb=" N LEU C 240 " --> pdb=" O THR C 135 " (cutoff:3.500A) removed outlier: 8.673A pdb=" N LEU C 242 " --> pdb=" O PRO C 137 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N LEU C 139 " --> pdb=" O LEU C 242 " (cutoff:3.500A) removed outlier: 7.697A pdb=" N ARG C 244 " --> pdb=" O LEU C 139 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N VAL C 141 " --> pdb=" O ARG C 244 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLY C 101 " --> pdb=" O LEU C 239 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N ALA C 241 " --> pdb=" O ILE C 99 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N ILE C 99 " --> pdb=" O ALA C 241 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N ARG C 100 " --> pdb=" O ASN C 119 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 322 through 326 removed outlier: 4.812A pdb=" N ILE C 322 " --> pdb=" O CYS C 536 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 352 through 356 removed outlier: 4.337A pdb=" N VAL C 393 " --> pdb=" O ILE C 356 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 359 through 360 removed outlier: 6.737A pdb=" N CYS C 359 " --> pdb=" O CYS C 523 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N VAL C 522 " --> pdb=" O PHE C 390 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 450 through 452 Processing sheet with id=AE6, first strand: chain 'C' and resid 471 through 472 Processing sheet with id=AE7, first strand: chain 'C' and resid 594 through 596 Processing sheet with id=AE8, first strand: chain 'C' and resid 652 through 653 removed outlier: 6.440A pdb=" N ILE C 668 " --> pdb=" O VAL C 664 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 705 through 709 removed outlier: 3.699A pdb=" N ALA C1072 " --> pdb=" O PHE C1089 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N PHE C1089 " --> pdb=" O ALA C1072 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 712 through 722 removed outlier: 5.896A pdb=" N TYR C1061 " --> pdb=" O HIS C1042 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N HIS C1042 " --> pdb=" O TYR C1061 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 727 through 730 removed outlier: 4.306A pdb=" N LYS C 727 " --> pdb=" O LEU C 855 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 1114 through 1119 removed outlier: 4.212A pdb=" N ALA C1081 " --> pdb=" O SER C1117 " (cutoff:3.500A) 1086 hydrogen bonds defined for protein. 2970 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.99 Time building geometry restraints manager: 3.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5398 1.33 - 1.45: 7102 1.45 - 1.57: 15628 1.57 - 1.69: 0 1.69 - 1.81: 156 Bond restraints: 28284 Sorted by residual: bond pdb=" C12 EIC B1310 " pdb=" C13 EIC B1310 " ideal model delta sigma weight residual 1.332 1.528 -0.196 2.00e-02 2.50e+03 9.58e+01 bond pdb=" C12 EIC A1310 " pdb=" C13 EIC A1310 " ideal model delta sigma weight residual 1.332 1.528 -0.196 2.00e-02 2.50e+03 9.56e+01 bond pdb=" C10 EIC A1310 " pdb=" C9 EIC A1310 " ideal model delta sigma weight residual 1.332 1.527 -0.195 2.00e-02 2.50e+03 9.55e+01 bond pdb=" C12 EIC C1310 " pdb=" C13 EIC C1310 " ideal model delta sigma weight residual 1.332 1.527 -0.195 2.00e-02 2.50e+03 9.54e+01 bond pdb=" C10 EIC C1310 " pdb=" C9 EIC C1310 " ideal model delta sigma weight residual 1.332 1.527 -0.195 2.00e-02 2.50e+03 9.51e+01 ... (remaining 28279 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.03: 36614 3.03 - 6.07: 1817 6.07 - 9.10: 45 9.10 - 12.13: 4 12.13 - 15.16: 13 Bond angle restraints: 38493 Sorted by residual: angle pdb=" C THR B 248 " pdb=" CA THR B 248 " pdb=" CB THR B 248 " ideal model delta sigma weight residual 111.20 117.42 -6.22 7.10e-01 1.98e+00 7.67e+01 angle pdb=" C THR A 248 " pdb=" CA THR A 248 " pdb=" CB THR A 248 " ideal model delta sigma weight residual 111.20 117.42 -6.22 7.10e-01 1.98e+00 7.67e+01 angle pdb=" C THR C 248 " pdb=" CA THR C 248 " pdb=" CB THR C 248 " ideal model delta sigma weight residual 111.20 117.40 -6.20 7.10e-01 1.98e+00 7.62e+01 angle pdb=" N PRO C 980 " pdb=" CA PRO C 980 " pdb=" C PRO C 980 " ideal model delta sigma weight residual 110.70 119.56 -8.86 1.22e+00 6.72e-01 5.27e+01 angle pdb=" N PRO B 980 " pdb=" CA PRO B 980 " pdb=" C PRO B 980 " ideal model delta sigma weight residual 110.70 119.53 -8.83 1.22e+00 6.72e-01 5.23e+01 ... (remaining 38488 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.44: 17059 24.44 - 48.88: 805 48.88 - 73.33: 136 73.33 - 97.77: 51 97.77 - 122.21: 3 Dihedral angle restraints: 18054 sinusoidal: 8244 harmonic: 9810 Sorted by residual: dihedral pdb=" C CYS C 164 " pdb=" N CYS C 164 " pdb=" CA CYS C 164 " pdb=" CB CYS C 164 " ideal model delta harmonic sigma weight residual -122.60 -140.88 18.28 0 2.50e+00 1.60e-01 5.35e+01 dihedral pdb=" CB CYS C 478 " pdb=" SG CYS C 478 " pdb=" SG CYS C 486 " pdb=" CB CYS C 486 " ideal model delta sinusoidal sigma weight residual 93.00 152.38 -59.38 1 1.00e+01 1.00e-02 4.71e+01 dihedral pdb=" N CYS C 164 " pdb=" C CYS C 164 " pdb=" CA CYS C 164 " pdb=" CB CYS C 164 " ideal model delta harmonic sigma weight residual 122.80 139.00 -16.20 0 2.50e+00 1.60e-01 4.20e+01 ... (remaining 18051 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.164: 3971 0.164 - 0.329: 636 0.329 - 0.493: 24 0.493 - 0.657: 0 0.657 - 0.822: 4 Chirality restraints: 4635 Sorted by residual: chirality pdb=" C1 NAG K 2 " pdb=" O4 NAG K 1 " pdb=" C2 NAG K 2 " pdb=" O5 NAG K 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.94 -0.46 2.00e-02 2.50e+03 5.33e+02 chirality pdb=" C1 NAG Y 2 " pdb=" O4 NAG Y 1 " pdb=" C2 NAG Y 2 " pdb=" O5 NAG Y 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.12 -0.28 2.00e-02 2.50e+03 1.92e+02 chirality pdb=" C1 NAG O 2 " pdb=" O4 NAG O 1 " pdb=" C2 NAG O 2 " pdb=" O5 NAG O 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.19 -0.21 2.00e-02 2.50e+03 1.15e+02 ... (remaining 4632 not shown) Planarity restraints: 4920 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG O 1 " 0.344 2.00e-02 2.50e+03 2.98e-01 1.11e+03 pdb=" C7 NAG O 1 " -0.082 2.00e-02 2.50e+03 pdb=" C8 NAG O 1 " 0.124 2.00e-02 2.50e+03 pdb=" N2 NAG O 1 " -0.530 2.00e-02 2.50e+03 pdb=" O7 NAG O 1 " 0.144 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 EIC A1310 " 0.420 2.00e-02 2.50e+03 3.16e-01 1.00e+03 pdb=" C11 EIC A1310 " -0.155 2.00e-02 2.50e+03 pdb=" C8 EIC A1310 " 0.155 2.00e-02 2.50e+03 pdb=" C9 EIC A1310 " -0.419 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1301 " -0.323 2.00e-02 2.50e+03 2.81e-01 9.86e+02 pdb=" C7 NAG A1301 " 0.071 2.00e-02 2.50e+03 pdb=" C8 NAG A1301 " -0.125 2.00e-02 2.50e+03 pdb=" N2 NAG A1301 " 0.503 2.00e-02 2.50e+03 pdb=" O7 NAG A1301 " -0.126 2.00e-02 2.50e+03 ... (remaining 4917 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 118 2.63 - 3.20: 23174 3.20 - 3.76: 42329 3.76 - 4.33: 61160 4.33 - 4.90: 97345 Nonbonded interactions: 224126 Sorted by model distance: nonbonded pdb=" O3 NAG Y 2 " pdb=" O7 NAG Y 2 " model vdw 2.059 3.040 nonbonded pdb=" O3 NAG K 2 " pdb=" O7 NAG K 2 " model vdw 2.073 3.040 nonbonded pdb=" OG1 THR B 22 " pdb=" O LYS B 75 " model vdw 2.250 3.040 nonbonded pdb=" OG1 THR C 22 " pdb=" O LYS C 75 " model vdw 2.266 3.040 nonbonded pdb=" CG2 ILE A 838 " pdb=" OD2 ASP C 584 " model vdw 2.282 3.460 ... (remaining 224121 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'k' selection = chain 'l' selection = chain 'm' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.580 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.370 Check model and map are aligned: 0.080 Set scattering table: 0.080 Process input model: 25.210 Find NCS groups from input model: 0.760 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:5.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 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 : 0.014 0.670 28424 Z= 1.125 Angle : 1.609 30.335 38862 Z= 1.172 Chirality : 0.114 0.822 4635 Planarity : 0.022 0.316 4860 Dihedral : 14.476 122.211 11631 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.42 % Allowed : 3.53 % Favored : 96.05 % Rotamer: Outliers : 4.88 % Allowed : 9.46 % Favored : 85.66 % Cbeta Deviations : 0.70 % 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 are not related in a simple way. whole: 1.41 (0.14), residues: 3369 helix: 4.20 (0.19), residues: 690 sheet: 1.75 (0.19), residues: 609 loop : -0.52 (0.12), residues: 2070 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG C 759 TYR 0.022 0.002 TYR A 634 PHE 0.018 0.002 PHE C 131 TRP 0.022 0.003 TRP A 150 HIS 0.005 0.001 HIS A 243 Details of bonding type rmsd covalent geometry : bond 0.01321 (28284) covalent geometry : angle 1.57033 (38493) SS BOND : bond 0.00862 ( 45) SS BOND : angle 4.81247 ( 90) hydrogen bonds : bond 0.17955 ( 1086) hydrogen bonds : angle 7.79797 ( 2970) Misc. bond : bond 0.64751 ( 2) link_BETA1-4 : bond 0.00647 ( 33) link_BETA1-4 : angle 2.15307 ( 99) link_NAG-ASN : bond 0.01112 ( 60) link_NAG-ASN : angle 4.17544 ( 180) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6738 Ramachandran restraints generated. 3369 Oldfield, 0 Emsley, 3369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6738 Ramachandran restraints generated. 3369 Oldfield, 0 Emsley, 3369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 415 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 143 poor density : 272 time to evaluate : 0.853 Fit side-chains revert: symmetry clash REVERT: A 251 ASN cc_start: 0.7728 (t0) cc_final: 0.7473 (t0) REVERT: A 332 ASN cc_start: 0.8028 (p0) cc_final: 0.7696 (p0) REVERT: A 626 GLN cc_start: 0.7624 (pt0) cc_final: 0.7347 (pt0) REVERT: A 817 PHE cc_start: 0.7591 (t80) cc_final: 0.7375 (t80) REVERT: A 1044 MET cc_start: 0.8850 (ptm) cc_final: 0.8561 (ptm) REVERT: A 1132 TYR cc_start: 0.7761 (t80) cc_final: 0.7551 (t80) REVERT: B 916 LEU cc_start: 0.8890 (tp) cc_final: 0.8666 (tp) REVERT: B 1044 MET cc_start: 0.8838 (ptm) cc_final: 0.8612 (ptm) REVERT: B 1132 TYR cc_start: 0.7795 (t80) cc_final: 0.7283 (t80) REVERT: C 626 GLN cc_start: 0.7433 (pt0) cc_final: 0.7082 (pm20) REVERT: C 863 MET cc_start: 0.8986 (mtt) cc_final: 0.8760 (mtm) REVERT: C 1044 MET cc_start: 0.8870 (ptm) cc_final: 0.8491 (ptp) REVERT: C 1132 TYR cc_start: 0.7832 (t80) cc_final: 0.7588 (t80) outliers start: 143 outliers final: 22 residues processed: 397 average time/residue: 0.4986 time to fit residues: 239.7389 Evaluate side-chains 144 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 122 time to evaluate : 1.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 LYS Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 129 CYS Chi-restraints excluded: chain A residue 334 CYS Chi-restraints excluded: chain A residue 359 CYS Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 600 THR Chi-restraints excluded: chain A residue 643 THR Chi-restraints excluded: chain A residue 946 VAL Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 334 CYS Chi-restraints excluded: chain B residue 359 CYS Chi-restraints excluded: chain B residue 600 THR Chi-restraints excluded: chain B residue 946 VAL Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 129 CYS Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 334 CYS Chi-restraints excluded: chain C residue 393 VAL Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 946 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 197 optimal weight: 0.9980 chunk 215 optimal weight: 0.4980 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 0.6980 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 0.9980 chunk 155 optimal weight: 0.9980 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 1.9990 chunk 298 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 71 GLN A 85 ASN A 113 GLN A 119 ASN A 153 ASN A 472 GLN A 626 GLN A 758 ASN A 895 GLN A1113 ASN B 71 GLN B 85 ASN B 119 ASN B 153 ASN B 496 HIS B 626 GLN B 697 ASN B 758 ASN B 895 GLN C 71 GLN C 85 ASN C 113 GLN C 119 ASN C 472 GLN C 496 HIS C 626 GLN C 697 ASN C 758 ASN C 895 GLN C1113 ASN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.113410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.083820 restraints weight = 47801.607| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 2.73 r_work: 0.3113 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2977 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.1717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 28424 Z= 0.144 Angle : 0.699 13.301 38862 Z= 0.346 Chirality : 0.048 0.511 4635 Planarity : 0.004 0.039 4860 Dihedral : 11.399 106.385 5665 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.21 % Favored : 96.76 % Rotamer: Outliers : 2.97 % Allowed : 13.39 % Favored : 83.64 % 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 are not related in a simple way. whole: 0.75 (0.14), residues: 3369 helix: 3.02 (0.19), residues: 711 sheet: 1.19 (0.19), residues: 729 loop : -0.81 (0.13), residues: 1929 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 841 TYR 0.017 0.001 TYR A1061 PHE 0.021 0.001 PHE A 390 TRP 0.017 0.002 TRP A 150 HIS 0.004 0.001 HIS C 243 Details of bonding type rmsd covalent geometry : bond 0.00297 (28284) covalent geometry : angle 0.66208 (38493) SS BOND : bond 0.00297 ( 45) SS BOND : angle 1.08039 ( 90) hydrogen bonds : bond 0.05718 ( 1086) hydrogen bonds : angle 6.22422 ( 2970) Misc. bond : bond 0.00553 ( 2) link_BETA1-4 : bond 0.00705 ( 33) link_BETA1-4 : angle 2.07545 ( 99) link_NAG-ASN : bond 0.00454 ( 60) link_NAG-ASN : angle 2.97865 ( 180) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6738 Ramachandran restraints generated. 3369 Oldfield, 0 Emsley, 3369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6738 Ramachandran restraints generated. 3369 Oldfield, 0 Emsley, 3369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 149 time to evaluate : 0.995 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 146 ASN cc_start: 0.8458 (OUTLIER) cc_final: 0.8176 (p0) REVERT: A 251 ASN cc_start: 0.7688 (t0) cc_final: 0.7381 (t0) REVERT: A 258 THR cc_start: 0.7360 (OUTLIER) cc_final: 0.6967 (p) REVERT: A 562 GLN cc_start: 0.7086 (OUTLIER) cc_final: 0.6193 (tm130) REVERT: A 620 MET cc_start: 0.8077 (mpt) cc_final: 0.7818 (mpp) REVERT: A 817 PHE cc_start: 0.8110 (t80) cc_final: 0.7776 (t80) REVERT: A 1013 ARG cc_start: 0.8845 (tpt170) cc_final: 0.8550 (tmt-80) REVERT: A 1044 MET cc_start: 0.9218 (ptm) cc_final: 0.8927 (ptp) REVERT: B 817 PHE cc_start: 0.7391 (t80) cc_final: 0.7187 (m-80) REVERT: B 1044 MET cc_start: 0.9142 (ptm) cc_final: 0.8887 (ptp) REVERT: C 66 ASN cc_start: 0.8660 (p0) cc_final: 0.8434 (p0) REVERT: C 216 ARG cc_start: 0.7831 (OUTLIER) cc_final: 0.6465 (mmm160) REVERT: C 562 GLN cc_start: 0.7109 (OUTLIER) cc_final: 0.6675 (tm-30) REVERT: C 626 GLN cc_start: 0.7610 (pt0) cc_final: 0.7122 (pm20) REVERT: C 1044 MET cc_start: 0.9156 (ptm) cc_final: 0.8826 (ptp) REVERT: C 1100 GLN cc_start: 0.8312 (OUTLIER) cc_final: 0.8060 (pt0) REVERT: C 1132 TYR cc_start: 0.7829 (t80) cc_final: 0.7526 (t80) outliers start: 87 outliers final: 29 residues processed: 223 average time/residue: 0.5073 time to fit residues: 137.2875 Evaluate side-chains 149 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 114 time to evaluate : 0.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 LYS Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 146 ASN Chi-restraints excluded: chain A residue 216 ARG Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 279 GLN Chi-restraints excluded: chain A residue 334 CYS Chi-restraints excluded: chain A residue 359 CYS Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain A residue 562 GLN Chi-restraints excluded: chain A residue 643 THR Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 334 CYS Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain B residue 643 THR Chi-restraints excluded: chain B residue 810 SER Chi-restraints excluded: chain B residue 1130 THR Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 129 CYS Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 209 ASP Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain C residue 216 ARG Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 334 CYS Chi-restraints excluded: chain C residue 562 GLN Chi-restraints excluded: chain C residue 643 THR Chi-restraints excluded: chain C residue 746 LEU Chi-restraints excluded: chain C residue 810 SER Chi-restraints excluded: chain C residue 1100 GLN Chi-restraints excluded: chain C residue 1130 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 277 optimal weight: 8.9990 chunk 214 optimal weight: 2.9990 chunk 307 optimal weight: 0.9980 chunk 217 optimal weight: 0.0060 chunk 318 optimal weight: 0.6980 chunk 244 optimal weight: 7.9990 chunk 104 optimal weight: 7.9990 chunk 304 optimal weight: 5.9990 chunk 187 optimal weight: 5.9990 chunk 51 optimal weight: 0.1980 chunk 14 optimal weight: 5.9990 overall best weight: 0.9798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 496 HIS B 144 HIS B 153 ASN C 153 ASN C 162 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.111756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.081745 restraints weight = 47838.741| |-----------------------------------------------------------------------------| r_work (start): 0.3203 rms_B_bonded: 2.77 r_work: 0.3072 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2935 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.2100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 28424 Z= 0.131 Angle : 0.640 9.940 38862 Z= 0.316 Chirality : 0.047 0.466 4635 Planarity : 0.004 0.041 4860 Dihedral : 10.692 104.132 5649 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.42 % Favored : 95.55 % Rotamer: Outliers : 2.53 % Allowed : 13.83 % Favored : 83.64 % 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 are not related in a simple way. whole: 0.44 (0.14), residues: 3369 helix: 2.54 (0.19), residues: 711 sheet: 1.11 (0.19), residues: 717 loop : -0.95 (0.13), residues: 1941 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 841 TYR 0.018 0.001 TYR A1061 PHE 0.027 0.001 PHE A 390 TRP 0.017 0.002 TRP B 150 HIS 0.006 0.001 HIS B 243 Details of bonding type rmsd covalent geometry : bond 0.00280 (28284) covalent geometry : angle 0.60831 (38493) SS BOND : bond 0.00403 ( 45) SS BOND : angle 1.27721 ( 90) hydrogen bonds : bond 0.05168 ( 1086) hydrogen bonds : angle 5.88938 ( 2970) Misc. bond : bond 0.01163 ( 2) link_BETA1-4 : bond 0.00591 ( 33) link_BETA1-4 : angle 2.01678 ( 99) link_NAG-ASN : bond 0.00436 ( 60) link_NAG-ASN : angle 2.49446 ( 180) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6738 Ramachandran restraints generated. 3369 Oldfield, 0 Emsley, 3369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6738 Ramachandran restraints generated. 3369 Oldfield, 0 Emsley, 3369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 129 time to evaluate : 1.014 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 186 ASN cc_start: 0.7290 (m-40) cc_final: 0.6682 (m-40) REVERT: A 251 ASN cc_start: 0.7710 (t0) cc_final: 0.7408 (t0) REVERT: A 562 GLN cc_start: 0.7329 (OUTLIER) cc_final: 0.6357 (tm130) REVERT: A 626 GLN cc_start: 0.7997 (pt0) cc_final: 0.7638 (pm20) REVERT: A 817 PHE cc_start: 0.8158 (t80) cc_final: 0.7831 (t80) REVERT: A 951 GLN cc_start: 0.8919 (OUTLIER) cc_final: 0.8621 (tm-30) REVERT: A 1132 TYR cc_start: 0.7753 (t80) cc_final: 0.7491 (t80) REVERT: B 1132 TYR cc_start: 0.7826 (t80) cc_final: 0.7148 (t80) REVERT: C 17 ASN cc_start: 0.6904 (m-40) cc_final: 0.6688 (m-40) REVERT: C 562 GLN cc_start: 0.7206 (OUTLIER) cc_final: 0.6742 (tm-30) REVERT: C 620 MET cc_start: 0.7744 (mpp) cc_final: 0.7532 (pmm) REVERT: C 626 GLN cc_start: 0.7727 (pt0) cc_final: 0.7224 (pm20) REVERT: C 1044 MET cc_start: 0.9140 (ptm) cc_final: 0.8883 (ptp) REVERT: C 1100 GLN cc_start: 0.8271 (OUTLIER) cc_final: 0.7981 (pt0) REVERT: C 1132 TYR cc_start: 0.7873 (t80) cc_final: 0.7581 (t80) outliers start: 74 outliers final: 28 residues processed: 191 average time/residue: 0.4028 time to fit residues: 97.5747 Evaluate side-chains 144 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 112 time to evaluate : 0.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 LYS Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 279 GLN Chi-restraints excluded: chain A residue 334 CYS Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain A residue 562 GLN Chi-restraints excluded: chain A residue 951 GLN Chi-restraints excluded: chain A residue 1130 THR Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 334 CYS Chi-restraints excluded: chain B residue 369 SER Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain B residue 708 ILE Chi-restraints excluded: chain B residue 1130 THR Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 75 LYS Chi-restraints excluded: chain C residue 129 CYS Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 334 CYS Chi-restraints excluded: chain C residue 369 SER Chi-restraints excluded: chain C residue 562 GLN Chi-restraints excluded: chain C residue 746 LEU Chi-restraints excluded: chain C residue 910 LEU Chi-restraints excluded: chain C residue 1100 GLN Chi-restraints excluded: chain C residue 1130 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 189 optimal weight: 7.9990 chunk 16 optimal weight: 7.9990 chunk 173 optimal weight: 10.0000 chunk 206 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 chunk 294 optimal weight: 1.9990 chunk 308 optimal weight: 0.0050 chunk 313 optimal weight: 1.9990 chunk 77 optimal weight: 0.0970 chunk 95 optimal weight: 6.9990 chunk 169 optimal weight: 3.9990 overall best weight: 0.9996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 153 ASN C 153 ASN C 162 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.110773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.080638 restraints weight = 47734.784| |-----------------------------------------------------------------------------| r_work (start): 0.3184 rms_B_bonded: 2.77 r_work: 0.3052 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2914 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.2347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 28424 Z= 0.128 Angle : 0.614 10.078 38862 Z= 0.302 Chirality : 0.046 0.446 4635 Planarity : 0.004 0.041 4860 Dihedral : 10.392 99.358 5647 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 2.63 % Allowed : 14.14 % Favored : 83.23 % 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 are not related in a simple way. whole: 0.32 (0.14), residues: 3369 helix: 2.52 (0.19), residues: 693 sheet: 0.96 (0.19), residues: 696 loop : -0.98 (0.12), residues: 1980 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 841 TYR 0.016 0.001 TYR A1061 PHE 0.031 0.001 PHE A 390 TRP 0.014 0.001 TRP A 150 HIS 0.004 0.001 HIS B 243 Details of bonding type rmsd covalent geometry : bond 0.00275 (28284) covalent geometry : angle 0.58191 (38493) SS BOND : bond 0.00262 ( 45) SS BOND : angle 1.21342 ( 90) hydrogen bonds : bond 0.04834 ( 1086) hydrogen bonds : angle 5.75738 ( 2970) Misc. bond : bond 0.00660 ( 2) link_BETA1-4 : bond 0.00575 ( 33) link_BETA1-4 : angle 1.98487 ( 99) link_NAG-ASN : bond 0.00389 ( 60) link_NAG-ASN : angle 2.45499 ( 180) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6738 Ramachandran restraints generated. 3369 Oldfield, 0 Emsley, 3369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6738 Ramachandran restraints generated. 3369 Oldfield, 0 Emsley, 3369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 122 time to evaluate : 1.046 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 146 ASN cc_start: 0.8485 (OUTLIER) cc_final: 0.7967 (p0) REVERT: A 251 ASN cc_start: 0.7533 (t0) cc_final: 0.7281 (t0) REVERT: A 562 GLN cc_start: 0.7434 (OUTLIER) cc_final: 0.6804 (tm130) REVERT: A 675 MET cc_start: 0.5912 (mmt) cc_final: 0.5587 (mmp) REVERT: A 817 PHE cc_start: 0.8188 (t80) cc_final: 0.7856 (t80) REVERT: A 1132 TYR cc_start: 0.7849 (t80) cc_final: 0.7586 (t80) REVERT: B 1117 SER cc_start: 0.8579 (t) cc_final: 0.8321 (m) REVERT: B 1132 TYR cc_start: 0.7842 (t80) cc_final: 0.7146 (t80) REVERT: C 79 ASN cc_start: 0.7734 (t0) cc_final: 0.7500 (t0) REVERT: C 159 SER cc_start: 0.8749 (OUTLIER) cc_final: 0.8435 (m) REVERT: C 558 LEU cc_start: 0.8255 (OUTLIER) cc_final: 0.8030 (mt) REVERT: C 562 GLN cc_start: 0.7383 (OUTLIER) cc_final: 0.6774 (tm130) REVERT: C 626 GLN cc_start: 0.7627 (pt0) cc_final: 0.7146 (pm20) REVERT: C 673 HIS cc_start: 0.7842 (OUTLIER) cc_final: 0.7599 (t-170) REVERT: C 817 PHE cc_start: 0.8277 (t80) cc_final: 0.7705 (m-80) REVERT: C 1044 MET cc_start: 0.9121 (ptm) cc_final: 0.8905 (ptp) REVERT: C 1100 GLN cc_start: 0.8296 (OUTLIER) cc_final: 0.7998 (pt0) REVERT: C 1132 TYR cc_start: 0.7894 (t80) cc_final: 0.7568 (t80) outliers start: 77 outliers final: 32 residues processed: 192 average time/residue: 0.4390 time to fit residues: 105.3901 Evaluate side-chains 144 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 105 time to evaluate : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 146 ASN Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 279 GLN Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 334 CYS Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain A residue 562 GLN Chi-restraints excluded: chain A residue 628 THR Chi-restraints excluded: chain A residue 1130 THR Chi-restraints excluded: chain B residue 15 CYS Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 159 SER Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 334 CYS Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain B residue 628 THR Chi-restraints excluded: chain B residue 708 ILE Chi-restraints excluded: chain B residue 1100 GLN Chi-restraints excluded: chain B residue 1130 THR Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 75 LYS Chi-restraints excluded: chain C residue 129 CYS Chi-restraints excluded: chain C residue 159 SER Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain C residue 334 CYS Chi-restraints excluded: chain C residue 369 SER Chi-restraints excluded: chain C residue 558 LEU Chi-restraints excluded: chain C residue 562 GLN Chi-restraints excluded: chain C residue 628 THR Chi-restraints excluded: chain C residue 673 HIS Chi-restraints excluded: chain C residue 746 LEU Chi-restraints excluded: chain C residue 1100 GLN Chi-restraints excluded: chain C residue 1130 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 190 optimal weight: 1.9990 chunk 288 optimal weight: 4.9990 chunk 326 optimal weight: 0.0020 chunk 259 optimal weight: 0.8980 chunk 332 optimal weight: 6.9990 chunk 182 optimal weight: 4.9990 chunk 69 optimal weight: 0.9980 chunk 60 optimal weight: 8.9990 chunk 254 optimal weight: 7.9990 chunk 256 optimal weight: 2.9990 chunk 285 optimal weight: 4.9990 overall best weight: 1.3792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 153 ASN B 895 GLN C 153 ASN C 162 ASN C 895 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.108896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.078593 restraints weight = 47788.143| |-----------------------------------------------------------------------------| r_work (start): 0.3147 rms_B_bonded: 2.77 r_work: 0.3012 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2874 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.2564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 28424 Z= 0.144 Angle : 0.628 9.966 38862 Z= 0.310 Chirality : 0.047 0.433 4635 Planarity : 0.004 0.044 4860 Dihedral : 10.058 95.727 5643 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 2.63 % Allowed : 14.11 % Favored : 83.27 % 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 are not related in a simple way. whole: 0.16 (0.14), residues: 3369 helix: 2.37 (0.19), residues: 693 sheet: 0.67 (0.19), residues: 717 loop : -1.00 (0.13), residues: 1959 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 841 TYR 0.017 0.001 TYR C 263 PHE 0.022 0.001 PHE A 390 TRP 0.010 0.002 TRP B 64 HIS 0.004 0.001 HIS B 243 Details of bonding type rmsd covalent geometry : bond 0.00323 (28284) covalent geometry : angle 0.59556 (38493) SS BOND : bond 0.00302 ( 45) SS BOND : angle 1.28033 ( 90) hydrogen bonds : bond 0.05072 ( 1086) hydrogen bonds : angle 5.77334 ( 2970) Misc. bond : bond 0.00438 ( 2) link_BETA1-4 : bond 0.00573 ( 33) link_BETA1-4 : angle 2.00590 ( 99) link_NAG-ASN : bond 0.00395 ( 60) link_NAG-ASN : angle 2.50136 ( 180) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6738 Ramachandran restraints generated. 3369 Oldfield, 0 Emsley, 3369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6738 Ramachandran restraints generated. 3369 Oldfield, 0 Emsley, 3369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 125 time to evaluate : 1.045 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 146 ASN cc_start: 0.8532 (OUTLIER) cc_final: 0.8013 (p0) REVERT: A 251 ASN cc_start: 0.7538 (t0) cc_final: 0.7315 (t0) REVERT: A 562 GLN cc_start: 0.7659 (OUTLIER) cc_final: 0.6792 (tm130) REVERT: A 626 GLN cc_start: 0.7951 (pt0) cc_final: 0.7638 (pm20) REVERT: A 675 MET cc_start: 0.6082 (mmt) cc_final: 0.5735 (mmp) REVERT: A 780 LYS cc_start: 0.8103 (mmtt) cc_final: 0.7756 (mmmm) REVERT: A 817 PHE cc_start: 0.8247 (t80) cc_final: 0.7909 (t80) REVERT: A 1132 TYR cc_start: 0.7894 (t80) cc_final: 0.7646 (t80) REVERT: B 269 GLN cc_start: 0.8948 (OUTLIER) cc_final: 0.8734 (mm-40) REVERT: B 1117 SER cc_start: 0.8665 (t) cc_final: 0.8374 (m) REVERT: B 1132 TYR cc_start: 0.7914 (t80) cc_final: 0.7221 (t80) REVERT: C 159 SER cc_start: 0.8743 (OUTLIER) cc_final: 0.8508 (m) REVERT: C 162 ASN cc_start: 0.6432 (OUTLIER) cc_final: 0.6230 (t0) REVERT: C 216 ARG cc_start: 0.7982 (OUTLIER) cc_final: 0.6301 (mmm160) REVERT: C 558 LEU cc_start: 0.8354 (OUTLIER) cc_final: 0.8150 (mt) REVERT: C 562 GLN cc_start: 0.7592 (OUTLIER) cc_final: 0.6958 (tm130) REVERT: C 673 HIS cc_start: 0.7947 (OUTLIER) cc_final: 0.7717 (t-170) REVERT: C 1044 MET cc_start: 0.9135 (ptm) cc_final: 0.8874 (ptp) REVERT: C 1100 GLN cc_start: 0.8353 (OUTLIER) cc_final: 0.8031 (pt0) REVERT: C 1117 SER cc_start: 0.8831 (t) cc_final: 0.8494 (m) REVERT: C 1132 TYR cc_start: 0.7903 (t80) cc_final: 0.7590 (t80) outliers start: 77 outliers final: 34 residues processed: 193 average time/residue: 0.5161 time to fit residues: 120.8967 Evaluate side-chains 156 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 112 time to evaluate : 0.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 CYS Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 146 ASN Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 216 ARG Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 279 GLN Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 334 CYS Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain A residue 562 GLN Chi-restraints excluded: chain A residue 628 THR Chi-restraints excluded: chain A residue 673 HIS Chi-restraints excluded: chain A residue 1130 THR Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 159 SER Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 269 GLN Chi-restraints excluded: chain B residue 334 CYS Chi-restraints excluded: chain B residue 369 SER Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain B residue 628 THR Chi-restraints excluded: chain B residue 708 ILE Chi-restraints excluded: chain B residue 1130 THR Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 129 CYS Chi-restraints excluded: chain C residue 134 CYS Chi-restraints excluded: chain C residue 159 SER Chi-restraints excluded: chain C residue 162 ASN Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 216 ARG Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 334 CYS Chi-restraints excluded: chain C residue 369 SER Chi-restraints excluded: chain C residue 558 LEU Chi-restraints excluded: chain C residue 562 GLN Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 628 THR Chi-restraints excluded: chain C residue 673 HIS Chi-restraints excluded: chain C residue 1100 GLN Chi-restraints excluded: chain C residue 1130 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 185 optimal weight: 0.9980 chunk 275 optimal weight: 0.4980 chunk 166 optimal weight: 0.4980 chunk 265 optimal weight: 0.6980 chunk 310 optimal weight: 4.9990 chunk 4 optimal weight: 4.9990 chunk 116 optimal weight: 6.9990 chunk 303 optimal weight: 0.8980 chunk 140 optimal weight: 2.9990 chunk 68 optimal weight: 9.9990 chunk 10 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 119 ASN C 951 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.109830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.079958 restraints weight = 47784.216| |-----------------------------------------------------------------------------| r_work (start): 0.3172 rms_B_bonded: 2.73 r_work: 0.3039 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2902 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.2652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 28424 Z= 0.112 Angle : 0.598 10.197 38862 Z= 0.293 Chirality : 0.045 0.418 4635 Planarity : 0.004 0.044 4860 Dihedral : 9.817 91.786 5642 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 2.22 % Allowed : 14.79 % Favored : 82.99 % 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 are not related in a simple way. whole: 0.17 (0.14), residues: 3369 helix: 2.36 (0.20), residues: 693 sheet: 0.87 (0.19), residues: 696 loop : -1.06 (0.13), residues: 1980 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 841 TYR 0.018 0.001 TYR C 246 PHE 0.012 0.001 PHE A 390 TRP 0.011 0.001 TRP A 256 HIS 0.003 0.001 HIS B 243 Details of bonding type rmsd covalent geometry : bond 0.00233 (28284) covalent geometry : angle 0.56745 (38493) SS BOND : bond 0.00230 ( 45) SS BOND : angle 0.96695 ( 90) hydrogen bonds : bond 0.04519 ( 1086) hydrogen bonds : angle 5.65965 ( 2970) Misc. bond : bond 0.00274 ( 2) link_BETA1-4 : bond 0.00598 ( 33) link_BETA1-4 : angle 1.96650 ( 99) link_NAG-ASN : bond 0.00394 ( 60) link_NAG-ASN : angle 2.41300 ( 180) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6738 Ramachandran restraints generated. 3369 Oldfield, 0 Emsley, 3369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6738 Ramachandran restraints generated. 3369 Oldfield, 0 Emsley, 3369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 118 time to evaluate : 0.838 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 146 ASN cc_start: 0.8593 (OUTLIER) cc_final: 0.8015 (p0) REVERT: A 251 ASN cc_start: 0.7490 (t0) cc_final: 0.7256 (t0) REVERT: A 269 GLN cc_start: 0.8918 (OUTLIER) cc_final: 0.8376 (mp10) REVERT: A 562 GLN cc_start: 0.7604 (OUTLIER) cc_final: 0.6898 (tm130) REVERT: A 626 GLN cc_start: 0.7954 (pt0) cc_final: 0.7532 (pm20) REVERT: A 675 MET cc_start: 0.6074 (mmt) cc_final: 0.5843 (mmp) REVERT: A 780 LYS cc_start: 0.8032 (mmtt) cc_final: 0.7706 (mmmm) REVERT: A 817 PHE cc_start: 0.8206 (t80) cc_final: 0.7860 (t80) REVERT: A 951 GLN cc_start: 0.8918 (tt0) cc_final: 0.8610 (tm-30) REVERT: A 1132 TYR cc_start: 0.7899 (t80) cc_final: 0.7637 (t80) REVERT: B 269 GLN cc_start: 0.8902 (OUTLIER) cc_final: 0.8695 (mm-40) REVERT: B 1117 SER cc_start: 0.8655 (t) cc_final: 0.8360 (m) REVERT: B 1132 TYR cc_start: 0.7846 (t80) cc_final: 0.7155 (t80) REVERT: C 162 ASN cc_start: 0.6954 (t0) cc_final: 0.6738 (t0) REVERT: C 216 ARG cc_start: 0.8064 (OUTLIER) cc_final: 0.6372 (mmm160) REVERT: C 562 GLN cc_start: 0.7519 (OUTLIER) cc_final: 0.6914 (tm130) REVERT: C 673 HIS cc_start: 0.7909 (OUTLIER) cc_final: 0.7696 (t-170) REVERT: C 1044 MET cc_start: 0.9112 (ptm) cc_final: 0.8895 (ptp) REVERT: C 1100 GLN cc_start: 0.8316 (OUTLIER) cc_final: 0.7961 (pt0) REVERT: C 1117 SER cc_start: 0.8816 (t) cc_final: 0.8485 (m) REVERT: C 1132 TYR cc_start: 0.7926 (t80) cc_final: 0.7599 (t80) outliers start: 65 outliers final: 29 residues processed: 179 average time/residue: 0.4791 time to fit residues: 104.9644 Evaluate side-chains 145 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 108 time to evaluate : 0.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 CYS Chi-restraints excluded: chain A residue 146 ASN Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 216 ARG Chi-restraints excluded: chain A residue 269 GLN Chi-restraints excluded: chain A residue 279 GLN Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 334 CYS Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain A residue 562 GLN Chi-restraints excluded: chain A residue 628 THR Chi-restraints excluded: chain A residue 1130 THR Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 269 GLN Chi-restraints excluded: chain B residue 334 CYS Chi-restraints excluded: chain B residue 369 SER Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain B residue 628 THR Chi-restraints excluded: chain B residue 708 ILE Chi-restraints excluded: chain B residue 1130 THR Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 129 CYS Chi-restraints excluded: chain C residue 134 CYS Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 216 ARG Chi-restraints excluded: chain C residue 334 CYS Chi-restraints excluded: chain C residue 562 GLN Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 628 THR Chi-restraints excluded: chain C residue 673 HIS Chi-restraints excluded: chain C residue 1100 GLN Chi-restraints excluded: chain C residue 1130 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 248 optimal weight: 10.0000 chunk 228 optimal weight: 0.7980 chunk 255 optimal weight: 5.9990 chunk 180 optimal weight: 9.9990 chunk 66 optimal weight: 0.4980 chunk 60 optimal weight: 6.9990 chunk 29 optimal weight: 5.9990 chunk 48 optimal weight: 0.9980 chunk 294 optimal weight: 0.9980 chunk 292 optimal weight: 10.0000 chunk 188 optimal weight: 6.9990 overall best weight: 1.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 895 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.107143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.076921 restraints weight = 47742.755| |-----------------------------------------------------------------------------| r_work (start): 0.3116 rms_B_bonded: 2.74 r_work: 0.2979 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2840 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 moved from start: 0.2810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 28424 Z= 0.177 Angle : 0.655 9.969 38862 Z= 0.324 Chirality : 0.048 0.427 4635 Planarity : 0.004 0.045 4860 Dihedral : 9.761 86.541 5642 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 2.29 % Allowed : 14.92 % Favored : 82.79 % 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 are not related in a simple way. whole: -0.05 (0.14), residues: 3369 helix: 2.03 (0.20), residues: 717 sheet: 0.54 (0.19), residues: 723 loop : -1.12 (0.13), residues: 1929 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 841 TYR 0.019 0.002 TYR C 263 PHE 0.015 0.002 PHE A 84 TRP 0.015 0.002 TRP B 64 HIS 0.003 0.001 HIS C1058 Details of bonding type rmsd covalent geometry : bond 0.00413 (28284) covalent geometry : angle 0.62208 (38493) SS BOND : bond 0.00423 ( 45) SS BOND : angle 1.31102 ( 90) hydrogen bonds : bond 0.05449 ( 1086) hydrogen bonds : angle 5.83577 ( 2970) Misc. bond : bond 0.00402 ( 2) link_BETA1-4 : bond 0.00535 ( 33) link_BETA1-4 : angle 1.99969 ( 99) link_NAG-ASN : bond 0.00398 ( 60) link_NAG-ASN : angle 2.58855 ( 180) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6738 Ramachandran restraints generated. 3369 Oldfield, 0 Emsley, 3369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6738 Ramachandran restraints generated. 3369 Oldfield, 0 Emsley, 3369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 123 time to evaluate : 1.063 Fit side-chains REVERT: A 146 ASN cc_start: 0.8613 (OUTLIER) cc_final: 0.8008 (p0) REVERT: A 251 ASN cc_start: 0.7596 (t0) cc_final: 0.7363 (t0) REVERT: A 269 GLN cc_start: 0.9038 (OUTLIER) cc_final: 0.8309 (mp10) REVERT: A 562 GLN cc_start: 0.7824 (OUTLIER) cc_final: 0.6876 (tm130) REVERT: A 626 GLN cc_start: 0.8030 (pt0) cc_final: 0.7626 (pm20) REVERT: A 675 MET cc_start: 0.6220 (mmt) cc_final: 0.5872 (mmp) REVERT: A 817 PHE cc_start: 0.8287 (t80) cc_final: 0.8018 (t80) REVERT: A 1132 TYR cc_start: 0.7916 (t80) cc_final: 0.7665 (t80) REVERT: B 269 GLN cc_start: 0.8986 (OUTLIER) cc_final: 0.8743 (mm-40) REVERT: B 1117 SER cc_start: 0.8725 (t) cc_final: 0.8446 (m) REVERT: B 1132 TYR cc_start: 0.7886 (t80) cc_final: 0.7205 (t80) REVERT: C 162 ASN cc_start: 0.7195 (t0) cc_final: 0.6862 (t0) REVERT: C 216 ARG cc_start: 0.8239 (OUTLIER) cc_final: 0.6582 (mmm160) REVERT: C 269 GLN cc_start: 0.9025 (OUTLIER) cc_final: 0.8519 (mt0) REVERT: C 562 GLN cc_start: 0.7707 (OUTLIER) cc_final: 0.6980 (tm130) REVERT: C 673 HIS cc_start: 0.8020 (OUTLIER) cc_final: 0.7761 (t-170) REVERT: C 1044 MET cc_start: 0.9179 (ptm) cc_final: 0.8903 (ptp) REVERT: C 1117 SER cc_start: 0.8897 (t) cc_final: 0.8554 (m) REVERT: C 1132 TYR cc_start: 0.7910 (t80) cc_final: 0.7640 (t80) outliers start: 67 outliers final: 37 residues processed: 181 average time/residue: 0.5556 time to fit residues: 120.7655 Evaluate side-chains 157 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 112 time to evaluate : 0.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 ASN Chi-restraints excluded: chain A residue 134 CYS Chi-restraints excluded: chain A residue 146 ASN Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 216 ARG Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 269 GLN Chi-restraints excluded: chain A residue 279 GLN Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 334 CYS Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain A residue 562 GLN Chi-restraints excluded: chain A residue 600 THR Chi-restraints excluded: chain A residue 628 THR Chi-restraints excluded: chain A residue 673 HIS Chi-restraints excluded: chain A residue 733 THR Chi-restraints excluded: chain A residue 1130 THR Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 75 LYS Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 269 GLN Chi-restraints excluded: chain B residue 334 CYS Chi-restraints excluded: chain B residue 369 SER Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain B residue 600 THR Chi-restraints excluded: chain B residue 628 THR Chi-restraints excluded: chain B residue 708 ILE Chi-restraints excluded: chain B residue 1130 THR Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 134 CYS Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 216 ARG Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 269 GLN Chi-restraints excluded: chain C residue 334 CYS Chi-restraints excluded: chain C residue 562 GLN Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 628 THR Chi-restraints excluded: chain C residue 673 HIS Chi-restraints excluded: chain C residue 1130 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 305 optimal weight: 3.9990 chunk 158 optimal weight: 6.9990 chunk 69 optimal weight: 0.5980 chunk 330 optimal weight: 7.9990 chunk 88 optimal weight: 0.6980 chunk 264 optimal weight: 0.8980 chunk 256 optimal weight: 0.2980 chunk 8 optimal weight: 7.9990 chunk 145 optimal weight: 0.9990 chunk 215 optimal weight: 0.1980 chunk 173 optimal weight: 5.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 162 ASN ** B 237 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 = 0.3673 r_free = 0.3673 target = 0.109587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.079449 restraints weight = 47830.347| |-----------------------------------------------------------------------------| r_work (start): 0.3163 rms_B_bonded: 2.77 r_work: 0.3032 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2894 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.2870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 28424 Z= 0.109 Angle : 0.596 10.170 38862 Z= 0.290 Chirality : 0.045 0.410 4635 Planarity : 0.004 0.045 4860 Dihedral : 9.444 86.266 5641 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 1.88 % Allowed : 15.51 % Favored : 82.62 % 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 are not related in a simple way. whole: -0.04 (0.14), residues: 3369 helix: 2.01 (0.19), residues: 732 sheet: 0.50 (0.19), residues: 723 loop : -1.11 (0.13), residues: 1914 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 841 TYR 0.015 0.001 TYR C 503 PHE 0.012 0.001 PHE A 173 TRP 0.012 0.001 TRP A 256 HIS 0.003 0.001 HIS B 243 Details of bonding type rmsd covalent geometry : bond 0.00224 (28284) covalent geometry : angle 0.56437 (38493) SS BOND : bond 0.00243 ( 45) SS BOND : angle 1.23830 ( 90) hydrogen bonds : bond 0.04308 ( 1086) hydrogen bonds : angle 5.61684 ( 2970) Misc. bond : bond 0.00238 ( 2) link_BETA1-4 : bond 0.00614 ( 33) link_BETA1-4 : angle 1.97715 ( 99) link_NAG-ASN : bond 0.00396 ( 60) link_NAG-ASN : angle 2.39280 ( 180) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6738 Ramachandran restraints generated. 3369 Oldfield, 0 Emsley, 3369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6738 Ramachandran restraints generated. 3369 Oldfield, 0 Emsley, 3369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 120 time to evaluate : 1.051 Fit side-chains revert: symmetry clash REVERT: A 146 ASN cc_start: 0.8592 (OUTLIER) cc_final: 0.7958 (p0) REVERT: A 269 GLN cc_start: 0.8963 (OUTLIER) cc_final: 0.8264 (mp10) REVERT: A 626 GLN cc_start: 0.8045 (pt0) cc_final: 0.7655 (pm20) REVERT: A 780 LYS cc_start: 0.8100 (mmtt) cc_final: 0.7842 (mmmt) REVERT: A 817 PHE cc_start: 0.8243 (t80) cc_final: 0.7909 (t80) REVERT: A 1132 TYR cc_start: 0.7885 (t80) cc_final: 0.7587 (t80) REVERT: B 1117 SER cc_start: 0.8694 (t) cc_final: 0.8400 (m) REVERT: B 1132 TYR cc_start: 0.7903 (t80) cc_final: 0.7201 (t80) REVERT: C 162 ASN cc_start: 0.7046 (t0) cc_final: 0.6743 (t0) REVERT: C 216 ARG cc_start: 0.8216 (OUTLIER) cc_final: 0.6549 (mmm160) REVERT: C 269 GLN cc_start: 0.8984 (OUTLIER) cc_final: 0.8531 (mt0) REVERT: C 562 GLN cc_start: 0.7620 (OUTLIER) cc_final: 0.7112 (tm-30) REVERT: C 673 HIS cc_start: 0.8000 (OUTLIER) cc_final: 0.7748 (t-170) REVERT: C 1117 SER cc_start: 0.8846 (t) cc_final: 0.8539 (m) REVERT: C 1132 TYR cc_start: 0.7913 (t80) cc_final: 0.7631 (t80) outliers start: 55 outliers final: 29 residues processed: 171 average time/residue: 0.5380 time to fit residues: 110.8609 Evaluate side-chains 148 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 113 time to evaluate : 1.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 CYS Chi-restraints excluded: chain A residue 146 ASN Chi-restraints excluded: chain A residue 156 ARG Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 269 GLN Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 334 CYS Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain A residue 514 GLU Chi-restraints excluded: chain A residue 600 THR Chi-restraints excluded: chain A residue 628 THR Chi-restraints excluded: chain A residue 733 THR Chi-restraints excluded: chain A residue 1130 THR Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 134 CYS Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 334 CYS Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 628 THR Chi-restraints excluded: chain B residue 708 ILE Chi-restraints excluded: chain B residue 971 LEU Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 134 CYS Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 216 ARG Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 269 GLN Chi-restraints excluded: chain C residue 334 CYS Chi-restraints excluded: chain C residue 562 GLN Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 628 THR Chi-restraints excluded: chain C residue 673 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 127 optimal weight: 6.9990 chunk 69 optimal weight: 0.8980 chunk 3 optimal weight: 6.9990 chunk 225 optimal weight: 9.9990 chunk 135 optimal weight: 7.9990 chunk 145 optimal weight: 1.9990 chunk 252 optimal weight: 0.7980 chunk 85 optimal weight: 4.9990 chunk 316 optimal weight: 2.9990 chunk 237 optimal weight: 4.9990 chunk 174 optimal weight: 5.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 278 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.106071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.075794 restraints weight = 47780.098| |-----------------------------------------------------------------------------| r_work (start): 0.3094 rms_B_bonded: 2.75 r_work: 0.2957 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2818 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8578 moved from start: 0.2991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 28424 Z= 0.212 Angle : 0.683 10.362 38862 Z= 0.338 Chirality : 0.049 0.435 4635 Planarity : 0.004 0.045 4860 Dihedral : 9.493 79.078 5641 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 1.54 % Allowed : 15.78 % Favored : 82.68 % 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 are not related in a simple way. whole: -0.20 (0.14), residues: 3369 helix: 1.81 (0.19), residues: 735 sheet: 0.57 (0.19), residues: 732 loop : -1.26 (0.13), residues: 1902 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C1085 TYR 0.021 0.002 TYR A 168 PHE 0.017 0.002 PHE A 173 TRP 0.018 0.002 TRP B 64 HIS 0.004 0.001 HIS C1058 Details of bonding type rmsd covalent geometry : bond 0.00502 (28284) covalent geometry : angle 0.64885 (38493) SS BOND : bond 0.00464 ( 45) SS BOND : angle 1.54981 ( 90) hydrogen bonds : bond 0.05750 ( 1086) hydrogen bonds : angle 5.88088 ( 2970) Misc. bond : bond 0.00443 ( 2) link_BETA1-4 : bond 0.00533 ( 33) link_BETA1-4 : angle 2.04864 ( 99) link_NAG-ASN : bond 0.00398 ( 60) link_NAG-ASN : angle 2.68808 ( 180) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6738 Ramachandran restraints generated. 3369 Oldfield, 0 Emsley, 3369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6738 Ramachandran restraints generated. 3369 Oldfield, 0 Emsley, 3369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 120 time to evaluate : 0.846 Fit side-chains revert: symmetry clash REVERT: A 146 ASN cc_start: 0.8602 (OUTLIER) cc_final: 0.7949 (p0) REVERT: A 269 GLN cc_start: 0.9056 (OUTLIER) cc_final: 0.8188 (mp10) REVERT: A 675 MET cc_start: 0.6279 (mmm) cc_final: 0.6046 (mmp) REVERT: A 817 PHE cc_start: 0.8328 (t80) cc_final: 0.8037 (t80) REVERT: A 1132 TYR cc_start: 0.7941 (t80) cc_final: 0.7700 (t80) REVERT: B 1117 SER cc_start: 0.8722 (t) cc_final: 0.8435 (m) REVERT: B 1132 TYR cc_start: 0.7919 (t80) cc_final: 0.7352 (t80) REVERT: C 162 ASN cc_start: 0.7288 (t0) cc_final: 0.7000 (t0) REVERT: C 216 ARG cc_start: 0.8305 (OUTLIER) cc_final: 0.6619 (mmm160) REVERT: C 269 GLN cc_start: 0.9055 (OUTLIER) cc_final: 0.8513 (mt0) REVERT: C 562 GLN cc_start: 0.7770 (OUTLIER) cc_final: 0.7017 (tm130) REVERT: C 1117 SER cc_start: 0.8894 (t) cc_final: 0.8564 (m) REVERT: C 1132 TYR cc_start: 0.7909 (t80) cc_final: 0.7647 (t80) outliers start: 45 outliers final: 27 residues processed: 162 average time/residue: 0.5211 time to fit residues: 102.9295 Evaluate side-chains 146 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 114 time to evaluate : 0.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 CYS Chi-restraints excluded: chain A residue 146 ASN Chi-restraints excluded: chain A residue 156 ARG Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 269 GLN Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 334 CYS Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain A residue 600 THR Chi-restraints excluded: chain A residue 733 THR Chi-restraints excluded: chain A residue 1130 THR Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 134 CYS Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 334 CYS Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 580 LEU Chi-restraints excluded: chain B residue 600 THR Chi-restraints excluded: chain B residue 708 ILE Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 134 CYS Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 216 ARG Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 269 GLN Chi-restraints excluded: chain C residue 334 CYS Chi-restraints excluded: chain C residue 401 LYS Chi-restraints excluded: chain C residue 562 GLN Chi-restraints excluded: chain C residue 600 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 125 optimal weight: 10.0000 chunk 253 optimal weight: 3.9990 chunk 211 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 297 optimal weight: 3.9990 chunk 51 optimal weight: 0.8980 chunk 284 optimal weight: 0.0470 chunk 335 optimal weight: 0.9990 chunk 195 optimal weight: 0.9990 chunk 292 optimal weight: 9.9990 chunk 179 optimal weight: 2.9990 overall best weight: 0.9884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 929 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.108135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.077773 restraints weight = 47786.770| |-----------------------------------------------------------------------------| r_work (start): 0.3131 rms_B_bonded: 2.78 r_work: 0.2997 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2860 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 moved from start: 0.3015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 28424 Z= 0.122 Angle : 0.615 10.218 38862 Z= 0.301 Chirality : 0.046 0.424 4635 Planarity : 0.004 0.045 4860 Dihedral : 9.226 74.013 5641 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 1.33 % Allowed : 16.12 % Favored : 82.55 % 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 are not related in a simple way. whole: -0.22 (0.14), residues: 3369 helix: 1.87 (0.19), residues: 735 sheet: 0.48 (0.19), residues: 714 loop : -1.26 (0.13), residues: 1920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 841 TYR 0.016 0.001 TYR C 503 PHE 0.017 0.001 PHE A 173 TRP 0.013 0.002 TRP A 880 HIS 0.003 0.001 HIS B 243 Details of bonding type rmsd covalent geometry : bond 0.00263 (28284) covalent geometry : angle 0.58135 (38493) SS BOND : bond 0.00279 ( 45) SS BOND : angle 1.23784 ( 90) hydrogen bonds : bond 0.04718 ( 1086) hydrogen bonds : angle 5.70372 ( 2970) Misc. bond : bond 0.00282 ( 2) link_BETA1-4 : bond 0.00601 ( 33) link_BETA1-4 : angle 2.01293 ( 99) link_NAG-ASN : bond 0.00378 ( 60) link_NAG-ASN : angle 2.52573 ( 180) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6738 Ramachandran restraints generated. 3369 Oldfield, 0 Emsley, 3369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6738 Ramachandran restraints generated. 3369 Oldfield, 0 Emsley, 3369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 119 time to evaluate : 0.775 Fit side-chains revert: symmetry clash REVERT: A 146 ASN cc_start: 0.8589 (OUTLIER) cc_final: 0.7921 (p0) REVERT: A 156 ARG cc_start: 0.7502 (OUTLIER) cc_final: 0.7240 (ptp-170) REVERT: A 269 GLN cc_start: 0.9021 (OUTLIER) cc_final: 0.8134 (mp10) REVERT: A 558 LEU cc_start: 0.8400 (OUTLIER) cc_final: 0.8146 (mt) REVERT: A 626 GLN cc_start: 0.8017 (pt0) cc_final: 0.7628 (pm20) REVERT: A 675 MET cc_start: 0.6323 (mmm) cc_final: 0.5984 (mmp) REVERT: A 817 PHE cc_start: 0.8290 (t80) cc_final: 0.8012 (t80) REVERT: A 1132 TYR cc_start: 0.7921 (t80) cc_final: 0.7629 (t80) REVERT: B 1117 SER cc_start: 0.8705 (t) cc_final: 0.8436 (m) REVERT: B 1132 TYR cc_start: 0.7952 (t80) cc_final: 0.7262 (t80) REVERT: C 162 ASN cc_start: 0.7229 (t0) cc_final: 0.6908 (t0) REVERT: C 216 ARG cc_start: 0.8379 (OUTLIER) cc_final: 0.6451 (mmm160) REVERT: C 269 GLN cc_start: 0.9040 (OUTLIER) cc_final: 0.8536 (mt0) REVERT: C 562 GLN cc_start: 0.7671 (OUTLIER) cc_final: 0.7180 (tm-30) REVERT: C 675 MET cc_start: 0.5670 (mmp) cc_final: 0.5464 (mmp) REVERT: C 1117 SER cc_start: 0.8822 (t) cc_final: 0.8514 (m) REVERT: C 1132 TYR cc_start: 0.7923 (t80) cc_final: 0.7624 (t80) outliers start: 39 outliers final: 22 residues processed: 157 average time/residue: 0.5318 time to fit residues: 100.7534 Evaluate side-chains 141 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 112 time to evaluate : 0.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 CYS Chi-restraints excluded: chain A residue 146 ASN Chi-restraints excluded: chain A residue 156 ARG Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 269 GLN Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 334 CYS Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain A residue 600 THR Chi-restraints excluded: chain A residue 1130 THR Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 134 CYS Chi-restraints excluded: chain B residue 334 CYS Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 600 THR Chi-restraints excluded: chain B residue 708 ILE Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 134 CYS Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 216 ARG Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 269 GLN Chi-restraints excluded: chain C residue 334 CYS Chi-restraints excluded: chain C residue 562 GLN Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 1130 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 189 optimal weight: 7.9990 chunk 220 optimal weight: 4.9990 chunk 199 optimal weight: 0.0010 chunk 119 optimal weight: 4.9990 chunk 193 optimal weight: 6.9990 chunk 191 optimal weight: 3.9990 chunk 12 optimal weight: 7.9990 chunk 108 optimal weight: 2.9990 chunk 325 optimal weight: 4.9990 chunk 214 optimal weight: 0.7980 chunk 139 optimal weight: 8.9990 overall best weight: 2.5592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 830 GLN B 929 GLN C 270 GLN C 830 GLN C 929 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.105309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.075031 restraints weight = 47713.207| |-----------------------------------------------------------------------------| r_work (start): 0.3082 rms_B_bonded: 2.74 r_work: 0.2944 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2805 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8591 moved from start: 0.3135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 28424 Z= 0.222 Angle : 0.696 10.134 38862 Z= 0.346 Chirality : 0.049 0.456 4635 Planarity : 0.005 0.045 4860 Dihedral : 9.325 77.006 5641 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 1.50 % Allowed : 15.74 % Favored : 82.75 % 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 are not related in a simple way. whole: -0.34 (0.14), residues: 3369 helix: 1.70 (0.19), residues: 735 sheet: 0.40 (0.19), residues: 759 loop : -1.35 (0.13), residues: 1875 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C1085 TYR 0.022 0.002 TYR A 168 PHE 0.019 0.002 PHE A 173 TRP 0.022 0.003 TRP C 150 HIS 0.004 0.001 HIS C1058 Details of bonding type rmsd covalent geometry : bond 0.00524 (28284) covalent geometry : angle 0.65897 (38493) SS BOND : bond 0.00472 ( 45) SS BOND : angle 1.58644 ( 90) hydrogen bonds : bond 0.05938 ( 1086) hydrogen bonds : angle 5.94209 ( 2970) Misc. bond : bond 0.00455 ( 2) link_BETA1-4 : bond 0.00540 ( 33) link_BETA1-4 : angle 2.09054 ( 99) link_NAG-ASN : bond 0.00402 ( 60) link_NAG-ASN : angle 2.83324 ( 180) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11275.22 seconds wall clock time: 191 minutes 54.58 seconds (11514.58 seconds total)