Starting phenix.real_space_refine on Mon Aug 25 16:50:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bt0_44878/08_2025/9bt0_44878.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bt0_44878/08_2025/9bt0_44878.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.23 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9bt0_44878/08_2025/9bt0_44878.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bt0_44878/08_2025/9bt0_44878.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9bt0_44878/08_2025/9bt0_44878.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bt0_44878/08_2025/9bt0_44878.map" } resolution = 2.23 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= -0.002 sd= 0.085 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 174 5.16 5 C 18651 2.51 5 N 4686 2.21 5 O 5862 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 98 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 29373 Number of models: 1 Model: "" Number of chains: 27 Chain: "C" Number of atoms: 9369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1194, 9369 Classifications: {'peptide': 1194} Link IDs: {'PCIS': 3, 'PTRANS': 46, 'TRANS': 1144} Chain breaks: 1 Chain: "B" Number of atoms: 9369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1194, 9369 Classifications: {'peptide': 1194} Link IDs: {'PCIS': 3, 'PTRANS': 46, 'TRANS': 1144} Chain breaks: 1 Chain: "A" Number of atoms: 9369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1194, 9369 Classifications: {'peptide': 1194} Link IDs: {'PCIS': 3, 'PTRANS': 46, 'TRANS': 1144} Chain breaks: 1 Chain: "D" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 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: "J" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "K" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "R" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Chain: "B" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Chain: "A" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Time building chain proxies: 6.45, per 1000 atoms: 0.22 Number of scatterers: 29373 At special positions: 0 Unit cell: (149.219, 148.32, 161.804, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 174 16.00 O 5862 8.00 N 4686 7.00 C 18651 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=72, symmetry=0 Simple disulfide: pdb=" SG CYS C 20 " - pdb=" SG CYS C 156 " distance=2.03 Simple disulfide: pdb=" SG CYS C 151 " - pdb=" SG CYS C 183 " distance=2.06 Simple disulfide: pdb=" SG CYS C 163 " - pdb=" SG CYS C 242 " distance=2.03 Simple disulfide: pdb=" SG CYS C 282 " - pdb=" SG CYS C 292 " distance=2.03 Simple disulfide: pdb=" SG CYS C 327 " - pdb=" SG CYS C 352 " distance=2.03 Simple disulfide: pdb=" SG CYS C 370 " - pdb=" SG CYS C 423 " distance=2.03 Simple disulfide: pdb=" SG CYS C 382 " - pdb=" SG CYS C 605 " distance=2.03 Simple disulfide: pdb=" SG CYS C 466 " - pdb=" SG CYS C 546 " distance=2.03 Simple disulfide: pdb=" SG CYS C 474 " - pdb=" SG CYS C 495 " distance=2.03 Simple disulfide: pdb=" SG CYS C 476 " - pdb=" SG CYS C 567 " distance=2.03 Simple disulfide: pdb=" SG CYS C 485 " - pdb=" SG CYS C 516 " distance=2.03 Simple disulfide: pdb=" SG CYS C 504 " - pdb=" SG CYS C 518 " distance=2.03 Simple disulfide: pdb=" SG CYS C 520 " - pdb=" SG CYS C 533 " distance=2.03 Simple disulfide: pdb=" SG CYS C 556 " - pdb=" SG CYS C 569 " distance=2.03 Simple disulfide: pdb=" SG CYS C 582 " - pdb=" SG CYS C 588 " distance=2.04 Simple disulfide: pdb=" SG CYS C 621 " - pdb=" SG CYS C 674 " distance=2.03 Simple disulfide: pdb=" SG CYS C 699 " - pdb=" SG CYS C 720 " distance=2.03 Simple disulfide: pdb=" SG CYS C 735 " - pdb=" SG CYS C 744 " distance=2.03 Simple disulfide: pdb=" SG CYS C 818 " - pdb=" SG CYS C 840 " distance=2.05 Simple disulfide: pdb=" SG CYS C 823 " - pdb=" SG CYS C 829 " distance=2.04 Simple disulfide: pdb=" SG CYS C 894 " - pdb=" SG CYS C 899 " distance=2.03 Simple disulfide: pdb=" SG CYS C 929 " - pdb=" SG CYS C 940 " distance=2.03 Simple disulfide: pdb=" SG CYS C1117 " - pdb=" SG CYS C1128 " distance=2.03 Simple disulfide: pdb=" SG CYS C1167 " - pdb=" SG CYS C1212 " distance=2.03 Simple disulfide: pdb=" SG CYS B 20 " - pdb=" SG CYS B 156 " distance=2.03 Simple disulfide: pdb=" SG CYS B 151 " - pdb=" SG CYS B 183 " distance=2.05 Simple disulfide: pdb=" SG CYS B 163 " - pdb=" SG CYS B 242 " distance=2.03 Simple disulfide: pdb=" SG CYS B 282 " - pdb=" SG CYS B 292 " distance=2.03 Simple disulfide: pdb=" SG CYS B 327 " - pdb=" SG CYS B 352 " distance=2.03 Simple disulfide: pdb=" SG CYS B 370 " - pdb=" SG CYS B 423 " distance=2.03 Simple disulfide: pdb=" SG CYS B 382 " - pdb=" SG CYS B 605 " distance=2.03 Simple disulfide: pdb=" SG CYS B 466 " - pdb=" SG CYS B 546 " distance=2.03 Simple disulfide: pdb=" SG CYS B 474 " - pdb=" SG CYS B 495 " distance=2.03 Simple disulfide: pdb=" SG CYS B 476 " - pdb=" SG CYS B 567 " distance=2.03 Simple disulfide: pdb=" SG CYS B 485 " - pdb=" SG CYS B 516 " distance=2.03 Simple disulfide: pdb=" SG CYS B 504 " - pdb=" SG CYS B 518 " distance=2.03 Simple disulfide: pdb=" SG CYS B 520 " - pdb=" SG CYS B 533 " distance=2.03 Simple disulfide: pdb=" SG CYS B 556 " - pdb=" SG CYS B 569 " distance=2.03 Simple disulfide: pdb=" SG CYS B 582 " - pdb=" SG CYS B 588 " distance=2.05 Simple disulfide: pdb=" SG CYS B 621 " - pdb=" SG CYS B 674 " distance=2.03 Simple disulfide: pdb=" SG CYS B 699 " - pdb=" SG CYS B 720 " distance=2.03 Simple disulfide: pdb=" SG CYS B 735 " - pdb=" SG CYS B 744 " distance=2.03 Simple disulfide: pdb=" SG CYS B 818 " - pdb=" SG CYS B 840 " distance=2.04 Simple disulfide: pdb=" SG CYS B 823 " - pdb=" SG CYS B 829 " distance=2.04 Simple disulfide: pdb=" SG CYS B 894 " - pdb=" SG CYS B 899 " distance=2.03 Simple disulfide: pdb=" SG CYS B 929 " - pdb=" SG CYS B 940 " distance=2.03 Simple disulfide: pdb=" SG CYS B1117 " - pdb=" SG CYS B1128 " distance=2.03 Simple disulfide: pdb=" SG CYS B1167 " - pdb=" SG CYS B1212 " distance=2.03 Simple disulfide: pdb=" SG CYS A 20 " - pdb=" SG CYS A 156 " distance=2.03 Simple disulfide: pdb=" SG CYS A 151 " - pdb=" SG CYS A 183 " distance=2.05 Simple disulfide: pdb=" SG CYS A 163 " - pdb=" SG CYS A 242 " distance=2.03 Simple disulfide: pdb=" SG CYS A 282 " - pdb=" SG CYS A 292 " distance=2.03 Simple disulfide: pdb=" SG CYS A 327 " - pdb=" SG CYS A 352 " distance=2.03 Simple disulfide: pdb=" SG CYS A 370 " - pdb=" SG CYS A 423 " distance=2.03 Simple disulfide: pdb=" SG CYS A 382 " - pdb=" SG CYS A 605 " distance=2.03 Simple disulfide: pdb=" SG CYS A 466 " - pdb=" SG CYS A 546 " distance=2.03 Simple disulfide: pdb=" SG CYS A 474 " - pdb=" SG CYS A 495 " distance=2.03 Simple disulfide: pdb=" SG CYS A 476 " - pdb=" SG CYS A 567 " distance=2.03 Simple disulfide: pdb=" SG CYS A 485 " - pdb=" SG CYS A 516 " distance=2.03 Simple disulfide: pdb=" SG CYS A 504 " - pdb=" SG CYS A 518 " distance=2.03 Simple disulfide: pdb=" SG CYS A 520 " - pdb=" SG CYS A 533 " distance=2.03 Simple disulfide: pdb=" SG CYS A 556 " - pdb=" SG CYS A 569 " distance=2.03 Simple disulfide: pdb=" SG CYS A 582 " - pdb=" SG CYS A 588 " distance=2.04 Simple disulfide: pdb=" SG CYS A 621 " - pdb=" SG CYS A 674 " distance=2.03 Simple disulfide: pdb=" SG CYS A 699 " - pdb=" SG CYS A 720 " distance=2.03 Simple disulfide: pdb=" SG CYS A 735 " - pdb=" SG CYS A 744 " distance=2.03 Simple disulfide: pdb=" SG CYS A 818 " - pdb=" SG CYS A 840 " distance=2.04 Simple disulfide: pdb=" SG CYS A 823 " - pdb=" SG CYS A 829 " distance=2.04 Simple disulfide: pdb=" SG CYS A 894 " - pdb=" SG CYS A 899 " distance=2.03 Simple disulfide: pdb=" SG CYS A 929 " - pdb=" SG CYS A 940 " distance=2.03 Simple disulfide: pdb=" SG CYS A1117 " - pdb=" SG CYS A1128 " distance=2.03 Simple disulfide: pdb=" SG CYS A1167 " - pdb=" SG CYS A1212 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA D 3 " - " MAN D 4 " " BMA K 3 " - " MAN K 4 " " BMA R 3 " - " MAN R 4 " ALPHA1-6 " BMA D 3 " - " MAN D 5 " " BMA K 3 " - " MAN K 5 " " BMA R 3 " - " MAN R 5 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " 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 J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " NAG-ASN " NAG A1401 " - " ASN A 19 " " NAG A1402 " - " ASN A 58 " " NAG A1403 " - " ASN A 171 " " NAG A1404 " - " ASN A 192 " " NAG A1405 " - " ASN A 251 " " NAG A1406 " - " ASN A 433 " " NAG A1407 " - " ASN A 454 " " NAG A1408 " - " ASN A 470 " " NAG A1409 " - " ASN A 564 " " NAG A1410 " - " ASN A 775 " " NAG A1411 " - " ASN A 780 " " NAG A1412 " - " ASN A 797 " " NAG A1413 " - " ASN A 928 " " NAG B1401 " - " ASN B 19 " " NAG B1402 " - " ASN B 58 " " NAG B1403 " - " ASN B 171 " " NAG B1404 " - " ASN B 192 " " NAG B1405 " - " ASN B 251 " " NAG B1406 " - " ASN B 433 " " NAG B1407 " - " ASN B 454 " " NAG B1408 " - " ASN B 470 " " NAG B1409 " - " ASN B 564 " " NAG B1410 " - " ASN B 775 " " NAG B1411 " - " ASN B 780 " " NAG B1412 " - " ASN B 797 " " NAG B1413 " - " ASN B 928 " " NAG C1401 " - " ASN C 19 " " NAG C1402 " - " ASN C 58 " " NAG C1403 " - " ASN C 171 " " NAG C1404 " - " ASN C 192 " " NAG C1405 " - " ASN C 251 " " NAG C1406 " - " ASN C 433 " " NAG C1407 " - " ASN C 454 " " NAG C1408 " - " ASN C 470 " " NAG C1409 " - " ASN C 564 " " NAG C1410 " - " ASN C 775 " " NAG C1411 " - " ASN C 780 " " NAG C1412 " - " ASN C 797 " " NAG C1413 " - " ASN C 928 " " NAG D 1 " - " ASN C 132 " " NAG E 1 " - " ASN C 188 " " NAG F 1 " - " ASN C 355 " " NAG G 1 " - " ASN C 666 " " NAG H 1 " - " ASN C 705 " " NAG I 1 " - " ASN C 726 " " NAG J 1 " - " ASN C1215 " " NAG K 1 " - " ASN B 132 " " NAG L 1 " - " ASN B 188 " " NAG M 1 " - " ASN B 355 " " NAG N 1 " - " ASN B 666 " " NAG O 1 " - " ASN B 705 " " NAG P 1 " - " ASN B 726 " " NAG Q 1 " - " ASN B1215 " " NAG R 1 " - " ASN A 132 " " NAG S 1 " - " ASN A 188 " " NAG T 1 " - " ASN A 355 " " NAG U 1 " - " ASN A 666 " " NAG V 1 " - " ASN A 705 " " NAG W 1 " - " ASN A 726 " " NAG X 1 " - " ASN A1215 " Time building additional restraints: 1.94 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 953.7 nanoseconds 7140 Ramachandran restraints generated. 3570 Oldfield, 0 Emsley, 3570 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6756 Finding SS restraints... Secondary structure from input PDB file: 92 helices and 67 sheets defined 27.2% alpha, 32.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.49 Creating SS restraints... Processing helix chain 'C' and resid 88 through 91 Processing helix chain 'C' and resid 285 through 295 Processing helix chain 'C' and resid 328 through 334 Processing helix chain 'C' and resid 341 through 344 removed outlier: 3.614A pdb=" N TRP C 344 " --> pdb=" O PRO C 341 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 341 through 344' Processing helix chain 'C' and resid 355 through 363 Processing helix chain 'C' and resid 374 through 379 removed outlier: 3.508A pdb=" N ILE C 378 " --> pdb=" O ASP C 374 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N TYR C 379 " --> pdb=" O GLU C 375 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 374 through 379' Processing helix chain 'C' and resid 394 through 402 removed outlier: 4.967A pdb=" N SER C 399 " --> pdb=" O SER C 396 " (cutoff:3.500A) Processing helix chain 'C' and resid 407 through 413 Processing helix chain 'C' and resid 442 through 448 Processing helix chain 'C' and resid 478 through 485 removed outlier: 3.627A pdb=" N SER C 484 " --> pdb=" O SER C 480 " (cutoff:3.500A) Processing helix chain 'C' and resid 552 through 556 Processing helix chain 'C' and resid 570 through 574 removed outlier: 3.697A pdb=" N PHE C 574 " --> pdb=" O THR C 571 " (cutoff:3.500A) Processing helix chain 'C' and resid 698 through 706 Processing helix chain 'C' and resid 817 through 824 Processing helix chain 'C' and resid 826 through 836 removed outlier: 3.547A pdb=" N TYR C 836 " --> pdb=" O LEU C 832 " (cutoff:3.500A) Processing helix chain 'C' and resid 838 through 867 Processing helix chain 'C' and resid 889 through 892 Processing helix chain 'C' and resid 896 through 900 removed outlier: 3.859A pdb=" N CYS C 899 " --> pdb=" O GLY C 896 " (cutoff:3.500A) Processing helix chain 'C' and resid 905 through 914 removed outlier: 3.959A pdb=" N LYS C 914 " --> pdb=" O LEU C 910 " (cutoff:3.500A) Processing helix chain 'C' and resid 918 through 928 Processing helix chain 'C' and resid 929 through 931 No H-bonds generated for 'chain 'C' and resid 929 through 931' Processing helix chain 'C' and resid 937 through 945 Processing helix chain 'C' and resid 955 through 969 Processing helix chain 'C' and resid 982 through 993 Processing helix chain 'C' and resid 997 through 1004 removed outlier: 3.567A pdb=" N LEU C1001 " --> pdb=" O THR C 997 " (cutoff:3.500A) Processing helix chain 'C' and resid 1004 through 1022 Processing helix chain 'C' and resid 1023 through 1025 No H-bonds generated for 'chain 'C' and resid 1023 through 1025' Processing helix chain 'C' and resid 1027 through 1050 removed outlier: 3.523A pdb=" N VAL C1037 " --> pdb=" O ILE C1033 " (cutoff:3.500A) Processing helix chain 'C' and resid 1051 through 1053 No H-bonds generated for 'chain 'C' and resid 1051 through 1053' Processing helix chain 'C' and resid 1061 through 1069 Processing helix chain 'C' and resid 1070 through 1117 removed outlier: 3.962A pdb=" N VAL C1076 " --> pdb=" O PRO C1072 " (cutoff:3.500A) Processing helix chain 'C' and resid 1202 through 1204 No H-bonds generated for 'chain 'C' and resid 1202 through 1204' Processing helix chain 'B' and resid 88 through 91 Processing helix chain 'B' and resid 285 through 295 Processing helix chain 'B' and resid 328 through 334 Processing helix chain 'B' and resid 355 through 363 Processing helix chain 'B' and resid 374 through 379 removed outlier: 3.977A pdb=" N TYR B 379 " --> pdb=" O GLU B 375 " (cutoff:3.500A) Processing helix chain 'B' and resid 394 through 402 removed outlier: 4.874A pdb=" N SER B 399 " --> pdb=" O SER B 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 413 Processing helix chain 'B' and resid 432 through 434 No H-bonds generated for 'chain 'B' and resid 432 through 434' Processing helix chain 'B' and resid 442 through 448 Processing helix chain 'B' and resid 478 through 485 removed outlier: 3.780A pdb=" N SER B 484 " --> pdb=" O SER B 480 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N CYS B 485 " --> pdb=" O PHE B 481 " (cutoff:3.500A) Processing helix chain 'B' and resid 552 through 556 Processing helix chain 'B' and resid 570 through 574 Processing helix chain 'B' and resid 698 through 706 Processing helix chain 'B' and resid 817 through 824 Processing helix chain 'B' and resid 826 through 836 removed outlier: 3.530A pdb=" N GLU B 835 " --> pdb=" O ASP B 831 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N TYR B 836 " --> pdb=" O LEU B 832 " (cutoff:3.500A) Processing helix chain 'B' and resid 837 through 867 removed outlier: 4.563A pdb=" N ASP B 841 " --> pdb=" O GLY B 837 " (cutoff:3.500A) Processing helix chain 'B' and resid 896 through 904 removed outlier: 3.518A pdb=" N CYS B 899 " --> pdb=" O GLY B 896 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N SER B 901 " --> pdb=" O HIS B 898 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N SER B 902 " --> pdb=" O CYS B 899 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N SER B 903 " --> pdb=" O GLY B 900 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ARG B 904 " --> pdb=" O SER B 901 " (cutoff:3.500A) Processing helix chain 'B' and resid 905 through 913 Processing helix chain 'B' and resid 918 through 928 Processing helix chain 'B' and resid 929 through 931 No H-bonds generated for 'chain 'B' and resid 929 through 931' Processing helix chain 'B' and resid 937 through 945 Processing helix chain 'B' and resid 955 through 972 removed outlier: 4.046A pdb=" N ALA B 970 " --> pdb=" O ALA B 966 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N MET B 971 " --> pdb=" O THR B 967 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N PHE B 972 " --> pdb=" O VAL B 968 " (cutoff:3.500A) Processing helix chain 'B' and resid 982 through 993 Processing helix chain 'B' and resid 997 through 1004 removed outlier: 3.553A pdb=" N LEU B1001 " --> pdb=" O THR B 997 " (cutoff:3.500A) Processing helix chain 'B' and resid 1004 through 1023 Processing helix chain 'B' and resid 1027 through 1050 removed outlier: 3.503A pdb=" N VAL B1036 " --> pdb=" O LYS B1032 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N VAL B1037 " --> pdb=" O ILE B1033 " (cutoff:3.500A) Processing helix chain 'B' and resid 1051 through 1053 No H-bonds generated for 'chain 'B' and resid 1051 through 1053' Processing helix chain 'B' and resid 1061 through 1069 Processing helix chain 'B' and resid 1070 through 1117 removed outlier: 3.676A pdb=" N VAL B1076 " --> pdb=" O PRO B1072 " (cutoff:3.500A) Processing helix chain 'B' and resid 1202 through 1204 No H-bonds generated for 'chain 'B' and resid 1202 through 1204' Processing helix chain 'A' and resid 88 through 91 removed outlier: 3.554A pdb=" N GLN A 91 " --> pdb=" O LEU A 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 88 through 91' Processing helix chain 'A' and resid 285 through 295 Processing helix chain 'A' and resid 328 through 334 Processing helix chain 'A' and resid 341 through 344 removed outlier: 3.577A pdb=" N TRP A 344 " --> pdb=" O PRO A 341 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 341 through 344' Processing helix chain 'A' and resid 355 through 363 Processing helix chain 'A' and resid 374 through 378 Processing helix chain 'A' and resid 394 through 402 removed outlier: 4.821A pdb=" N SER A 399 " --> pdb=" O SER A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 413 Processing helix chain 'A' and resid 442 through 448 Processing helix chain 'A' and resid 478 through 485 Processing helix chain 'A' and resid 552 through 556 Processing helix chain 'A' and resid 570 through 574 removed outlier: 3.809A pdb=" N PHE A 574 " --> pdb=" O THR A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 698 through 706 Processing helix chain 'A' and resid 817 through 824 Processing helix chain 'A' and resid 826 through 835 removed outlier: 3.527A pdb=" N GLU A 835 " --> pdb=" O ASP A 831 " (cutoff:3.500A) Processing helix chain 'A' and resid 838 through 867 Processing helix chain 'A' and resid 896 through 904 removed outlier: 6.964A pdb=" N SER A 901 " --> pdb=" O HIS A 898 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N SER A 902 " --> pdb=" O CYS A 899 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N SER A 903 " --> pdb=" O GLY A 900 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ARG A 904 " --> pdb=" O SER A 901 " (cutoff:3.500A) Processing helix chain 'A' and resid 905 through 913 Processing helix chain 'A' and resid 918 through 928 Processing helix chain 'A' and resid 929 through 931 No H-bonds generated for 'chain 'A' and resid 929 through 931' Processing helix chain 'A' and resid 937 through 945 Processing helix chain 'A' and resid 955 through 972 removed outlier: 4.059A pdb=" N ALA A 970 " --> pdb=" O ALA A 966 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N MET A 971 " --> pdb=" O THR A 967 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N PHE A 972 " --> pdb=" O VAL A 968 " (cutoff:3.500A) Processing helix chain 'A' and resid 982 through 993 Processing helix chain 'A' and resid 997 through 1004 removed outlier: 3.575A pdb=" N LEU A1001 " --> pdb=" O THR A 997 " (cutoff:3.500A) Processing helix chain 'A' and resid 1004 through 1022 Processing helix chain 'A' and resid 1027 through 1050 removed outlier: 3.516A pdb=" N VAL A1036 " --> pdb=" O LYS A1032 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N VAL A1037 " --> pdb=" O ILE A1033 " (cutoff:3.500A) Processing helix chain 'A' and resid 1051 through 1053 No H-bonds generated for 'chain 'A' and resid 1051 through 1053' Processing helix chain 'A' and resid 1061 through 1069 Processing helix chain 'A' and resid 1070 through 1117 removed outlier: 3.868A pdb=" N VAL A1076 " --> pdb=" O PRO A1072 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ARG A1080 " --> pdb=" O VAL A1076 " (cutoff:3.500A) Processing helix chain 'A' and resid 1202 through 1204 No H-bonds generated for 'chain 'A' and resid 1202 through 1204' Processing sheet with id=AA1, first strand: chain 'C' and resid 25 through 26 Processing sheet with id=AA2, first strand: chain 'C' and resid 37 through 39 removed outlier: 8.189A pdb=" N ASN C 73 " --> pdb=" O PRO C 260 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N GLY C 101 " --> pdb=" O LEU C 261 " (cutoff:3.500A) removed outlier: 5.833A pdb=" N TYR C 213 " --> pdb=" O PHE C 222 " (cutoff:3.500A) removed outlier: 5.244A pdb=" N PHE C 222 " --> pdb=" O TYR C 213 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 59 through 68 removed outlier: 3.755A pdb=" N ASN C 278 " --> pdb=" O LYS C 269 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 54 through 56 removed outlier: 5.984A pdb=" N VAL C 55 " --> pdb=" O TYR A 651 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N ILE A 658 " --> pdb=" O ILE A 671 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N THR A 668 " --> pdb=" O VAL A 638 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ALA A 315 " --> pdb=" O CYS A 621 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 80 through 81 removed outlier: 8.044A pdb=" N THR C 241 " --> pdb=" O PRO C 159 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N THR C 161 " --> pdb=" O THR C 241 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N TRP C 174 " --> pdb=" O CYS C 156 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 96 through 97 removed outlier: 4.283A pdb=" N THR C 123 " --> pdb=" O LEU C 238 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N PHE C 185 " --> pdb=" O ALA C 150 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 109 through 113 Processing sheet with id=AA8, first strand: chain 'C' and resid 302 through 305 Processing sheet with id=AA9, first strand: chain 'C' and resid 309 through 310 Processing sheet with id=AB1, first strand: chain 'C' and resid 315 through 319 removed outlier: 3.964A pdb=" N ALA C 315 " --> pdb=" O CYS C 621 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N THR C 668 " --> pdb=" O VAL C 638 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N ILE C 658 " --> pdb=" O ILE C 671 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 337 through 339 removed outlier: 6.728A pdb=" N VAL C 338 " --> pdb=" O ASN C 437 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'C' and resid 345 through 349 removed outlier: 6.413A pdb=" N PHE C 383 " --> pdb=" O ILE C 599 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N ILE C 599 " --> pdb=" O PHE C 383 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N SER C 428 " --> pdb=" O THR C 365 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N THR C 365 " --> pdb=" O SER C 428 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 353 through 354 removed outlier: 6.413A pdb=" N PHE C 383 " --> pdb=" O ILE C 599 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N ILE C 599 " --> pdb=" O PHE C 383 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 459 through 463 Processing sheet with id=AB6, first strand: chain 'C' and resid 466 through 468 removed outlier: 4.207A pdb=" N CYS C 466 " --> pdb=" O SER C 538 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 504 through 507 Processing sheet with id=AB8, first strand: chain 'C' and resid 724 through 732 removed outlier: 6.398A pdb=" N ASP C 725 " --> pdb=" O PHE C 768 " (cutoff:3.500A) removed outlier: 8.319A pdb=" N THR C 770 " --> pdb=" O ASP C 725 " (cutoff:3.500A) removed outlier: 9.362A pdb=" N LEU C 727 " --> pdb=" O THR C 770 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N PHE C 743 " --> pdb=" O MET C 739 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 777 through 779 removed outlier: 6.135A pdb=" N SER C 777 " --> pdb=" O LEU B 871 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'C' and resid 790 through 808 removed outlier: 6.839A pdb=" N GLU C 791 " --> pdb=" O LEU C1161 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N LEU C1161 " --> pdb=" O GLU C 791 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N LYS C 793 " --> pdb=" O THR C1159 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N THR C1159 " --> pdb=" O LYS C 793 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N PHE C1157 " --> pdb=" O PRO C 795 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N ASN C 797 " --> pdb=" O ILE C1155 " (cutoff:3.500A) removed outlier: 5.925A pdb=" N TYR C1152 " --> pdb=" O HIS C1133 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N HIS C1133 " --> pdb=" O TYR C1152 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 790 through 808 removed outlier: 6.839A pdb=" N GLU C 791 " --> pdb=" O LEU C1161 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N LEU C1161 " --> pdb=" O GLU C 791 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N LYS C 793 " --> pdb=" O THR C1159 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N THR C1159 " --> pdb=" O LYS C 793 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N PHE C1157 " --> pdb=" O PRO C 795 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N ASN C 797 " --> pdb=" O ILE C1155 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N LEU C1161 " --> pdb=" O LYS C1183 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N LYS C1183 " --> pdb=" O LEU C1161 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N GLY C1192 " --> pdb=" O TYR C1197 " (cutoff:3.500A) removed outlier: 5.390A pdb=" N TYR C1197 " --> pdb=" O GLY C1192 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 813 through 816 removed outlier: 3.934A pdb=" N LYS C 813 " --> pdb=" O LEU C 950 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 870 through 872 Processing sheet with id=AC5, first strand: chain 'C' and resid 882 through 883 Processing sheet with id=AC6, first strand: chain 'C' and resid 1206 through 1209 removed outlier: 5.862A pdb=" N CYS C1167 " --> pdb=" O ALA C1219 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 25 through 26 Processing sheet with id=AC8, first strand: chain 'B' and resid 37 through 39 removed outlier: 8.208A pdb=" N ASN B 73 " --> pdb=" O PRO B 260 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N GLY B 101 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N TYR B 213 " --> pdb=" O PHE B 222 " (cutoff:3.500A) removed outlier: 5.247A pdb=" N PHE B 222 " --> pdb=" O TYR B 213 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 59 through 68 removed outlier: 3.768A pdb=" N ASN B 278 " --> pdb=" O LYS B 269 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 80 through 81 removed outlier: 8.044A pdb=" N THR B 241 " --> pdb=" O PRO B 159 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N THR B 161 " --> pdb=" O THR B 241 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N TRP B 174 " --> pdb=" O CYS B 156 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 96 through 97 Processing sheet with id=AD3, first strand: chain 'B' and resid 109 through 113 Processing sheet with id=AD4, first strand: chain 'B' and resid 302 through 305 Processing sheet with id=AD5, first strand: chain 'B' and resid 309 through 310 Processing sheet with id=AD6, first strand: chain 'B' and resid 315 through 319 removed outlier: 3.884A pdb=" N ALA B 315 " --> pdb=" O CYS B 621 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N THR B 668 " --> pdb=" O VAL B 638 " (cutoff:3.500A) removed outlier: 5.217A pdb=" N ILE B 658 " --> pdb=" O ILE B 671 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 337 through 339 removed outlier: 6.679A pdb=" N VAL B 338 " --> pdb=" O ASN B 437 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD7 Processing sheet with id=AD8, first strand: chain 'B' and resid 345 through 349 removed outlier: 6.399A pdb=" N PHE B 383 " --> pdb=" O ILE B 599 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N ILE B 599 " --> pdb=" O PHE B 383 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N SER B 428 " --> pdb=" O THR B 365 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N THR B 365 " --> pdb=" O SER B 428 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 353 through 354 removed outlier: 6.399A pdb=" N PHE B 383 " --> pdb=" O ILE B 599 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N ILE B 599 " --> pdb=" O PHE B 383 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 459 through 463 Processing sheet with id=AE2, first strand: chain 'B' and resid 467 through 468 Processing sheet with id=AE3, first strand: chain 'B' and resid 504 through 507 Processing sheet with id=AE4, first strand: chain 'B' and resid 724 through 732 removed outlier: 6.389A pdb=" N ASP B 725 " --> pdb=" O PHE B 768 " (cutoff:3.500A) removed outlier: 8.346A pdb=" N THR B 770 " --> pdb=" O ASP B 725 " (cutoff:3.500A) removed outlier: 9.373A pdb=" N LEU B 727 " --> pdb=" O THR B 770 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N PHE B 743 " --> pdb=" O MET B 739 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'B' and resid 777 through 779 removed outlier: 6.086A pdb=" N SER B 777 " --> pdb=" O LEU A 871 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE5 Processing sheet with id=AE6, first strand: chain 'B' and resid 790 through 808 removed outlier: 6.848A pdb=" N GLU B 791 " --> pdb=" O LEU B1161 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N LEU B1161 " --> pdb=" O GLU B 791 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N LYS B 793 " --> pdb=" O THR B1159 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N THR B1159 " --> pdb=" O LYS B 793 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N PHE B1157 " --> pdb=" O PRO B 795 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N ASN B 797 " --> pdb=" O ILE B1155 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N TYR B1152 " --> pdb=" O HIS B1133 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N HIS B1133 " --> pdb=" O TYR B1152 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'B' and resid 790 through 808 removed outlier: 6.848A pdb=" N GLU B 791 " --> pdb=" O LEU B1161 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N LEU B1161 " --> pdb=" O GLU B 791 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N LYS B 793 " --> pdb=" O THR B1159 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N THR B1159 " --> pdb=" O LYS B 793 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N PHE B1157 " --> pdb=" O PRO B 795 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N ASN B 797 " --> pdb=" O ILE B1155 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N LEU B1161 " --> pdb=" O LYS B1183 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N LYS B1183 " --> pdb=" O LEU B1161 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N GLY B1192 " --> pdb=" O TYR B1197 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N TYR B1197 " --> pdb=" O GLY B1192 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'B' and resid 813 through 816 removed outlier: 3.977A pdb=" N LYS B 813 " --> pdb=" O LEU B 950 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'B' and resid 882 through 883 Processing sheet with id=AF1, first strand: chain 'B' and resid 1206 through 1209 removed outlier: 5.780A pdb=" N CYS B1167 " --> pdb=" O ALA B1219 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'A' and resid 25 through 26 Processing sheet with id=AF3, first strand: chain 'A' and resid 37 through 39 removed outlier: 8.240A pdb=" N ASN A 73 " --> pdb=" O PRO A 260 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N GLY A 101 " --> pdb=" O LEU A 261 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N PHE A 209 " --> pdb=" O SER A 225 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N SER A 225 " --> pdb=" O PHE A 209 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N ALA A 211 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'A' and resid 59 through 67 removed outlier: 3.722A pdb=" N ASN A 278 " --> pdb=" O LYS A 269 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'A' and resid 80 through 81 removed outlier: 8.073A pdb=" N THR A 241 " --> pdb=" O PRO A 159 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N THR A 161 " --> pdb=" O THR A 241 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N TRP A 174 " --> pdb=" O CYS A 156 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'A' and resid 96 through 97 Processing sheet with id=AF7, first strand: chain 'A' and resid 109 through 113 Processing sheet with id=AF8, first strand: chain 'A' and resid 302 through 305 Processing sheet with id=AF9, first strand: chain 'A' and resid 309 through 310 Processing sheet with id=AG1, first strand: chain 'A' and resid 337 through 339 removed outlier: 6.763A pdb=" N VAL A 338 " --> pdb=" O ASN A 437 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG1 Processing sheet with id=AG2, first strand: chain 'A' and resid 345 through 349 removed outlier: 6.625A pdb=" N SER A 428 " --> pdb=" O THR A 365 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N THR A 365 " --> pdb=" O SER A 428 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'A' and resid 345 through 349 Processing sheet with id=AG4, first strand: chain 'A' and resid 353 through 354 Processing sheet with id=AG5, first strand: chain 'A' and resid 459 through 463 Processing sheet with id=AG6, first strand: chain 'A' and resid 467 through 468 Processing sheet with id=AG7, first strand: chain 'A' and resid 504 through 509 removed outlier: 5.904A pdb=" N VAL A 509 " --> pdb=" O THR A 513 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N THR A 513 " --> pdb=" O VAL A 509 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'A' and resid 724 through 732 removed outlier: 6.436A pdb=" N ASP A 725 " --> pdb=" O PHE A 768 " (cutoff:3.500A) removed outlier: 8.339A pdb=" N THR A 770 " --> pdb=" O ASP A 725 " (cutoff:3.500A) removed outlier: 9.464A pdb=" N LEU A 727 " --> pdb=" O THR A 770 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N PHE A 743 " --> pdb=" O MET A 739 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'A' and resid 790 through 808 removed outlier: 6.880A pdb=" N GLU A 791 " --> pdb=" O LEU A1161 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N LEU A1161 " --> pdb=" O GLU A 791 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N LYS A 793 " --> pdb=" O THR A1159 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N THR A1159 " --> pdb=" O LYS A 793 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N PHE A1157 " --> pdb=" O PRO A 795 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N ASN A 797 " --> pdb=" O ILE A1155 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N TYR A1152 " --> pdb=" O HIS A1133 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N HIS A1133 " --> pdb=" O TYR A1152 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'A' and resid 790 through 808 removed outlier: 6.880A pdb=" N GLU A 791 " --> pdb=" O LEU A1161 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N LEU A1161 " --> pdb=" O GLU A 791 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N LYS A 793 " --> pdb=" O THR A1159 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N THR A1159 " --> pdb=" O LYS A 793 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N PHE A1157 " --> pdb=" O PRO A 795 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N ASN A 797 " --> pdb=" O ILE A1155 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N LEU A1161 " --> pdb=" O LYS A1183 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N LYS A1183 " --> pdb=" O LEU A1161 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'A' and resid 813 through 816 removed outlier: 3.964A pdb=" N LYS A 813 " --> pdb=" O LEU A 950 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'A' and resid 882 through 883 Processing sheet with id=AH4, first strand: chain 'A' and resid 1206 through 1209 removed outlier: 5.763A pdb=" N CYS A1167 " --> pdb=" O ALA A1219 " (cutoff:3.500A) 1243 hydrogen bonds defined for protein. 3411 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: 6.73 Time building geometry restraints manager: 2.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 9042 1.34 - 1.46: 7814 1.46 - 1.59: 13014 1.59 - 1.71: 1 1.71 - 1.84: 204 Bond restraints: 30075 Sorted by residual: bond pdb=" C3 BMA D 3 " pdb=" O3 BMA D 3 " ideal model delta sigma weight residual 1.406 1.484 -0.078 2.00e-02 2.50e+03 1.53e+01 bond pdb=" C3 BMA K 3 " pdb=" O3 BMA K 3 " ideal model delta sigma weight residual 1.406 1.482 -0.076 2.00e-02 2.50e+03 1.44e+01 bond pdb=" C3 BMA R 3 " pdb=" O3 BMA R 3 " ideal model delta sigma weight residual 1.406 1.480 -0.074 2.00e-02 2.50e+03 1.38e+01 bond pdb=" C1 MAN R 4 " pdb=" O5 MAN R 4 " ideal model delta sigma weight residual 1.399 1.473 -0.074 2.00e-02 2.50e+03 1.37e+01 bond pdb=" C1 MAN K 5 " pdb=" O5 MAN K 5 " ideal model delta sigma weight residual 1.399 1.473 -0.074 2.00e-02 2.50e+03 1.36e+01 ... (remaining 30070 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.66: 40073 2.66 - 5.32: 824 5.32 - 7.99: 34 7.99 - 10.65: 4 10.65 - 13.31: 3 Bond angle restraints: 40938 Sorted by residual: angle pdb=" N CYS C 183 " pdb=" CA CYS C 183 " pdb=" C CYS C 183 " ideal model delta sigma weight residual 108.79 122.10 -13.31 1.53e+00 4.27e-01 7.57e+01 angle pdb=" CA PRO B 490 " pdb=" N PRO B 490 " pdb=" CD PRO B 490 " ideal model delta sigma weight residual 112.00 101.58 10.42 1.40e+00 5.10e-01 5.54e+01 angle pdb=" CA ASP C 366 " pdb=" CB ASP C 366 " pdb=" CG ASP C 366 " ideal model delta sigma weight residual 112.60 118.84 -6.24 1.00e+00 1.00e+00 3.90e+01 angle pdb=" C LEU C 52 " pdb=" CA LEU C 52 " pdb=" CB LEU C 52 " ideal model delta sigma weight residual 116.54 110.00 6.54 1.15e+00 7.56e-01 3.24e+01 angle pdb=" CB HIS B 234 " pdb=" CG HIS B 234 " pdb=" CD2 HIS B 234 " ideal model delta sigma weight residual 131.20 124.16 7.04 1.30e+00 5.92e-01 2.94e+01 ... (remaining 40933 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.66: 17980 21.66 - 43.31: 821 43.31 - 64.97: 173 64.97 - 86.63: 61 86.63 - 108.28: 27 Dihedral angle restraints: 19062 sinusoidal: 8535 harmonic: 10527 Sorted by residual: dihedral pdb=" CB CYS C 20 " pdb=" SG CYS C 20 " pdb=" SG CYS C 156 " pdb=" CB CYS C 156 " ideal model delta sinusoidal sigma weight residual 93.00 28.62 64.38 1 1.00e+01 1.00e-02 5.45e+01 dihedral pdb=" CB CYS B 894 " pdb=" SG CYS B 894 " pdb=" SG CYS B 899 " pdb=" CB CYS B 899 " ideal model delta sinusoidal sigma weight residual 93.00 39.61 53.39 1 1.00e+01 1.00e-02 3.88e+01 dihedral pdb=" CB CYS C 894 " pdb=" SG CYS C 894 " pdb=" SG CYS C 899 " pdb=" CB CYS C 899 " ideal model delta sinusoidal sigma weight residual 93.00 42.39 50.61 1 1.00e+01 1.00e-02 3.51e+01 ... (remaining 19059 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.097: 4452 0.097 - 0.194: 368 0.194 - 0.291: 31 0.291 - 0.388: 4 0.388 - 0.485: 2 Chirality restraints: 4857 Sorted by residual: chirality pdb=" C1 NAG D 2 " pdb=" O4 NAG D 1 " pdb=" C2 NAG D 2 " pdb=" O5 NAG D 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.56 0.16 2.00e-02 2.50e+03 6.76e+01 chirality pdb=" C1 BMA D 3 " pdb=" O4 NAG D 2 " pdb=" C2 BMA D 3 " pdb=" O5 BMA D 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.56 0.16 2.00e-02 2.50e+03 6.08e+01 chirality pdb=" C1 BMA R 3 " pdb=" O4 NAG R 2 " pdb=" C2 BMA R 3 " pdb=" O5 BMA R 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.55 0.15 2.00e-02 2.50e+03 5.62e+01 ... (remaining 4854 not shown) Planarity restraints: 5190 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 132 " 0.105 2.00e-02 2.50e+03 1.06e-01 1.41e+02 pdb=" CG ASN A 132 " -0.075 2.00e-02 2.50e+03 pdb=" OD1 ASN A 132 " -0.001 2.00e-02 2.50e+03 pdb=" ND2 ASN A 132 " -0.155 2.00e-02 2.50e+03 pdb=" C1 NAG R 1 " 0.126 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 132 " -0.098 2.00e-02 2.50e+03 9.75e-02 1.19e+02 pdb=" CG ASN B 132 " 0.073 2.00e-02 2.50e+03 pdb=" OD1 ASN B 132 " 0.000 2.00e-02 2.50e+03 pdb=" ND2 ASN B 132 " 0.140 2.00e-02 2.50e+03 pdb=" C1 NAG K 1 " -0.115 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 132 " 0.084 2.00e-02 2.50e+03 8.28e-02 8.57e+01 pdb=" CG ASN C 132 " -0.062 2.00e-02 2.50e+03 pdb=" OD1 ASN C 132 " -0.003 2.00e-02 2.50e+03 pdb=" ND2 ASN C 132 " -0.118 2.00e-02 2.50e+03 pdb=" C1 NAG D 1 " 0.098 2.00e-02 2.50e+03 ... (remaining 5187 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 3002 2.75 - 3.29: 29164 3.29 - 3.83: 51100 3.83 - 4.36: 63086 4.36 - 4.90: 105444 Nonbonded interactions: 251796 Sorted by model distance: nonbonded pdb=" OG SER B 562 " pdb=" OD1 ASN B 564 " model vdw 2.214 3.040 nonbonded pdb=" OG SER A 562 " pdb=" OD1 ASN A 564 " model vdw 2.226 3.040 nonbonded pdb=" O PHE B 23 " pdb=" NH2 ARG B 170 " model vdw 2.237 3.120 nonbonded pdb=" OG SER C 562 " pdb=" OD1 ASN C 564 " model vdw 2.239 3.040 nonbonded pdb=" O PRO C 68 " pdb=" OH TYR C 266 " model vdw 2.262 3.040 ... (remaining 251791 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'K' selection = chain 'R' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' } ncs_group { reference = chain 'J' selection = chain 'Q' selection = chain 'X' } 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: 5.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.330 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 25.160 Find NCS groups from input model: 0.550 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9096 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 : 0.006 0.145 30240 Z= 0.332 Angle : 0.857 13.310 41361 Z= 0.507 Chirality : 0.055 0.485 4857 Planarity : 0.006 0.108 5130 Dihedral : 14.012 108.283 12090 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 0.53 % Allowed : 5.44 % Favored : 94.04 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 6.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.58 (0.14), residues: 3570 helix: 1.36 (0.18), residues: 822 sheet: 0.49 (0.18), residues: 795 loop : 0.00 (0.14), residues: 1953 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 34 TYR 0.120 0.004 TYR A 826 PHE 0.046 0.002 PHE B 591 TRP 0.062 0.003 TRP C 444 HIS 0.007 0.001 HIS B 458 Details of bonding type rmsd covalent geometry : bond 0.00623 (30075) covalent geometry : angle 0.84011 (40938) SS BOND : bond 0.00595 ( 72) SS BOND : angle 1.17743 ( 144) hydrogen bonds : bond 0.17066 ( 1180) hydrogen bonds : angle 7.51353 ( 3411) link_ALPHA1-3 : bond 0.02453 ( 3) link_ALPHA1-3 : angle 3.06324 ( 9) link_ALPHA1-6 : bond 0.02185 ( 3) link_ALPHA1-6 : angle 2.59951 ( 9) link_BETA1-4 : bond 0.01028 ( 27) link_BETA1-4 : angle 2.34940 ( 81) link_NAG-ASN : bond 0.00412 ( 60) link_NAG-ASN : angle 1.94743 ( 180) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7140 Ramachandran restraints generated. 3570 Oldfield, 0 Emsley, 3570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7140 Ramachandran restraints generated. 3570 Oldfield, 0 Emsley, 3570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 3219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 207 time to evaluate : 0.942 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 23 PHE cc_start: 0.8657 (t80) cc_final: 0.8416 (OUTLIER) REVERT: C 133 ASN cc_start: 0.7913 (m-40) cc_final: 0.7668 (m-40) REVERT: C 451 ASN cc_start: 0.8290 (p0) cc_final: 0.7992 (p0) REVERT: C 515 TRP cc_start: 0.8225 (t60) cc_final: 0.7512 (t60) REVERT: C 888 PHE cc_start: 0.8006 (m-80) cc_final: 0.7747 (m-10) REVERT: C 1006 LYS cc_start: 0.9021 (OUTLIER) cc_final: 0.8710 (tmtt) REVERT: C 1045 ASN cc_start: 0.8768 (t0) cc_final: 0.8362 (m-40) REVERT: B 218 MET cc_start: 0.9144 (mtm) cc_final: 0.8778 (mtm) REVERT: B 311 VAL cc_start: 0.8814 (t) cc_final: 0.8576 (m) REVERT: B 584 SER cc_start: 0.8728 (m) cc_final: 0.8527 (p) REVERT: B 888 PHE cc_start: 0.8470 (m-80) cc_final: 0.8217 (m-80) REVERT: B 902 SER cc_start: 0.7428 (m) cc_final: 0.7170 (p) REVERT: A 708 LEU cc_start: 0.8288 (mt) cc_final: 0.8078 (mp) REVERT: A 839 PHE cc_start: 0.8661 (t80) cc_final: 0.8318 (t80) REVERT: A 894 CYS cc_start: 0.6009 (t) cc_final: 0.5653 (t) REVERT: A 1042 GLN cc_start: 0.8621 (tm-30) cc_final: 0.8409 (tm-30) REVERT: A 1070 ASP cc_start: 0.7892 (p0) cc_final: 0.7523 (p0) outliers start: 17 outliers final: 9 residues processed: 220 average time/residue: 0.5545 time to fit residues: 145.9753 Evaluate side-chains 148 residues out of total 3219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 139 time to evaluate : 1.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 971 MET Chi-restraints excluded: chain C residue 1006 LYS Chi-restraints excluded: chain C residue 1093 VAL Chi-restraints excluded: chain C residue 1206 VAL Chi-restraints excluded: chain B residue 213 TYR Chi-restraints excluded: chain A residue 709 THR Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 1155 ILE Chi-restraints excluded: chain A residue 1171 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 0.3980 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 0.9990 chunk 183 optimal weight: 3.9990 chunk 298 optimal weight: 6.9990 overall best weight: 1.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 825 ASN A 825 ASN A 885 ASN A1075 GLN A1095 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.083928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2807 r_free = 0.2807 target = 0.057571 restraints weight = 50351.671| |-----------------------------------------------------------------------------| r_work (start): 0.2767 rms_B_bonded: 2.53 r_work: 0.2634 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2513 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9090 moved from start: 0.1121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 30240 Z= 0.209 Angle : 0.603 12.664 41361 Z= 0.313 Chirality : 0.045 0.191 4857 Planarity : 0.004 0.056 5130 Dihedral : 9.190 80.852 5813 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 2.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 1.34 % Allowed : 5.90 % Favored : 92.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.62 (0.14), residues: 3570 helix: 1.58 (0.18), residues: 843 sheet: 0.42 (0.17), residues: 813 loop : -0.04 (0.14), residues: 1914 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 531 TYR 0.018 0.002 TYR C1152 PHE 0.018 0.002 PHE B 907 TRP 0.026 0.002 TRP A 444 HIS 0.003 0.001 HIS C 684 Details of bonding type rmsd covalent geometry : bond 0.00472 (30075) covalent geometry : angle 0.58501 (40938) SS BOND : bond 0.00298 ( 72) SS BOND : angle 0.80992 ( 144) hydrogen bonds : bond 0.05069 ( 1180) hydrogen bonds : angle 5.99508 ( 3411) link_ALPHA1-3 : bond 0.00829 ( 3) link_ALPHA1-3 : angle 2.45210 ( 9) link_ALPHA1-6 : bond 0.00297 ( 3) link_ALPHA1-6 : angle 1.79256 ( 9) link_BETA1-4 : bond 0.00355 ( 27) link_BETA1-4 : angle 1.86737 ( 81) link_NAG-ASN : bond 0.00320 ( 60) link_NAG-ASN : angle 1.77434 ( 180) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7140 Ramachandran restraints generated. 3570 Oldfield, 0 Emsley, 3570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7140 Ramachandran restraints generated. 3570 Oldfield, 0 Emsley, 3570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 3219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 157 time to evaluate : 1.034 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 1045 ASN cc_start: 0.8769 (t0) cc_final: 0.8279 (m110) REVERT: C 1080 ARG cc_start: 0.9076 (OUTLIER) cc_final: 0.8735 (mtt-85) REVERT: B 176 PHE cc_start: 0.8279 (t80) cc_final: 0.8066 (t80) REVERT: B 311 VAL cc_start: 0.8739 (t) cc_final: 0.8486 (m) REVERT: B 584 SER cc_start: 0.8742 (m) cc_final: 0.8478 (p) REVERT: B 888 PHE cc_start: 0.8546 (m-80) cc_final: 0.8253 (m-80) REVERT: B 902 SER cc_start: 0.7436 (m) cc_final: 0.7116 (p) REVERT: A 615 GLU cc_start: 0.8118 (OUTLIER) cc_final: 0.7769 (pp20) REVERT: A 623 ASP cc_start: 0.8887 (OUTLIER) cc_final: 0.8481 (m-30) REVERT: A 839 PHE cc_start: 0.8624 (t80) cc_final: 0.8209 (t80) REVERT: A 846 ILE cc_start: 0.9260 (mt) cc_final: 0.9046 (mp) REVERT: A 894 CYS cc_start: 0.6771 (t) cc_final: 0.6184 (t) REVERT: A 1042 GLN cc_start: 0.8713 (tm-30) cc_final: 0.8497 (tm-30) REVERT: A 1095 GLN cc_start: 0.8933 (tt0) cc_final: 0.8728 (tt0) outliers start: 43 outliers final: 12 residues processed: 193 average time/residue: 0.5416 time to fit residues: 125.6249 Evaluate side-chains 155 residues out of total 3219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 140 time to evaluate : 0.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 435 THR Chi-restraints excluded: chain C residue 776 VAL Chi-restraints excluded: chain C residue 1080 ARG Chi-restraints excluded: chain C residue 1093 VAL Chi-restraints excluded: chain C residue 1206 VAL Chi-restraints excluded: chain B residue 213 TYR Chi-restraints excluded: chain B residue 776 VAL Chi-restraints excluded: chain B residue 894 CYS Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 374 ASP Chi-restraints excluded: chain A residue 435 THR Chi-restraints excluded: chain A residue 508 THR Chi-restraints excluded: chain A residue 615 GLU Chi-restraints excluded: chain A residue 623 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 4.9990 chunk 67 optimal weight: 3.9990 chunk 201 optimal weight: 4.9990 chunk 31 optimal weight: 0.9990 chunk 308 optimal weight: 3.9990 chunk 295 optimal weight: 3.9990 chunk 321 optimal weight: 0.9990 chunk 83 optimal weight: 1.9990 chunk 345 optimal weight: 4.9990 chunk 333 optimal weight: 2.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 114 ASN B 825 ASN B 842 ASN A1083 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.082520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2776 r_free = 0.2776 target = 0.056164 restraints weight = 50500.256| |-----------------------------------------------------------------------------| r_work (start): 0.2735 rms_B_bonded: 2.49 r_work: 0.2605 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2485 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2485 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9109 moved from start: 0.1509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 30240 Z= 0.262 Angle : 0.613 10.424 41361 Z= 0.317 Chirality : 0.046 0.194 4857 Planarity : 0.004 0.059 5130 Dihedral : 8.111 72.596 5800 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 2.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 1.40 % Allowed : 6.65 % Favored : 91.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.50 (0.14), residues: 3570 helix: 1.49 (0.18), residues: 846 sheet: 0.29 (0.17), residues: 813 loop : -0.11 (0.14), residues: 1911 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 446 TYR 0.018 0.002 TYR B 50 PHE 0.020 0.002 PHE C 121 TRP 0.022 0.002 TRP C 444 HIS 0.003 0.001 HIS C 684 Details of bonding type rmsd covalent geometry : bond 0.00596 (30075) covalent geometry : angle 0.59589 (40938) SS BOND : bond 0.00334 ( 72) SS BOND : angle 1.04549 ( 144) hydrogen bonds : bond 0.05111 ( 1180) hydrogen bonds : angle 5.89998 ( 3411) link_ALPHA1-3 : bond 0.01196 ( 3) link_ALPHA1-3 : angle 1.60192 ( 9) link_ALPHA1-6 : bond 0.00610 ( 3) link_ALPHA1-6 : angle 1.85453 ( 9) link_BETA1-4 : bond 0.00317 ( 27) link_BETA1-4 : angle 1.66822 ( 81) link_NAG-ASN : bond 0.00376 ( 60) link_NAG-ASN : angle 1.80667 ( 180) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7140 Ramachandran restraints generated. 3570 Oldfield, 0 Emsley, 3570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7140 Ramachandran restraints generated. 3570 Oldfield, 0 Emsley, 3570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 3219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 148 time to evaluate : 1.039 Fit side-chains revert: symmetry clash REVERT: C 888 PHE cc_start: 0.8055 (m-80) cc_final: 0.7747 (m-80) REVERT: C 1075 GLN cc_start: 0.8725 (OUTLIER) cc_final: 0.8511 (tt0) REVERT: C 1080 ARG cc_start: 0.9070 (OUTLIER) cc_final: 0.8766 (mtt-85) REVERT: B 311 VAL cc_start: 0.8806 (t) cc_final: 0.8523 (m) REVERT: B 531 ARG cc_start: 0.8474 (ttm170) cc_final: 0.8174 (mtt-85) REVERT: B 888 PHE cc_start: 0.8588 (m-80) cc_final: 0.8317 (m-80) REVERT: B 1070 ASP cc_start: 0.8235 (OUTLIER) cc_final: 0.7739 (m-30) REVERT: A 623 ASP cc_start: 0.8855 (OUTLIER) cc_final: 0.8453 (m-30) REVERT: A 839 PHE cc_start: 0.8641 (t80) cc_final: 0.8188 (t80) REVERT: A 846 ILE cc_start: 0.9293 (mt) cc_final: 0.9073 (mp) REVERT: A 894 CYS cc_start: 0.6720 (t) cc_final: 0.6146 (t) REVERT: A 1042 GLN cc_start: 0.8726 (tm-30) cc_final: 0.8496 (tm-30) outliers start: 45 outliers final: 19 residues processed: 188 average time/residue: 0.5343 time to fit residues: 121.0067 Evaluate side-chains 160 residues out of total 3219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 137 time to evaluate : 1.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 435 THR Chi-restraints excluded: chain C residue 776 VAL Chi-restraints excluded: chain C residue 849 GLU Chi-restraints excluded: chain C residue 1075 GLN Chi-restraints excluded: chain C residue 1080 ARG Chi-restraints excluded: chain C residue 1093 VAL Chi-restraints excluded: chain C residue 1125 ILE Chi-restraints excluded: chain C residue 1206 VAL Chi-restraints excluded: chain B residue 213 TYR Chi-restraints excluded: chain B residue 776 VAL Chi-restraints excluded: chain B residue 894 CYS Chi-restraints excluded: chain B residue 1070 ASP Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 374 ASP Chi-restraints excluded: chain A residue 435 THR Chi-restraints excluded: chain A residue 584 SER Chi-restraints excluded: chain A residue 623 ASP Chi-restraints excluded: chain A residue 657 ILE Chi-restraints excluded: chain A residue 708 LEU Chi-restraints excluded: chain A residue 709 THR Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 1125 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 14 optimal weight: 3.9990 chunk 198 optimal weight: 1.9990 chunk 340 optimal weight: 2.9990 chunk 264 optimal weight: 0.9990 chunk 95 optimal weight: 1.9990 chunk 258 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 232 optimal weight: 0.0060 chunk 311 optimal weight: 2.9990 chunk 262 optimal weight: 5.9990 overall best weight: 1.4004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C1090 ASN B 842 ASN A1095 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.083262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2796 r_free = 0.2796 target = 0.057030 restraints weight = 50246.677| |-----------------------------------------------------------------------------| r_work (start): 0.2755 rms_B_bonded: 2.48 r_work: 0.2623 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2501 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9098 moved from start: 0.1656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 30240 Z= 0.197 Angle : 0.571 9.255 41361 Z= 0.295 Chirality : 0.044 0.225 4857 Planarity : 0.004 0.061 5130 Dihedral : 7.486 66.048 5800 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 1.46 % Allowed : 7.30 % Favored : 91.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.47 (0.14), residues: 3570 helix: 1.54 (0.18), residues: 846 sheet: 0.26 (0.17), residues: 813 loop : -0.15 (0.14), residues: 1911 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 517 TYR 0.016 0.002 TYR C1152 PHE 0.020 0.002 PHE C 176 TRP 0.019 0.002 TRP C 444 HIS 0.004 0.001 HIS C 488 Details of bonding type rmsd covalent geometry : bond 0.00446 (30075) covalent geometry : angle 0.55419 (40938) SS BOND : bond 0.00286 ( 72) SS BOND : angle 0.92255 ( 144) hydrogen bonds : bond 0.04552 ( 1180) hydrogen bonds : angle 5.73351 ( 3411) link_ALPHA1-3 : bond 0.01162 ( 3) link_ALPHA1-3 : angle 1.85215 ( 9) link_ALPHA1-6 : bond 0.00615 ( 3) link_ALPHA1-6 : angle 1.91163 ( 9) link_BETA1-4 : bond 0.00317 ( 27) link_BETA1-4 : angle 1.54980 ( 81) link_NAG-ASN : bond 0.00288 ( 60) link_NAG-ASN : angle 1.70470 ( 180) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7140 Ramachandran restraints generated. 3570 Oldfield, 0 Emsley, 3570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7140 Ramachandran restraints generated. 3570 Oldfield, 0 Emsley, 3570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 3219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 147 time to evaluate : 0.870 Fit side-chains revert: symmetry clash REVERT: C 515 TRP cc_start: 0.8307 (OUTLIER) cc_final: 0.8069 (t60) REVERT: C 888 PHE cc_start: 0.7930 (m-80) cc_final: 0.7475 (m-80) REVERT: C 1080 ARG cc_start: 0.9035 (OUTLIER) cc_final: 0.8735 (mtt-85) REVERT: B 311 VAL cc_start: 0.8749 (t) cc_final: 0.8456 (m) REVERT: B 531 ARG cc_start: 0.8493 (ttm170) cc_final: 0.8196 (mtt-85) REVERT: B 888 PHE cc_start: 0.8540 (m-80) cc_final: 0.8324 (m-80) REVERT: B 1070 ASP cc_start: 0.8116 (OUTLIER) cc_final: 0.7606 (m-30) REVERT: A 623 ASP cc_start: 0.8836 (OUTLIER) cc_final: 0.8397 (m-30) REVERT: A 839 PHE cc_start: 0.8581 (t80) cc_final: 0.8089 (t80) REVERT: A 846 ILE cc_start: 0.9254 (mt) cc_final: 0.9030 (mp) REVERT: A 894 CYS cc_start: 0.6705 (t) cc_final: 0.6128 (t) REVERT: A 1042 GLN cc_start: 0.8713 (tm-30) cc_final: 0.8483 (tm-30) outliers start: 47 outliers final: 20 residues processed: 181 average time/residue: 0.5640 time to fit residues: 122.2744 Evaluate side-chains 163 residues out of total 3219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 139 time to evaluate : 0.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 435 THR Chi-restraints excluded: chain C residue 515 TRP Chi-restraints excluded: chain C residue 559 LEU Chi-restraints excluded: chain C residue 709 THR Chi-restraints excluded: chain C residue 776 VAL Chi-restraints excluded: chain C residue 1080 ARG Chi-restraints excluded: chain C residue 1093 VAL Chi-restraints excluded: chain C residue 1206 VAL Chi-restraints excluded: chain B residue 213 TYR Chi-restraints excluded: chain B residue 435 THR Chi-restraints excluded: chain B residue 776 VAL Chi-restraints excluded: chain B residue 894 CYS Chi-restraints excluded: chain B residue 1070 ASP Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 435 THR Chi-restraints excluded: chain A residue 584 SER Chi-restraints excluded: chain A residue 623 ASP Chi-restraints excluded: chain A residue 657 ILE Chi-restraints excluded: chain A residue 709 THR Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 1003 LYS Chi-restraints excluded: chain A residue 1006 LYS Chi-restraints excluded: chain A residue 1209 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 331 optimal weight: 0.9990 chunk 112 optimal weight: 1.9990 chunk 342 optimal weight: 0.8980 chunk 251 optimal weight: 2.9990 chunk 191 optimal weight: 2.9990 chunk 209 optimal weight: 0.9990 chunk 315 optimal weight: 4.9990 chunk 56 optimal weight: 6.9990 chunk 113 optimal weight: 1.9990 chunk 247 optimal weight: 2.9990 chunk 205 optimal weight: 5.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 152 GLN C 488 HIS A 114 ASN A1095 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.083245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2795 r_free = 0.2795 target = 0.057000 restraints weight = 50218.382| |-----------------------------------------------------------------------------| r_work (start): 0.2755 rms_B_bonded: 2.49 r_work: 0.2623 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2502 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9098 moved from start: 0.1760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 30240 Z= 0.196 Angle : 0.563 10.334 41361 Z= 0.290 Chirality : 0.044 0.240 4857 Planarity : 0.004 0.060 5130 Dihedral : 7.139 60.211 5800 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 1.49 % Allowed : 7.89 % Favored : 90.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.46 (0.14), residues: 3570 helix: 1.55 (0.18), residues: 846 sheet: 0.22 (0.17), residues: 813 loop : -0.15 (0.14), residues: 1911 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 531 TYR 0.016 0.002 TYR C1152 PHE 0.018 0.002 PHE C 176 TRP 0.017 0.001 TRP C 444 HIS 0.003 0.001 HIS C 201 Details of bonding type rmsd covalent geometry : bond 0.00442 (30075) covalent geometry : angle 0.54689 (40938) SS BOND : bond 0.00265 ( 72) SS BOND : angle 0.84307 ( 144) hydrogen bonds : bond 0.04452 ( 1180) hydrogen bonds : angle 5.66710 ( 3411) link_ALPHA1-3 : bond 0.01152 ( 3) link_ALPHA1-3 : angle 1.74326 ( 9) link_ALPHA1-6 : bond 0.00772 ( 3) link_ALPHA1-6 : angle 1.96747 ( 9) link_BETA1-4 : bond 0.00324 ( 27) link_BETA1-4 : angle 1.47051 ( 81) link_NAG-ASN : bond 0.00294 ( 60) link_NAG-ASN : angle 1.67983 ( 180) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7140 Ramachandran restraints generated. 3570 Oldfield, 0 Emsley, 3570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7140 Ramachandran restraints generated. 3570 Oldfield, 0 Emsley, 3570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 3219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 143 time to evaluate : 1.035 Fit side-chains revert: symmetry clash REVERT: C 488 HIS cc_start: 0.8253 (m-70) cc_final: 0.7356 (m-70) REVERT: C 839 PHE cc_start: 0.8660 (t80) cc_final: 0.8426 (t80) REVERT: C 1075 GLN cc_start: 0.8670 (OUTLIER) cc_final: 0.8369 (tm-30) REVERT: C 1080 ARG cc_start: 0.9028 (OUTLIER) cc_final: 0.8704 (mtt-85) REVERT: B 311 VAL cc_start: 0.8727 (t) cc_final: 0.8433 (m) REVERT: B 531 ARG cc_start: 0.8504 (ttm170) cc_final: 0.8156 (mtt-85) REVERT: B 842 ASN cc_start: 0.9067 (m-40) cc_final: 0.8774 (m110) REVERT: B 1070 ASP cc_start: 0.8097 (OUTLIER) cc_final: 0.7612 (m-30) REVERT: A 615 GLU cc_start: 0.8191 (OUTLIER) cc_final: 0.7979 (pp20) REVERT: A 623 ASP cc_start: 0.8814 (OUTLIER) cc_final: 0.8396 (m-30) REVERT: A 839 PHE cc_start: 0.8568 (t80) cc_final: 0.8135 (t80) REVERT: A 846 ILE cc_start: 0.9259 (mt) cc_final: 0.9059 (mp) REVERT: A 894 CYS cc_start: 0.6756 (t) cc_final: 0.6191 (t) REVERT: A 1042 GLN cc_start: 0.8718 (tm-30) cc_final: 0.8489 (tm-30) outliers start: 48 outliers final: 27 residues processed: 181 average time/residue: 0.5444 time to fit residues: 118.7264 Evaluate side-chains 170 residues out of total 3219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 138 time to evaluate : 1.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 435 THR Chi-restraints excluded: chain C residue 559 LEU Chi-restraints excluded: chain C residue 709 THR Chi-restraints excluded: chain C residue 776 VAL Chi-restraints excluded: chain C residue 849 GLU Chi-restraints excluded: chain C residue 1075 GLN Chi-restraints excluded: chain C residue 1080 ARG Chi-restraints excluded: chain C residue 1093 VAL Chi-restraints excluded: chain C residue 1206 VAL Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 213 TYR Chi-restraints excluded: chain B residue 776 VAL Chi-restraints excluded: chain B residue 894 CYS Chi-restraints excluded: chain B residue 1070 ASP Chi-restraints excluded: chain A residue 194 SER Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 374 ASP Chi-restraints excluded: chain A residue 435 THR Chi-restraints excluded: chain A residue 508 THR Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 584 SER Chi-restraints excluded: chain A residue 615 GLU Chi-restraints excluded: chain A residue 623 ASP Chi-restraints excluded: chain A residue 657 ILE Chi-restraints excluded: chain A residue 709 THR Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 1003 LYS Chi-restraints excluded: chain A residue 1006 LYS Chi-restraints excluded: chain A residue 1125 ILE Chi-restraints excluded: chain A residue 1209 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 196 optimal weight: 3.9990 chunk 131 optimal weight: 3.9990 chunk 165 optimal weight: 2.9990 chunk 348 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 246 optimal weight: 3.9990 chunk 166 optimal weight: 0.9980 chunk 222 optimal weight: 0.7980 chunk 205 optimal weight: 5.9990 chunk 344 optimal weight: 0.9980 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1095 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.083351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2837 r_free = 0.2837 target = 0.057837 restraints weight = 50212.273| |-----------------------------------------------------------------------------| r_work (start): 0.2784 rms_B_bonded: 2.42 r_work: 0.2658 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2542 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2542 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9115 moved from start: 0.1841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 30240 Z= 0.172 Angle : 0.545 8.642 41361 Z= 0.282 Chirality : 0.043 0.245 4857 Planarity : 0.004 0.059 5130 Dihedral : 6.911 58.136 5800 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.77 % Allowed : 8.05 % Favored : 90.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.47 (0.14), residues: 3570 helix: 1.62 (0.18), residues: 846 sheet: 0.17 (0.17), residues: 810 loop : -0.15 (0.14), residues: 1914 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 531 TYR 0.016 0.001 TYR C1152 PHE 0.025 0.001 PHE B 23 TRP 0.017 0.001 TRP C 444 HIS 0.003 0.001 HIS C 201 Details of bonding type rmsd covalent geometry : bond 0.00387 (30075) covalent geometry : angle 0.52937 (40938) SS BOND : bond 0.00268 ( 72) SS BOND : angle 0.81177 ( 144) hydrogen bonds : bond 0.04258 ( 1180) hydrogen bonds : angle 5.58789 ( 3411) link_ALPHA1-3 : bond 0.01193 ( 3) link_ALPHA1-3 : angle 1.76620 ( 9) link_ALPHA1-6 : bond 0.00771 ( 3) link_ALPHA1-6 : angle 1.93519 ( 9) link_BETA1-4 : bond 0.00326 ( 27) link_BETA1-4 : angle 1.41507 ( 81) link_NAG-ASN : bond 0.00254 ( 60) link_NAG-ASN : angle 1.63293 ( 180) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7140 Ramachandran restraints generated. 3570 Oldfield, 0 Emsley, 3570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7140 Ramachandran restraints generated. 3570 Oldfield, 0 Emsley, 3570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 3219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 142 time to evaluate : 0.925 Fit side-chains revert: symmetry clash REVERT: C 488 HIS cc_start: 0.8189 (m-70) cc_final: 0.7949 (m-70) REVERT: C 1045 ASN cc_start: 0.8773 (t0) cc_final: 0.8324 (m110) REVERT: C 1075 GLN cc_start: 0.8646 (OUTLIER) cc_final: 0.8368 (tm-30) REVERT: C 1080 ARG cc_start: 0.9037 (OUTLIER) cc_final: 0.8705 (mtt-85) REVERT: B 311 VAL cc_start: 0.8771 (t) cc_final: 0.8495 (m) REVERT: B 531 ARG cc_start: 0.8488 (ttm170) cc_final: 0.8135 (mtt-85) REVERT: B 1070 ASP cc_start: 0.8082 (OUTLIER) cc_final: 0.7589 (m-30) REVERT: A 623 ASP cc_start: 0.8808 (OUTLIER) cc_final: 0.8430 (m-30) REVERT: A 836 TYR cc_start: 0.8734 (OUTLIER) cc_final: 0.8174 (m-80) REVERT: A 839 PHE cc_start: 0.8569 (t80) cc_final: 0.8136 (t80) REVERT: A 846 ILE cc_start: 0.9277 (mt) cc_final: 0.9063 (mp) REVERT: A 894 CYS cc_start: 0.6756 (t) cc_final: 0.6218 (t) REVERT: A 910 LEU cc_start: 0.9044 (tp) cc_final: 0.8692 (mp) REVERT: A 1042 GLN cc_start: 0.8718 (tm-30) cc_final: 0.8495 (tm-30) outliers start: 57 outliers final: 34 residues processed: 185 average time/residue: 0.5377 time to fit residues: 119.9436 Evaluate side-chains 176 residues out of total 3219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 137 time to evaluate : 0.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 435 THR Chi-restraints excluded: chain C residue 559 LEU Chi-restraints excluded: chain C residue 709 THR Chi-restraints excluded: chain C residue 776 VAL Chi-restraints excluded: chain C residue 836 TYR Chi-restraints excluded: chain C residue 849 GLU Chi-restraints excluded: chain C residue 1075 GLN Chi-restraints excluded: chain C residue 1080 ARG Chi-restraints excluded: chain C residue 1093 VAL Chi-restraints excluded: chain C residue 1206 VAL Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 213 TYR Chi-restraints excluded: chain B residue 435 THR Chi-restraints excluded: chain B residue 575 LEU Chi-restraints excluded: chain B residue 776 VAL Chi-restraints excluded: chain B residue 894 CYS Chi-restraints excluded: chain B residue 1070 ASP Chi-restraints excluded: chain A residue 194 SER Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 374 ASP Chi-restraints excluded: chain A residue 435 THR Chi-restraints excluded: chain A residue 508 THR Chi-restraints excluded: chain A residue 516 CYS Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 623 ASP Chi-restraints excluded: chain A residue 657 ILE Chi-restraints excluded: chain A residue 708 LEU Chi-restraints excluded: chain A residue 709 THR Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 836 TYR Chi-restraints excluded: chain A residue 1003 LYS Chi-restraints excluded: chain A residue 1006 LYS Chi-restraints excluded: chain A residue 1007 LEU Chi-restraints excluded: chain A residue 1125 ILE Chi-restraints excluded: chain A residue 1135 LEU Chi-restraints excluded: chain A residue 1209 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 158 optimal weight: 2.9990 chunk 203 optimal weight: 3.9990 chunk 97 optimal weight: 2.9990 chunk 237 optimal weight: 4.9990 chunk 191 optimal weight: 3.9990 chunk 147 optimal weight: 1.9990 chunk 290 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 chunk 73 optimal weight: 3.9990 chunk 177 optimal weight: 1.9990 chunk 41 optimal weight: 3.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 22 ASN B 842 ASN A 114 ASN A 825 ASN A1095 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.082066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2769 r_free = 0.2769 target = 0.055773 restraints weight = 50510.739| |-----------------------------------------------------------------------------| r_work (start): 0.2728 rms_B_bonded: 2.48 r_work: 0.2595 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2474 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9117 moved from start: 0.1922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 30240 Z= 0.280 Angle : 0.605 9.811 41361 Z= 0.312 Chirality : 0.045 0.248 4857 Planarity : 0.004 0.059 5130 Dihedral : 7.048 59.739 5800 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.80 % Allowed : 8.17 % Favored : 90.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.37 (0.14), residues: 3570 helix: 1.49 (0.18), residues: 846 sheet: 0.17 (0.18), residues: 777 loop : -0.21 (0.14), residues: 1947 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 517 TYR 0.018 0.002 TYR B 50 PHE 0.024 0.002 PHE C 176 TRP 0.020 0.002 TRP C 515 HIS 0.004 0.001 HIS C 201 Details of bonding type rmsd covalent geometry : bond 0.00641 (30075) covalent geometry : angle 0.58907 (40938) SS BOND : bond 0.00379 ( 72) SS BOND : angle 0.94964 ( 144) hydrogen bonds : bond 0.04778 ( 1180) hydrogen bonds : angle 5.74316 ( 3411) link_ALPHA1-3 : bond 0.01082 ( 3) link_ALPHA1-3 : angle 1.89181 ( 9) link_ALPHA1-6 : bond 0.00700 ( 3) link_ALPHA1-6 : angle 1.92771 ( 9) link_BETA1-4 : bond 0.00300 ( 27) link_BETA1-4 : angle 1.50277 ( 81) link_NAG-ASN : bond 0.00423 ( 60) link_NAG-ASN : angle 1.79013 ( 180) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7140 Ramachandran restraints generated. 3570 Oldfield, 0 Emsley, 3570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7140 Ramachandran restraints generated. 3570 Oldfield, 0 Emsley, 3570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 3219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 139 time to evaluate : 1.067 Fit side-chains revert: symmetry clash REVERT: C 273 ARG cc_start: 0.9055 (OUTLIER) cc_final: 0.8761 (ptm-80) REVERT: C 488 HIS cc_start: 0.8265 (m-70) cc_final: 0.7954 (m170) REVERT: C 888 PHE cc_start: 0.7892 (m-80) cc_final: 0.7583 (m-80) REVERT: C 1075 GLN cc_start: 0.8685 (OUTLIER) cc_final: 0.8360 (tm-30) REVERT: C 1080 ARG cc_start: 0.9037 (OUTLIER) cc_final: 0.8742 (mtt-85) REVERT: B 311 VAL cc_start: 0.8814 (t) cc_final: 0.8504 (m) REVERT: B 531 ARG cc_start: 0.8529 (ttm170) cc_final: 0.8191 (ttm-80) REVERT: B 1070 ASP cc_start: 0.8111 (OUTLIER) cc_final: 0.7625 (m-30) REVERT: A 623 ASP cc_start: 0.8822 (OUTLIER) cc_final: 0.8377 (m-30) REVERT: A 836 TYR cc_start: 0.8760 (OUTLIER) cc_final: 0.8313 (m-80) REVERT: A 839 PHE cc_start: 0.8578 (t80) cc_final: 0.8143 (t80) REVERT: A 894 CYS cc_start: 0.6838 (t) cc_final: 0.6270 (t) REVERT: A 910 LEU cc_start: 0.9075 (tp) cc_final: 0.8719 (mp) REVERT: A 1042 GLN cc_start: 0.8728 (tm-30) cc_final: 0.8490 (tm-30) REVERT: A 1073 GLU cc_start: 0.8749 (OUTLIER) cc_final: 0.8281 (mp0) outliers start: 58 outliers final: 34 residues processed: 183 average time/residue: 0.5364 time to fit residues: 117.6723 Evaluate side-chains 178 residues out of total 3219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 137 time to evaluate : 0.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 273 ARG Chi-restraints excluded: chain C residue 435 THR Chi-restraints excluded: chain C residue 559 LEU Chi-restraints excluded: chain C residue 709 THR Chi-restraints excluded: chain C residue 734 SER Chi-restraints excluded: chain C residue 776 VAL Chi-restraints excluded: chain C residue 836 TYR Chi-restraints excluded: chain C residue 849 GLU Chi-restraints excluded: chain C residue 1075 GLN Chi-restraints excluded: chain C residue 1080 ARG Chi-restraints excluded: chain C residue 1093 VAL Chi-restraints excluded: chain C residue 1206 VAL Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 213 TYR Chi-restraints excluded: chain B residue 435 THR Chi-restraints excluded: chain B residue 776 VAL Chi-restraints excluded: chain B residue 894 CYS Chi-restraints excluded: chain B residue 964 THR Chi-restraints excluded: chain B residue 1070 ASP Chi-restraints excluded: chain B residue 1125 ILE Chi-restraints excluded: chain A residue 194 SER Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 374 ASP Chi-restraints excluded: chain A residue 435 THR Chi-restraints excluded: chain A residue 508 THR Chi-restraints excluded: chain A residue 516 CYS Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 623 ASP Chi-restraints excluded: chain A residue 657 ILE Chi-restraints excluded: chain A residue 709 THR Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 836 TYR Chi-restraints excluded: chain A residue 880 HIS Chi-restraints excluded: chain A residue 1003 LYS Chi-restraints excluded: chain A residue 1006 LYS Chi-restraints excluded: chain A residue 1007 LEU Chi-restraints excluded: chain A residue 1073 GLU Chi-restraints excluded: chain A residue 1125 ILE Chi-restraints excluded: chain A residue 1209 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 17 optimal weight: 0.6980 chunk 40 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 146 optimal weight: 0.9980 chunk 160 optimal weight: 0.9990 chunk 190 optimal weight: 1.9990 chunk 179 optimal weight: 0.9990 chunk 91 optimal weight: 0.8980 chunk 59 optimal weight: 4.9990 chunk 61 optimal weight: 1.9990 chunk 0 optimal weight: 8.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 22 ASN B 825 ASN A1095 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.084033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2838 r_free = 0.2838 target = 0.058004 restraints weight = 50102.506| |-----------------------------------------------------------------------------| r_work (start): 0.2789 rms_B_bonded: 2.48 r_work: 0.2663 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2546 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9111 moved from start: 0.1959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 30240 Z= 0.150 Angle : 0.538 8.959 41361 Z= 0.279 Chirality : 0.043 0.241 4857 Planarity : 0.004 0.060 5130 Dihedral : 6.695 58.002 5800 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.34 % Allowed : 8.70 % Favored : 89.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.44 (0.14), residues: 3570 helix: 1.62 (0.18), residues: 846 sheet: 0.12 (0.17), residues: 810 loop : -0.17 (0.14), residues: 1914 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 517 TYR 0.017 0.001 TYR C1152 PHE 0.020 0.001 PHE C 176 TRP 0.042 0.002 TRP C 515 HIS 0.004 0.001 HIS C 488 Details of bonding type rmsd covalent geometry : bond 0.00334 (30075) covalent geometry : angle 0.52352 (40938) SS BOND : bond 0.00256 ( 72) SS BOND : angle 0.72393 ( 144) hydrogen bonds : bond 0.04109 ( 1180) hydrogen bonds : angle 5.55146 ( 3411) link_ALPHA1-3 : bond 0.01204 ( 3) link_ALPHA1-3 : angle 1.65999 ( 9) link_ALPHA1-6 : bond 0.00783 ( 3) link_ALPHA1-6 : angle 1.88686 ( 9) link_BETA1-4 : bond 0.00347 ( 27) link_BETA1-4 : angle 1.37401 ( 81) link_NAG-ASN : bond 0.00217 ( 60) link_NAG-ASN : angle 1.60923 ( 180) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7140 Ramachandran restraints generated. 3570 Oldfield, 0 Emsley, 3570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7140 Ramachandran restraints generated. 3570 Oldfield, 0 Emsley, 3570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 3219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 145 time to evaluate : 1.233 Fit side-chains revert: symmetry clash REVERT: C 836 TYR cc_start: 0.8619 (OUTLIER) cc_final: 0.8337 (t80) REVERT: C 1075 GLN cc_start: 0.8660 (OUTLIER) cc_final: 0.8382 (tm-30) REVERT: C 1080 ARG cc_start: 0.9037 (OUTLIER) cc_final: 0.8705 (mtt-85) REVERT: B 182 LEU cc_start: 0.8901 (OUTLIER) cc_final: 0.8656 (tm) REVERT: B 218 MET cc_start: 0.9251 (OUTLIER) cc_final: 0.8976 (mtm) REVERT: B 311 VAL cc_start: 0.8772 (t) cc_final: 0.8498 (m) REVERT: B 531 ARG cc_start: 0.8504 (ttm170) cc_final: 0.8152 (mtt-85) REVERT: B 842 ASN cc_start: 0.9117 (m-40) cc_final: 0.8870 (m110) REVERT: B 1070 ASP cc_start: 0.8080 (OUTLIER) cc_final: 0.7640 (m-30) REVERT: A 623 ASP cc_start: 0.8785 (OUTLIER) cc_final: 0.8417 (m-30) REVERT: A 836 TYR cc_start: 0.8726 (OUTLIER) cc_final: 0.8187 (m-80) REVERT: A 839 PHE cc_start: 0.8579 (t80) cc_final: 0.8132 (t80) REVERT: A 894 CYS cc_start: 0.6749 (OUTLIER) cc_final: 0.6209 (t) REVERT: A 910 LEU cc_start: 0.9045 (tp) cc_final: 0.8693 (mp) REVERT: A 1042 GLN cc_start: 0.8735 (tm-30) cc_final: 0.8513 (tm-30) outliers start: 43 outliers final: 24 residues processed: 175 average time/residue: 0.5803 time to fit residues: 121.6474 Evaluate side-chains 171 residues out of total 3219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 138 time to evaluate : 1.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 435 THR Chi-restraints excluded: chain C residue 709 THR Chi-restraints excluded: chain C residue 776 VAL Chi-restraints excluded: chain C residue 836 TYR Chi-restraints excluded: chain C residue 849 GLU Chi-restraints excluded: chain C residue 1075 GLN Chi-restraints excluded: chain C residue 1080 ARG Chi-restraints excluded: chain C residue 1093 VAL Chi-restraints excluded: chain C residue 1125 ILE Chi-restraints excluded: chain C residue 1206 VAL Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 213 TYR Chi-restraints excluded: chain B residue 218 MET Chi-restraints excluded: chain B residue 435 THR Chi-restraints excluded: chain B residue 894 CYS Chi-restraints excluded: chain B residue 1070 ASP Chi-restraints excluded: chain A residue 194 SER Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 374 ASP Chi-restraints excluded: chain A residue 435 THR Chi-restraints excluded: chain A residue 508 THR Chi-restraints excluded: chain A residue 516 CYS Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 623 ASP Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 836 TYR Chi-restraints excluded: chain A residue 880 HIS Chi-restraints excluded: chain A residue 894 CYS Chi-restraints excluded: chain A residue 1003 LYS Chi-restraints excluded: chain A residue 1006 LYS Chi-restraints excluded: chain A residue 1209 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 41 optimal weight: 2.9990 chunk 349 optimal weight: 0.6980 chunk 118 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 271 optimal weight: 0.6980 chunk 204 optimal weight: 3.9990 chunk 99 optimal weight: 0.9990 chunk 62 optimal weight: 3.9990 chunk 268 optimal weight: 5.9990 chunk 139 optimal weight: 0.9980 chunk 0 optimal weight: 8.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 22 ASN C 488 HIS B 825 ASN A 114 ASN A1095 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.083374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2800 r_free = 0.2800 target = 0.057204 restraints weight = 50227.555| |-----------------------------------------------------------------------------| r_work (start): 0.2759 rms_B_bonded: 2.50 r_work: 0.2630 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2511 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9095 moved from start: 0.1974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 30240 Z= 0.186 Angle : 0.554 9.219 41361 Z= 0.287 Chirality : 0.043 0.228 4857 Planarity : 0.004 0.058 5130 Dihedral : 6.654 58.166 5800 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.40 % Allowed : 8.82 % Favored : 89.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.43 (0.14), residues: 3570 helix: 1.62 (0.18), residues: 846 sheet: 0.11 (0.17), residues: 810 loop : -0.17 (0.14), residues: 1914 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 531 TYR 0.016 0.001 TYR A 579 PHE 0.027 0.002 PHE C 176 TRP 0.049 0.002 TRP C 515 HIS 0.010 0.001 HIS C 488 Details of bonding type rmsd covalent geometry : bond 0.00420 (30075) covalent geometry : angle 0.53937 (40938) SS BOND : bond 0.00288 ( 72) SS BOND : angle 0.74783 ( 144) hydrogen bonds : bond 0.04271 ( 1180) hydrogen bonds : angle 5.56736 ( 3411) link_ALPHA1-3 : bond 0.01113 ( 3) link_ALPHA1-3 : angle 1.70471 ( 9) link_ALPHA1-6 : bond 0.00761 ( 3) link_ALPHA1-6 : angle 1.82633 ( 9) link_BETA1-4 : bond 0.00325 ( 27) link_BETA1-4 : angle 1.42077 ( 81) link_NAG-ASN : bond 0.00283 ( 60) link_NAG-ASN : angle 1.65117 ( 180) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7140 Ramachandran restraints generated. 3570 Oldfield, 0 Emsley, 3570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7140 Ramachandran restraints generated. 3570 Oldfield, 0 Emsley, 3570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 3219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 140 time to evaluate : 1.155 Fit side-chains revert: symmetry clash REVERT: C 176 PHE cc_start: 0.8407 (t80) cc_final: 0.7913 (t80) REVERT: C 515 TRP cc_start: 0.7745 (t-100) cc_final: 0.7512 (t-100) REVERT: C 836 TYR cc_start: 0.8634 (OUTLIER) cc_final: 0.8354 (t80) REVERT: C 1075 GLN cc_start: 0.8640 (OUTLIER) cc_final: 0.8358 (tm-30) REVERT: C 1080 ARG cc_start: 0.9013 (OUTLIER) cc_final: 0.8683 (mtt-85) REVERT: B 176 PHE cc_start: 0.8263 (t80) cc_final: 0.8014 (t80) REVERT: B 182 LEU cc_start: 0.8853 (OUTLIER) cc_final: 0.8620 (tm) REVERT: B 311 VAL cc_start: 0.8728 (t) cc_final: 0.8448 (m) REVERT: B 531 ARG cc_start: 0.8503 (ttm170) cc_final: 0.8145 (mtt-85) REVERT: B 842 ASN cc_start: 0.9085 (m-40) cc_final: 0.8840 (m110) REVERT: B 1070 ASP cc_start: 0.8065 (OUTLIER) cc_final: 0.7618 (m-30) REVERT: A 623 ASP cc_start: 0.8767 (OUTLIER) cc_final: 0.8343 (m-30) REVERT: A 836 TYR cc_start: 0.8751 (OUTLIER) cc_final: 0.8246 (m-80) REVERT: A 839 PHE cc_start: 0.8581 (t80) cc_final: 0.8130 (t80) REVERT: A 846 ILE cc_start: 0.9222 (mp) cc_final: 0.8992 (mp) REVERT: A 894 CYS cc_start: 0.6782 (OUTLIER) cc_final: 0.6221 (t) REVERT: A 910 LEU cc_start: 0.9041 (tp) cc_final: 0.8684 (mp) REVERT: A 1042 GLN cc_start: 0.8702 (tm-30) cc_final: 0.8469 (tm-30) outliers start: 45 outliers final: 29 residues processed: 174 average time/residue: 0.5820 time to fit residues: 121.7885 Evaluate side-chains 175 residues out of total 3219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 138 time to evaluate : 1.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 133 ASN Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 435 THR Chi-restraints excluded: chain C residue 709 THR Chi-restraints excluded: chain C residue 734 SER Chi-restraints excluded: chain C residue 776 VAL Chi-restraints excluded: chain C residue 836 TYR Chi-restraints excluded: chain C residue 849 GLU Chi-restraints excluded: chain C residue 1075 GLN Chi-restraints excluded: chain C residue 1080 ARG Chi-restraints excluded: chain C residue 1093 VAL Chi-restraints excluded: chain C residue 1125 ILE Chi-restraints excluded: chain C residue 1206 VAL Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 213 TYR Chi-restraints excluded: chain B residue 435 THR Chi-restraints excluded: chain B residue 776 VAL Chi-restraints excluded: chain B residue 894 CYS Chi-restraints excluded: chain B residue 964 THR Chi-restraints excluded: chain B residue 1070 ASP Chi-restraints excluded: chain B residue 1125 ILE Chi-restraints excluded: chain A residue 194 SER Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 374 ASP Chi-restraints excluded: chain A residue 435 THR Chi-restraints excluded: chain A residue 516 CYS Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 623 ASP Chi-restraints excluded: chain A residue 709 THR Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 836 TYR Chi-restraints excluded: chain A residue 880 HIS Chi-restraints excluded: chain A residue 894 CYS Chi-restraints excluded: chain A residue 1003 LYS Chi-restraints excluded: chain A residue 1006 LYS Chi-restraints excluded: chain A residue 1209 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 93 optimal weight: 0.9980 chunk 61 optimal weight: 1.9990 chunk 135 optimal weight: 2.9990 chunk 109 optimal weight: 1.9990 chunk 311 optimal weight: 0.7980 chunk 5 optimal weight: 0.6980 chunk 196 optimal weight: 3.9990 chunk 152 optimal weight: 0.8980 chunk 206 optimal weight: 3.9990 chunk 234 optimal weight: 2.9990 chunk 341 optimal weight: 3.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 22 ASN A 114 ASN A1095 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.083927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2835 r_free = 0.2835 target = 0.057881 restraints weight = 49895.180| |-----------------------------------------------------------------------------| r_work (start): 0.2785 rms_B_bonded: 2.47 r_work: 0.2659 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2542 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2542 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9112 moved from start: 0.2004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 30240 Z= 0.164 Angle : 0.548 11.665 41361 Z= 0.283 Chirality : 0.043 0.218 4857 Planarity : 0.004 0.059 5130 Dihedral : 6.549 57.868 5800 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.37 % Allowed : 9.01 % Favored : 89.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.45 (0.14), residues: 3570 helix: 1.64 (0.18), residues: 846 sheet: 0.11 (0.17), residues: 810 loop : -0.16 (0.14), residues: 1914 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 517 TYR 0.017 0.001 TYR A 579 PHE 0.036 0.001 PHE C 176 TRP 0.048 0.001 TRP C 515 HIS 0.007 0.001 HIS C 488 Details of bonding type rmsd covalent geometry : bond 0.00368 (30075) covalent geometry : angle 0.53441 (40938) SS BOND : bond 0.00261 ( 72) SS BOND : angle 0.69051 ( 144) hydrogen bonds : bond 0.04122 ( 1180) hydrogen bonds : angle 5.52466 ( 3411) link_ALPHA1-3 : bond 0.01120 ( 3) link_ALPHA1-3 : angle 1.60908 ( 9) link_ALPHA1-6 : bond 0.00789 ( 3) link_ALPHA1-6 : angle 1.69240 ( 9) link_BETA1-4 : bond 0.00334 ( 27) link_BETA1-4 : angle 1.39728 ( 81) link_NAG-ASN : bond 0.00242 ( 60) link_NAG-ASN : angle 1.60227 ( 180) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7140 Ramachandran restraints generated. 3570 Oldfield, 0 Emsley, 3570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7140 Ramachandran restraints generated. 3570 Oldfield, 0 Emsley, 3570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 3219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 142 time to evaluate : 1.003 Fit side-chains revert: symmetry clash REVERT: C 836 TYR cc_start: 0.8627 (OUTLIER) cc_final: 0.8355 (t80) REVERT: C 1075 GLN cc_start: 0.8627 (OUTLIER) cc_final: 0.8153 (mp10) REVERT: C 1080 ARG cc_start: 0.9034 (OUTLIER) cc_final: 0.8701 (mtt-85) REVERT: B 182 LEU cc_start: 0.8768 (OUTLIER) cc_final: 0.8469 (pt) REVERT: B 311 VAL cc_start: 0.8759 (t) cc_final: 0.8487 (m) REVERT: B 531 ARG cc_start: 0.8504 (ttm170) cc_final: 0.8150 (mtt-85) REVERT: B 842 ASN cc_start: 0.9103 (m-40) cc_final: 0.8857 (m110) REVERT: B 1070 ASP cc_start: 0.8032 (OUTLIER) cc_final: 0.7621 (m-30) REVERT: A 623 ASP cc_start: 0.8776 (OUTLIER) cc_final: 0.8387 (m-30) REVERT: A 708 LEU cc_start: 0.8606 (OUTLIER) cc_final: 0.8375 (mm) REVERT: A 836 TYR cc_start: 0.8742 (OUTLIER) cc_final: 0.8139 (m-80) REVERT: A 839 PHE cc_start: 0.8575 (t80) cc_final: 0.8137 (t80) REVERT: A 846 ILE cc_start: 0.9256 (mp) cc_final: 0.9013 (mp) REVERT: A 894 CYS cc_start: 0.6752 (OUTLIER) cc_final: 0.6217 (t) REVERT: A 910 LEU cc_start: 0.9051 (tp) cc_final: 0.8702 (mp) REVERT: A 1042 GLN cc_start: 0.8730 (tm-30) cc_final: 0.8506 (tm-30) REVERT: A 1095 GLN cc_start: 0.8915 (tt0) cc_final: 0.8403 (tp40) outliers start: 44 outliers final: 30 residues processed: 175 average time/residue: 0.5599 time to fit residues: 117.3287 Evaluate side-chains 177 residues out of total 3219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 138 time to evaluate : 0.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 133 ASN Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 435 THR Chi-restraints excluded: chain C residue 559 LEU Chi-restraints excluded: chain C residue 709 THR Chi-restraints excluded: chain C residue 734 SER Chi-restraints excluded: chain C residue 776 VAL Chi-restraints excluded: chain C residue 836 TYR Chi-restraints excluded: chain C residue 849 GLU Chi-restraints excluded: chain C residue 1075 GLN Chi-restraints excluded: chain C residue 1080 ARG Chi-restraints excluded: chain C residue 1093 VAL Chi-restraints excluded: chain C residue 1125 ILE Chi-restraints excluded: chain C residue 1206 VAL Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 213 TYR Chi-restraints excluded: chain B residue 435 THR Chi-restraints excluded: chain B residue 776 VAL Chi-restraints excluded: chain B residue 894 CYS Chi-restraints excluded: chain B residue 964 THR Chi-restraints excluded: chain B residue 1070 ASP Chi-restraints excluded: chain A residue 194 SER Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 374 ASP Chi-restraints excluded: chain A residue 435 THR Chi-restraints excluded: chain A residue 516 CYS Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 623 ASP Chi-restraints excluded: chain A residue 708 LEU Chi-restraints excluded: chain A residue 709 THR Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 836 TYR Chi-restraints excluded: chain A residue 880 HIS Chi-restraints excluded: chain A residue 894 CYS Chi-restraints excluded: chain A residue 1003 LYS Chi-restraints excluded: chain A residue 1006 LYS Chi-restraints excluded: chain A residue 1209 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 105 optimal weight: 3.9990 chunk 238 optimal weight: 0.7980 chunk 146 optimal weight: 0.6980 chunk 236 optimal weight: 0.0170 chunk 288 optimal weight: 8.9990 chunk 107 optimal weight: 0.6980 chunk 334 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 353 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 chunk 200 optimal weight: 3.9990 overall best weight: 0.8420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 22 ASN A 114 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.084339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2824 r_free = 0.2824 target = 0.058249 restraints weight = 50426.087| |-----------------------------------------------------------------------------| r_work (start): 0.2785 rms_B_bonded: 2.50 r_work: 0.2654 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2534 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9080 moved from start: 0.2042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 30240 Z= 0.141 Angle : 0.534 9.665 41361 Z= 0.276 Chirality : 0.042 0.215 4857 Planarity : 0.004 0.059 5130 Dihedral : 6.367 56.849 5800 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 1.30 % Allowed : 9.13 % Favored : 89.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.46 (0.14), residues: 3570 helix: 1.68 (0.18), residues: 849 sheet: 0.03 (0.17), residues: 831 loop : -0.13 (0.14), residues: 1890 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 531 TYR 0.018 0.001 TYR A 579 PHE 0.032 0.001 PHE B 23 TRP 0.054 0.002 TRP C 515 HIS 0.002 0.000 HIS C 201 Details of bonding type rmsd covalent geometry : bond 0.00312 (30075) covalent geometry : angle 0.52045 (40938) SS BOND : bond 0.00257 ( 72) SS BOND : angle 0.64097 ( 144) hydrogen bonds : bond 0.03965 ( 1180) hydrogen bonds : angle 5.45528 ( 3411) link_ALPHA1-3 : bond 0.01163 ( 3) link_ALPHA1-3 : angle 1.51961 ( 9) link_ALPHA1-6 : bond 0.00871 ( 3) link_ALPHA1-6 : angle 1.49965 ( 9) link_BETA1-4 : bond 0.00347 ( 27) link_BETA1-4 : angle 1.38159 ( 81) link_NAG-ASN : bond 0.00207 ( 60) link_NAG-ASN : angle 1.55653 ( 180) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10922.64 seconds wall clock time: 186 minutes 20.21 seconds (11180.21 seconds total)