Starting phenix.real_space_refine on Wed Jun 25 10:19:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bt0_44878/06_2025/9bt0_44878.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bt0_44878/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9bt0_44878/06_2025/9bt0_44878.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bt0_44878/06_2025/9bt0_44878.map" model { file = "/net/cci-nas-00/data/ceres_data/9bt0_44878/06_2025/9bt0_44878.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bt0_44878/06_2025/9bt0_44878.cif" } resolution = 2.23 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 1.54s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 18.99, per 1000 atoms: 0.65 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: 8.48 Conformation dependent library (CDL) restraints added in 3.9 seconds 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: 5.34 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: 16.26 Time building geometry restraints manager: 10.00 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: 0.00 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: 5.530 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: 1.270 Check model and map are aligned: 0.210 Set scattering table: 0.290 Process input model: 77.180 Find NCS groups from input model: 1.990 Set up NCS constraints: 0.250 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:16.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 102.940 ------------------------------------------------------------------------------- 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 : 3.15 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.062 0.003 TRP C 444 HIS 0.007 0.001 HIS B 458 PHE 0.046 0.002 PHE B 591 TYR 0.120 0.004 TYR A 826 ARG 0.009 0.001 ARG C 34 Details of bonding type rmsd link_NAG-ASN : bond 0.00412 ( 60) link_NAG-ASN : angle 1.94743 ( 180) 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_ALPHA1-3 : bond 0.02453 ( 3) link_ALPHA1-3 : angle 3.06324 ( 9) hydrogen bonds : bond 0.17066 ( 1180) hydrogen bonds : angle 7.51353 ( 3411) SS BOND : bond 0.00595 ( 72) SS BOND : angle 1.17743 ( 144) covalent geometry : bond 0.00623 (30075) covalent geometry : angle 0.84011 (40938) *********************** 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 : 3.146 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: 1.2415 time to fit residues: 330.1759 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 : 3.327 ------------------------------------------------------------------------------- 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 301 optimal weight: 4.9990 chunk 270 optimal weight: 2.9990 chunk 150 optimal weight: 0.8980 chunk 92 optimal weight: 3.9990 chunk 182 optimal weight: 2.9990 chunk 144 optimal weight: 3.9990 chunk 279 optimal weight: 0.3980 chunk 108 optimal weight: 0.6980 chunk 170 optimal weight: 0.9980 chunk 208 optimal weight: 0.5980 chunk 324 optimal weight: 3.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3326 r_free = 0.3326 target = 0.085652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.059562 restraints weight = 50247.887| |-----------------------------------------------------------------------------| r_work (start): 0.2810 rms_B_bonded: 2.51 r_work: 0.2684 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2567 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2567 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9056 moved from start: 0.1019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 30240 Z= 0.139 Angle : 0.566 12.040 41361 Z= 0.294 Chirality : 0.044 0.184 4857 Planarity : 0.004 0.055 5130 Dihedral : 9.096 81.697 5813 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.30 % Allowed : 5.93 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.14), residues: 3570 helix: 1.78 (0.18), residues: 822 sheet: 0.44 (0.18), residues: 765 loop : -0.03 (0.14), residues: 1983 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 444 HIS 0.003 0.001 HIS B 201 PHE 0.017 0.001 PHE A 74 TYR 0.017 0.001 TYR C1152 ARG 0.006 0.001 ARG C 531 Details of bonding type rmsd link_NAG-ASN : bond 0.00226 ( 60) link_NAG-ASN : angle 1.65937 ( 180) link_ALPHA1-6 : bond 0.00481 ( 3) link_ALPHA1-6 : angle 1.78490 ( 9) link_BETA1-4 : bond 0.00384 ( 27) link_BETA1-4 : angle 1.81944 ( 81) link_ALPHA1-3 : bond 0.00928 ( 3) link_ALPHA1-3 : angle 2.09798 ( 9) hydrogen bonds : bond 0.04768 ( 1180) hydrogen bonds : angle 5.94276 ( 3411) SS BOND : bond 0.00236 ( 72) SS BOND : angle 0.71283 ( 144) covalent geometry : bond 0.00301 (30075) covalent geometry : angle 0.54935 (40938) *********************** 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: 42 poor density : 158 time to evaluate : 3.997 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 515 TRP cc_start: 0.8302 (t60) cc_final: 0.7919 (t60) REVERT: C 1045 ASN cc_start: 0.8743 (t0) cc_final: 0.8210 (m-40) REVERT: C 1080 ARG cc_start: 0.9040 (OUTLIER) cc_final: 0.8693 (mtt-85) REVERT: B 218 MET cc_start: 0.9192 (mtm) cc_final: 0.8720 (mtm) REVERT: B 311 VAL cc_start: 0.8685 (t) cc_final: 0.8421 (m) REVERT: B 584 SER cc_start: 0.8707 (m) cc_final: 0.8429 (p) REVERT: B 888 PHE cc_start: 0.8483 (m-80) cc_final: 0.8039 (m-80) REVERT: B 902 SER cc_start: 0.7365 (m) cc_final: 0.7055 (p) REVERT: B 1075 GLN cc_start: 0.8770 (OUTLIER) cc_final: 0.8405 (tm-30) REVERT: A 615 GLU cc_start: 0.8068 (OUTLIER) cc_final: 0.7745 (pp20) REVERT: A 623 ASP cc_start: 0.8857 (OUTLIER) cc_final: 0.8452 (m-30) REVERT: A 839 PHE cc_start: 0.8596 (t80) cc_final: 0.8175 (t80) REVERT: A 846 ILE cc_start: 0.9202 (mt) cc_final: 0.8978 (mp) REVERT: A 894 CYS cc_start: 0.6674 (t) cc_final: 0.6106 (t) REVERT: A 1042 GLN cc_start: 0.8671 (tm-30) cc_final: 0.8466 (tm-30) outliers start: 42 outliers final: 13 residues processed: 193 average time/residue: 1.2262 time to fit residues: 286.3335 Evaluate side-chains 158 residues out of total 3219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 141 time to evaluate : 3.032 ------------------------------------------------------------------------------- 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 894 CYS Chi-restraints excluded: chain B residue 1075 GLN 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 Chi-restraints excluded: chain A residue 657 ILE Chi-restraints excluded: chain A residue 1135 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 278 optimal weight: 6.9990 chunk 356 optimal weight: 3.9990 chunk 143 optimal weight: 2.9990 chunk 177 optimal weight: 1.9990 chunk 13 optimal weight: 8.9990 chunk 28 optimal weight: 2.9990 chunk 124 optimal weight: 1.9990 chunk 264 optimal weight: 4.9990 chunk 285 optimal weight: 9.9990 chunk 168 optimal weight: 1.9990 chunk 222 optimal weight: 3.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 825 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 = 0.3269 r_free = 0.3269 target = 0.082382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2771 r_free = 0.2771 target = 0.055942 restraints weight = 50442.022| |-----------------------------------------------------------------------------| r_work (start): 0.2730 rms_B_bonded: 2.50 r_work: 0.2600 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2480 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9112 moved from start: 0.1427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.076 30240 Z= 0.302 Angle : 0.634 10.740 41361 Z= 0.328 Chirality : 0.047 0.186 4857 Planarity : 0.004 0.058 5130 Dihedral : 8.327 74.130 5800 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 2.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.27 % Allowed : 6.59 % Favored : 92.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.14), residues: 3570 helix: 1.47 (0.18), residues: 846 sheet: 0.32 (0.17), residues: 813 loop : -0.10 (0.14), residues: 1911 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 444 HIS 0.004 0.001 HIS C 201 PHE 0.021 0.002 PHE B 907 TYR 0.019 0.002 TYR B 50 ARG 0.005 0.001 ARG C 531 Details of bonding type rmsd link_NAG-ASN : bond 0.00403 ( 60) link_NAG-ASN : angle 1.82636 ( 180) link_ALPHA1-6 : bond 0.00557 ( 3) link_ALPHA1-6 : angle 1.79787 ( 9) link_BETA1-4 : bond 0.00323 ( 27) link_BETA1-4 : angle 1.73392 ( 81) link_ALPHA1-3 : bond 0.01144 ( 3) link_ALPHA1-3 : angle 1.79607 ( 9) hydrogen bonds : bond 0.05239 ( 1180) hydrogen bonds : angle 5.95809 ( 3411) SS BOND : bond 0.00390 ( 72) SS BOND : angle 1.08624 ( 144) covalent geometry : bond 0.00696 (30075) covalent geometry : angle 0.61628 (40938) *********************** 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 187 residues out of total 3219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 146 time to evaluate : 4.004 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 515 TRP cc_start: 0.8253 (t60) cc_final: 0.7909 (t60) REVERT: C 888 PHE cc_start: 0.8035 (m-80) cc_final: 0.7772 (m-80) REVERT: C 1075 GLN cc_start: 0.8720 (OUTLIER) cc_final: 0.8509 (tt0) REVERT: C 1080 ARG cc_start: 0.9078 (OUTLIER) cc_final: 0.8774 (mtt-85) REVERT: B 218 MET cc_start: 0.9293 (mtm) cc_final: 0.8925 (mtm) REVERT: B 311 VAL cc_start: 0.8830 (t) cc_final: 0.8553 (m) REVERT: B 531 ARG cc_start: 0.8463 (ttm170) cc_final: 0.8161 (mtt-85) REVERT: B 584 SER cc_start: 0.8814 (m) cc_final: 0.8600 (p) REVERT: B 888 PHE cc_start: 0.8593 (m-80) cc_final: 0.8338 (m-80) REVERT: B 1070 ASP cc_start: 0.8274 (OUTLIER) cc_final: 0.7763 (m-30) REVERT: A 623 ASP cc_start: 0.8861 (OUTLIER) cc_final: 0.8461 (m-30) REVERT: A 839 PHE cc_start: 0.8650 (t80) cc_final: 0.8236 (t80) REVERT: A 894 CYS cc_start: 0.6765 (t) cc_final: 0.6177 (t) REVERT: A 1042 GLN cc_start: 0.8740 (tm-30) cc_final: 0.8510 (tm-30) outliers start: 41 outliers final: 15 residues processed: 181 average time/residue: 1.6735 time to fit residues: 369.1510 Evaluate side-chains 156 residues out of total 3219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 137 time to evaluate : 3.575 ------------------------------------------------------------------------------- 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 559 LEU Chi-restraints excluded: chain C residue 734 SER Chi-restraints excluded: chain C residue 776 VAL 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 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 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 99 optimal weight: 0.5980 chunk 300 optimal weight: 0.5980 chunk 295 optimal weight: 3.9990 chunk 75 optimal weight: 0.0670 chunk 202 optimal weight: 0.8980 chunk 23 optimal weight: 8.9990 chunk 248 optimal weight: 5.9990 chunk 142 optimal weight: 7.9990 chunk 150 optimal weight: 0.1980 chunk 308 optimal weight: 1.9990 chunk 137 optimal weight: 1.9990 overall best weight: 0.4718 ------------------------------------------------------------------------------- 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 A1095 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.085383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2850 r_free = 0.2850 target = 0.059375 restraints weight = 50359.498| |-----------------------------------------------------------------------------| r_work (start): 0.2808 rms_B_bonded: 2.50 r_work: 0.2682 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2564 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9059 moved from start: 0.1576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 30240 Z= 0.114 Angle : 0.527 9.293 41361 Z= 0.272 Chirality : 0.042 0.227 4857 Planarity : 0.004 0.059 5130 Dihedral : 7.253 65.703 5800 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 1.12 % Allowed : 7.55 % Favored : 91.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.14), residues: 3570 helix: 1.68 (0.18), residues: 846 sheet: 0.42 (0.18), residues: 783 loop : -0.13 (0.14), residues: 1941 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 444 HIS 0.003 0.000 HIS C 488 PHE 0.042 0.001 PHE B 176 TYR 0.017 0.001 TYR C1152 ARG 0.011 0.001 ARG B 517 Details of bonding type rmsd link_NAG-ASN : bond 0.00176 ( 60) link_NAG-ASN : angle 1.54801 ( 180) link_ALPHA1-6 : bond 0.00689 ( 3) link_ALPHA1-6 : angle 1.87553 ( 9) link_BETA1-4 : bond 0.00364 ( 27) link_BETA1-4 : angle 1.48102 ( 81) link_ALPHA1-3 : bond 0.01178 ( 3) link_ALPHA1-3 : angle 1.57782 ( 9) hydrogen bonds : bond 0.04052 ( 1180) hydrogen bonds : angle 5.55814 ( 3411) SS BOND : bond 0.00303 ( 72) SS BOND : angle 0.80465 ( 144) covalent geometry : bond 0.00240 (30075) covalent geometry : angle 0.51173 (40938) *********************** 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 199 residues out of total 3219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 163 time to evaluate : 4.815 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 488 HIS cc_start: 0.8533 (m170) cc_final: 0.8292 (m90) REVERT: C 888 PHE cc_start: 0.7943 (m-80) cc_final: 0.7613 (m-80) REVERT: C 1045 ASN cc_start: 0.8740 (t0) cc_final: 0.8227 (m-40) REVERT: C 1080 ARG cc_start: 0.9005 (OUTLIER) cc_final: 0.8677 (mtt-85) REVERT: B 155 MET cc_start: 0.9522 (mmm) cc_final: 0.9168 (mmm) REVERT: B 311 VAL cc_start: 0.8641 (t) cc_final: 0.8342 (m) REVERT: B 531 ARG cc_start: 0.8414 (ttm170) cc_final: 0.8078 (mtt-85) REVERT: B 584 SER cc_start: 0.8818 (m) cc_final: 0.8591 (p) REVERT: B 842 ASN cc_start: 0.9088 (m-40) cc_final: 0.8818 (m110) REVERT: B 902 SER cc_start: 0.7390 (m) cc_final: 0.7091 (p) REVERT: B 1070 ASP cc_start: 0.8121 (OUTLIER) cc_final: 0.7658 (m-30) REVERT: A 531 ARG cc_start: 0.8748 (mtt-85) cc_final: 0.8540 (mtt90) REVERT: A 623 ASP cc_start: 0.8813 (OUTLIER) cc_final: 0.8420 (m-30) REVERT: A 839 PHE cc_start: 0.8547 (t80) cc_final: 0.8099 (t80) REVERT: A 846 ILE cc_start: 0.9188 (mt) cc_final: 0.8950 (mp) REVERT: A 894 CYS cc_start: 0.6628 (t) cc_final: 0.6072 (t) REVERT: A 1042 GLN cc_start: 0.8701 (tm-30) cc_final: 0.8479 (tm-30) outliers start: 36 outliers final: 16 residues processed: 186 average time/residue: 1.8873 time to fit residues: 431.5782 Evaluate side-chains 163 residues out of total 3219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 144 time to evaluate : 3.711 ------------------------------------------------------------------------------- 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 623 ASP 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 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 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 880 HIS Chi-restraints excluded: chain A residue 1003 LYS Chi-restraints excluded: chain A residue 1006 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 183 optimal weight: 0.9980 chunk 54 optimal weight: 10.0000 chunk 176 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 90 optimal weight: 3.9990 chunk 10 optimal weight: 7.9990 chunk 307 optimal weight: 7.9990 chunk 21 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 83 optimal weight: 1.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C1090 ASN B 825 ASN A 825 ASN A1095 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.082502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2778 r_free = 0.2778 target = 0.056168 restraints weight = 50190.739| |-----------------------------------------------------------------------------| r_work (start): 0.2736 rms_B_bonded: 2.48 r_work: 0.2606 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2486 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9110 moved from start: 0.1708 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= 0.264 Angle : 0.601 9.329 41361 Z= 0.310 Chirality : 0.045 0.237 4857 Planarity : 0.004 0.058 5130 Dihedral : 7.270 61.481 5800 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 1.62 % Allowed : 7.67 % Favored : 90.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.14), residues: 3570 helix: 1.54 (0.18), residues: 846 sheet: 0.25 (0.17), residues: 813 loop : -0.13 (0.14), residues: 1911 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 444 HIS 0.003 0.001 HIS C 830 PHE 0.021 0.002 PHE C 176 TYR 0.018 0.002 TYR B 50 ARG 0.007 0.001 ARG C 531 Details of bonding type rmsd link_NAG-ASN : bond 0.00389 ( 60) link_NAG-ASN : angle 1.75850 ( 180) link_ALPHA1-6 : bond 0.00639 ( 3) link_ALPHA1-6 : angle 1.90125 ( 9) link_BETA1-4 : bond 0.00302 ( 27) link_BETA1-4 : angle 1.55999 ( 81) link_ALPHA1-3 : bond 0.01170 ( 3) link_ALPHA1-3 : angle 1.92049 ( 9) hydrogen bonds : bond 0.04815 ( 1180) hydrogen bonds : angle 5.74041 ( 3411) SS BOND : bond 0.00405 ( 72) SS BOND : angle 0.96578 ( 144) covalent geometry : bond 0.00603 (30075) covalent geometry : angle 0.58416 (40938) *********************** 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 192 residues out of total 3219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 140 time to evaluate : 3.129 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 1075 GLN cc_start: 0.8679 (OUTLIER) cc_final: 0.8353 (tm-30) REVERT: C 1080 ARG cc_start: 0.9043 (OUTLIER) cc_final: 0.8722 (mtt-85) REVERT: B 311 VAL cc_start: 0.8795 (t) cc_final: 0.8507 (m) REVERT: B 531 ARG cc_start: 0.8471 (ttm170) cc_final: 0.8179 (mtt-85) REVERT: B 1070 ASP cc_start: 0.8131 (OUTLIER) cc_final: 0.7642 (m-30) REVERT: A 531 ARG cc_start: 0.8745 (mtt-85) cc_final: 0.8464 (mtt90) REVERT: A 623 ASP cc_start: 0.8814 (OUTLIER) cc_final: 0.8369 (m-30) REVERT: A 839 PHE cc_start: 0.8595 (t80) cc_final: 0.8110 (t80) REVERT: A 894 CYS cc_start: 0.6828 (t) cc_final: 0.6280 (t) REVERT: A 1042 GLN cc_start: 0.8722 (tm-30) cc_final: 0.8484 (tm-30) outliers start: 52 outliers final: 30 residues processed: 181 average time/residue: 1.1932 time to fit residues: 265.0425 Evaluate side-chains 168 residues out of total 3219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 134 time to evaluate : 3.210 ------------------------------------------------------------------------------- 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 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 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 182 LEU 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 708 LEU Chi-restraints excluded: chain A residue 709 THR 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 295 optimal weight: 4.9990 chunk 346 optimal weight: 0.9990 chunk 162 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 111 optimal weight: 0.6980 chunk 118 optimal weight: 0.8980 chunk 351 optimal weight: 1.9990 chunk 128 optimal weight: 1.9990 chunk 186 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 152 GLN B 825 ASN B 842 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 = 0.3290 r_free = 0.3290 target = 0.083034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2828 r_free = 0.2828 target = 0.057449 restraints weight = 50325.784| |-----------------------------------------------------------------------------| r_work (start): 0.2774 rms_B_bonded: 2.43 r_work: 0.2646 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2529 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9121 moved from start: 0.1774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 30240 Z= 0.189 Angle : 0.562 9.838 41361 Z= 0.290 Chirality : 0.043 0.243 4857 Planarity : 0.004 0.058 5130 Dihedral : 7.054 59.025 5800 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 1.52 % Allowed : 8.14 % Favored : 90.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.14), residues: 3570 helix: 1.56 (0.18), residues: 846 sheet: 0.20 (0.17), residues: 810 loop : -0.15 (0.14), residues: 1914 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 444 HIS 0.003 0.001 HIS C 201 PHE 0.023 0.001 PHE C 176 TYR 0.016 0.001 TYR C1152 ARG 0.009 0.000 ARG C 531 Details of bonding type rmsd link_NAG-ASN : bond 0.00288 ( 60) link_NAG-ASN : angle 1.67312 ( 180) link_ALPHA1-6 : bond 0.00712 ( 3) link_ALPHA1-6 : angle 1.93807 ( 9) link_BETA1-4 : bond 0.00317 ( 27) link_BETA1-4 : angle 1.45285 ( 81) link_ALPHA1-3 : bond 0.01165 ( 3) link_ALPHA1-3 : angle 1.78112 ( 9) hydrogen bonds : bond 0.04418 ( 1180) hydrogen bonds : angle 5.65362 ( 3411) SS BOND : bond 0.00275 ( 72) SS BOND : angle 0.84412 ( 144) covalent geometry : bond 0.00425 (30075) covalent geometry : angle 0.54641 (40938) *********************** 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 193 residues out of total 3219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 144 time to evaluate : 3.425 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 133 ASN cc_start: 0.8782 (OUTLIER) cc_final: 0.8566 (t160) REVERT: C 1075 GLN cc_start: 0.8677 (OUTLIER) cc_final: 0.8363 (tm-30) REVERT: C 1080 ARG cc_start: 0.9045 (OUTLIER) cc_final: 0.8719 (mtt-85) REVERT: B 218 MET cc_start: 0.9295 (OUTLIER) cc_final: 0.8991 (mtm) REVERT: B 311 VAL cc_start: 0.8794 (t) cc_final: 0.8518 (m) REVERT: B 531 ARG cc_start: 0.8479 (ttm170) cc_final: 0.8175 (mtt-85) REVERT: B 1070 ASP cc_start: 0.8107 (OUTLIER) cc_final: 0.7645 (m-30) REVERT: A 623 ASP cc_start: 0.8813 (OUTLIER) cc_final: 0.8425 (m-30) REVERT: A 836 TYR cc_start: 0.8822 (OUTLIER) cc_final: 0.8302 (m-80) REVERT: A 839 PHE cc_start: 0.8596 (t80) cc_final: 0.8150 (t80) REVERT: A 846 ILE cc_start: 0.9227 (mp) cc_final: 0.8987 (mp) REVERT: A 894 CYS cc_start: 0.6748 (t) cc_final: 0.6216 (t) REVERT: A 1042 GLN cc_start: 0.8734 (tm-30) cc_final: 0.8512 (tm-30) outliers start: 49 outliers final: 27 residues processed: 178 average time/residue: 1.2722 time to fit residues: 275.3364 Evaluate side-chains 173 residues out of total 3219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 139 time to evaluate : 3.992 ------------------------------------------------------------------------------- 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 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 218 MET 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 182 LEU 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 709 THR 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 1125 ILE 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 313 optimal weight: 0.0060 chunk 59 optimal weight: 5.9990 chunk 40 optimal weight: 3.9990 chunk 170 optimal weight: 6.9990 chunk 82 optimal weight: 1.9990 chunk 49 optimal weight: 0.7980 chunk 217 optimal weight: 2.9990 chunk 145 optimal weight: 4.9990 chunk 321 optimal weight: 2.9990 chunk 277 optimal weight: 0.9980 chunk 67 optimal weight: 2.9990 overall best weight: 1.3600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 825 ASN A1095 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.083292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2798 r_free = 0.2798 target = 0.057067 restraints weight = 50174.088| |-----------------------------------------------------------------------------| r_work (start): 0.2758 rms_B_bonded: 2.48 r_work: 0.2626 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2505 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9098 moved from start: 0.1856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 30240 Z= 0.193 Angle : 0.555 8.727 41361 Z= 0.288 Chirality : 0.043 0.248 4857 Planarity : 0.004 0.059 5130 Dihedral : 6.872 58.511 5800 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 1.62 % Allowed : 8.23 % Favored : 90.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.14), residues: 3570 helix: 1.58 (0.18), residues: 846 sheet: 0.17 (0.17), residues: 810 loop : -0.17 (0.14), residues: 1914 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP C 515 HIS 0.003 0.001 HIS C 201 PHE 0.049 0.002 PHE B 176 TYR 0.016 0.001 TYR C1152 ARG 0.008 0.000 ARG C 531 Details of bonding type rmsd link_NAG-ASN : bond 0.00291 ( 60) link_NAG-ASN : angle 1.65433 ( 180) link_ALPHA1-6 : bond 0.00766 ( 3) link_ALPHA1-6 : angle 1.92381 ( 9) link_BETA1-4 : bond 0.00321 ( 27) link_BETA1-4 : angle 1.42348 ( 81) link_ALPHA1-3 : bond 0.01183 ( 3) link_ALPHA1-3 : angle 1.76445 ( 9) hydrogen bonds : bond 0.04354 ( 1180) hydrogen bonds : angle 5.61264 ( 3411) SS BOND : bond 0.00296 ( 72) SS BOND : angle 0.84200 ( 144) covalent geometry : bond 0.00437 (30075) covalent geometry : angle 0.53963 (40938) *********************** 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 196 residues out of total 3219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 144 time to evaluate : 4.010 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 133 ASN cc_start: 0.8768 (OUTLIER) cc_final: 0.8520 (t160) REVERT: C 273 ARG cc_start: 0.9031 (OUTLIER) cc_final: 0.8742 (ptm-80) REVERT: C 488 HIS cc_start: 0.8645 (m170) cc_final: 0.7346 (m90) REVERT: C 1075 GLN cc_start: 0.8679 (OUTLIER) cc_final: 0.8131 (mp10) REVERT: C 1080 ARG cc_start: 0.9024 (OUTLIER) cc_final: 0.8701 (mtt-85) REVERT: B 311 VAL cc_start: 0.8744 (t) cc_final: 0.8459 (m) REVERT: B 507 THR cc_start: 0.8629 (OUTLIER) cc_final: 0.8381 (p) REVERT: B 531 ARG cc_start: 0.8489 (ttm170) cc_final: 0.8133 (mtt-85) REVERT: B 842 ASN cc_start: 0.9075 (m-40) cc_final: 0.8812 (m110) REVERT: B 1070 ASP cc_start: 0.8120 (OUTLIER) cc_final: 0.7670 (m-30) REVERT: A 623 ASP cc_start: 0.8777 (OUTLIER) cc_final: 0.8368 (m-30) REVERT: A 836 TYR cc_start: 0.8807 (OUTLIER) cc_final: 0.8254 (m-80) REVERT: A 839 PHE cc_start: 0.8580 (t80) cc_final: 0.8115 (t80) REVERT: A 846 ILE cc_start: 0.9203 (mp) cc_final: 0.8937 (mp) REVERT: A 894 CYS cc_start: 0.6853 (t) cc_final: 0.6298 (t) REVERT: A 1042 GLN cc_start: 0.8713 (tm-30) cc_final: 0.8481 (tm-30) outliers start: 52 outliers final: 30 residues processed: 182 average time/residue: 1.2694 time to fit residues: 283.1309 Evaluate side-chains 177 residues out of total 3219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 139 time to evaluate : 3.528 ------------------------------------------------------------------------------- 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 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 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 507 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 182 LEU 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 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 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 171 optimal weight: 0.9990 chunk 114 optimal weight: 4.9990 chunk 191 optimal weight: 3.9990 chunk 294 optimal weight: 0.4980 chunk 195 optimal weight: 0.6980 chunk 282 optimal weight: 2.9990 chunk 242 optimal weight: 1.9990 chunk 6 optimal weight: 5.9990 chunk 110 optimal weight: 0.0980 chunk 138 optimal weight: 0.5980 chunk 43 optimal weight: 1.9990 overall best weight: 0.5782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 825 ASN A1095 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.085266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.059270 restraints weight = 50239.034| |-----------------------------------------------------------------------------| r_work (start): 0.2818 rms_B_bonded: 2.49 r_work: 0.2694 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2578 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9091 moved from start: 0.1931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 30240 Z= 0.117 Angle : 0.516 8.313 41361 Z= 0.267 Chirality : 0.042 0.243 4857 Planarity : 0.003 0.058 5130 Dihedral : 6.493 57.217 5800 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 1.30 % Allowed : 8.51 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.14), residues: 3570 helix: 1.71 (0.18), residues: 849 sheet: 0.18 (0.18), residues: 795 loop : -0.16 (0.14), residues: 1926 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 444 HIS 0.015 0.001 HIS C 488 PHE 0.043 0.001 PHE B 176 TYR 0.017 0.001 TYR C1152 ARG 0.010 0.000 ARG C 531 Details of bonding type rmsd link_NAG-ASN : bond 0.00165 ( 60) link_NAG-ASN : angle 1.50999 ( 180) link_ALPHA1-6 : bond 0.00860 ( 3) link_ALPHA1-6 : angle 1.87298 ( 9) link_BETA1-4 : bond 0.00362 ( 27) link_BETA1-4 : angle 1.34118 ( 81) link_ALPHA1-3 : bond 0.01247 ( 3) link_ALPHA1-3 : angle 1.60552 ( 9) hydrogen bonds : bond 0.03835 ( 1180) hydrogen bonds : angle 5.42159 ( 3411) SS BOND : bond 0.00201 ( 72) SS BOND : angle 0.64308 ( 144) covalent geometry : bond 0.00254 (30075) covalent geometry : angle 0.50235 (40938) *********************** 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 201 residues out of total 3219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 159 time to evaluate : 5.239 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 133 ASN cc_start: 0.8744 (OUTLIER) cc_final: 0.8515 (t160) REVERT: C 176 PHE cc_start: 0.8382 (t80) cc_final: 0.8059 (t80) REVERT: C 1045 ASN cc_start: 0.8776 (t0) cc_final: 0.8275 (m-40) REVERT: C 1075 GLN cc_start: 0.8654 (OUTLIER) cc_final: 0.8174 (mp10) REVERT: C 1080 ARG cc_start: 0.9012 (OUTLIER) cc_final: 0.8676 (mtt-85) REVERT: B 182 LEU cc_start: 0.8735 (OUTLIER) cc_final: 0.8434 (OUTLIER) REVERT: B 311 VAL cc_start: 0.8713 (t) cc_final: 0.8425 (m) REVERT: B 531 ARG cc_start: 0.8452 (ttm170) cc_final: 0.8103 (mtt-85) REVERT: B 842 ASN cc_start: 0.9084 (m-40) cc_final: 0.8830 (m110) REVERT: B 1070 ASP cc_start: 0.8065 (OUTLIER) cc_final: 0.7704 (m-30) REVERT: A 623 ASP cc_start: 0.8770 (OUTLIER) cc_final: 0.8410 (m-30) REVERT: A 708 LEU cc_start: 0.8617 (OUTLIER) cc_final: 0.8296 (mm) REVERT: A 836 TYR cc_start: 0.8751 (OUTLIER) cc_final: 0.8155 (m-80) REVERT: A 839 PHE cc_start: 0.8545 (t80) cc_final: 0.8119 (t80) REVERT: A 846 ILE cc_start: 0.9149 (OUTLIER) cc_final: 0.8841 (mp) REVERT: A 894 CYS cc_start: 0.6720 (t) cc_final: 0.6193 (t) REVERT: A 1042 GLN cc_start: 0.8727 (tm-30) cc_final: 0.8508 (tm-30) REVERT: A 1095 GLN cc_start: 0.8863 (tt0) cc_final: 0.8323 (tp40) outliers start: 42 outliers final: 23 residues processed: 188 average time/residue: 1.4417 time to fit residues: 330.6007 Evaluate side-chains 179 residues out of total 3219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 148 time to evaluate : 3.585 ------------------------------------------------------------------------------- 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 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 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 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 836 TYR Chi-restraints excluded: chain A residue 846 ILE Chi-restraints excluded: chain A residue 880 HIS Chi-restraints excluded: chain A residue 1003 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 164 optimal weight: 6.9990 chunk 204 optimal weight: 3.9990 chunk 153 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 319 optimal weight: 1.9990 chunk 279 optimal weight: 2.9990 chunk 230 optimal weight: 3.9990 chunk 333 optimal weight: 0.7980 chunk 336 optimal weight: 0.5980 chunk 139 optimal weight: 0.0470 chunk 172 optimal weight: 0.9980 overall best weight: 0.8880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.084411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2828 r_free = 0.2828 target = 0.058363 restraints weight = 50136.061| |-----------------------------------------------------------------------------| r_work (start): 0.2788 rms_B_bonded: 2.48 r_work: 0.2658 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2538 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9079 moved from start: 0.1966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 30240 Z= 0.146 Angle : 0.525 8.474 41361 Z= 0.272 Chirality : 0.042 0.233 4857 Planarity : 0.004 0.058 5130 Dihedral : 6.430 57.240 5800 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.18 % Allowed : 9.01 % Favored : 89.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.14), residues: 3570 helix: 1.74 (0.18), residues: 849 sheet: 0.28 (0.18), residues: 780 loop : -0.15 (0.14), residues: 1941 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP C 515 HIS 0.006 0.001 HIS C 488 PHE 0.034 0.001 PHE B 23 TYR 0.017 0.001 TYR A 579 ARG 0.009 0.000 ARG C 531 Details of bonding type rmsd link_NAG-ASN : bond 0.00214 ( 60) link_NAG-ASN : angle 1.54466 ( 180) link_ALPHA1-6 : bond 0.00802 ( 3) link_ALPHA1-6 : angle 1.84405 ( 9) link_BETA1-4 : bond 0.00338 ( 27) link_BETA1-4 : angle 1.37934 ( 81) link_ALPHA1-3 : bond 0.01174 ( 3) link_ALPHA1-3 : angle 1.65307 ( 9) hydrogen bonds : bond 0.03980 ( 1180) hydrogen bonds : angle 5.41527 ( 3411) SS BOND : bond 0.00245 ( 72) SS BOND : angle 0.65291 ( 144) covalent geometry : bond 0.00324 (30075) covalent geometry : angle 0.51074 (40938) *********************** 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 184 residues out of total 3219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 146 time to evaluate : 3.214 Fit side-chains revert: symmetry clash REVERT: C 1045 ASN cc_start: 0.8735 (t0) cc_final: 0.8235 (m-40) REVERT: C 1075 GLN cc_start: 0.8613 (OUTLIER) cc_final: 0.8104 (mp10) REVERT: C 1080 ARG cc_start: 0.8988 (OUTLIER) cc_final: 0.8658 (mtt-85) REVERT: B 182 LEU cc_start: 0.8640 (OUTLIER) cc_final: 0.8414 (pt) REVERT: B 311 VAL cc_start: 0.8683 (t) cc_final: 0.8404 (m) REVERT: B 531 ARG cc_start: 0.8461 (ttm170) cc_final: 0.8110 (mtt-85) REVERT: B 842 ASN cc_start: 0.9036 (m-40) cc_final: 0.8761 (m110) REVERT: B 1070 ASP cc_start: 0.8067 (OUTLIER) cc_final: 0.7738 (m-30) REVERT: A 623 ASP cc_start: 0.8738 (OUTLIER) cc_final: 0.8340 (m-30) REVERT: A 836 TYR cc_start: 0.8738 (OUTLIER) cc_final: 0.8183 (m-80) REVERT: A 839 PHE cc_start: 0.8533 (t80) cc_final: 0.8111 (t80) REVERT: A 846 ILE cc_start: 0.9142 (OUTLIER) cc_final: 0.8847 (mp) REVERT: A 894 CYS cc_start: 0.6807 (t) cc_final: 0.6261 (t) REVERT: A 1042 GLN cc_start: 0.8707 (tm-30) cc_final: 0.8474 (tm-30) REVERT: A 1095 GLN cc_start: 0.8830 (tt0) cc_final: 0.8302 (tp40) outliers start: 38 outliers final: 21 residues processed: 173 average time/residue: 1.2393 time to fit residues: 261.7983 Evaluate side-chains 175 residues out of total 3219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 147 time to evaluate : 3.141 ------------------------------------------------------------------------------- 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 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 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 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 836 TYR Chi-restraints excluded: chain A residue 846 ILE Chi-restraints excluded: chain A residue 880 HIS Chi-restraints excluded: chain A residue 1003 LYS Chi-restraints excluded: chain A residue 1007 LEU 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 331 optimal weight: 2.9990 chunk 9 optimal weight: 5.9990 chunk 88 optimal weight: 3.9990 chunk 327 optimal weight: 0.5980 chunk 232 optimal weight: 4.9990 chunk 205 optimal weight: 0.4980 chunk 238 optimal weight: 4.9990 chunk 296 optimal weight: 5.9990 chunk 62 optimal weight: 2.9990 chunk 109 optimal weight: 0.9980 chunk 319 optimal weight: 1.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- 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 = 0.3294 r_free = 0.3294 target = 0.083190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2832 r_free = 0.2832 target = 0.057617 restraints weight = 50444.122| |-----------------------------------------------------------------------------| r_work (start): 0.2778 rms_B_bonded: 2.44 r_work: 0.2651 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2534 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9119 moved from start: 0.1982 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= 0.199 Angle : 0.567 9.581 41361 Z= 0.292 Chirality : 0.044 0.216 4857 Planarity : 0.004 0.058 5130 Dihedral : 6.547 58.606 5800 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 1.18 % Allowed : 9.07 % Favored : 89.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.14), residues: 3570 helix: 1.67 (0.18), residues: 846 sheet: 0.26 (0.18), residues: 780 loop : -0.17 (0.14), residues: 1944 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP C 515 HIS 0.012 0.001 HIS C 488 PHE 0.030 0.002 PHE B 23 TYR 0.018 0.002 TYR A 579 ARG 0.009 0.001 ARG C 531 Details of bonding type rmsd link_NAG-ASN : bond 0.00298 ( 60) link_NAG-ASN : angle 1.62842 ( 180) link_ALPHA1-6 : bond 0.00763 ( 3) link_ALPHA1-6 : angle 1.73633 ( 9) link_BETA1-4 : bond 0.00319 ( 27) link_BETA1-4 : angle 1.42385 ( 81) link_ALPHA1-3 : bond 0.01102 ( 3) link_ALPHA1-3 : angle 1.68943 ( 9) hydrogen bonds : bond 0.04299 ( 1180) hydrogen bonds : angle 5.53303 ( 3411) SS BOND : bond 0.00296 ( 72) SS BOND : angle 0.74221 ( 144) covalent geometry : bond 0.00450 (30075) covalent geometry : angle 0.55313 (40938) ********************** 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 179 residues out of total 3219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 141 time to evaluate : 4.632 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 176 PHE cc_start: 0.8174 (t80) cc_final: 0.7846 (t80) REVERT: C 1075 GLN cc_start: 0.8654 (OUTLIER) cc_final: 0.8163 (mp10) REVERT: C 1080 ARG cc_start: 0.9030 (OUTLIER) cc_final: 0.8700 (mtt-85) REVERT: B 182 LEU cc_start: 0.8696 (OUTLIER) cc_final: 0.8483 (pt) REVERT: B 311 VAL cc_start: 0.8788 (t) cc_final: 0.8518 (m) REVERT: B 531 ARG cc_start: 0.8473 (ttm170) cc_final: 0.8116 (mtt-85) REVERT: B 842 ASN cc_start: 0.9064 (m-40) cc_final: 0.8803 (m110) REVERT: B 1070 ASP cc_start: 0.8081 (OUTLIER) cc_final: 0.7696 (m-30) REVERT: A 623 ASP cc_start: 0.8755 (OUTLIER) cc_final: 0.8358 (m-30) REVERT: A 708 LEU cc_start: 0.8644 (OUTLIER) cc_final: 0.8386 (mm) REVERT: A 836 TYR cc_start: 0.8771 (OUTLIER) cc_final: 0.8270 (m-80) REVERT: A 839 PHE cc_start: 0.8569 (t80) cc_final: 0.8160 (t80) REVERT: A 846 ILE cc_start: 0.9205 (OUTLIER) cc_final: 0.8913 (mp) REVERT: A 894 CYS cc_start: 0.6823 (t) cc_final: 0.6295 (t) REVERT: A 910 LEU cc_start: 0.9045 (tp) cc_final: 0.8686 (mp) REVERT: A 1042 GLN cc_start: 0.8727 (tm-30) cc_final: 0.8501 (tm-30) REVERT: A 1095 GLN cc_start: 0.8911 (tt0) cc_final: 0.8411 (tp40) outliers start: 38 outliers final: 27 residues processed: 166 average time/residue: 1.6887 time to fit residues: 342.7335 Evaluate side-chains 174 residues out of total 3219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 139 time to evaluate : 8.177 ------------------------------------------------------------------------------- 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 178 LYS 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 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 708 LEU Chi-restraints excluded: chain A residue 836 TYR Chi-restraints excluded: chain A residue 846 ILE Chi-restraints excluded: chain A residue 880 HIS Chi-restraints excluded: chain A residue 1003 LYS Chi-restraints excluded: chain A residue 1007 LEU 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 186 optimal weight: 2.9990 chunk 164 optimal weight: 0.1980 chunk 230 optimal weight: 0.7980 chunk 185 optimal weight: 3.9990 chunk 283 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 268 optimal weight: 1.9990 chunk 259 optimal weight: 2.9990 chunk 67 optimal weight: 3.9990 chunk 73 optimal weight: 1.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- 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 = 0.3294 r_free = 0.3294 target = 0.083742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2809 r_free = 0.2809 target = 0.057573 restraints weight = 50227.025| |-----------------------------------------------------------------------------| r_work (start): 0.2767 rms_B_bonded: 2.51 r_work: 0.2642 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2524 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9088 moved from start: 0.2008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 30240 Z= 0.175 Angle : 0.549 9.857 41361 Z= 0.283 Chirality : 0.043 0.213 4857 Planarity : 0.004 0.058 5130 Dihedral : 6.472 58.857 5800 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 1.09 % Allowed : 9.20 % Favored : 89.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.14), residues: 3570 helix: 1.67 (0.18), residues: 849 sheet: 0.16 (0.18), residues: 801 loop : -0.16 (0.14), residues: 1920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP C 515 HIS 0.003 0.001 HIS C 488 PHE 0.031 0.001 PHE C 176 TYR 0.018 0.001 TYR A 579 ARG 0.009 0.000 ARG C 531 Details of bonding type rmsd link_NAG-ASN : bond 0.00250 ( 60) link_NAG-ASN : angle 1.58621 ( 180) link_ALPHA1-6 : bond 0.00825 ( 3) link_ALPHA1-6 : angle 1.54940 ( 9) link_BETA1-4 : bond 0.00333 ( 27) link_BETA1-4 : angle 1.39751 ( 81) link_ALPHA1-3 : bond 0.01119 ( 3) link_ALPHA1-3 : angle 1.59290 ( 9) hydrogen bonds : bond 0.04155 ( 1180) hydrogen bonds : angle 5.50375 ( 3411) SS BOND : bond 0.00270 ( 72) SS BOND : angle 0.69246 ( 144) covalent geometry : bond 0.00393 (30075) covalent geometry : angle 0.53558 (40938) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 26598.24 seconds wall clock time: 466 minutes 41.59 seconds (28001.59 seconds total)