Starting phenix.real_space_refine on Mon Aug 25 16:50:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bsw_44874/08_2025/9bsw_44874.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bsw_44874/08_2025/9bsw_44874.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.06 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9bsw_44874/08_2025/9bsw_44874.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bsw_44874/08_2025/9bsw_44874.map" model { file = "/net/cci-nas-00/data/ceres_data/9bsw_44874/08_2025/9bsw_44874.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bsw_44874/08_2025/9bsw_44874.cif" } resolution = 2.06 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 sd= 0.087 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 174 5.16 5 C 18659 2.51 5 N 4687 2.21 5 O 5867 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 99 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 29387 Number of models: 1 Model: "" Number of chains: 29 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: "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: "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: "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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 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: "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: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 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: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 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: "A" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "B" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 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 Time building chain proxies: 5.75, per 1000 atoms: 0.20 Number of scatterers: 29387 At special positions: 0 Unit cell: (150.118, 150.118, 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 5867 8.00 N 4687 7.00 C 18659 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=72, symmetry=0 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=2.04 Simple disulfide: pdb=" SG CYS A 163 " - pdb=" SG CYS A 242 " distance=2.02 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=2.05 Simple disulfide: pdb=" SG CYS A 466 " - pdb=" SG CYS A 546 " distance=2.04 Simple disulfide: pdb=" SG CYS A 474 " - pdb=" SG CYS A 495 " distance=2.02 Simple disulfide: pdb=" SG CYS A 476 " - pdb=" SG CYS A 567 " distance=2.02 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=2.05 Simple disulfide: pdb=" SG CYS A 621 " - pdb=" SG CYS A 674 " distance=2.04 Simple disulfide: pdb=" SG CYS A 699 " - pdb=" SG CYS A 720 " distance=2.04 Simple disulfide: pdb=" SG CYS A 735 " - pdb=" SG CYS A 744 " distance=2.02 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=2.03 Simple disulfide: pdb=" SG CYS A 894 " - pdb=" SG CYS A 899 " distance=2.04 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=2.02 Simple disulfide: pdb=" SG CYS A1167 " - pdb=" SG CYS A1212 " distance=2.05 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=2.03 Simple disulfide: pdb=" SG CYS B 163 " - pdb=" SG CYS B 242 " distance=2.02 Simple disulfide: pdb=" SG CYS B 282 " - pdb=" SG CYS B 292 " distance=2.02 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=2.04 Simple disulfide: pdb=" SG CYS B 382 " - pdb=" SG CYS B 605 " distance=2.05 Simple disulfide: pdb=" SG CYS B 466 " - pdb=" SG CYS B 546 " distance=2.05 Simple disulfide: pdb=" SG CYS B 474 " - pdb=" SG CYS B 495 " distance=2.02 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=2.04 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=2.04 Simple disulfide: pdb=" SG CYS B 735 " - pdb=" SG CYS B 744 " distance=2.02 Simple disulfide: pdb=" SG CYS B 818 " - pdb=" SG CYS B 840 " distance=2.05 Simple disulfide: pdb=" SG CYS B 823 " - pdb=" SG CYS B 829 " distance=2.03 Simple disulfide: pdb=" SG CYS B 894 " - pdb=" SG CYS B 899 " distance=2.04 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=2.01 Simple disulfide: pdb=" SG CYS B1167 " - pdb=" SG CYS B1212 " distance=2.04 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=2.05 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=2.02 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=2.04 Simple disulfide: pdb=" SG CYS C 466 " - pdb=" SG CYS C 546 " distance=2.04 Simple disulfide: pdb=" SG CYS C 474 " - pdb=" SG CYS C 495 " distance=2.02 Simple disulfide: pdb=" SG CYS C 476 " - pdb=" SG CYS C 567 " distance=2.02 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=2.04 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=2.04 Simple disulfide: pdb=" SG CYS C 582 " - pdb=" SG CYS C 588 " distance=2.05 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=2.04 Simple disulfide: pdb=" SG CYS C 735 " - pdb=" SG CYS C 744 " distance=2.02 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=2.04 Simple disulfide: pdb=" SG CYS C 929 " - pdb=" SG CYS C 940 " distance=2.04 Simple disulfide: pdb=" SG CYS C1117 " - pdb=" SG CYS C1128 " distance=2.02 Simple disulfide: pdb=" SG CYS C1167 " - pdb=" SG CYS C1212 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA D 3 " - " MAN D 4 " " BMA M 3 " - " MAN M 6 " " BMA T 3 " - " MAN T 4 " ALPHA1-6 " BMA D 3 " - " MAN D 5 " " BMA M 3 " - " MAN M 4 " " MAN M 4 " - " MAN M 5 " " BMA T 3 " - " MAN T 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 K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " NAG-ASN " NAG A1401 " - " ASN A 19 " " NAG A1402 " - " ASN A 58 " " NAG A1403 " - " ASN A 192 " " NAG A1404 " - " ASN A 251 " " NAG A1405 " - " ASN A 433 " " NAG A1406 " - " ASN A 470 " " NAG A1407 " - " ASN A 564 " " NAG A1408 " - " ASN A 775 " " NAG A1409 " - " ASN A 780 " " NAG A1410 " - " ASN A 797 " " NAG A1411 " - " ASN A 928 " " NAG B1401 " - " ASN B 29 " " NAG B1402 " - " ASN B 58 " " NAG B1403 " - " ASN B 192 " " NAG B1404 " - " ASN B 251 " " NAG B1405 " - " ASN B 433 " " NAG B1406 " - " ASN B 470 " " NAG B1407 " - " ASN B 564 " " NAG B1408 " - " ASN B 686 " " NAG B1409 " - " ASN B 775 " " NAG B1410 " - " ASN B 780 " " NAG B1411 " - " ASN B 797 " " NAG B1412 " - " 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 A 132 " " NAG E 1 " - " ASN A 188 " " NAG F 1 " - " ASN A 355 " " NAG G 1 " - " ASN A 666 " " NAG H 1 " - " ASN A 686 " " NAG I 1 " - " ASN A 705 " " NAG J 1 " - " ASN A 726 " " NAG K 1 " - " ASN A1215 " " NAG L 1 " - " ASN B 19 " " NAG M 1 " - " ASN B 132 " " NAG N 1 " - " ASN B 188 " " NAG O 1 " - " ASN B 355 " " NAG P 1 " - " ASN B 666 " " NAG Q 1 " - " ASN B 705 " " NAG R 1 " - " ASN B 726 " " NAG S 1 " - " ASN B1215 " " NAG T 1 " - " ASN C 132 " " NAG U 1 " - " ASN C 188 " " NAG V 1 " - " ASN C 355 " " NAG W 1 " - " ASN C 666 " " NAG X 1 " - " ASN C 705 " " NAG Y 1 " - " ASN C 726 " " NAG Z 1 " - " ASN C1215 " Time building additional restraints: 2.38 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 715.3 nanoseconds 7140 Ramachandran restraints generated. 3570 Oldfield, 0 Emsley, 3570 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6756 Finding SS restraints... Secondary structure from input PDB file: 93 helices and 69 sheets defined 26.9% alpha, 32.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.56 Creating SS restraints... Processing helix chain 'A' and resid 88 through 91 removed outlier: 3.514A 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 294 Processing helix chain 'A' and resid 328 through 334 Processing helix chain 'A' and resid 341 through 344 removed outlier: 3.542A 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 379 removed outlier: 3.914A pdb=" N TYR A 379 " --> pdb=" O GLU A 375 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 402 removed outlier: 5.106A 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 432 through 434 No H-bonds generated for 'chain 'A' and resid 432 through 434' Processing helix chain 'A' and resid 442 through 448 removed outlier: 3.521A pdb=" N TYR A 448 " --> pdb=" O TRP A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 484 removed outlier: 3.809A pdb=" N SER A 484 " --> pdb=" O SER A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 553 through 556 Processing helix chain 'A' and resid 570 through 572 No H-bonds generated for 'chain 'A' and resid 570 through 572' Processing helix chain 'A' and resid 698 through 706 Processing helix chain 'A' and resid 817 through 823 Processing helix chain 'A' and resid 826 through 835 removed outlier: 3.583A pdb=" N LEU A 832 " --> pdb=" O ALA A 828 " (cutoff:3.500A) Processing helix chain 'A' and resid 838 through 867 Processing helix chain 'A' and resid 889 through 892 Processing helix chain 'A' and resid 895 through 899 removed outlier: 3.808A pdb=" N HIS A 898 " --> pdb=" O LEU A 895 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N CYS A 899 " --> pdb=" O GLY A 896 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 895 through 899' 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: 3.972A pdb=" N ALA A 970 " --> pdb=" O ALA A 966 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N MET A 971 " --> pdb=" O THR A 967 " (cutoff:3.500A) removed outlier: 3.562A 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: 3.572A pdb=" N LEU A1001 " --> pdb=" O THR A 997 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LYS A1003 " --> pdb=" O ASP A 999 " (cutoff:3.500A) Processing helix chain 'A' and resid 1004 through 1023 removed outlier: 3.759A pdb=" N PHE A1023 " --> pdb=" O ILE A1019 " (cutoff:3.500A) Processing helix chain 'A' and resid 1027 through 1050 removed outlier: 3.542A pdb=" N VAL A1037 " --> pdb=" O ILE A1033 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLN A1050 " --> pdb=" O SER A1046 " (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 1118 removed outlier: 3.875A pdb=" N VAL A1076 " --> pdb=" O PRO A1072 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU A1102 " --> pdb=" O SER A1098 " (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 helix chain 'B' and resid 88 through 91 removed outlier: 3.598A pdb=" N GLN B 91 " --> pdb=" O LEU B 88 " (cutoff:3.500A) No H-bonds generated for '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 341 through 344 removed outlier: 3.553A pdb=" N TRP B 344 " --> pdb=" O PRO B 341 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 341 through 344' Processing helix chain 'B' and resid 355 through 363 removed outlier: 3.622A pdb=" N ARG B 361 " --> pdb=" O SER B 357 " (cutoff:3.500A) Processing helix chain 'B' and resid 374 through 379 removed outlier: 3.897A pdb=" N TYR B 379 " --> pdb=" O GLU B 375 " (cutoff:3.500A) Processing helix chain 'B' and resid 394 through 402 removed outlier: 5.215A 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 442 through 448 Processing helix chain 'B' and resid 478 through 483 Processing helix chain 'B' and resid 553 through 556 Processing helix chain 'B' and resid 570 through 572 No H-bonds generated for 'chain 'B' and resid 570 through 572' Processing helix chain 'B' and resid 698 through 706 Processing helix chain 'B' and resid 817 through 823 Processing helix chain 'B' and resid 826 through 835 removed outlier: 3.841A pdb=" N GLU B 835 " --> pdb=" O ASP B 831 " (cutoff:3.500A) Processing helix chain 'B' and resid 836 through 867 removed outlier: 3.871A pdb=" N CYS B 840 " --> pdb=" O TYR B 836 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ASP B 841 " --> pdb=" O GLY B 837 " (cutoff:3.500A) Processing helix chain 'B' and resid 889 through 892 Processing helix chain 'B' and resid 895 through 899 removed outlier: 3.646A pdb=" N HIS B 898 " --> pdb=" O LEU B 895 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N CYS B 899 " --> pdb=" O GLY B 896 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 895 through 899' 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 969 Processing helix chain 'B' and resid 982 through 993 Processing helix chain 'B' and resid 997 through 1004 removed outlier: 3.559A pdb=" N LEU B1001 " --> pdb=" O THR B 997 " (cutoff:3.500A) Processing helix chain 'B' and resid 1004 through 1023 removed outlier: 3.777A pdb=" N PHE B1023 " --> pdb=" O ILE B1019 " (cutoff:3.500A) Processing helix chain 'B' and resid 1027 through 1050 removed outlier: 3.566A 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 1067 Processing helix chain 'B' and resid 1070 through 1118 Processing helix chain 'C' and resid 88 through 91 removed outlier: 3.544A pdb=" N GLN C 91 " --> pdb=" O LEU C 88 " (cutoff:3.500A) No H-bonds generated for '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: 3.514A 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: 3.894A pdb=" N TYR C 379 " --> pdb=" O GLU C 375 " (cutoff:3.500A) Processing helix chain 'C' and resid 394 through 402 removed outlier: 5.103A 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 removed outlier: 3.519A pdb=" N TYR C 448 " --> pdb=" O TRP C 444 " (cutoff:3.500A) Processing helix chain 'C' and resid 478 through 485 removed outlier: 3.528A pdb=" N SER C 484 " --> pdb=" O SER C 480 " (cutoff:3.500A) Processing helix chain 'C' and resid 553 through 556 Processing helix chain 'C' and resid 570 through 572 No H-bonds generated for 'chain 'C' and resid 570 through 572' 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 835 removed outlier: 3.827A pdb=" N GLU C 835 " --> pdb=" O ASP C 831 " (cutoff:3.500A) Processing helix chain 'C' and resid 837 through 867 removed outlier: 4.203A pdb=" N ASP C 841 " --> pdb=" O GLY C 837 " (cutoff:3.500A) Processing helix chain 'C' and resid 889 through 892 removed outlier: 3.564A pdb=" N VAL C 892 " --> pdb=" O LYS C 889 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 889 through 892' Processing helix chain 'C' and resid 896 through 900 removed outlier: 3.909A pdb=" N CYS C 899 " --> pdb=" O GLY C 896 " (cutoff:3.500A) Processing helix chain 'C' and resid 905 through 913 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 972 removed outlier: 3.962A pdb=" N ALA C 970 " --> pdb=" O ALA C 966 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N MET C 971 " --> pdb=" O THR C 967 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N PHE C 972 " --> pdb=" O VAL C 968 " (cutoff:3.500A) Processing helix chain 'C' and resid 982 through 994 removed outlier: 3.629A pdb=" N LEU C 994 " --> pdb=" O ARG C 990 " (cutoff:3.500A) Processing helix chain 'C' and resid 997 through 1004 removed outlier: 3.631A pdb=" N LEU C1001 " --> pdb=" O THR C 997 " (cutoff:3.500A) Processing helix chain 'C' and resid 1004 through 1023 removed outlier: 3.779A pdb=" N PHE C1023 " --> pdb=" O ILE C1019 " (cutoff:3.500A) Processing helix chain 'C' and resid 1027 through 1050 removed outlier: 3.729A 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 1118 removed outlier: 3.757A pdb=" N VAL C1076 " --> pdb=" O PRO C1072 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ARG C1080 " --> pdb=" O VAL C1076 " (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 sheet with id=AA1, first strand: chain 'A' and resid 25 through 26 Processing sheet with id=AA2, first strand: chain 'A' and resid 37 through 39 removed outlier: 8.165A pdb=" N ASN A 73 " --> pdb=" O PRO A 260 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N GLY A 101 " --> pdb=" O LEU A 261 " (cutoff:3.500A) removed outlier: 5.836A pdb=" N TYR A 213 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N PHE A 222 " --> pdb=" O TYR A 213 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 59 through 68 removed outlier: 3.731A pdb=" N ASN A 278 " --> pdb=" O LYS A 269 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 54 through 56 removed outlier: 6.139A pdb=" N VAL A 55 " --> pdb=" O TYR C 651 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N LEU C 650 " --> pdb=" O ILE C 658 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N ILE C 658 " --> pdb=" O ILE C 671 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N THR C 668 " --> pdb=" O VAL C 638 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ALA C 315 " --> pdb=" O CYS C 621 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 80 through 81 removed outlier: 7.978A pdb=" N THR A 241 " --> pdb=" O PRO A 159 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N THR A 161 " --> pdb=" O THR A 241 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N TRP A 174 " --> pdb=" O CYS A 156 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 96 through 97 Processing sheet with id=AA7, first strand: chain 'A' and resid 109 through 113 Processing sheet with id=AA8, first strand: chain 'A' and resid 302 through 305 Processing sheet with id=AA9, first strand: chain 'A' and resid 309 through 310 Processing sheet with id=AB1, first strand: chain 'A' and resid 315 through 319 removed outlier: 4.026A pdb=" N ALA A 315 " --> pdb=" O CYS A 621 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N THR A 668 " --> pdb=" O VAL A 638 " (cutoff:3.500A) removed outlier: 5.112A pdb=" N ILE A 658 " --> pdb=" O ILE A 671 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 337 through 339 removed outlier: 6.629A pdb=" N VAL A 338 " --> pdb=" O ASN A 437 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 345 through 349 removed outlier: 6.553A pdb=" N PHE A 383 " --> pdb=" O ILE A 599 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N ILE A 599 " --> pdb=" O PHE A 383 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N SER A 385 " --> pdb=" O ASN A 597 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N SER A 428 " --> pdb=" O THR A 365 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N THR A 365 " --> pdb=" O SER A 428 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 353 through 354 removed outlier: 6.553A pdb=" N PHE A 383 " --> pdb=" O ILE A 599 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N ILE A 599 " --> pdb=" O PHE A 383 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N SER A 385 " --> pdb=" O ASN A 597 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 459 through 463 Processing sheet with id=AB6, first strand: chain 'A' and resid 467 through 468 Processing sheet with id=AB7, first strand: chain 'A' and resid 504 through 506 Processing sheet with id=AB8, first strand: chain 'A' and resid 550 through 551 removed outlier: 3.705A pdb=" N GLY A 550 " --> pdb=" O LEU A 575 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 724 through 732 removed outlier: 6.306A pdb=" N ASP A 725 " --> pdb=" O PHE A 768 " (cutoff:3.500A) removed outlier: 8.377A pdb=" N THR A 770 " --> pdb=" O ASP A 725 " (cutoff:3.500A) removed outlier: 9.396A pdb=" N LEU A 727 " --> pdb=" O THR A 770 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N PHE A 743 " --> pdb=" O MET A 739 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 777 through 779 removed outlier: 6.136A pdb=" N SER A 777 " --> pdb=" O LEU B 871 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'A' and resid 790 through 808 removed outlier: 6.840A pdb=" N GLU A 791 " --> pdb=" O LEU A1161 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N LEU A1161 " --> pdb=" O GLU A 791 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N LYS A 793 " --> pdb=" O THR A1159 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N THR A1159 " --> pdb=" O LYS A 793 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N PHE A1157 " --> pdb=" O PRO A 795 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N ASN A 797 " --> pdb=" O ILE A1155 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N GLY A1144 " --> pdb=" O ASN A1140 " (cutoff:3.500A) removed outlier: 5.494A pdb=" N ASN A1140 " --> pdb=" O GLY A1144 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N LEU A1146 " --> pdb=" O VAL A1138 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N VAL A1138 " --> pdb=" O LEU A1146 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N MET A1148 " --> pdb=" O SER A1136 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N SER A1136 " --> pdb=" O MET A1148 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N PHE A1150 " --> pdb=" O ILE A1134 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N ASN A1132 " --> pdb=" O TYR A1152 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 790 through 808 removed outlier: 6.840A pdb=" N GLU A 791 " --> pdb=" O LEU A1161 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N LEU A1161 " --> pdb=" O GLU A 791 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N LYS A 793 " --> pdb=" O THR A1159 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N THR A1159 " --> pdb=" O LYS A 793 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N PHE A1157 " --> pdb=" O PRO A 795 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N ASN A 797 " --> pdb=" O ILE A1155 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N LEU A1161 " --> pdb=" O LYS A1183 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N LYS A1183 " --> pdb=" O LEU A1161 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N GLY A1192 " --> pdb=" O TYR A1197 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N TYR A1197 " --> pdb=" O GLY A1192 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 813 through 816 removed outlier: 4.010A pdb=" N LYS A 813 " --> pdb=" O LEU A 950 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 870 through 872 Processing sheet with id=AC6, first strand: chain 'A' and resid 882 through 883 Processing sheet with id=AC7, first strand: chain 'A' and resid 1206 through 1209 removed outlier: 5.892A pdb=" N CYS A1167 " --> pdb=" O ALA A1219 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 25 through 26 Processing sheet with id=AC9, first strand: chain 'B' and resid 35 through 39 removed outlier: 4.887A pdb=" N PHE B 74 " --> pdb=" O SER B 36 " (cutoff:3.500A) removed outlier: 8.562A pdb=" N ASN B 73 " --> pdb=" O PRO B 260 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N GLY B 101 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N PHE B 209 " --> pdb=" O SER B 225 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N SER B 225 " --> pdb=" O PHE B 209 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N ALA B 211 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 59 through 68 removed outlier: 3.667A pdb=" N ASN B 278 " --> pdb=" O LYS B 269 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 80 through 81 removed outlier: 8.206A pdb=" N THR B 241 " --> pdb=" O PRO B 159 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N THR B 161 " --> pdb=" O THR B 241 " (cutoff:3.500A) removed outlier: 7.361A pdb=" N TRP B 174 " --> pdb=" O CYS B 156 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 96 through 97 removed outlier: 3.697A pdb=" N PHE B 185 " --> pdb=" O ALA B 150 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 109 through 113 Processing sheet with id=AD5, first strand: chain 'B' and resid 302 through 305 Processing sheet with id=AD6, first strand: chain 'B' and resid 309 through 310 Processing sheet with id=AD7, first strand: chain 'B' and resid 315 through 319 removed outlier: 3.935A pdb=" N ALA B 315 " --> pdb=" O CYS B 621 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N THR B 668 " --> pdb=" O VAL B 638 " (cutoff:3.500A) removed outlier: 5.180A pdb=" N ILE B 658 " --> pdb=" O ILE B 671 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N LEU B 650 " --> pdb=" O ILE B 658 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 337 through 339 removed outlier: 6.430A pdb=" N VAL B 338 " --> pdb=" O ASN B 437 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'B' and resid 345 through 349 removed outlier: 6.443A pdb=" N PHE B 383 " --> pdb=" O ILE B 599 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N ILE B 599 " --> pdb=" O PHE B 383 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N SER B 428 " --> pdb=" O THR B 365 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N THR B 365 " --> pdb=" O SER B 428 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 353 through 354 removed outlier: 6.443A pdb=" N PHE B 383 " --> pdb=" O ILE B 599 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N ILE B 599 " --> pdb=" O PHE B 383 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 459 through 463 Processing sheet with id=AE3, first strand: chain 'B' and resid 466 through 468 removed outlier: 4.027A pdb=" N CYS B 466 " --> pdb=" O SER B 538 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'B' and resid 504 through 509 removed outlier: 5.546A pdb=" N VAL B 509 " --> pdb=" O THR B 513 " (cutoff:3.500A) removed outlier: 5.249A pdb=" N THR B 513 " --> pdb=" O VAL B 509 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'B' and resid 550 through 551 removed outlier: 3.661A pdb=" N GLY B 550 " --> pdb=" O LEU B 575 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'B' and resid 724 through 732 removed outlier: 6.274A pdb=" N ASP B 725 " --> pdb=" O PHE B 768 " (cutoff:3.500A) removed outlier: 8.315A pdb=" N THR B 770 " --> pdb=" O ASP B 725 " (cutoff:3.500A) removed outlier: 9.458A pdb=" N LEU B 727 " --> pdb=" O THR B 770 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N PHE B 743 " --> pdb=" O MET B 739 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'B' and resid 777 through 779 Processing sheet with id=AE8, first strand: chain 'B' and resid 790 through 808 removed outlier: 6.812A pdb=" N GLU B 791 " --> pdb=" O LEU B1161 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N LEU B1161 " --> pdb=" O GLU B 791 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N LYS B 793 " --> pdb=" O THR B1159 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N THR B1159 " --> pdb=" O LYS B 793 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N PHE B1157 " --> pdb=" O PRO B 795 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ASN B 797 " --> pdb=" O ILE B1155 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N TYR B1152 " --> pdb=" O HIS B1133 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N HIS B1133 " --> pdb=" O TYR B1152 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'B' and resid 790 through 808 removed outlier: 6.812A pdb=" N GLU B 791 " --> pdb=" O LEU B1161 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N LEU B1161 " --> pdb=" O GLU B 791 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N LYS B 793 " --> pdb=" O THR B1159 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N THR B1159 " --> pdb=" O LYS B 793 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N PHE B1157 " --> pdb=" O PRO B 795 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ASN B 797 " --> pdb=" O ILE B1155 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N LEU B1161 " --> pdb=" O LYS B1183 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N LYS B1183 " --> pdb=" O LEU B1161 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'B' and resid 813 through 816 removed outlier: 4.023A pdb=" N LYS B 813 " --> pdb=" O LEU B 950 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'B' and resid 882 through 883 Processing sheet with id=AF3, first strand: chain 'B' and resid 1206 through 1209 removed outlier: 5.882A pdb=" N CYS B1167 " --> pdb=" O ALA B1219 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 25 through 26 Processing sheet with id=AF5, first strand: chain 'C' and resid 37 through 39 removed outlier: 8.259A pdb=" N ASN C 73 " --> pdb=" O PRO C 260 " (cutoff:3.500A) removed outlier: 5.804A pdb=" N TYR C 213 " --> pdb=" O PHE C 222 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N PHE C 222 " --> pdb=" O TYR C 213 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 59 through 67 removed outlier: 3.695A pdb=" N ASN C 278 " --> pdb=" O LYS C 269 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 80 through 81 removed outlier: 8.112A pdb=" N THR C 241 " --> pdb=" O PRO C 159 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N THR C 161 " --> pdb=" O THR C 241 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N TRP C 174 " --> pdb=" O CYS C 156 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'C' and resid 96 through 97 removed outlier: 3.552A pdb=" N PHE C 185 " --> pdb=" O ALA C 150 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'C' and resid 109 through 113 Processing sheet with id=AG1, first strand: chain 'C' and resid 302 through 305 Processing sheet with id=AG2, first strand: chain 'C' and resid 309 through 310 Processing sheet with id=AG3, first strand: chain 'C' and resid 337 through 339 removed outlier: 6.610A pdb=" N VAL C 338 " --> pdb=" O ASN C 437 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG3 Processing sheet with id=AG4, first strand: chain 'C' and resid 345 through 349 removed outlier: 6.503A pdb=" N PHE C 383 " --> pdb=" O ILE C 599 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N ILE C 599 " --> pdb=" O PHE C 383 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N SER C 428 " --> pdb=" O THR C 365 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N THR C 365 " --> pdb=" O SER C 428 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'C' and resid 353 through 354 removed outlier: 6.503A pdb=" N PHE C 383 " --> pdb=" O ILE C 599 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N ILE C 599 " --> pdb=" O PHE C 383 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'C' and resid 459 through 463 Processing sheet with id=AG7, first strand: chain 'C' and resid 466 through 468 removed outlier: 4.181A pdb=" N CYS C 466 " --> pdb=" O SER C 538 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'C' and resid 504 through 509 removed outlier: 6.170A pdb=" N VAL C 509 " --> pdb=" O THR C 513 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N THR C 513 " --> pdb=" O VAL C 509 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'C' and resid 550 through 551 removed outlier: 3.660A pdb=" N GLY C 550 " --> pdb=" O LEU C 575 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'C' and resid 724 through 732 removed outlier: 6.384A pdb=" N ASP C 725 " --> pdb=" O PHE C 768 " (cutoff:3.500A) removed outlier: 8.472A pdb=" N THR C 770 " --> pdb=" O ASP C 725 " (cutoff:3.500A) removed outlier: 9.457A pdb=" N LEU C 727 " --> pdb=" O THR C 770 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N PHE C 743 " --> pdb=" O MET C 739 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N LEU C 737 " --> pdb=" O VAL C 745 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'C' and resid 790 through 808 removed outlier: 6.789A pdb=" N GLU C 791 " --> pdb=" O LEU C1161 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N LEU C1161 " --> pdb=" O GLU C 791 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N LYS C 793 " --> pdb=" O THR C1159 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N THR C1159 " --> pdb=" O LYS C 793 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N PHE C1157 " --> pdb=" O PRO C 795 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N ASN C 797 " --> pdb=" O ILE C1155 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N TYR C1152 " --> pdb=" O HIS C1133 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N HIS C1133 " --> pdb=" O TYR C1152 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'C' and resid 790 through 808 removed outlier: 6.789A pdb=" N GLU C 791 " --> pdb=" O LEU C1161 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N LEU C1161 " --> pdb=" O GLU C 791 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N LYS C 793 " --> pdb=" O THR C1159 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N THR C1159 " --> pdb=" O LYS C 793 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N PHE C1157 " --> pdb=" O PRO C 795 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N ASN C 797 " --> pdb=" O ILE C1155 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N LEU C1161 " --> pdb=" O LYS C1183 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N LYS C1183 " --> pdb=" O LEU C1161 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N GLY C1192 " --> pdb=" O TYR C1197 " (cutoff:3.500A) removed outlier: 5.541A pdb=" N TYR C1197 " --> pdb=" O GLY C1192 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'C' and resid 813 through 816 removed outlier: 4.007A pdb=" N LYS C 813 " --> pdb=" O LEU C 950 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'C' and resid 882 through 883 Processing sheet with id=AH6, first strand: chain 'C' and resid 1206 through 1209 removed outlier: 5.843A pdb=" N CYS C1167 " --> pdb=" O ALA C1219 " (cutoff:3.500A) 1214 hydrogen bonds defined for protein. 3363 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.00 Time building geometry restraints manager: 3.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 7839 1.33 - 1.46: 6190 1.46 - 1.58: 15856 1.58 - 1.70: 0 1.70 - 1.82: 204 Bond restraints: 30089 Sorted by residual: bond pdb=" C3 BMA M 3 " pdb=" O3 BMA M 3 " ideal model delta sigma weight residual 1.406 1.489 -0.083 2.00e-02 2.50e+03 1.71e+01 bond pdb=" CA PRO C 973 " pdb=" C PRO C 973 " ideal model delta sigma weight residual 1.514 1.537 -0.022 5.50e-03 3.31e+04 1.66e+01 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 1.51e+01 bond pdb=" C1 MAN T 5 " pdb=" O5 MAN T 5 " ideal model delta sigma weight residual 1.399 1.475 -0.076 2.00e-02 2.50e+03 1.44e+01 bond pdb=" C5 NAG E 2 " pdb=" O5 NAG E 2 " ideal model delta sigma weight residual 1.413 1.488 -0.075 2.00e-02 2.50e+03 1.41e+01 ... (remaining 30084 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.91: 30998 1.91 - 3.82: 8916 3.82 - 5.73: 943 5.73 - 7.64: 92 7.64 - 9.55: 8 Bond angle restraints: 40957 Sorted by residual: angle pdb=" N ILE B1125 " pdb=" CA ILE B1125 " pdb=" C ILE B1125 " ideal model delta sigma weight residual 110.42 118.42 -8.00 9.60e-01 1.09e+00 6.94e+01 angle pdb=" N ILE C1125 " pdb=" CA ILE C1125 " pdb=" C ILE C1125 " ideal model delta sigma weight residual 110.30 117.58 -7.28 9.70e-01 1.06e+00 5.64e+01 angle pdb=" N ILE A1125 " pdb=" CA ILE A1125 " pdb=" C ILE A1125 " ideal model delta sigma weight residual 110.30 117.51 -7.21 9.70e-01 1.06e+00 5.53e+01 angle pdb=" CA ASP A 366 " pdb=" CB ASP A 366 " pdb=" CG ASP A 366 " ideal model delta sigma weight residual 112.60 119.30 -6.70 1.00e+00 1.00e+00 4.49e+01 angle pdb=" N PRO B1071 " pdb=" CA PRO B1071 " pdb=" C PRO B1071 " ideal model delta sigma weight residual 110.70 118.43 -7.73 1.22e+00 6.72e-01 4.01e+01 ... (remaining 40952 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.66: 18043 20.66 - 41.31: 805 41.31 - 61.97: 154 61.97 - 82.62: 49 82.62 - 103.28: 32 Dihedral angle restraints: 19083 sinusoidal: 8556 harmonic: 10527 Sorted by residual: 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 35.74 57.26 1 1.00e+01 1.00e-02 4.41e+01 dihedral pdb=" CA TYR A 266 " pdb=" C TYR A 266 " pdb=" N LEU A 267 " pdb=" CA LEU A 267 " ideal model delta harmonic sigma weight residual 180.00 153.43 26.57 0 5.00e+00 4.00e-02 2.82e+01 dihedral pdb=" C ILE A 15 " pdb=" N ILE A 15 " pdb=" CA ILE A 15 " pdb=" CB ILE A 15 " ideal model delta harmonic sigma weight residual -122.00 -134.56 12.56 0 2.50e+00 1.60e-01 2.52e+01 ... (remaining 19080 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 2812 0.083 - 0.166: 1690 0.166 - 0.249: 310 0.249 - 0.332: 46 0.332 - 0.414: 4 Chirality restraints: 4862 Sorted by residual: chirality pdb=" C1 NAG U 2 " pdb=" O4 NAG U 1 " pdb=" C2 NAG U 2 " pdb=" O5 NAG U 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.59 0.19 2.00e-02 2.50e+03 9.50e+01 chirality pdb=" C1 BMA K 3 " pdb=" O4 NAG K 2 " pdb=" C2 BMA K 3 " pdb=" O5 BMA K 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.58 0.18 2.00e-02 2.50e+03 7.87e+01 chirality pdb=" C1 NAG Z 2 " pdb=" O4 NAG Z 1 " pdb=" C2 NAG Z 2 " pdb=" O5 NAG Z 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.57 0.17 2.00e-02 2.50e+03 7.40e+01 ... (remaining 4859 not shown) Planarity restraints: 5190 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR C1092 " -0.144 2.00e-02 2.50e+03 7.97e-02 1.27e+02 pdb=" CG TYR C1092 " 0.043 2.00e-02 2.50e+03 pdb=" CD1 TYR C1092 " 0.068 2.00e-02 2.50e+03 pdb=" CD2 TYR C1092 " 0.057 2.00e-02 2.50e+03 pdb=" CE1 TYR C1092 " 0.040 2.00e-02 2.50e+03 pdb=" CE2 TYR C1092 " 0.051 2.00e-02 2.50e+03 pdb=" CZ TYR C1092 " 0.010 2.00e-02 2.50e+03 pdb=" OH TYR C1092 " -0.126 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A1092 " 0.136 2.00e-02 2.50e+03 7.41e-02 1.10e+02 pdb=" CG TYR A1092 " -0.046 2.00e-02 2.50e+03 pdb=" CD1 TYR A1092 " -0.060 2.00e-02 2.50e+03 pdb=" CD2 TYR A1092 " -0.056 2.00e-02 2.50e+03 pdb=" CE1 TYR A1092 " -0.039 2.00e-02 2.50e+03 pdb=" CE2 TYR A1092 " -0.042 2.00e-02 2.50e+03 pdb=" CZ TYR A1092 " -0.008 2.00e-02 2.50e+03 pdb=" OH TYR A1092 " 0.115 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B1092 " -0.134 2.00e-02 2.50e+03 7.27e-02 1.06e+02 pdb=" CG TYR B1092 " 0.046 2.00e-02 2.50e+03 pdb=" CD1 TYR B1092 " 0.058 2.00e-02 2.50e+03 pdb=" CD2 TYR B1092 " 0.056 2.00e-02 2.50e+03 pdb=" CE1 TYR B1092 " 0.040 2.00e-02 2.50e+03 pdb=" CE2 TYR B1092 " 0.040 2.00e-02 2.50e+03 pdb=" CZ TYR B1092 " 0.006 2.00e-02 2.50e+03 pdb=" OH TYR B1092 " -0.112 2.00e-02 2.50e+03 ... (remaining 5187 not shown) Histogram of nonbonded interaction distances: 2.50 - 2.98: 14366 2.98 - 3.46: 28821 3.46 - 3.94: 52180 3.94 - 4.42: 57539 4.42 - 4.90: 95340 Nonbonded interactions: 248246 Sorted by model distance: nonbonded pdb=" OD2 ASP A 374 " pdb=" OG SER A 376 " model vdw 2.503 3.040 nonbonded pdb=" OG1 THR A 195 " pdb=" O ASP A 215 " model vdw 2.522 3.040 nonbonded pdb=" OG SER A 487 " pdb=" O THR A 513 " model vdw 2.531 3.040 nonbonded pdb=" OG SER C 570 " pdb=" OD1 ASP C 572 " model vdw 2.531 3.040 nonbonded pdb=" OG SER B 570 " pdb=" OD1 ASP B 572 " model vdw 2.531 3.040 ... (remaining 248241 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' and resid 14 through 1411) selection = (chain 'C' and resid 14 through 1411) } ncs_group { reference = chain 'D' selection = chain 'T' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'L' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' } ncs_group { reference = chain 'K' selection = chain 'Z' } 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: 5.760 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: 0.030 Extract box with map and model: 0.530 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 26.580 Find NCS groups from input model: 0.580 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:5.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9154 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 : 0.013 0.083 30255 Z= 0.742 Angle : 1.704 9.550 41383 Z= 1.111 Chirality : 0.098 0.414 4862 Planarity : 0.014 0.196 5131 Dihedral : 13.097 103.276 12111 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 0.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 0.40 % Allowed : 4.85 % Favored : 94.75 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 6.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.41 (0.13), residues: 3570 helix: 1.26 (0.18), residues: 805 sheet: 0.57 (0.18), residues: 755 loop : -0.20 (0.13), residues: 2010 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.002 ARG B 936 TYR 0.144 0.020 TYR C1092 PHE 0.080 0.013 PHE C 74 TRP 0.089 0.021 TRP C 197 HIS 0.013 0.003 HIS B 545 Details of bonding type rmsd covalent geometry : bond 0.01331 (30089) covalent geometry : angle 1.67532 (40957) SS BOND : bond 0.00910 ( 72) SS BOND : angle 1.67560 ( 144) hydrogen bonds : bond 0.14630 ( 1158) hydrogen bonds : angle 7.40294 ( 3363) link_ALPHA1-3 : bond 0.02497 ( 3) link_ALPHA1-3 : angle 3.96582 ( 9) link_ALPHA1-6 : bond 0.02581 ( 4) link_ALPHA1-6 : angle 3.14726 ( 12) link_BETA1-4 : bond 0.02372 ( 28) link_BETA1-4 : angle 4.17016 ( 84) link_NAG-ASN : bond 0.00994 ( 59) link_NAG-ASN : angle 4.20673 ( 177) *********************** 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 216 residues out of total 3219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 203 time to evaluate : 0.924 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 565 VAL cc_start: 0.8717 (t) cc_final: 0.8513 (p) REVERT: A 730 TYR cc_start: 0.8411 (t80) cc_final: 0.8211 (t80) REVERT: A 866 MET cc_start: 0.9619 (mmm) cc_final: 0.9381 (mmm) REVERT: B 531 ARG cc_start: 0.8513 (mtt-85) cc_final: 0.8278 (mmt90) REVERT: B 611 GLN cc_start: 0.8826 (mm110) cc_final: 0.8434 (mp10) REVERT: B 1070 ASP cc_start: 0.7920 (p0) cc_final: 0.7506 (p0) REVERT: B 1073 GLU cc_start: 0.8720 (mp0) cc_final: 0.8469 (mp0) REVERT: C 488 HIS cc_start: 0.8700 (m170) cc_final: 0.8275 (m170) REVERT: C 517 ARG cc_start: 0.8044 (tmm-80) cc_final: 0.7785 (tmm-80) REVERT: C 1189 MET cc_start: 0.9117 (OUTLIER) cc_final: 0.8717 (mtp) outliers start: 13 outliers final: 6 residues processed: 211 average time/residue: 0.5787 time to fit residues: 144.3279 Evaluate side-chains 155 residues out of total 3219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 148 time to evaluate : 0.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 783 ILE Chi-restraints excluded: chain A residue 1073 GLU Chi-restraints excluded: chain A residue 1093 VAL Chi-restraints excluded: chain B residue 1206 VAL Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 1189 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 197 optimal weight: 0.9990 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 0.8980 chunk 132 optimal weight: 0.8980 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 8.9990 chunk 207 optimal weight: 0.6980 chunk 155 optimal weight: 0.7980 chunk 244 optimal weight: 0.7980 chunk 183 optimal weight: 0.9990 chunk 298 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1083 ASN A1185 ASN A1210 ASN B 488 HIS B 842 ASN B1042 GLN B1075 GLN B1095 GLN C 133 ASN C 880 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.081574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2785 r_free = 0.2785 target = 0.057800 restraints weight = 47587.212| |-----------------------------------------------------------------------------| r_work (start): 0.2755 rms_B_bonded: 2.40 r_work: 0.2625 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2508 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9147 moved from start: 0.1209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 30255 Z= 0.146 Angle : 0.585 8.672 41383 Z= 0.304 Chirality : 0.044 0.212 4862 Planarity : 0.004 0.045 5131 Dihedral : 8.450 79.561 5831 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 1.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 0.90 % Allowed : 6.09 % Favored : 93.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.51 (0.14), residues: 3570 helix: 1.46 (0.18), residues: 839 sheet: 0.39 (0.17), residues: 796 loop : -0.11 (0.14), residues: 1935 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 264 TYR 0.017 0.001 TYR B1152 PHE 0.017 0.001 PHE B 121 TRP 0.030 0.002 TRP B 515 HIS 0.003 0.001 HIS B 488 Details of bonding type rmsd covalent geometry : bond 0.00313 (30089) covalent geometry : angle 0.56161 (40957) SS BOND : bond 0.00241 ( 72) SS BOND : angle 0.69671 ( 144) hydrogen bonds : bond 0.04764 ( 1158) hydrogen bonds : angle 5.95377 ( 3363) link_ALPHA1-3 : bond 0.00973 ( 3) link_ALPHA1-3 : angle 2.24146 ( 9) link_ALPHA1-6 : bond 0.00548 ( 4) link_ALPHA1-6 : angle 1.84617 ( 12) link_BETA1-4 : bond 0.00446 ( 28) link_BETA1-4 : angle 2.09302 ( 84) link_NAG-ASN : bond 0.00246 ( 59) link_NAG-ASN : angle 1.98961 ( 177) *********************** 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 188 residues out of total 3219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 159 time to evaluate : 1.132 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 384 LYS cc_start: 0.9139 (OUTLIER) cc_final: 0.8815 (tttp) REVERT: A 866 MET cc_start: 0.9590 (mmm) cc_final: 0.9355 (mmm) REVERT: A 1070 ASP cc_start: 0.8164 (m-30) cc_final: 0.7835 (m-30) REVERT: B 104 SER cc_start: 0.9490 (m) cc_final: 0.9282 (p) REVERT: B 611 GLN cc_start: 0.8971 (mm110) cc_final: 0.8743 (mm110) REVERT: B 1070 ASP cc_start: 0.7889 (p0) cc_final: 0.7630 (p0) REVERT: B 1073 GLU cc_start: 0.8803 (mp0) cc_final: 0.8565 (mp0) REVERT: C 488 HIS cc_start: 0.8863 (m170) cc_final: 0.8480 (m170) REVERT: C 842 ASN cc_start: 0.9089 (m-40) cc_final: 0.8857 (m110) REVERT: C 1189 MET cc_start: 0.9062 (mtt) cc_final: 0.8717 (mtp) outliers start: 29 outliers final: 14 residues processed: 181 average time/residue: 0.7107 time to fit residues: 153.5160 Evaluate side-chains 158 residues out of total 3219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 143 time to evaluate : 0.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 384 LYS Chi-restraints excluded: chain A residue 451 ASN Chi-restraints excluded: chain A residue 1073 GLU Chi-restraints excluded: chain A residue 1093 VAL Chi-restraints excluded: chain A residue 1101 SER Chi-restraints excluded: chain A residue 1206 VAL Chi-restraints excluded: chain B residue 435 THR Chi-restraints excluded: chain B residue 451 ASN Chi-restraints excluded: chain B residue 776 VAL Chi-restraints excluded: chain B residue 1206 VAL Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 435 THR Chi-restraints excluded: chain C residue 1093 VAL Chi-restraints excluded: chain C residue 1159 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 334 optimal weight: 3.9990 chunk 71 optimal weight: 2.9990 chunk 240 optimal weight: 0.0980 chunk 156 optimal weight: 0.9980 chunk 109 optimal weight: 3.9990 chunk 227 optimal weight: 2.9990 chunk 311 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 chunk 326 optimal weight: 3.9990 chunk 89 optimal weight: 0.9980 chunk 116 optimal weight: 3.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 424 GLN A1075 GLN B1042 GLN B1095 GLN C 114 ASN C 133 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.079700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2744 r_free = 0.2744 target = 0.055546 restraints weight = 48210.319| |-----------------------------------------------------------------------------| r_work (start): 0.2709 rms_B_bonded: 2.44 r_work: 0.2574 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2456 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2456 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9153 moved from start: 0.1377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 30255 Z= 0.222 Angle : 0.601 11.751 41383 Z= 0.313 Chirality : 0.045 0.237 4862 Planarity : 0.004 0.049 5131 Dihedral : 7.822 71.414 5826 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 2.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 1.34 % Allowed : 6.09 % Favored : 92.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.46 (0.14), residues: 3570 helix: 1.49 (0.18), residues: 823 sheet: 0.26 (0.17), residues: 788 loop : -0.12 (0.14), residues: 1959 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 34 TYR 0.018 0.002 TYR B 66 PHE 0.019 0.002 PHE C 121 TRP 0.022 0.002 TRP B 444 HIS 0.003 0.001 HIS B 488 Details of bonding type rmsd covalent geometry : bond 0.00501 (30089) covalent geometry : angle 0.57915 (40957) SS BOND : bond 0.00306 ( 72) SS BOND : angle 0.98729 ( 144) hydrogen bonds : bond 0.04949 ( 1158) hydrogen bonds : angle 5.85311 ( 3363) link_ALPHA1-3 : bond 0.01009 ( 3) link_ALPHA1-3 : angle 1.51496 ( 9) link_ALPHA1-6 : bond 0.00794 ( 4) link_ALPHA1-6 : angle 1.60630 ( 12) link_BETA1-4 : bond 0.00353 ( 28) link_BETA1-4 : angle 1.91351 ( 84) link_NAG-ASN : bond 0.00308 ( 59) link_NAG-ASN : angle 1.97508 ( 177) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7140 Ramachandran restraints generated. 3570 Oldfield, 0 Emsley, 3570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7140 Ramachandran restraints generated. 3570 Oldfield, 0 Emsley, 3570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 3219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 150 time to evaluate : 0.996 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 384 LYS cc_start: 0.9147 (OUTLIER) cc_final: 0.8750 (ttmm) REVERT: A 531 ARG cc_start: 0.8756 (OUTLIER) cc_final: 0.8241 (ttm170) REVERT: A 1070 ASP cc_start: 0.8251 (m-30) cc_final: 0.7940 (m-30) REVERT: B 104 SER cc_start: 0.9508 (m) cc_final: 0.9276 (p) REVERT: B 611 GLN cc_start: 0.9012 (mm110) cc_final: 0.8753 (mm110) REVERT: B 1070 ASP cc_start: 0.7751 (p0) cc_final: 0.7441 (p0) REVERT: B 1073 GLU cc_start: 0.8828 (mp0) cc_final: 0.8473 (mp0) REVERT: C 488 HIS cc_start: 0.8900 (m170) cc_final: 0.8551 (m170) REVERT: C 531 ARG cc_start: 0.8639 (mpt-90) cc_final: 0.8434 (mpt-90) REVERT: C 842 ASN cc_start: 0.9046 (m-40) cc_final: 0.8802 (m110) REVERT: C 1189 MET cc_start: 0.9083 (mtt) cc_final: 0.8650 (mtp) outliers start: 43 outliers final: 23 residues processed: 184 average time/residue: 0.5819 time to fit residues: 129.8944 Evaluate side-chains 168 residues out of total 3219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 143 time to evaluate : 1.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 384 LYS Chi-restraints excluded: chain A residue 435 THR Chi-restraints excluded: chain A residue 531 ARG Chi-restraints excluded: chain A residue 836 TYR Chi-restraints excluded: chain A residue 881 PHE Chi-restraints excluded: chain A residue 1073 GLU Chi-restraints excluded: chain A residue 1093 VAL Chi-restraints excluded: chain A residue 1101 SER Chi-restraints excluded: chain A residue 1206 VAL Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 435 THR Chi-restraints excluded: chain B residue 451 ASN Chi-restraints excluded: chain B residue 776 VAL Chi-restraints excluded: chain B residue 1007 LEU Chi-restraints excluded: chain B residue 1125 ILE Chi-restraints excluded: chain B residue 1159 THR Chi-restraints excluded: chain B residue 1206 VAL Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 435 THR Chi-restraints excluded: chain C residue 709 THR Chi-restraints excluded: chain C residue 776 VAL Chi-restraints excluded: chain C residue 849 GLU Chi-restraints excluded: chain C residue 1093 VAL Chi-restraints excluded: chain C residue 1159 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 243 optimal weight: 0.0970 chunk 264 optimal weight: 1.9990 chunk 350 optimal weight: 0.6980 chunk 61 optimal weight: 2.9990 chunk 246 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 109 optimal weight: 2.9990 chunk 138 optimal weight: 2.9990 chunk 341 optimal weight: 3.9990 chunk 212 optimal weight: 3.9990 chunk 147 optimal weight: 0.7980 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 91 GLN B1042 GLN B1095 GLN C 114 ASN C 133 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.079946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2751 r_free = 0.2751 target = 0.055936 restraints weight = 47704.994| |-----------------------------------------------------------------------------| r_work (start): 0.2716 rms_B_bonded: 2.43 r_work: 0.2583 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2465 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9146 moved from start: 0.1520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 30255 Z= 0.191 Angle : 0.564 11.569 41383 Z= 0.294 Chirality : 0.044 0.248 4862 Planarity : 0.004 0.049 5131 Dihedral : 7.317 63.190 5826 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 2.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 1.37 % Allowed : 6.40 % Favored : 92.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.44 (0.14), residues: 3570 helix: 1.53 (0.18), residues: 821 sheet: 0.22 (0.18), residues: 782 loop : -0.14 (0.14), residues: 1967 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 34 TYR 0.016 0.001 TYR C 675 PHE 0.017 0.002 PHE C 121 TRP 0.021 0.002 TRP B 444 HIS 0.005 0.001 HIS B 488 Details of bonding type rmsd covalent geometry : bond 0.00429 (30089) covalent geometry : angle 0.54510 (40957) SS BOND : bond 0.00335 ( 72) SS BOND : angle 0.86107 ( 144) hydrogen bonds : bond 0.04564 ( 1158) hydrogen bonds : angle 5.73101 ( 3363) link_ALPHA1-3 : bond 0.01129 ( 3) link_ALPHA1-3 : angle 1.60671 ( 9) link_ALPHA1-6 : bond 0.00885 ( 4) link_ALPHA1-6 : angle 1.66052 ( 12) link_BETA1-4 : bond 0.00326 ( 28) link_BETA1-4 : angle 1.74134 ( 84) link_NAG-ASN : bond 0.00259 ( 59) link_NAG-ASN : angle 1.81313 ( 177) *********************** 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 197 residues out of total 3219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 153 time to evaluate : 1.060 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 384 LYS cc_start: 0.9149 (OUTLIER) cc_final: 0.8922 (tttp) REVERT: A 531 ARG cc_start: 0.8769 (OUTLIER) cc_final: 0.8342 (ttm170) REVERT: A 657 ILE cc_start: 0.9355 (mp) cc_final: 0.9003 (tt) REVERT: A 1070 ASP cc_start: 0.8227 (m-30) cc_final: 0.7912 (m-30) REVERT: B 374 ASP cc_start: 0.8620 (OUTLIER) cc_final: 0.8240 (m-30) REVERT: B 611 GLN cc_start: 0.9021 (mm110) cc_final: 0.8758 (mm110) REVERT: B 1070 ASP cc_start: 0.7743 (p0) cc_final: 0.7440 (p0) REVERT: B 1073 GLU cc_start: 0.8849 (mp0) cc_final: 0.8479 (mp0) REVERT: C 488 HIS cc_start: 0.8900 (m170) cc_final: 0.8562 (m170) REVERT: C 842 ASN cc_start: 0.9028 (m-40) cc_final: 0.8791 (m110) REVERT: C 888 PHE cc_start: 0.8057 (m-80) cc_final: 0.7798 (m-80) REVERT: C 1189 MET cc_start: 0.9131 (mtt) cc_final: 0.8715 (mtp) outliers start: 44 outliers final: 21 residues processed: 186 average time/residue: 0.5997 time to fit residues: 134.8062 Evaluate side-chains 168 residues out of total 3219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 144 time to evaluate : 1.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 384 LYS Chi-restraints excluded: chain A residue 435 THR Chi-restraints excluded: chain A residue 451 ASN Chi-restraints excluded: chain A residue 531 ARG Chi-restraints excluded: chain A residue 836 TYR Chi-restraints excluded: chain A residue 881 PHE Chi-restraints excluded: chain A residue 1073 GLU Chi-restraints excluded: chain A residue 1093 VAL Chi-restraints excluded: chain A residue 1101 SER Chi-restraints excluded: chain A residue 1206 VAL Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 374 ASP Chi-restraints excluded: chain B residue 435 THR Chi-restraints excluded: chain B residue 776 VAL Chi-restraints excluded: chain B residue 1007 LEU Chi-restraints excluded: chain B residue 1206 VAL Chi-restraints excluded: chain C residue 178 LYS Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 435 THR Chi-restraints excluded: chain C residue 565 VAL Chi-restraints excluded: chain C residue 615 GLU Chi-restraints excluded: chain C residue 1093 VAL Chi-restraints excluded: chain C residue 1159 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 272 optimal weight: 0.7980 chunk 107 optimal weight: 5.9990 chunk 117 optimal weight: 1.9990 chunk 289 optimal weight: 1.9990 chunk 203 optimal weight: 4.9990 chunk 33 optimal weight: 0.6980 chunk 356 optimal weight: 0.6980 chunk 204 optimal weight: 0.9980 chunk 215 optimal weight: 1.9990 chunk 197 optimal weight: 2.9990 chunk 61 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 597 ASN B1042 GLN B1095 GLN C 114 ASN C 133 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.080987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2780 r_free = 0.2780 target = 0.057149 restraints weight = 48098.172| |-----------------------------------------------------------------------------| r_work (start): 0.2743 rms_B_bonded: 2.43 r_work: 0.2614 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2498 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9126 moved from start: 0.1619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 30255 Z= 0.138 Angle : 0.523 9.823 41383 Z= 0.273 Chirality : 0.043 0.249 4862 Planarity : 0.003 0.047 5131 Dihedral : 6.894 56.504 5826 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 2.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 1.37 % Allowed : 6.68 % Favored : 91.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.46 (0.14), residues: 3570 helix: 1.55 (0.18), residues: 841 sheet: 0.21 (0.18), residues: 779 loop : -0.13 (0.14), residues: 1950 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 531 TYR 0.016 0.001 TYR B1152 PHE 0.018 0.001 PHE C1105 TRP 0.022 0.001 TRP B 515 HIS 0.003 0.001 HIS B 488 Details of bonding type rmsd covalent geometry : bond 0.00301 (30089) covalent geometry : angle 0.50516 (40957) SS BOND : bond 0.00230 ( 72) SS BOND : angle 0.67083 ( 144) hydrogen bonds : bond 0.04147 ( 1158) hydrogen bonds : angle 5.55516 ( 3363) link_ALPHA1-3 : bond 0.01239 ( 3) link_ALPHA1-3 : angle 1.50288 ( 9) link_ALPHA1-6 : bond 0.00974 ( 4) link_ALPHA1-6 : angle 1.64976 ( 12) link_BETA1-4 : bond 0.00335 ( 28) link_BETA1-4 : angle 1.58726 ( 84) link_NAG-ASN : bond 0.00195 ( 59) link_NAG-ASN : angle 1.71475 ( 177) *********************** 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 200 residues out of total 3219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 156 time to evaluate : 0.784 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 384 LYS cc_start: 0.9136 (OUTLIER) cc_final: 0.8917 (tttp) REVERT: A 531 ARG cc_start: 0.8765 (OUTLIER) cc_final: 0.8401 (ttm170) REVERT: A 657 ILE cc_start: 0.9322 (mp) cc_final: 0.9031 (tt) REVERT: A 888 PHE cc_start: 0.8094 (m-80) cc_final: 0.7539 (m-80) REVERT: A 1070 ASP cc_start: 0.8185 (m-30) cc_final: 0.7921 (m-30) REVERT: B 611 GLN cc_start: 0.8998 (mm110) cc_final: 0.8781 (mm110) REVERT: B 1070 ASP cc_start: 0.7715 (p0) cc_final: 0.7425 (p0) REVERT: B 1073 GLU cc_start: 0.8820 (mp0) cc_final: 0.8482 (mp0) REVERT: C 488 HIS cc_start: 0.8871 (m170) cc_final: 0.8537 (m170) REVERT: C 842 ASN cc_start: 0.9049 (m-40) cc_final: 0.8816 (m110) REVERT: C 1189 MET cc_start: 0.9104 (mtt) cc_final: 0.8669 (mtp) outliers start: 44 outliers final: 23 residues processed: 184 average time/residue: 0.5806 time to fit residues: 129.1502 Evaluate side-chains 168 residues out of total 3219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 143 time to evaluate : 1.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 384 LYS Chi-restraints excluded: chain A residue 435 THR Chi-restraints excluded: chain A residue 451 ASN Chi-restraints excluded: chain A residue 531 ARG Chi-restraints excluded: chain A residue 836 TYR Chi-restraints excluded: chain A residue 881 PHE Chi-restraints excluded: chain A residue 1093 VAL Chi-restraints excluded: chain A residue 1206 VAL Chi-restraints excluded: chain A residue 1209 MET Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 435 THR Chi-restraints excluded: chain B residue 776 VAL Chi-restraints excluded: chain B residue 1007 LEU Chi-restraints excluded: chain B residue 1206 VAL Chi-restraints excluded: chain C residue 178 LYS Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 435 THR Chi-restraints excluded: chain C residue 565 VAL Chi-restraints excluded: chain C residue 615 GLU Chi-restraints excluded: chain C residue 709 THR Chi-restraints excluded: chain C residue 776 VAL Chi-restraints excluded: chain C residue 1093 VAL Chi-restraints excluded: chain C residue 1159 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 312 optimal weight: 2.9990 chunk 250 optimal weight: 4.9990 chunk 9 optimal weight: 3.9990 chunk 62 optimal weight: 0.9980 chunk 82 optimal weight: 2.9990 chunk 247 optimal weight: 3.9990 chunk 268 optimal weight: 0.8980 chunk 279 optimal weight: 3.9990 chunk 48 optimal weight: 5.9990 chunk 322 optimal weight: 5.9990 chunk 202 optimal weight: 1.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1042 GLN B1095 GLN C 114 ASN C 133 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.078767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2727 r_free = 0.2727 target = 0.054815 restraints weight = 47614.721| |-----------------------------------------------------------------------------| r_work (start): 0.2689 rms_B_bonded: 2.40 r_work: 0.2557 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2439 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9159 moved from start: 0.1671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.076 30255 Z= 0.265 Angle : 0.604 10.722 41383 Z= 0.313 Chirality : 0.046 0.246 4862 Planarity : 0.004 0.058 5131 Dihedral : 7.015 59.488 5823 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.34 % Allowed : 7.08 % Favored : 91.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.40 (0.14), residues: 3570 helix: 1.49 (0.18), residues: 821 sheet: 0.11 (0.17), residues: 794 loop : -0.12 (0.14), residues: 1955 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 990 TYR 0.018 0.002 TYR B 66 PHE 0.021 0.002 PHE C1105 TRP 0.021 0.002 TRP B 515 HIS 0.003 0.001 HIS C 201 Details of bonding type rmsd covalent geometry : bond 0.00603 (30089) covalent geometry : angle 0.58412 (40957) SS BOND : bond 0.00392 ( 72) SS BOND : angle 0.91886 ( 144) hydrogen bonds : bond 0.04863 ( 1158) hydrogen bonds : angle 5.76007 ( 3363) link_ALPHA1-3 : bond 0.01070 ( 3) link_ALPHA1-3 : angle 1.73035 ( 9) link_ALPHA1-6 : bond 0.00917 ( 4) link_ALPHA1-6 : angle 1.59496 ( 12) link_BETA1-4 : bond 0.00297 ( 28) link_BETA1-4 : angle 1.69309 ( 84) link_NAG-ASN : bond 0.00378 ( 59) link_NAG-ASN : angle 1.99059 ( 177) *********************** 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 188 residues out of total 3219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 145 time to evaluate : 1.105 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 384 LYS cc_start: 0.9153 (OUTLIER) cc_final: 0.8924 (tttp) REVERT: A 531 ARG cc_start: 0.8800 (OUTLIER) cc_final: 0.8401 (ttm170) REVERT: A 836 TYR cc_start: 0.8806 (OUTLIER) cc_final: 0.7967 (m-80) REVERT: A 888 PHE cc_start: 0.8132 (m-80) cc_final: 0.7923 (m-80) REVERT: B 374 ASP cc_start: 0.8604 (OUTLIER) cc_final: 0.8287 (m-30) REVERT: B 611 GLN cc_start: 0.9045 (mm110) cc_final: 0.8789 (mm110) REVERT: B 1070 ASP cc_start: 0.7714 (p0) cc_final: 0.7372 (p0) REVERT: B 1073 GLU cc_start: 0.8868 (mp0) cc_final: 0.8457 (mp0) REVERT: C 22 ASN cc_start: 0.8881 (t0) cc_final: 0.8629 (p0) REVERT: C 488 HIS cc_start: 0.8883 (m170) cc_final: 0.8521 (m170) REVERT: C 842 ASN cc_start: 0.9031 (m-40) cc_final: 0.8799 (m110) REVERT: C 1189 MET cc_start: 0.9129 (mtt) cc_final: 0.8652 (mtp) outliers start: 43 outliers final: 26 residues processed: 179 average time/residue: 0.6144 time to fit residues: 131.6590 Evaluate side-chains 170 residues out of total 3219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 140 time to evaluate : 1.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 384 LYS Chi-restraints excluded: chain A residue 435 THR Chi-restraints excluded: chain A residue 451 ASN Chi-restraints excluded: chain A residue 531 ARG Chi-restraints excluded: chain A residue 836 TYR Chi-restraints excluded: chain A residue 849 GLU Chi-restraints excluded: chain A residue 881 PHE Chi-restraints excluded: chain A residue 1093 VAL Chi-restraints excluded: chain A residue 1101 SER Chi-restraints excluded: chain A residue 1206 VAL Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 374 ASP Chi-restraints excluded: chain B residue 435 THR Chi-restraints excluded: chain B residue 776 VAL Chi-restraints excluded: chain B residue 1007 LEU Chi-restraints excluded: chain B residue 1125 ILE Chi-restraints excluded: chain B residue 1159 THR Chi-restraints excluded: chain B residue 1206 VAL Chi-restraints excluded: chain C residue 178 LYS Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 435 THR Chi-restraints excluded: chain C residue 565 VAL Chi-restraints excluded: chain C residue 615 GLU Chi-restraints excluded: chain C residue 709 THR Chi-restraints excluded: chain C residue 776 VAL Chi-restraints excluded: chain C residue 1093 VAL Chi-restraints excluded: chain C residue 1125 ILE Chi-restraints excluded: chain C residue 1159 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 86 optimal weight: 0.0040 chunk 114 optimal weight: 0.0570 chunk 351 optimal weight: 0.9980 chunk 106 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 264 optimal weight: 0.9980 chunk 21 optimal weight: 0.5980 chunk 55 optimal weight: 8.9990 chunk 143 optimal weight: 2.9990 chunk 261 optimal weight: 0.9990 chunk 240 optimal weight: 1.9990 overall best weight: 0.5310 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1042 GLN B1095 GLN C 114 ASN C 133 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.081462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2792 r_free = 0.2792 target = 0.057728 restraints weight = 47722.571| |-----------------------------------------------------------------------------| r_work (start): 0.2754 rms_B_bonded: 2.42 r_work: 0.2624 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2508 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9120 moved from start: 0.1750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.116 30255 Z= 0.123 Angle : 0.523 13.808 41383 Z= 0.272 Chirality : 0.043 0.243 4862 Planarity : 0.003 0.047 5131 Dihedral : 6.574 56.081 5823 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 1.15 % Allowed : 7.55 % Favored : 91.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.49 (0.14), residues: 3570 helix: 1.66 (0.18), residues: 835 sheet: 0.17 (0.18), residues: 779 loop : -0.12 (0.14), residues: 1956 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 531 TYR 0.019 0.001 TYR B1152 PHE 0.020 0.001 PHE C1105 TRP 0.023 0.001 TRP B 515 HIS 0.005 0.001 HIS B 488 Details of bonding type rmsd covalent geometry : bond 0.00269 (30089) covalent geometry : angle 0.50530 (40957) SS BOND : bond 0.00395 ( 72) SS BOND : angle 1.00408 ( 144) hydrogen bonds : bond 0.03944 ( 1158) hydrogen bonds : angle 5.48058 ( 3363) link_ALPHA1-3 : bond 0.01262 ( 3) link_ALPHA1-3 : angle 1.44844 ( 9) link_ALPHA1-6 : bond 0.00983 ( 4) link_ALPHA1-6 : angle 1.63393 ( 12) link_BETA1-4 : bond 0.00356 ( 28) link_BETA1-4 : angle 1.47537 ( 84) link_NAG-ASN : bond 0.00180 ( 59) link_NAG-ASN : angle 1.68877 ( 177) *********************** 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 189 residues out of total 3219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 152 time to evaluate : 1.263 Fit side-chains revert: symmetry clash REVERT: A 531 ARG cc_start: 0.8780 (OUTLIER) cc_final: 0.8441 (ttm170) REVERT: A 836 TYR cc_start: 0.8747 (OUTLIER) cc_final: 0.7852 (m-80) REVERT: B 374 ASP cc_start: 0.8468 (OUTLIER) cc_final: 0.8110 (m-30) REVERT: B 611 GLN cc_start: 0.9010 (mm110) cc_final: 0.8803 (mm110) REVERT: B 1070 ASP cc_start: 0.7735 (p0) cc_final: 0.7410 (p0) REVERT: B 1073 GLU cc_start: 0.8803 (mp0) cc_final: 0.8446 (mp0) REVERT: C 178 LYS cc_start: 0.8229 (OUTLIER) cc_final: 0.8025 (mmtt) REVERT: C 488 HIS cc_start: 0.8887 (m170) cc_final: 0.8561 (m170) REVERT: C 842 ASN cc_start: 0.9031 (m-40) cc_final: 0.8791 (m110) REVERT: C 1189 MET cc_start: 0.9114 (mtt) cc_final: 0.8673 (mtp) outliers start: 37 outliers final: 21 residues processed: 178 average time/residue: 0.6635 time to fit residues: 142.1775 Evaluate side-chains 171 residues out of total 3219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 146 time to evaluate : 1.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 435 THR Chi-restraints excluded: chain A residue 451 ASN Chi-restraints excluded: chain A residue 531 ARG Chi-restraints excluded: chain A residue 836 TYR Chi-restraints excluded: chain A residue 881 PHE Chi-restraints excluded: chain A residue 1093 VAL Chi-restraints excluded: chain A residue 1101 SER Chi-restraints excluded: chain A residue 1206 VAL Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 374 ASP Chi-restraints excluded: chain B residue 435 THR Chi-restraints excluded: chain B residue 776 VAL Chi-restraints excluded: chain B residue 1007 LEU Chi-restraints excluded: chain B residue 1206 VAL Chi-restraints excluded: chain C residue 178 LYS Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 435 THR Chi-restraints excluded: chain C residue 565 VAL Chi-restraints excluded: chain C residue 615 GLU 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 1093 VAL Chi-restraints excluded: chain C residue 1159 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 327 optimal weight: 0.6980 chunk 167 optimal weight: 0.0470 chunk 137 optimal weight: 1.9990 chunk 245 optimal weight: 0.9980 chunk 305 optimal weight: 2.9990 chunk 95 optimal weight: 0.7980 chunk 197 optimal weight: 1.9990 chunk 316 optimal weight: 0.8980 chunk 42 optimal weight: 4.9990 chunk 104 optimal weight: 0.6980 chunk 212 optimal weight: 1.9990 overall best weight: 0.6278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1042 GLN B1095 GLN C 114 ASN C 133 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.081517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2794 r_free = 0.2794 target = 0.057784 restraints weight = 47890.455| |-----------------------------------------------------------------------------| r_work (start): 0.2756 rms_B_bonded: 2.43 r_work: 0.2626 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2510 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9119 moved from start: 0.1789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 30255 Z= 0.125 Angle : 0.522 10.451 41383 Z= 0.271 Chirality : 0.043 0.240 4862 Planarity : 0.003 0.048 5131 Dihedral : 6.434 55.087 5823 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.06 % Allowed : 7.80 % Favored : 91.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.53 (0.14), residues: 3570 helix: 1.70 (0.18), residues: 835 sheet: 0.17 (0.18), residues: 768 loop : -0.09 (0.14), residues: 1967 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 34 TYR 0.017 0.001 TYR B1152 PHE 0.022 0.001 PHE C1105 TRP 0.026 0.001 TRP B 515 HIS 0.004 0.001 HIS B 488 Details of bonding type rmsd covalent geometry : bond 0.00272 (30089) covalent geometry : angle 0.50560 (40957) SS BOND : bond 0.00309 ( 72) SS BOND : angle 0.73072 ( 144) hydrogen bonds : bond 0.03936 ( 1158) hydrogen bonds : angle 5.41348 ( 3363) link_ALPHA1-3 : bond 0.01237 ( 3) link_ALPHA1-3 : angle 1.49926 ( 9) link_ALPHA1-6 : bond 0.00999 ( 4) link_ALPHA1-6 : angle 1.58351 ( 12) link_BETA1-4 : bond 0.00329 ( 28) link_BETA1-4 : angle 1.48720 ( 84) link_NAG-ASN : bond 0.00169 ( 59) link_NAG-ASN : angle 1.63955 ( 177) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7140 Ramachandran restraints generated. 3570 Oldfield, 0 Emsley, 3570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7140 Ramachandran restraints generated. 3570 Oldfield, 0 Emsley, 3570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 3219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 154 time to evaluate : 1.246 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 384 LYS cc_start: 0.9137 (OUTLIER) cc_final: 0.8925 (tttp) REVERT: A 531 ARG cc_start: 0.8766 (OUTLIER) cc_final: 0.8438 (ttm170) REVERT: A 836 TYR cc_start: 0.8763 (OUTLIER) cc_final: 0.7870 (m-80) REVERT: B 374 ASP cc_start: 0.8476 (OUTLIER) cc_final: 0.8137 (m-30) REVERT: B 611 GLN cc_start: 0.8987 (mm110) cc_final: 0.8762 (mm110) REVERT: B 1070 ASP cc_start: 0.7678 (p0) cc_final: 0.7314 (p0) REVERT: B 1073 GLU cc_start: 0.8811 (mp0) cc_final: 0.8461 (mp0) REVERT: C 488 HIS cc_start: 0.8872 (m170) cc_final: 0.8540 (m170) REVERT: C 842 ASN cc_start: 0.9041 (m-40) cc_final: 0.8826 (m110) REVERT: C 1189 MET cc_start: 0.9132 (mtt) cc_final: 0.8685 (mtp) outliers start: 34 outliers final: 22 residues processed: 176 average time/residue: 0.6615 time to fit residues: 140.1870 Evaluate side-chains 173 residues out of total 3219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 147 time to evaluate : 1.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 384 LYS Chi-restraints excluded: chain A residue 435 THR Chi-restraints excluded: chain A residue 451 ASN Chi-restraints excluded: chain A residue 531 ARG Chi-restraints excluded: chain A residue 792 ILE Chi-restraints excluded: chain A residue 836 TYR Chi-restraints excluded: chain A residue 881 PHE Chi-restraints excluded: chain A residue 1093 VAL Chi-restraints excluded: chain A residue 1101 SER Chi-restraints excluded: chain A residue 1206 VAL Chi-restraints excluded: chain B residue 374 ASP Chi-restraints excluded: chain B residue 435 THR Chi-restraints excluded: chain B residue 776 VAL Chi-restraints excluded: chain B residue 1007 LEU Chi-restraints excluded: chain B residue 1206 VAL Chi-restraints excluded: chain C residue 178 LYS Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 435 THR Chi-restraints excluded: chain C residue 565 VAL Chi-restraints excluded: chain C residue 615 GLU 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 1093 VAL Chi-restraints excluded: chain C residue 1159 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 293 optimal weight: 3.9990 chunk 214 optimal weight: 1.9990 chunk 267 optimal weight: 3.9990 chunk 209 optimal weight: 7.9990 chunk 107 optimal weight: 5.9990 chunk 236 optimal weight: 4.9990 chunk 304 optimal weight: 5.9990 chunk 187 optimal weight: 0.0970 chunk 93 optimal weight: 3.9990 chunk 170 optimal weight: 0.6980 chunk 35 optimal weight: 4.9990 overall best weight: 2.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 488 HIS B1042 GLN B1095 GLN C 114 ASN C 133 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.078583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2723 r_free = 0.2723 target = 0.054610 restraints weight = 47874.666| |-----------------------------------------------------------------------------| r_work (start): 0.2684 rms_B_bonded: 2.41 r_work: 0.2552 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2435 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9161 moved from start: 0.1781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.078 30255 Z= 0.282 Angle : 0.611 9.097 41383 Z= 0.318 Chirality : 0.046 0.239 4862 Planarity : 0.004 0.063 5131 Dihedral : 6.819 59.790 5823 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 1.03 % Allowed : 8.01 % Favored : 90.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.41 (0.14), residues: 3570 helix: 1.52 (0.18), residues: 818 sheet: 0.10 (0.17), residues: 793 loop : -0.12 (0.14), residues: 1959 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 34 TYR 0.019 0.002 TYR C 675 PHE 0.025 0.002 PHE C1105 TRP 0.032 0.002 TRP B 515 HIS 0.010 0.001 HIS B 488 Details of bonding type rmsd covalent geometry : bond 0.00642 (30089) covalent geometry : angle 0.59379 (40957) SS BOND : bond 0.00410 ( 72) SS BOND : angle 0.94701 ( 144) hydrogen bonds : bond 0.04889 ( 1158) hydrogen bonds : angle 5.76193 ( 3363) link_ALPHA1-3 : bond 0.01086 ( 3) link_ALPHA1-3 : angle 1.74168 ( 9) link_ALPHA1-6 : bond 0.01139 ( 4) link_ALPHA1-6 : angle 1.58122 ( 12) link_BETA1-4 : bond 0.00294 ( 28) link_BETA1-4 : angle 1.65715 ( 84) link_NAG-ASN : bond 0.00415 ( 59) link_NAG-ASN : angle 1.84361 ( 177) *********************** 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 175 residues out of total 3219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 142 time to evaluate : 1.226 Fit side-chains revert: symmetry clash REVERT: A 384 LYS cc_start: 0.9154 (OUTLIER) cc_final: 0.8929 (tttp) REVERT: A 531 ARG cc_start: 0.8805 (OUTLIER) cc_final: 0.8461 (ttm170) REVERT: A 836 TYR cc_start: 0.8807 (OUTLIER) cc_final: 0.8004 (m-80) REVERT: A 1070 ASP cc_start: 0.8145 (m-30) cc_final: 0.7809 (m-30) REVERT: B 374 ASP cc_start: 0.8623 (OUTLIER) cc_final: 0.8300 (m-30) REVERT: B 611 GLN cc_start: 0.9042 (mm110) cc_final: 0.8816 (mm110) REVERT: B 1070 ASP cc_start: 0.7727 (p0) cc_final: 0.7349 (p0) REVERT: B 1073 GLU cc_start: 0.8863 (mp0) cc_final: 0.8476 (mp0) REVERT: C 22 ASN cc_start: 0.8843 (t0) cc_final: 0.8605 (p0) REVERT: C 488 HIS cc_start: 0.8869 (m170) cc_final: 0.8509 (m170) REVERT: C 1070 ASP cc_start: 0.8514 (m-30) cc_final: 0.8303 (m-30) REVERT: C 1189 MET cc_start: 0.9093 (mtt) cc_final: 0.8593 (mtp) outliers start: 33 outliers final: 22 residues processed: 167 average time/residue: 0.7076 time to fit residues: 140.5016 Evaluate side-chains 161 residues out of total 3219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 135 time to evaluate : 1.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 384 LYS Chi-restraints excluded: chain A residue 435 THR Chi-restraints excluded: chain A residue 451 ASN Chi-restraints excluded: chain A residue 531 ARG Chi-restraints excluded: chain A residue 792 ILE Chi-restraints excluded: chain A residue 836 TYR Chi-restraints excluded: chain A residue 849 GLU Chi-restraints excluded: chain A residue 881 PHE Chi-restraints excluded: chain A residue 1093 VAL Chi-restraints excluded: chain A residue 1101 SER Chi-restraints excluded: chain A residue 1206 VAL Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 374 ASP Chi-restraints excluded: chain B residue 435 THR Chi-restraints excluded: chain B residue 776 VAL Chi-restraints excluded: chain B residue 1007 LEU Chi-restraints excluded: chain B residue 1206 VAL Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 435 THR Chi-restraints excluded: chain C residue 565 VAL Chi-restraints excluded: chain C residue 615 GLU Chi-restraints excluded: chain C residue 709 THR Chi-restraints excluded: chain C residue 776 VAL Chi-restraints excluded: chain C residue 1093 VAL Chi-restraints excluded: chain C residue 1159 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 79 optimal weight: 0.6980 chunk 19 optimal weight: 0.9980 chunk 73 optimal weight: 2.9990 chunk 56 optimal weight: 7.9990 chunk 110 optimal weight: 1.9990 chunk 123 optimal weight: 0.9980 chunk 95 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 235 optimal weight: 2.9990 chunk 296 optimal weight: 0.9990 chunk 245 optimal weight: 4.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 488 HIS B1042 GLN B1095 GLN C 114 ASN C 133 ASN C 842 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.079954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2754 r_free = 0.2754 target = 0.056043 restraints weight = 47815.106| |-----------------------------------------------------------------------------| r_work (start): 0.2717 rms_B_bonded: 2.43 r_work: 0.2586 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2469 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.2469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9141 moved from start: 0.1814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 30255 Z= 0.176 Angle : 0.559 8.449 41383 Z= 0.291 Chirality : 0.044 0.236 4862 Planarity : 0.004 0.056 5131 Dihedral : 6.605 57.910 5823 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 0.90 % Allowed : 8.17 % Favored : 90.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.43 (0.14), residues: 3570 helix: 1.59 (0.18), residues: 830 sheet: 0.12 (0.18), residues: 772 loop : -0.15 (0.14), residues: 1968 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 34 TYR 0.020 0.001 TYR C 675 PHE 0.023 0.001 PHE C1105 TRP 0.033 0.001 TRP B 515 HIS 0.007 0.001 HIS B 488 Details of bonding type rmsd covalent geometry : bond 0.00392 (30089) covalent geometry : angle 0.54281 (40957) SS BOND : bond 0.00326 ( 72) SS BOND : angle 0.80639 ( 144) hydrogen bonds : bond 0.04330 ( 1158) hydrogen bonds : angle 5.61299 ( 3363) link_ALPHA1-3 : bond 0.01184 ( 3) link_ALPHA1-3 : angle 1.53524 ( 9) link_ALPHA1-6 : bond 0.00978 ( 4) link_ALPHA1-6 : angle 1.58249 ( 12) link_BETA1-4 : bond 0.00307 ( 28) link_BETA1-4 : angle 1.51402 ( 84) link_NAG-ASN : bond 0.00255 ( 59) link_NAG-ASN : angle 1.70000 ( 177) ********************** 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 172 residues out of total 3219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 143 time to evaluate : 1.274 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 384 LYS cc_start: 0.9135 (OUTLIER) cc_final: 0.8917 (tttp) REVERT: A 531 ARG cc_start: 0.8790 (OUTLIER) cc_final: 0.8468 (ttm170) REVERT: A 836 TYR cc_start: 0.8808 (OUTLIER) cc_final: 0.7941 (m-80) REVERT: A 866 MET cc_start: 0.9501 (mmm) cc_final: 0.9286 (mmm) REVERT: B 374 ASP cc_start: 0.8560 (OUTLIER) cc_final: 0.8244 (m-30) REVERT: B 611 GLN cc_start: 0.9031 (mm110) cc_final: 0.8829 (mm110) REVERT: B 1070 ASP cc_start: 0.7722 (p0) cc_final: 0.7372 (p0) REVERT: B 1073 GLU cc_start: 0.8832 (mp0) cc_final: 0.8448 (mp0) REVERT: C 22 ASN cc_start: 0.8836 (t0) cc_final: 0.8611 (p0) REVERT: C 488 HIS cc_start: 0.8982 (m170) cc_final: 0.8626 (m170) REVERT: C 1189 MET cc_start: 0.9094 (mtt) cc_final: 0.8622 (mtp) outliers start: 29 outliers final: 23 residues processed: 166 average time/residue: 0.7008 time to fit residues: 138.8591 Evaluate side-chains 167 residues out of total 3219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 140 time to evaluate : 1.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 384 LYS Chi-restraints excluded: chain A residue 435 THR Chi-restraints excluded: chain A residue 451 ASN Chi-restraints excluded: chain A residue 531 ARG Chi-restraints excluded: chain A residue 792 ILE Chi-restraints excluded: chain A residue 836 TYR Chi-restraints excluded: chain A residue 849 GLU Chi-restraints excluded: chain A residue 881 PHE Chi-restraints excluded: chain A residue 1093 VAL Chi-restraints excluded: chain A residue 1101 SER Chi-restraints excluded: chain A residue 1206 VAL Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 374 ASP Chi-restraints excluded: chain B residue 435 THR Chi-restraints excluded: chain B residue 776 VAL Chi-restraints excluded: chain B residue 1007 LEU Chi-restraints excluded: chain B residue 1206 VAL Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 435 THR Chi-restraints excluded: chain C residue 565 VAL Chi-restraints excluded: chain C residue 615 GLU 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 1093 VAL Chi-restraints excluded: chain C residue 1159 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 29 optimal weight: 1.9990 chunk 98 optimal weight: 3.9990 chunk 290 optimal weight: 6.9990 chunk 322 optimal weight: 0.9990 chunk 104 optimal weight: 0.6980 chunk 5 optimal weight: 0.9990 chunk 14 optimal weight: 0.7980 chunk 342 optimal weight: 0.9980 chunk 308 optimal weight: 3.9990 chunk 61 optimal weight: 0.5980 chunk 167 optimal weight: 3.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 488 HIS B1042 GLN B1095 GLN C 114 ASN C 133 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.080764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2774 r_free = 0.2774 target = 0.056897 restraints weight = 48085.049| |-----------------------------------------------------------------------------| r_work (start): 0.2737 rms_B_bonded: 2.44 r_work: 0.2606 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2489 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9132 moved from start: 0.1854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 30255 Z= 0.144 Angle : 0.534 7.858 41383 Z= 0.278 Chirality : 0.043 0.233 4862 Planarity : 0.004 0.053 5131 Dihedral : 6.430 56.028 5823 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 0.93 % Allowed : 8.11 % Favored : 90.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.48 (0.14), residues: 3570 helix: 1.68 (0.18), residues: 829 sheet: 0.13 (0.18), residues: 774 loop : -0.13 (0.14), residues: 1967 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 34 TYR 0.019 0.001 TYR C 675 PHE 0.031 0.001 PHE A 888 TRP 0.037 0.001 TRP B 515 HIS 0.006 0.001 HIS B 488 Details of bonding type rmsd covalent geometry : bond 0.00318 (30089) covalent geometry : angle 0.51901 (40957) SS BOND : bond 0.00296 ( 72) SS BOND : angle 0.73203 ( 144) hydrogen bonds : bond 0.04103 ( 1158) hydrogen bonds : angle 5.49550 ( 3363) link_ALPHA1-3 : bond 0.01198 ( 3) link_ALPHA1-3 : angle 1.47413 ( 9) link_ALPHA1-6 : bond 0.00983 ( 4) link_ALPHA1-6 : angle 1.55563 ( 12) link_BETA1-4 : bond 0.00323 ( 28) link_BETA1-4 : angle 1.47821 ( 84) link_NAG-ASN : bond 0.00200 ( 59) link_NAG-ASN : angle 1.63593 ( 177) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13299.38 seconds wall clock time: 227 minutes 1.27 seconds (13621.27 seconds total)