Starting phenix.real_space_refine on Sun Jul 5 18:29:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8ohn_16882/07_2026/8ohn_16882.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ohn_16882/07_2026/8ohn_16882.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/8ohn_16882/07_2026/8ohn_16882.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8ohn_16882/07_2026/8ohn_16882.cif" model { file = "/net/cci-nas-00/data/ceres_data/8ohn_16882/07_2026/8ohn_16882.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ohn_16882/07_2026/8ohn_16882.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ohn_16882/07_2026/8ohn_16882.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ohn_16882/07_2026/8ohn_16882.map" } resolution = 3.4 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= 0.020 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 18633 2.51 5 N 4689 2.21 5 O 5832 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 29328 Number of models: 1 Model: "" Number of chains: 33 Chain: "A" Number of atoms: 9373 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1195, 9373 Classifications: {'peptide': 1195} Link IDs: {'PCIS': 3, 'PTRANS': 43, 'TRANS': 1148} Chain breaks: 1 Chain: "B" Number of atoms: 9373 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1195, 9373 Classifications: {'peptide': 1195} Link IDs: {'PCIS': 3, 'PTRANS': 43, 'TRANS': 1148} Chain breaks: 1 Chain: "C" Number of atoms: 9373 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1195, 9373 Classifications: {'peptide': 1195} Link IDs: {'PCIS': 3, 'PTRANS': 43, 'TRANS': 1148} Chain breaks: 1 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen 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 chiralities: 2 Chain: "G" 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 chiralities: 3 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 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 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 chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen 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 chiralities: 2 Chain: "P" 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 chiralities: 3 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 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 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 chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen 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 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 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 chiralities: 2 Chain: "Y" 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 chiralities: 3 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen chiralities: 10 Chain: "B" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen chiralities: 10 Chain: "C" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen chiralities: 10 Time building chain proxies: 6.33, per 1000 atoms: 0.22 Number of scatterers: 29328 At special positions: 0 Unit cell: (150.511, 159.365, 164.898, 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 5832 8.00 N 4689 7.00 C 18633 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=2.04 Simple disulfide: pdb=" SG CYS A 282 " - pdb=" SG CYS A 292 " distance=2.03 Simple disulfide: pdb=" SG CYS A 327 " - pdb=" SG CYS A 352 " distance=2.03 Simple disulfide: pdb=" SG CYS A 370 " - pdb=" SG CYS A 423 " distance=2.03 Simple disulfide: pdb=" SG CYS A 382 " - pdb=" SG CYS A 605 " distance=2.03 Simple disulfide: pdb=" SG CYS A 466 " - pdb=" SG CYS A 546 " distance=2.03 Simple disulfide: pdb=" SG CYS A 474 " - pdb=" SG CYS A 495 " distance=2.03 Simple disulfide: pdb=" SG CYS A 476 " - pdb=" SG CYS A 567 " distance=2.03 Simple disulfide: pdb=" SG CYS A 485 " - pdb=" SG CYS A 516 " distance=2.03 Simple disulfide: pdb=" SG CYS A 504 " - pdb=" SG CYS A 518 " distance=2.03 Simple disulfide: pdb=" SG CYS A 520 " - pdb=" SG CYS A 533 " distance=2.03 Simple disulfide: pdb=" SG CYS A 556 " - pdb=" SG CYS A 569 " distance=2.04 Simple disulfide: pdb=" SG CYS A 582 " - pdb=" SG CYS A 588 " distance=2.04 Simple disulfide: pdb=" SG CYS A 621 " - pdb=" SG CYS A 674 " distance=2.03 Simple disulfide: pdb=" SG CYS A 699 " - pdb=" SG CYS A 720 " distance=2.03 Simple disulfide: pdb=" SG CYS A 735 " - pdb=" SG CYS A 744 " distance=2.03 Simple disulfide: pdb=" SG CYS A 818 " - pdb=" SG CYS A 840 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS A 929 " - pdb=" SG CYS A 940 " distance=2.03 Simple disulfide: pdb=" SG CYS A1117 " - pdb=" SG CYS A1128 " distance=2.03 Simple disulfide: pdb=" SG CYS A1167 " - pdb=" SG CYS A1212 " distance=2.03 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=2.04 Simple disulfide: pdb=" SG CYS B 163 " - pdb=" SG CYS B 242 " distance=2.03 Simple disulfide: pdb=" SG CYS B 282 " - pdb=" SG CYS B 292 " distance=2.02 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=2.03 Simple disulfide: pdb=" SG CYS B 382 " - pdb=" SG CYS B 605 " distance=2.03 Simple disulfide: pdb=" SG CYS B 466 " - pdb=" SG CYS B 546 " distance=2.03 Simple disulfide: pdb=" SG CYS B 474 " - pdb=" SG CYS B 495 " distance=2.03 Simple disulfide: pdb=" SG CYS B 476 " - pdb=" SG CYS B 567 " distance=2.03 Simple disulfide: pdb=" SG CYS B 485 " - pdb=" SG CYS B 516 " distance=2.03 Simple disulfide: pdb=" SG CYS B 504 " - pdb=" SG CYS B 518 " distance=2.03 Simple disulfide: pdb=" SG CYS B 520 " - pdb=" SG CYS B 533 " distance=2.03 Simple disulfide: pdb=" SG CYS B 556 " - pdb=" SG CYS B 569 " distance=2.04 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=2.03 Simple disulfide: pdb=" SG CYS B 735 " - pdb=" SG CYS B 744 " distance=2.03 Simple disulfide: pdb=" SG CYS B 818 " - pdb=" SG CYS B 840 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS B 929 " - pdb=" SG CYS B 940 " distance=2.03 Simple disulfide: pdb=" SG CYS B1117 " - pdb=" SG CYS B1128 " distance=2.03 Simple disulfide: pdb=" SG CYS B1167 " - pdb=" SG CYS B1212 " distance=2.03 Simple disulfide: pdb=" SG CYS C 20 " - pdb=" SG CYS C 156 " distance=2.03 Simple disulfide: pdb=" SG CYS C 151 " - pdb=" SG CYS C 183 " distance=2.04 Simple disulfide: pdb=" SG CYS C 163 " - pdb=" SG CYS C 242 " distance=2.04 Simple disulfide: pdb=" SG CYS C 282 " - pdb=" SG CYS C 292 " distance=2.03 Simple disulfide: pdb=" SG CYS C 327 " - pdb=" SG CYS C 352 " distance=2.03 Simple disulfide: pdb=" SG CYS C 370 " - pdb=" SG CYS C 423 " distance=2.03 Simple disulfide: pdb=" SG CYS C 382 " - pdb=" SG CYS C 605 " distance=2.03 Simple disulfide: pdb=" SG CYS C 466 " - pdb=" SG CYS C 546 " distance=2.03 Simple disulfide: pdb=" SG CYS C 474 " - pdb=" SG CYS C 495 " distance=2.03 Simple disulfide: pdb=" SG CYS C 476 " - pdb=" SG CYS C 567 " distance=2.03 Simple disulfide: pdb=" SG CYS C 485 " - pdb=" SG CYS C 516 " distance=2.03 Simple disulfide: pdb=" SG CYS C 504 " - pdb=" SG CYS C 518 " distance=2.03 Simple disulfide: pdb=" SG CYS C 520 " - pdb=" SG CYS C 533 " distance=2.03 Simple disulfide: pdb=" SG CYS C 556 " - pdb=" SG CYS C 569 " distance=2.04 Simple disulfide: pdb=" SG CYS C 582 " - pdb=" SG CYS C 588 " distance=2.04 Simple disulfide: pdb=" SG CYS C 621 " - pdb=" SG CYS C 674 " distance=2.03 Simple disulfide: pdb=" SG CYS C 699 " - pdb=" SG CYS C 720 " distance=2.03 Simple disulfide: pdb=" SG CYS C 735 " - pdb=" SG CYS C 744 " distance=2.03 Simple disulfide: pdb=" SG CYS C 818 " - pdb=" SG CYS C 840 " distance=2.03 Simple disulfide: pdb=" SG CYS C 823 " - pdb=" SG CYS C 829 " distance=2.03 Simple disulfide: pdb=" SG CYS C 894 " - pdb=" SG CYS C 899 " distance=2.03 Simple disulfide: pdb=" SG CYS C 929 " - pdb=" SG CYS C 940 " distance=2.03 Simple disulfide: pdb=" SG CYS C1117 " - pdb=" SG CYS C1128 " distance=2.03 Simple disulfide: pdb=" SG CYS C1167 " - pdb=" SG CYS C1212 " distance=2.03 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 BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " NAG-ASN " NAG A1401 " - " ASN A 19 " " NAG A1402 " - " ASN A 171 " " NAG A1403 " - " ASN A 192 " " NAG A1404 " - " ASN A 454 " " NAG A1405 " - " ASN A 470 " " NAG A1406 " - " ASN A 775 " " NAG A1407 " - " ASN A 780 " " NAG A1408 " - " ASN A 797 " " NAG A1409 " - " ASN A 928 " " NAG A1410 " - " ASN A 433 " " NAG B1401 " - " ASN B 19 " " NAG B1402 " - " ASN B 171 " " NAG B1403 " - " ASN B 192 " " NAG B1404 " - " ASN B 454 " " NAG B1405 " - " ASN B 470 " " NAG B1406 " - " ASN B 775 " " NAG B1407 " - " ASN B 780 " " NAG B1408 " - " ASN B 797 " " NAG B1409 " - " ASN B 928 " " NAG B1410 " - " ASN B 433 " " NAG C1401 " - " ASN C 19 " " NAG C1402 " - " ASN C 171 " " NAG C1403 " - " ASN C 192 " " NAG C1404 " - " ASN C 454 " " NAG C1405 " - " ASN C 470 " " NAG C1406 " - " ASN C 775 " " NAG C1407 " - " ASN C 780 " " NAG C1408 " - " ASN C 797 " " NAG C1409 " - " ASN C 928 " " NAG C1410 " - " ASN C 433 " " NAG D 1 " - " ASN A 188 " " NAG E 1 " - " ASN A 705 " " NAG F 1 " - " ASN A 355 " " NAG G 1 " - " ASN A 132 " " NAG H 1 " - " ASN A 686 " " NAG I 1 " - " ASN A 726 " " NAG J 1 " - " ASN A1215 " " NAG K 1 " - " ASN A 58 " " NAG L 1 " - " ASN A 666 " " NAG M 1 " - " ASN B 188 " " NAG N 1 " - " ASN B 705 " " NAG O 1 " - " ASN B 355 " " NAG P 1 " - " ASN B 132 " " NAG Q 1 " - " ASN B 686 " " NAG R 1 " - " ASN B 726 " " NAG S 1 " - " ASN B1215 " " NAG T 1 " - " ASN B 58 " " NAG U 1 " - " ASN B 666 " " NAG V 1 " - " ASN C 188 " " NAG W 1 " - " ASN C 705 " " NAG X 1 " - " ASN C 355 " " NAG Y 1 " - " ASN C 132 " " NAG Z 1 " - " ASN C 686 " " NAG a 1 " - " ASN C 726 " " NAG b 1 " - " ASN C1215 " " NAG c 1 " - " ASN C 58 " " NAG d 1 " - " ASN C 666 " Time building additional restraints: 2.59 Conformation dependent library (CDL) restraints added in 1.0 seconds 7146 Ramachandran restraints generated. 3573 Oldfield, 0 Emsley, 3573 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6762 Finding SS restraints... Secondary structure from input PDB file: 76 helices and 60 sheets defined 24.2% alpha, 28.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.12 Creating SS restraints... Processing helix chain 'A' and resid 88 through 91 removed outlier: 4.175A pdb=" N GLN A 91 " --> pdb=" O LEU A 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 88 through 91' Processing helix chain 'A' and resid 285 through 295 Processing helix chain 'A' and resid 328 through 334 Processing helix chain 'A' and resid 355 through 363 removed outlier: 3.571A pdb=" N VAL A 363 " --> pdb=" O LEU A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 402 removed outlier: 3.545A pdb=" N LEU A 401 " --> pdb=" O ARG A 398 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLN A 402 " --> pdb=" O SER A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 413 Processing helix chain 'A' and resid 442 through 448 removed outlier: 3.765A pdb=" N TYR A 448 " --> pdb=" O TRP A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 485 removed outlier: 3.713A pdb=" N SER A 484 " --> pdb=" O SER A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 698 through 706 Processing helix chain 'A' and resid 785 through 789 removed outlier: 4.114A pdb=" N GLY A 788 " --> pdb=" O SER A 785 " (cutoff:3.500A) Processing helix chain 'A' and resid 817 through 822 Processing helix chain 'A' and resid 826 through 833 Processing helix chain 'A' and resid 836 through 865 removed outlier: 3.526A pdb=" N CYS A 840 " --> pdb=" O TYR A 836 " (cutoff:3.500A) Processing helix chain 'A' and resid 905 through 915 removed outlier: 4.033A pdb=" N LEU A 910 " --> pdb=" O PHE A 906 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N LEU A 911 " --> pdb=" O PHE A 907 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N VAL A 915 " --> pdb=" O LEU A 911 " (cutoff:3.500A) Processing helix chain 'A' and resid 918 through 928 Processing helix chain 'A' and resid 937 through 945 removed outlier: 4.236A pdb=" N VAL A 941 " --> pdb=" O ASP A 937 " (cutoff:3.500A) Processing helix chain 'A' and resid 955 through 972 Processing helix chain 'A' and resid 982 through 994 removed outlier: 3.804A pdb=" N LEU A 994 " --> pdb=" O ARG A 990 " (cutoff:3.500A) Processing helix chain 'A' and resid 998 through 1003 removed outlier: 3.671A pdb=" N ASN A1002 " --> pdb=" O MET A 998 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LYS A1003 " --> pdb=" O ASP A 999 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 998 through 1003' Processing helix chain 'A' and resid 1004 through 1022 Processing helix chain 'A' and resid 1023 through 1025 No H-bonds generated for 'chain 'A' and resid 1023 through 1025' Processing helix chain 'A' and resid 1027 through 1050 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 removed outlier: 3.570A pdb=" N ILE A1065 " --> pdb=" O SER A1061 " (cutoff:3.500A) Processing helix chain 'A' and resid 1073 through 1118 removed outlier: 3.920A pdb=" N GLN A1077 " --> pdb=" O GLU A1073 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL A1118 " --> pdb=" O VAL A1114 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 91 removed outlier: 4.285A 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 355 through 363 removed outlier: 3.590A pdb=" N VAL B 363 " --> pdb=" O LEU B 359 " (cutoff:3.500A) Processing helix chain 'B' and resid 398 through 402 removed outlier: 3.552A pdb=" N LEU B 401 " --> pdb=" O ARG B 398 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLN B 402 " --> pdb=" O SER B 399 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 398 through 402' Processing helix chain 'B' and resid 407 through 413 Processing helix chain 'B' and resid 442 through 448 removed outlier: 3.771A pdb=" N TYR B 448 " --> pdb=" O TRP B 444 " (cutoff:3.500A) Processing helix chain 'B' and resid 478 through 485 removed outlier: 3.680A pdb=" N SER B 484 " --> pdb=" O SER B 480 " (cutoff:3.500A) Processing helix chain 'B' and resid 698 through 706 Processing helix chain 'B' and resid 817 through 822 Processing helix chain 'B' and resid 826 through 833 Processing helix chain 'B' and resid 836 through 865 removed outlier: 3.555A pdb=" N CYS B 840 " --> pdb=" O TYR B 836 " (cutoff:3.500A) Processing helix chain 'B' and resid 905 through 915 removed outlier: 4.003A pdb=" N LEU B 910 " --> pdb=" O PHE B 906 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N LEU B 911 " --> pdb=" O PHE B 907 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N VAL B 915 " --> pdb=" O LEU B 911 " (cutoff:3.500A) Processing helix chain 'B' and resid 918 through 928 Processing helix chain 'B' and resid 937 through 945 removed outlier: 4.193A pdb=" N VAL B 941 " --> pdb=" O ASP B 937 " (cutoff:3.500A) Processing helix chain 'B' and resid 955 through 972 Processing helix chain 'B' and resid 982 through 994 removed outlier: 3.819A pdb=" N LEU B 994 " --> pdb=" O ARG B 990 " (cutoff:3.500A) Processing helix chain 'B' and resid 998 through 1003 removed outlier: 3.654A pdb=" N ASN B1002 " --> pdb=" O MET B 998 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LYS B1003 " --> pdb=" O ASP B 999 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 998 through 1003' Processing helix chain 'B' and resid 1004 through 1022 Processing helix chain 'B' and resid 1023 through 1025 No H-bonds generated for 'chain 'B' and resid 1023 through 1025' Processing helix chain 'B' and resid 1028 through 1050 Processing helix chain 'B' and resid 1051 through 1053 No H-bonds generated for 'chain 'B' and resid 1051 through 1053' Processing helix chain 'B' and resid 1061 through 1069 removed outlier: 3.544A pdb=" N ILE B1065 " --> pdb=" O SER B1061 " (cutoff:3.500A) Processing helix chain 'B' and resid 1073 through 1118 removed outlier: 3.915A pdb=" N GLN B1077 " --> pdb=" O GLU B1073 " (cutoff:3.500A) Processing helix chain 'C' and resid 88 through 91 removed outlier: 4.222A 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 355 through 363 removed outlier: 3.592A pdb=" N VAL C 363 " --> pdb=" O LEU C 359 " (cutoff:3.500A) Processing helix chain 'C' and resid 374 through 378 removed outlier: 3.646A pdb=" N LYS C 377 " --> pdb=" O ASP C 374 " (cutoff:3.500A) Processing helix chain 'C' and resid 397 through 402 removed outlier: 3.571A pdb=" N LEU C 401 " --> pdb=" O ARG C 398 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLN C 402 " --> pdb=" O SER C 399 " (cutoff:3.500A) Processing helix chain 'C' and resid 407 through 413 Processing helix chain 'C' and resid 442 through 448 removed outlier: 3.774A pdb=" N TYR C 448 " --> pdb=" O TRP C 444 " (cutoff:3.500A) Processing helix chain 'C' and resid 478 through 485 removed outlier: 3.703A pdb=" N SER C 484 " --> pdb=" O SER C 480 " (cutoff:3.500A) Processing helix chain 'C' and resid 698 through 706 Processing helix chain 'C' and resid 785 through 789 removed outlier: 4.122A pdb=" N GLY C 788 " --> pdb=" O SER C 785 " (cutoff:3.500A) Processing helix chain 'C' and resid 817 through 822 Processing helix chain 'C' and resid 826 through 833 Processing helix chain 'C' and resid 836 through 865 removed outlier: 3.539A pdb=" N CYS C 840 " --> pdb=" O TYR C 836 " (cutoff:3.500A) Processing helix chain 'C' and resid 905 through 915 removed outlier: 4.041A pdb=" N LEU C 910 " --> pdb=" O PHE C 906 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N LEU C 911 " --> pdb=" O PHE C 907 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N VAL C 915 " --> pdb=" O LEU C 911 " (cutoff:3.500A) Processing helix chain 'C' and resid 918 through 928 Processing helix chain 'C' and resid 937 through 945 removed outlier: 4.196A pdb=" N VAL C 941 " --> pdb=" O ASP C 937 " (cutoff:3.500A) Processing helix chain 'C' and resid 955 through 972 Processing helix chain 'C' and resid 975 through 979 removed outlier: 3.515A pdb=" N ALA C 978 " --> pdb=" O TRP C 975 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ALA C 979 " --> pdb=" O SER C 976 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 975 through 979' Processing helix chain 'C' and resid 982 through 993 Processing helix chain 'C' and resid 998 through 1003 removed outlier: 3.704A pdb=" N ASN C1002 " --> pdb=" O MET C 998 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LYS C1003 " --> pdb=" O ASP C 999 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 998 through 1003' Processing helix chain 'C' and resid 1004 through 1022 Processing helix chain 'C' and resid 1023 through 1025 No H-bonds generated for 'chain 'C' and resid 1023 through 1025' Processing helix chain 'C' and resid 1027 through 1050 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 removed outlier: 3.560A pdb=" N ILE C1065 " --> pdb=" O SER C1061 " (cutoff:3.500A) Processing helix chain 'C' and resid 1073 through 1118 removed outlier: 3.884A pdb=" N GLN C1077 " --> pdb=" O GLU C1073 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VAL C1118 " --> pdb=" O VAL C1114 " (cutoff:3.500A) 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 54 through 55 removed outlier: 6.090A pdb=" N VAL A 55 " --> pdb=" O TYR C 651 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLY C 659 " --> pdb=" O LEU C 650 " (cutoff:3.500A) removed outlier: 4.972A pdb=" N ILE C 658 " --> pdb=" O ILE C 671 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLY C 631 " --> pdb=" O TYR C 624 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N ALA C 315 " --> pdb=" O CYS C 621 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 60 through 68 removed outlier: 3.657A pdb=" N GLY A 65 " --> pdb=" O ARG A 264 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N GLY A 101 " --> pdb=" O LEU A 261 " (cutoff:3.500A) removed outlier: 5.239A pdb=" N TYR A 213 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N PHE A 222 " --> pdb=" O TYR A 213 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 60 through 68 removed outlier: 3.657A pdb=" N GLY A 65 " --> pdb=" O ARG A 264 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ASN A 278 " --> pdb=" O LYS A 269 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 80 through 81 Processing sheet with id=AA6, first strand: chain 'A' and resid 109 through 112 removed outlier: 3.754A pdb=" N THR A 109 " --> pdb=" O GLU A 120 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 185 through 190 removed outlier: 4.106A pdb=" N PHE A 185 " --> pdb=" O ALA A 150 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS A 187 " --> pdb=" O ILE A 148 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 302 through 306 removed outlier: 3.676A pdb=" N VAL A 679 " --> pdb=" O LEU A 306 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 315 through 319 removed outlier: 4.340A pdb=" N ALA A 315 " --> pdb=" O CYS A 621 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ARG A 319 " --> pdb=" O ASP A 625 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLY A 631 " --> pdb=" O TYR A 624 " (cutoff:3.500A) removed outlier: 5.056A pdb=" N ILE A 658 " --> pdb=" O ILE A 671 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLY A 659 " --> pdb=" O LEU A 650 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 337 through 339 Processing sheet with id=AB2, first strand: chain 'A' and resid 345 through 349 removed outlier: 3.670A pdb=" N LEU A 388 " --> pdb=" O LYS A 347 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N PHE A 383 " --> pdb=" O ILE A 599 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N ILE A 599 " --> pdb=" O PHE A 383 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N SER A 385 " --> pdb=" O ASN A 597 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ASN A 597 " --> pdb=" O SER A 385 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N SER A 428 " --> pdb=" O THR A 365 " (cutoff:3.500A) removed outlier: 5.669A pdb=" N THR A 365 " --> pdb=" O SER A 428 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 345 through 349 removed outlier: 3.670A pdb=" N LEU A 388 " --> pdb=" O LYS A 347 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 459 through 463 Processing sheet with id=AB5, first strand: chain 'A' and resid 466 through 468 removed outlier: 4.282A pdb=" N CYS A 466 " --> pdb=" O SER A 538 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LYS A 536 " --> pdb=" O SER A 468 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 505 through 507 Processing sheet with id=AB7, first strand: chain 'A' and resid 725 through 732 removed outlier: 9.011A pdb=" N PHE A 768 " --> pdb=" O THR A 728 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N TYR A 730 " --> pdb=" O PHE A 768 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N PHE A 743 " --> pdb=" O MET A 739 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 777 through 779 Processing sheet with id=AB9, first strand: chain 'A' and resid 790 through 807 removed outlier: 6.941A pdb=" N GLU A 791 " --> pdb=" O LEU A1161 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N LEU A1161 " --> pdb=" O GLU A 791 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N LYS A 793 " --> pdb=" O THR A1159 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N THR A1159 " --> pdb=" O LYS A 793 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N PHE A1157 " --> pdb=" O PRO A 795 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N ASN A 797 " --> pdb=" O ILE A1155 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLY A1144 " --> pdb=" O ALA A1141 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU A1135 " --> pdb=" O PHE A1150 " (cutoff:3.500A) removed outlier: 5.517A pdb=" N TYR A1152 " --> pdb=" O HIS A1133 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N HIS A1133 " --> pdb=" O TYR A1152 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 790 through 807 removed outlier: 6.941A pdb=" N GLU A 791 " --> pdb=" O LEU A1161 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N LEU A1161 " --> pdb=" O GLU A 791 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N LYS A 793 " --> pdb=" O THR A1159 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N THR A1159 " --> pdb=" O LYS A 793 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N PHE A1157 " --> pdb=" O PRO A 795 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N ASN A 797 " --> pdb=" O ILE A1155 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N LEU A1161 " --> pdb=" O LYS A1183 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N LYS A1183 " --> pdb=" O LEU A1161 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 813 through 815 removed outlier: 4.388A pdb=" N LYS A 813 " --> pdb=" O LEU A 950 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 871 through 872 removed outlier: 6.465A pdb=" N LEU A 871 " --> pdb=" O VAL C 779 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'A' and resid 1206 through 1209 removed outlier: 3.635A pdb=" N ILE A1174 " --> pdb=" O LEU A1166 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU A1166 " --> pdb=" O ILE A1174 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 25 through 26 Processing sheet with id=AC6, first strand: chain 'B' and resid 60 through 68 removed outlier: 3.643A pdb=" N GLY B 65 " --> pdb=" O ARG B 264 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N GLY B 101 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N TYR B 203 " --> pdb=" O TYR B 210 " (cutoff:3.500A) removed outlier: 5.161A pdb=" N TYR B 213 " --> pdb=" O PHE B 222 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N PHE B 222 " --> pdb=" O TYR B 213 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 60 through 68 removed outlier: 3.643A pdb=" N GLY B 65 " --> pdb=" O ARG B 264 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N LEU B 267 " --> pdb=" O ALA B 279 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N ALA B 279 " --> pdb=" O LEU B 267 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N LYS B 269 " --> pdb=" O THR B 277 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 80 through 81 Processing sheet with id=AC9, first strand: chain 'B' and resid 109 through 112 removed outlier: 3.821A pdb=" N THR B 109 " --> pdb=" O GLU B 120 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 185 through 190 removed outlier: 4.140A pdb=" N PHE B 185 " --> pdb=" O ALA B 150 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 302 through 306 removed outlier: 3.683A pdb=" N VAL B 679 " --> pdb=" O LEU B 306 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 315 through 319 removed outlier: 4.279A pdb=" N ALA B 315 " --> pdb=" O CYS B 621 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ASP B 623 " --> pdb=" O ALA B 315 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ARG B 319 " --> pdb=" O ASP B 625 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLY B 631 " --> pdb=" O TYR B 624 " (cutoff:3.500A) removed outlier: 5.074A pdb=" N ILE B 658 " --> pdb=" O ILE B 671 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLY B 659 " --> pdb=" O LEU B 650 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 337 through 339 removed outlier: 7.044A pdb=" N VAL B 338 " --> pdb=" O ASN B 437 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'B' and resid 345 through 349 removed outlier: 3.525A pdb=" N LYS B 390 " --> pdb=" O GLU B 345 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU B 388 " --> pdb=" O LYS B 347 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N PHE B 383 " --> pdb=" O ILE B 599 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N ILE B 599 " --> pdb=" O PHE B 383 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N SER B 385 " --> pdb=" O ASN B 597 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ASN B 597 " --> pdb=" O SER B 385 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N SER B 428 " --> pdb=" O THR B 365 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N THR B 365 " --> pdb=" O SER B 428 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 345 through 349 removed outlier: 3.525A pdb=" N LYS B 390 " --> pdb=" O GLU B 345 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU B 388 " --> pdb=" O LYS B 347 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 459 through 463 Processing sheet with id=AD8, first strand: chain 'B' and resid 466 through 468 removed outlier: 4.237A pdb=" N CYS B 466 " --> pdb=" O SER B 538 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LYS B 536 " --> pdb=" O SER B 468 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 505 through 507 Processing sheet with id=AE1, first strand: chain 'B' and resid 725 through 732 removed outlier: 9.276A pdb=" N PHE B 768 " --> pdb=" O THR B 728 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N TYR B 730 " --> pdb=" O PHE B 768 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N PHE B 743 " --> pdb=" O MET B 739 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 777 through 779 Processing sheet with id=AE3, first strand: chain 'B' and resid 790 through 807 removed outlier: 6.975A pdb=" N GLU B 791 " --> pdb=" O LEU B1161 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N LEU B1161 " --> pdb=" O GLU B 791 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N LYS B 793 " --> pdb=" O THR B1159 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N THR B1159 " --> pdb=" O LYS B 793 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N PHE B1157 " --> pdb=" O PRO B 795 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N ASN B 797 " --> pdb=" O ILE B1155 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLY B1144 " --> pdb=" O ALA B1141 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU B1135 " --> pdb=" O PHE B1150 " (cutoff:3.500A) removed outlier: 5.384A pdb=" N TYR B1152 " --> pdb=" O HIS B1133 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N HIS B1133 " --> pdb=" O TYR B1152 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'B' and resid 790 through 807 removed outlier: 6.975A pdb=" N GLU B 791 " --> pdb=" O LEU B1161 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N LEU B1161 " --> pdb=" O GLU B 791 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N LYS B 793 " --> pdb=" O THR B1159 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N THR B1159 " --> pdb=" O LYS B 793 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N PHE B1157 " --> pdb=" O PRO B 795 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N ASN B 797 " --> pdb=" O ILE B1155 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N LEU B1161 " --> pdb=" O LYS B1183 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N LYS B1183 " --> pdb=" O LEU B1161 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'B' and resid 813 through 815 removed outlier: 4.392A pdb=" N LYS B 813 " --> pdb=" O LEU B 950 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'B' and resid 1206 through 1209 removed outlier: 3.607A pdb=" N GLY B1173 " --> pdb=" O MET B1209 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ILE B1174 " --> pdb=" O LEU B1166 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU B1166 " --> pdb=" O ILE B1174 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 25 through 26 Processing sheet with id=AE8, first strand: chain 'C' and resid 60 through 68 removed outlier: 3.609A pdb=" N GLY C 65 " --> pdb=" O ARG C 264 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N GLY C 101 " --> pdb=" O LEU C 261 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N TYR C 203 " --> pdb=" O TYR C 210 " (cutoff:3.500A) removed outlier: 5.226A pdb=" N TYR C 213 " --> pdb=" O PHE C 222 " (cutoff:3.500A) removed outlier: 5.041A pdb=" N PHE C 222 " --> pdb=" O TYR C 213 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 60 through 68 removed outlier: 3.609A pdb=" N GLY C 65 " --> pdb=" O ARG C 264 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N LEU C 267 " --> pdb=" O ALA C 279 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N ALA C 279 " --> pdb=" O LEU C 267 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N LYS C 269 " --> pdb=" O THR C 277 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 80 through 81 Processing sheet with id=AF2, first strand: chain 'C' and resid 109 through 112 removed outlier: 3.752A pdb=" N THR C 109 " --> pdb=" O GLU C 120 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 185 through 190 removed outlier: 4.182A pdb=" N PHE C 185 " --> pdb=" O ALA C 150 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 302 through 306 removed outlier: 3.741A pdb=" N VAL C 679 " --> pdb=" O LEU C 306 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 337 through 339 Processing sheet with id=AF6, first strand: chain 'C' and resid 345 through 349 removed outlier: 3.506A pdb=" N GLU C 345 " --> pdb=" O LYS C 390 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU C 388 " --> pdb=" O LYS C 347 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N PHE C 383 " --> pdb=" O ILE C 599 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N ILE C 599 " --> pdb=" O PHE C 383 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N SER C 385 " --> pdb=" O ASN C 597 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ASN C 597 " --> pdb=" O SER C 385 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N SER C 428 " --> pdb=" O THR C 365 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N THR C 365 " --> pdb=" O SER C 428 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 345 through 349 removed outlier: 3.506A pdb=" N GLU C 345 " --> pdb=" O LYS C 390 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU C 388 " --> pdb=" O LYS C 347 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'C' and resid 459 through 463 Processing sheet with id=AF9, first strand: chain 'C' and resid 466 through 468 removed outlier: 4.288A pdb=" N CYS C 466 " --> pdb=" O SER C 538 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LYS C 536 " --> pdb=" O SER C 468 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'C' and resid 505 through 507 Processing sheet with id=AG2, first strand: chain 'C' and resid 725 through 732 removed outlier: 9.025A pdb=" N PHE C 768 " --> pdb=" O THR C 728 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N TYR C 730 " --> pdb=" O PHE C 768 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N PHE C 743 " --> pdb=" O MET C 739 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'C' and resid 790 through 807 removed outlier: 6.937A pdb=" N GLU C 791 " --> pdb=" O LEU C1161 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N LEU C1161 " --> pdb=" O GLU C 791 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N LYS C 793 " --> pdb=" O THR C1159 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N THR C1159 " --> pdb=" O LYS C 793 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N PHE C1157 " --> pdb=" O PRO C 795 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N ASN C 797 " --> pdb=" O ILE C1155 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLY C1144 " --> pdb=" O ALA C1141 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU C1137 " --> pdb=" O MET C1148 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU C1135 " --> pdb=" O PHE C1150 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N TYR C1152 " --> pdb=" O HIS C1133 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N HIS C1133 " --> pdb=" O TYR C1152 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'C' and resid 790 through 807 removed outlier: 6.937A pdb=" N GLU C 791 " --> pdb=" O LEU C1161 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N LEU C1161 " --> pdb=" O GLU C 791 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N LYS C 793 " --> pdb=" O THR C1159 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N THR C1159 " --> pdb=" O LYS C 793 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N PHE C1157 " --> pdb=" O PRO C 795 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N ASN C 797 " --> pdb=" O ILE C1155 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N LEU C1161 " --> pdb=" O LYS C1183 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N LYS C1183 " --> pdb=" O LEU C1161 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'C' and resid 813 through 815 removed outlier: 4.325A pdb=" N LYS C 813 " --> pdb=" O LEU C 950 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'C' and resid 1206 through 1209 removed outlier: 3.796A pdb=" N GLY C1173 " --> pdb=" O MET C1209 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU C1166 " --> pdb=" O ILE C1174 " (cutoff:3.500A) 1083 hydrogen bonds defined for protein. 3102 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.78 Time building geometry restraints manager: 3.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 8859 1.34 - 1.46: 7651 1.46 - 1.58: 13302 1.58 - 1.71: 2 1.71 - 1.83: 204 Bond restraints: 30018 Sorted by residual: bond pdb=" CB PRO B1220 " pdb=" CG PRO B1220 " ideal model delta sigma weight residual 1.492 1.633 -0.141 5.00e-02 4.00e+02 7.96e+00 bond pdb=" CB PRO A1220 " pdb=" CG PRO A1220 " ideal model delta sigma weight residual 1.492 1.606 -0.114 5.00e-02 4.00e+02 5.21e+00 bond pdb=" C1 NAG Q 2 " pdb=" O5 NAG Q 2 " ideal model delta sigma weight residual 1.406 1.447 -0.041 2.00e-02 2.50e+03 4.12e+00 bond pdb=" C1 NAG Z 1 " pdb=" O5 NAG Z 1 " ideal model delta sigma weight residual 1.406 1.446 -0.040 2.00e-02 2.50e+03 4.07e+00 bond pdb=" C1 NAG L 2 " pdb=" O5 NAG L 2 " ideal model delta sigma weight residual 1.406 1.446 -0.040 2.00e-02 2.50e+03 4.05e+00 ... (remaining 30013 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.82: 40506 2.82 - 5.63: 288 5.63 - 8.45: 44 8.45 - 11.27: 10 11.27 - 14.09: 3 Bond angle restraints: 40851 Sorted by residual: angle pdb=" CA PRO B1220 " pdb=" N PRO B1220 " pdb=" CD PRO B1220 " ideal model delta sigma weight residual 112.00 102.33 9.67 1.40e+00 5.10e-01 4.77e+01 angle pdb=" CA PRO C1220 " pdb=" N PRO C1220 " pdb=" CD PRO C1220 " ideal model delta sigma weight residual 112.00 104.82 7.18 1.40e+00 5.10e-01 2.63e+01 angle pdb=" CA PRO A1220 " pdb=" N PRO A1220 " pdb=" CD PRO A1220 " ideal model delta sigma weight residual 112.00 105.38 6.62 1.40e+00 5.10e-01 2.24e+01 angle pdb=" CA LEU B 510 " pdb=" CB LEU B 510 " pdb=" CG LEU B 510 " ideal model delta sigma weight residual 116.30 130.39 -14.09 3.50e+00 8.16e-02 1.62e+01 angle pdb=" CA LEU A 510 " pdb=" CB LEU A 510 " pdb=" CG LEU A 510 " ideal model delta sigma weight residual 116.30 130.06 -13.76 3.50e+00 8.16e-02 1.55e+01 ... (remaining 40846 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 15374 17.94 - 35.87: 1476 35.87 - 53.81: 220 53.81 - 71.75: 39 71.75 - 89.69: 21 Dihedral angle restraints: 17130 sinusoidal: 6597 harmonic: 10533 Sorted by residual: dihedral pdb=" CB CYS A 476 " pdb=" SG CYS A 476 " pdb=" SG CYS A 567 " pdb=" CB CYS A 567 " ideal model delta sinusoidal sigma weight residual -86.00 -169.84 83.84 1 1.00e+01 1.00e-02 8.57e+01 dihedral pdb=" CB CYS C 476 " pdb=" SG CYS C 476 " pdb=" SG CYS C 567 " pdb=" CB CYS C 567 " ideal model delta sinusoidal sigma weight residual -86.00 -168.96 82.96 1 1.00e+01 1.00e-02 8.42e+01 dihedral pdb=" CB CYS B 476 " pdb=" SG CYS B 476 " pdb=" SG CYS B 567 " pdb=" CB CYS B 567 " ideal model delta sinusoidal sigma weight residual -86.00 -168.38 82.38 1 1.00e+01 1.00e-02 8.33e+01 ... (remaining 17127 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 3907 0.059 - 0.118: 845 0.118 - 0.177: 72 0.177 - 0.236: 14 0.236 - 0.295: 4 Chirality restraints: 4842 Sorted by residual: chirality pdb=" CB THR C 31 " pdb=" CA THR C 31 " pdb=" OG1 THR C 31 " pdb=" CG2 THR C 31 " both_signs ideal model delta sigma weight residual False 2.55 2.26 0.30 2.00e-01 2.50e+01 2.18e+00 chirality pdb=" C5 BMA P 3 " pdb=" C4 BMA P 3 " pdb=" C6 BMA P 3 " pdb=" O5 BMA P 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.28 2.00e-01 2.50e+01 1.95e+00 chirality pdb=" C5 BMA G 3 " pdb=" C4 BMA G 3 " pdb=" C6 BMA G 3 " pdb=" O5 BMA G 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.28 2.00e-01 2.50e+01 1.89e+00 ... (remaining 4839 not shown) Planarity restraints: 5181 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA C1219 " 0.096 5.00e-02 4.00e+02 1.41e-01 3.17e+01 pdb=" N PRO C1220 " -0.243 5.00e-02 4.00e+02 pdb=" CA PRO C1220 " 0.075 5.00e-02 4.00e+02 pdb=" CD PRO C1220 " 0.073 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B1219 " 0.057 5.00e-02 4.00e+02 8.03e-02 1.03e+01 pdb=" N PRO B1220 " -0.139 5.00e-02 4.00e+02 pdb=" CA PRO B1220 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO B1220 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A1219 " -0.054 5.00e-02 4.00e+02 7.80e-02 9.74e+00 pdb=" N PRO A1220 " 0.135 5.00e-02 4.00e+02 pdb=" CA PRO A1220 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO A1220 " -0.043 5.00e-02 4.00e+02 ... (remaining 5178 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 2405 2.75 - 3.28: 27524 3.28 - 3.82: 48079 3.82 - 4.36: 54555 4.36 - 4.90: 96541 Nonbonded interactions: 229104 Sorted by model distance: nonbonded pdb=" O PRO C 68 " pdb=" OH TYR C 266 " model vdw 2.208 3.040 nonbonded pdb=" O PRO A 68 " pdb=" OH TYR A 266 " model vdw 2.240 3.040 nonbonded pdb=" O PRO B 68 " pdb=" OH TYR B 266 " model vdw 2.259 3.040 nonbonded pdb=" OG SER B 506 " pdb=" OD1 ASP B 514 " model vdw 2.275 3.040 nonbonded pdb=" OD1 ASN A 337 " pdb=" OG1 THR A 435 " model vdw 2.278 3.040 ... (remaining 229099 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: 0.09 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' } ncs_group { reference = chain 'G' selection = chain 'P' selection = chain 'Y' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.820 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: 0.520 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 26.500 Find NCS groups from input model: 0.910 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 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 : 0.004 0.141 30177 Z= 0.196 Angle : 0.719 14.086 41256 Z= 0.338 Chirality : 0.048 0.295 4842 Planarity : 0.006 0.141 5124 Dihedral : 13.840 89.686 10152 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 0.00 % Allowed : 0.34 % Favored : 99.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.30 (0.13), residues: 3573 helix: 0.76 (0.18), residues: 723 sheet: -0.68 (0.18), residues: 828 loop : -1.59 (0.13), residues: 2022 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 346 TYR 0.038 0.001 TYR C 266 PHE 0.026 0.001 PHE A 176 TRP 0.013 0.001 TRP C 444 HIS 0.005 0.001 HIS B 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00419 / 0.20 (30018) covalent geometry : angle 0.70027 / 0.33 (40851) SS BOND : bond 0.00320 / 0.19 ( 72) SS BOND : angle 1.00057 / 0.73 ( 144) hydrogen bonds : bond 0.21456 / 14.05 ( 1016) hydrogen bonds : angle 8.15339 / 5.46 ( 3102) link_BETA1-4 : bond 0.00832 / 0.50 ( 30) link_BETA1-4 : angle 2.12967 / 1.39 ( 90) link_NAG-ASN : bond 0.00373 / 0.25 ( 57) link_NAG-ASN : angle 2.04442 / 1.46 ( 171) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7146 Ramachandran restraints generated. 3573 Oldfield, 0 Emsley, 3573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7146 Ramachandran restraints generated. 3573 Oldfield, 0 Emsley, 3573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 696 residues out of total 3216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 696 time to evaluate : 1.041 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 ILE cc_start: 0.8880 (pt) cc_final: 0.8486 (mm) REVERT: A 133 ASN cc_start: 0.8449 (p0) cc_final: 0.8209 (p0) REVERT: A 142 HIS cc_start: 0.7828 (m90) cc_final: 0.6666 (m90) REVERT: A 174 TRP cc_start: 0.8455 (p-90) cc_final: 0.7738 (p-90) REVERT: A 175 HIS cc_start: 0.8443 (p-80) cc_final: 0.7851 (p-80) REVERT: A 186 LYS cc_start: 0.8085 (ttmt) cc_final: 0.7829 (ttmm) REVERT: A 206 ARG cc_start: 0.8309 (mtm110) cc_final: 0.7972 (ptp-110) REVERT: A 262 SER cc_start: 0.7690 (t) cc_final: 0.7267 (p) REVERT: A 316 THR cc_start: 0.8891 (m) cc_final: 0.8392 (p) REVERT: A 326 ASP cc_start: 0.7211 (t70) cc_final: 0.6388 (t0) REVERT: A 328 ASP cc_start: 0.7587 (m-30) cc_final: 0.7154 (m-30) REVERT: A 397 ARG cc_start: 0.8446 (mmt180) cc_final: 0.8207 (mmm-85) REVERT: A 417 ASP cc_start: 0.7999 (t70) cc_final: 0.7784 (t0) REVERT: A 437 ASN cc_start: 0.8829 (t0) cc_final: 0.8357 (p0) REVERT: A 553 GLU cc_start: 0.8386 (mm-30) cc_final: 0.7639 (mp0) REVERT: A 574 PHE cc_start: 0.8415 (m-80) cc_final: 0.7814 (m-80) REVERT: A 711 GLN cc_start: 0.7366 (pm20) cc_final: 0.6998 (mp10) REVERT: A 717 TYR cc_start: 0.8608 (t80) cc_final: 0.8380 (t80) REVERT: A 725 ASP cc_start: 0.7792 (p0) cc_final: 0.7490 (p0) REVERT: A 779 VAL cc_start: 0.8602 (t) cc_final: 0.7834 (m) REVERT: A 792 ILE cc_start: 0.8997 (tt) cc_final: 0.8528 (pt) REVERT: A 832 LEU cc_start: 0.8932 (mt) cc_final: 0.7898 (mm) REVERT: A 842 ASN cc_start: 0.8624 (m-40) cc_final: 0.8346 (m-40) REVERT: A 844 ASN cc_start: 0.8666 (m-40) cc_final: 0.7512 (m-40) REVERT: A 848 ASP cc_start: 0.8004 (m-30) cc_final: 0.7482 (m-30) REVERT: A 855 ASP cc_start: 0.7831 (m-30) cc_final: 0.7571 (m-30) REVERT: A 874 ASN cc_start: 0.8409 (m-40) cc_final: 0.7741 (p0) REVERT: A 887 ASN cc_start: 0.8967 (m-40) cc_final: 0.8552 (m-40) REVERT: A 889 LYS cc_start: 0.8783 (ttpt) cc_final: 0.8472 (ttmm) REVERT: A 909 ASP cc_start: 0.8275 (m-30) cc_final: 0.7382 (m-30) REVERT: A 910 LEU cc_start: 0.9257 (mp) cc_final: 0.8701 (mt) REVERT: A 938 LEU cc_start: 0.8547 (mm) cc_final: 0.8332 (mt) REVERT: A 999 ASP cc_start: 0.8080 (t0) cc_final: 0.7622 (t0) REVERT: A 1005 GLN cc_start: 0.8484 (tm-30) cc_final: 0.8079 (tm-30) REVERT: A 1010 THR cc_start: 0.9025 (m) cc_final: 0.8707 (p) REVERT: A 1054 LYS cc_start: 0.8876 (mttt) cc_final: 0.8559 (mmmm) REVERT: A 1079 ASP cc_start: 0.8305 (m-30) cc_final: 0.7666 (m-30) REVERT: A 1083 ASN cc_start: 0.8560 (m-40) cc_final: 0.8328 (m110) REVERT: A 1095 GLN cc_start: 0.7912 (tm-30) cc_final: 0.7579 (tm-30) REVERT: A 1209 MET cc_start: 0.7919 (mtt) cc_final: 0.7579 (mtt) REVERT: B 69 LYS cc_start: 0.8861 (tmtt) cc_final: 0.8601 (ttpp) REVERT: B 88 LEU cc_start: 0.9116 (mp) cc_final: 0.8888 (tp) REVERT: B 187 LYS cc_start: 0.8657 (tttt) cc_final: 0.7768 (ttmm) REVERT: B 197 TRP cc_start: 0.8455 (m100) cc_final: 0.7619 (m100) REVERT: B 316 THR cc_start: 0.8762 (m) cc_final: 0.8132 (p) REVERT: B 326 ASP cc_start: 0.6896 (t70) cc_final: 0.6031 (t0) REVERT: B 328 ASP cc_start: 0.7448 (m-30) cc_final: 0.6545 (m-30) REVERT: B 331 LYS cc_start: 0.8420 (mttt) cc_final: 0.8103 (mtpp) REVERT: B 397 ARG cc_start: 0.8419 (mmt180) cc_final: 0.7995 (mmm-85) REVERT: B 411 SER cc_start: 0.9234 (t) cc_final: 0.8855 (p) REVERT: B 448 TYR cc_start: 0.8409 (m-80) cc_final: 0.8012 (m-10) REVERT: B 450 PHE cc_start: 0.8419 (t80) cc_final: 0.7990 (t80) REVERT: B 462 TYR cc_start: 0.8109 (p90) cc_final: 0.7843 (p90) REVERT: B 578 SER cc_start: 0.7502 (p) cc_final: 0.6072 (p) REVERT: B 704 ASN cc_start: 0.7915 (p0) cc_final: 0.7579 (p0) REVERT: B 711 GLN cc_start: 0.7309 (pm20) cc_final: 0.7011 (mp10) REVERT: B 792 ILE cc_start: 0.9010 (tt) cc_final: 0.8657 (pt) REVERT: B 842 ASN cc_start: 0.8553 (m-40) cc_final: 0.8198 (m-40) REVERT: B 848 ASP cc_start: 0.8154 (m-30) cc_final: 0.7716 (m-30) REVERT: B 855 ASP cc_start: 0.7741 (m-30) cc_final: 0.7539 (m-30) REVERT: B 874 ASN cc_start: 0.8262 (m-40) cc_final: 0.7693 (p0) REVERT: B 908 GLU cc_start: 0.7822 (mt-10) cc_final: 0.7604 (mt-10) REVERT: B 910 LEU cc_start: 0.9275 (mp) cc_final: 0.8660 (mt) REVERT: B 914 LYS cc_start: 0.8972 (mmtt) cc_final: 0.8754 (mmmt) REVERT: B 916 LYS cc_start: 0.8209 (pttt) cc_final: 0.7879 (ptmm) REVERT: B 999 ASP cc_start: 0.8108 (t0) cc_final: 0.7764 (t0) REVERT: B 1003 LYS cc_start: 0.8928 (mtpt) cc_final: 0.8502 (mtpp) REVERT: B 1004 ASN cc_start: 0.8036 (m-40) cc_final: 0.6343 (t0) REVERT: B 1010 THR cc_start: 0.8932 (m) cc_final: 0.8674 (p) REVERT: B 1045 ASN cc_start: 0.8749 (t0) cc_final: 0.8428 (t0) REVERT: B 1054 LYS cc_start: 0.8664 (mttt) cc_final: 0.8340 (mmmm) REVERT: B 1075 GLN cc_start: 0.7878 (mm-40) cc_final: 0.7243 (mm-40) REVERT: B 1079 ASP cc_start: 0.8165 (m-30) cc_final: 0.7746 (m-30) REVERT: B 1095 GLN cc_start: 0.7941 (tm-30) cc_final: 0.6491 (tm-30) REVERT: B 1099 ASP cc_start: 0.8219 (m-30) cc_final: 0.7136 (m-30) REVERT: B 1177 LYS cc_start: 0.8308 (ttmm) cc_final: 0.7950 (mmmm) REVERT: B 1210 ASN cc_start: 0.8957 (t0) cc_final: 0.8751 (m-40) REVERT: C 22 ASN cc_start: 0.8398 (p0) cc_final: 0.8181 (p0) REVERT: C 53 ASP cc_start: 0.7702 (m-30) cc_final: 0.7313 (m-30) REVERT: C 69 LYS cc_start: 0.8876 (tmtt) cc_final: 0.8611 (tttp) REVERT: C 92 LYS cc_start: 0.9109 (mttt) cc_final: 0.8660 (mtpp) REVERT: C 142 HIS cc_start: 0.7473 (m90) cc_final: 0.6937 (m-70) REVERT: C 206 ARG cc_start: 0.8099 (mtm110) cc_final: 0.7830 (ptp-170) REVERT: C 208 THR cc_start: 0.8136 (p) cc_final: 0.7888 (p) REVERT: C 262 SER cc_start: 0.7214 (t) cc_final: 0.6790 (p) REVERT: C 288 SER cc_start: 0.8663 (m) cc_final: 0.8215 (p) REVERT: C 289 GLU cc_start: 0.8190 (mt-10) cc_final: 0.7640 (mm-30) REVERT: C 293 LYS cc_start: 0.8811 (ttpt) cc_final: 0.8491 (ptpp) REVERT: C 316 THR cc_start: 0.8845 (m) cc_final: 0.8230 (p) REVERT: C 331 LYS cc_start: 0.8451 (mttt) cc_final: 0.8185 (mtpp) REVERT: C 397 ARG cc_start: 0.8483 (mmt180) cc_final: 0.8184 (mmm-85) REVERT: C 437 ASN cc_start: 0.8499 (t0) cc_final: 0.8040 (p0) REVERT: C 439 TYR cc_start: 0.8164 (t80) cc_final: 0.7874 (t80) REVERT: C 448 TYR cc_start: 0.8718 (m-80) cc_final: 0.8379 (m-80) REVERT: C 460 VAL cc_start: 0.8550 (t) cc_final: 0.8344 (p) REVERT: C 481 PHE cc_start: 0.6684 (t80) cc_final: 0.6381 (t80) REVERT: C 500 ASN cc_start: 0.7551 (m-40) cc_final: 0.7318 (m-40) REVERT: C 574 PHE cc_start: 0.8432 (m-80) cc_final: 0.8086 (m-80) REVERT: C 580 ASP cc_start: 0.7889 (t0) cc_final: 0.7616 (t70) REVERT: C 713 TYR cc_start: 0.8026 (p90) cc_final: 0.7782 (p90) REVERT: C 779 VAL cc_start: 0.8517 (t) cc_final: 0.7667 (m) REVERT: C 792 ILE cc_start: 0.8957 (tt) cc_final: 0.8511 (tp) REVERT: C 832 LEU cc_start: 0.9135 (mt) cc_final: 0.8320 (mm) REVERT: C 842 ASN cc_start: 0.8599 (m-40) cc_final: 0.8354 (m-40) REVERT: C 848 ASP cc_start: 0.8080 (m-30) cc_final: 0.7643 (m-30) REVERT: C 849 GLU cc_start: 0.7800 (mm-30) cc_final: 0.7439 (mm-30) REVERT: C 874 ASN cc_start: 0.8374 (m-40) cc_final: 0.7785 (p0) REVERT: C 881 PHE cc_start: 0.7419 (p90) cc_final: 0.7186 (p90) REVERT: C 887 ASN cc_start: 0.8690 (m-40) cc_final: 0.8425 (m-40) REVERT: C 889 LYS cc_start: 0.8979 (ttpt) cc_final: 0.8678 (ttpp) REVERT: C 909 ASP cc_start: 0.8218 (m-30) cc_final: 0.7426 (m-30) REVERT: C 910 LEU cc_start: 0.9204 (mp) cc_final: 0.8835 (mt) REVERT: C 998 MET cc_start: 0.8861 (tpp) cc_final: 0.8126 (mmm) REVERT: C 999 ASP cc_start: 0.8059 (t70) cc_final: 0.7542 (t0) REVERT: C 1010 THR cc_start: 0.8834 (m) cc_final: 0.8474 (p) REVERT: C 1045 ASN cc_start: 0.8882 (t0) cc_final: 0.8623 (t0) REVERT: C 1054 LYS cc_start: 0.8860 (mttt) cc_final: 0.8642 (mtpp) REVERT: C 1095 GLN cc_start: 0.7995 (tm-30) cc_final: 0.6868 (tm-30) REVERT: C 1099 ASP cc_start: 0.8187 (m-30) cc_final: 0.6604 (m-30) REVERT: C 1126 ASN cc_start: 0.8536 (m-40) cc_final: 0.8185 (t0) outliers start: 0 outliers final: 0 residues processed: 696 average time/residue: 0.1893 time to fit residues: 206.3063 Evaluate side-chains 497 residues out of total 3216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 497 time to evaluate : 1.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 10.0000 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 0.9990 chunk 244 optimal weight: 0.9990 chunk 183 optimal weight: 0.8980 chunk 298 optimal weight: 0.2980 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 300 ASN A 413 ASN ** A 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 685 GLN A 867 GLN B 142 HIS B 364 HIS B 413 ASN ** B 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 586 ASN B 685 GLN B 858 GLN B 867 GLN B 945 ASN ** C 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 234 HIS C 334 ASN C 364 HIS C 413 ASN ** C 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 867 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.106905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.086399 restraints weight = 64234.023| |-----------------------------------------------------------------------------| r_work (start): 0.3184 rms_B_bonded: 3.84 r_work: 0.3004 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.2159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 30177 Z= 0.167 Angle : 0.620 11.504 41256 Z= 0.319 Chirality : 0.044 0.228 4842 Planarity : 0.005 0.081 5124 Dihedral : 4.502 27.064 3867 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 1.18 % Allowed : 8.08 % Favored : 90.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.80 (0.14), residues: 3573 helix: 1.53 (0.19), residues: 765 sheet: -0.28 (0.18), residues: 750 loop : -1.50 (0.13), residues: 2058 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 447 TYR 0.028 0.001 TYR A 713 PHE 0.024 0.002 PHE C 473 TRP 0.020 0.001 TRP B 174 HIS 0.005 0.001 HIS C 175 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.17 (30018) covalent geometry : angle 0.60488 / 0.32 (40851) SS BOND : bond 0.00289 / 0.18 ( 72) SS BOND : angle 1.17301 / 0.85 ( 144) hydrogen bonds : bond 0.04467 / 2.92 ( 1016) hydrogen bonds : angle 5.53355 / 3.72 ( 3102) link_BETA1-4 : bond 0.00401 / 0.26 ( 30) link_BETA1-4 : angle 1.68593 / 1.17 ( 90) link_NAG-ASN : bond 0.00293 / 0.17 ( 57) link_NAG-ASN : angle 1.63129 / 1.13 ( 171) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7146 Ramachandran restraints generated. 3573 Oldfield, 0 Emsley, 3573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7146 Ramachandran restraints generated. 3573 Oldfield, 0 Emsley, 3573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 578 residues out of total 3216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 540 time to evaluate : 0.999 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 SER cc_start: 0.8216 (m) cc_final: 0.7971 (t) REVERT: A 114 ASN cc_start: 0.8962 (m-40) cc_final: 0.8751 (m-40) REVERT: A 137 ILE cc_start: 0.9059 (mt) cc_final: 0.8838 (tt) REVERT: A 140 GLN cc_start: 0.7696 (tm-30) cc_final: 0.6913 (tm-30) REVERT: A 142 HIS cc_start: 0.8155 (m90) cc_final: 0.7418 (m90) REVERT: A 175 HIS cc_start: 0.8535 (p-80) cc_final: 0.8292 (p-80) REVERT: A 262 SER cc_start: 0.8184 (t) cc_final: 0.7807 (p) REVERT: A 289 GLU cc_start: 0.8763 (mt-10) cc_final: 0.8259 (mm-30) REVERT: A 326 ASP cc_start: 0.7486 (t70) cc_final: 0.6789 (t0) REVERT: A 331 LYS cc_start: 0.8785 (mtpt) cc_final: 0.8541 (mtpp) REVERT: A 376 SER cc_start: 0.9095 (m) cc_final: 0.8703 (p) REVERT: A 384 LYS cc_start: 0.8816 (pttt) cc_final: 0.8586 (pttt) REVERT: A 397 ARG cc_start: 0.8864 (mmt180) cc_final: 0.8582 (mmm-85) REVERT: A 437 ASN cc_start: 0.8975 (t0) cc_final: 0.8627 (t0) REVERT: A 446 ARG cc_start: 0.8779 (ttm-80) cc_final: 0.8106 (mtm-85) REVERT: A 481 PHE cc_start: 0.6670 (t80) cc_final: 0.6388 (t80) REVERT: A 535 GLN cc_start: 0.8397 (pt0) cc_final: 0.7833 (pt0) REVERT: A 536 LYS cc_start: 0.8573 (ptpp) cc_final: 0.8350 (mtmm) REVERT: A 553 GLU cc_start: 0.8386 (mm-30) cc_final: 0.7768 (mp0) REVERT: A 580 ASP cc_start: 0.8517 (t0) cc_final: 0.8255 (t0) REVERT: A 704 ASN cc_start: 0.7856 (p0) cc_final: 0.7545 (p0) REVERT: A 711 GLN cc_start: 0.8061 (pm20) cc_final: 0.7608 (mp10) REVERT: A 803 GLN cc_start: 0.8385 (tp40) cc_final: 0.8127 (tp-100) REVERT: A 842 ASN cc_start: 0.8895 (m-40) cc_final: 0.8594 (m-40) REVERT: A 844 ASN cc_start: 0.8851 (m-40) cc_final: 0.7973 (m-40) REVERT: A 848 ASP cc_start: 0.8498 (m-30) cc_final: 0.8063 (m-30) REVERT: A 858 GLN cc_start: 0.8683 (mm110) cc_final: 0.8419 (mm110) REVERT: A 867 GLN cc_start: 0.7846 (mm110) cc_final: 0.7575 (mm-40) REVERT: A 874 ASN cc_start: 0.8779 (m-40) cc_final: 0.8230 (p0) REVERT: A 889 LYS cc_start: 0.9063 (ttpt) cc_final: 0.8746 (ttpp) REVERT: A 909 ASP cc_start: 0.8542 (m-30) cc_final: 0.7817 (m-30) REVERT: A 999 ASP cc_start: 0.8536 (t0) cc_final: 0.8016 (t0) REVERT: A 1054 LYS cc_start: 0.9174 (mttt) cc_final: 0.8898 (mtpp) REVERT: A 1079 ASP cc_start: 0.8801 (m-30) cc_final: 0.8196 (m-30) REVERT: A 1095 GLN cc_start: 0.8693 (tm-30) cc_final: 0.8177 (tm-30) REVERT: A 1112 GLU cc_start: 0.8775 (tt0) cc_final: 0.8381 (tp30) REVERT: A 1177 LYS cc_start: 0.8399 (tppt) cc_final: 0.7971 (mptt) REVERT: A 1189 MET cc_start: 0.8294 (mtt) cc_final: 0.7969 (mtt) REVERT: A 1209 MET cc_start: 0.8311 (mtt) cc_final: 0.7985 (mtt) REVERT: B 69 LYS cc_start: 0.9124 (tmtt) cc_final: 0.8744 (ttpp) REVERT: B 88 LEU cc_start: 0.9162 (mp) cc_final: 0.8873 (tp) REVERT: B 107 LYS cc_start: 0.8534 (tttt) cc_final: 0.8119 (ttpp) REVERT: B 111 LEU cc_start: 0.8655 (mm) cc_final: 0.8191 (mt) REVERT: B 131 ILE cc_start: 0.9053 (mp) cc_final: 0.8821 (tp) REVERT: B 133 ASN cc_start: 0.8530 (p0) cc_final: 0.8224 (p0) REVERT: B 142 HIS cc_start: 0.8105 (m90) cc_final: 0.6948 (m-70) REVERT: B 175 HIS cc_start: 0.8668 (p-80) cc_final: 0.8232 (p-80) REVERT: B 197 TRP cc_start: 0.8363 (m100) cc_final: 0.7827 (m100) REVERT: B 326 ASP cc_start: 0.7447 (t70) cc_final: 0.6579 (t0) REVERT: B 328 ASP cc_start: 0.8047 (m-30) cc_final: 0.7415 (m-30) REVERT: B 331 LYS cc_start: 0.9030 (mttt) cc_final: 0.8596 (mtpp) REVERT: B 397 ARG cc_start: 0.8853 (mmt180) cc_final: 0.8269 (mmm-85) REVERT: B 400 ASP cc_start: 0.8355 (m-30) cc_final: 0.7879 (m-30) REVERT: B 411 SER cc_start: 0.9364 (t) cc_final: 0.8950 (p) REVERT: B 446 ARG cc_start: 0.8800 (ttm110) cc_final: 0.8372 (ttm110) REVERT: B 448 TYR cc_start: 0.8738 (m-80) cc_final: 0.8461 (m-10) REVERT: B 544 GLU cc_start: 0.8207 (tp30) cc_final: 0.7995 (tp30) REVERT: B 607 ASN cc_start: 0.8225 (t0) cc_final: 0.7967 (t0) REVERT: B 615 GLU cc_start: 0.7777 (tm-30) cc_final: 0.7517 (tm-30) REVERT: B 646 TRP cc_start: 0.8372 (p90) cc_final: 0.8106 (p90) REVERT: B 711 GLN cc_start: 0.7953 (pm20) cc_final: 0.7556 (mp10) REVERT: B 772 GLU cc_start: 0.8064 (mp0) cc_final: 0.7686 (mp0) REVERT: B 792 ILE cc_start: 0.9158 (tt) cc_final: 0.8885 (pt) REVERT: B 805 GLU cc_start: 0.8141 (tp30) cc_final: 0.7875 (tm-30) REVERT: B 842 ASN cc_start: 0.8872 (m-40) cc_final: 0.8460 (m-40) REVERT: B 848 ASP cc_start: 0.8669 (m-30) cc_final: 0.8268 (m-30) REVERT: B 855 ASP cc_start: 0.8268 (m-30) cc_final: 0.7966 (m-30) REVERT: B 867 GLN cc_start: 0.7618 (mm110) cc_final: 0.7401 (mm-40) REVERT: B 874 ASN cc_start: 0.8596 (m-40) cc_final: 0.8005 (p0) REVERT: B 889 LYS cc_start: 0.9107 (ttpt) cc_final: 0.8774 (ttmm) REVERT: B 916 LYS cc_start: 0.8620 (pttt) cc_final: 0.8241 (ptmm) REVERT: B 924 GLU cc_start: 0.8533 (OUTLIER) cc_final: 0.8232 (tm-30) REVERT: B 999 ASP cc_start: 0.8478 (t0) cc_final: 0.8054 (t0) REVERT: B 1003 LYS cc_start: 0.9118 (mtpt) cc_final: 0.8702 (mtpp) REVERT: B 1004 ASN cc_start: 0.8418 (m-40) cc_final: 0.6651 (t0) REVERT: B 1006 LYS cc_start: 0.9261 (mmmm) cc_final: 0.8899 (mmmm) REVERT: B 1010 THR cc_start: 0.9179 (m) cc_final: 0.8881 (p) REVERT: B 1045 ASN cc_start: 0.9095 (t0) cc_final: 0.8878 (t0) REVERT: B 1054 LYS cc_start: 0.9090 (mttt) cc_final: 0.8784 (mmmm) REVERT: B 1075 GLN cc_start: 0.8487 (mm-40) cc_final: 0.7778 (mm-40) REVERT: B 1079 ASP cc_start: 0.8682 (m-30) cc_final: 0.8386 (m-30) REVERT: B 1095 GLN cc_start: 0.8632 (tm-30) cc_final: 0.7558 (tm-30) REVERT: B 1099 ASP cc_start: 0.8843 (m-30) cc_final: 0.7937 (m-30) REVERT: B 1189 MET cc_start: 0.8428 (mtt) cc_final: 0.8123 (mtt) REVERT: B 1199 GLU cc_start: 0.8089 (mm-30) cc_final: 0.7876 (mm-30) REVERT: B 1208 PHE cc_start: 0.9115 (m-10) cc_final: 0.8769 (m-80) REVERT: B 1216 PHE cc_start: 0.7858 (m-10) cc_final: 0.7412 (m-80) REVERT: C 18 PHE cc_start: 0.7969 (t80) cc_final: 0.7482 (t80) REVERT: C 53 ASP cc_start: 0.8426 (m-30) cc_final: 0.7988 (m-30) REVERT: C 84 LYS cc_start: 0.8748 (mmmm) cc_final: 0.8238 (mmmt) REVERT: C 92 LYS cc_start: 0.9157 (mttt) cc_final: 0.8748 (mtpp) REVERT: C 140 GLN cc_start: 0.7913 (tm-30) cc_final: 0.7529 (tm-30) REVERT: C 262 SER cc_start: 0.8111 (t) cc_final: 0.7749 (p) REVERT: C 288 SER cc_start: 0.8888 (m) cc_final: 0.8387 (t) REVERT: C 289 GLU cc_start: 0.8735 (mt-10) cc_final: 0.8439 (tm-30) REVERT: C 293 LYS cc_start: 0.8979 (ttpt) cc_final: 0.8693 (ttpt) REVERT: C 330 ASP cc_start: 0.8280 (p0) cc_final: 0.7999 (p0) REVERT: C 331 LYS cc_start: 0.9022 (mttt) cc_final: 0.8421 (mtpp) REVERT: C 384 LYS cc_start: 0.8891 (pttt) cc_final: 0.8551 (pttt) REVERT: C 397 ARG cc_start: 0.8825 (mmt180) cc_final: 0.8431 (mmm-85) REVERT: C 437 ASN cc_start: 0.8724 (t0) cc_final: 0.8359 (t0) REVERT: C 439 TYR cc_start: 0.8456 (t80) cc_final: 0.8134 (t80) REVERT: C 460 VAL cc_start: 0.9053 (t) cc_final: 0.8774 (p) REVERT: C 481 PHE cc_start: 0.6730 (t80) cc_final: 0.6423 (t80) REVERT: C 500 ASN cc_start: 0.7747 (m-40) cc_final: 0.7484 (m-40) REVERT: C 579 TYR cc_start: 0.8604 (p90) cc_final: 0.8240 (p90) REVERT: C 580 ASP cc_start: 0.8208 (t0) cc_final: 0.7976 (t0) REVERT: C 587 ARG cc_start: 0.8492 (mtp85) cc_final: 0.8173 (ttt90) REVERT: C 632 GLN cc_start: 0.8739 (pt0) cc_final: 0.8424 (pp30) REVERT: C 678 ARG cc_start: 0.7377 (ttm-80) cc_final: 0.7089 (ttm170) REVERT: C 704 ASN cc_start: 0.7373 (p0) cc_final: 0.7092 (p0) REVERT: C 772 GLU cc_start: 0.8038 (mp0) cc_final: 0.7560 (mp0) REVERT: C 803 GLN cc_start: 0.8312 (tp-100) cc_final: 0.7803 (tp-100) REVERT: C 832 LEU cc_start: 0.9152 (mt) cc_final: 0.8824 (mm) REVERT: C 842 ASN cc_start: 0.8832 (m-40) cc_final: 0.8589 (m-40) REVERT: C 848 ASP cc_start: 0.8670 (m-30) cc_final: 0.8283 (m-30) REVERT: C 873 SER cc_start: 0.8888 (m) cc_final: 0.8661 (p) REVERT: C 874 ASN cc_start: 0.8710 (m-40) cc_final: 0.8074 (p0) REVERT: C 882 ASP cc_start: 0.7682 (m-30) cc_final: 0.7451 (m-30) REVERT: C 888 PHE cc_start: 0.8368 (m-10) cc_final: 0.8026 (m-10) REVERT: C 889 LYS cc_start: 0.9250 (ttpt) cc_final: 0.8954 (ttpp) REVERT: C 909 ASP cc_start: 0.8559 (m-30) cc_final: 0.8005 (m-30) REVERT: C 998 MET cc_start: 0.8999 (tpp) cc_final: 0.8404 (tpp) REVERT: C 999 ASP cc_start: 0.8271 (t70) cc_final: 0.7785 (t0) REVERT: C 1010 THR cc_start: 0.9115 (m) cc_final: 0.8744 (p) REVERT: C 1045 ASN cc_start: 0.9279 (t0) cc_final: 0.9063 (t0) REVERT: C 1058 ILE cc_start: 0.9481 (OUTLIER) cc_final: 0.9250 (pt) REVERT: C 1075 GLN cc_start: 0.8519 (mm-40) cc_final: 0.7646 (mm-40) REVERT: C 1079 ASP cc_start: 0.8652 (m-30) cc_final: 0.8298 (m-30) REVERT: C 1095 GLN cc_start: 0.8652 (tm-30) cc_final: 0.7575 (tm-30) REVERT: C 1099 ASP cc_start: 0.8838 (m-30) cc_final: 0.7542 (m-30) REVERT: C 1104 LYS cc_start: 0.9011 (tptt) cc_final: 0.8796 (tptp) REVERT: C 1105 LEU cc_start: 0.9043 (mt) cc_final: 0.8750 (tt) REVERT: C 1112 GLU cc_start: 0.8699 (tp30) cc_final: 0.8293 (tp30) REVERT: C 1126 ASN cc_start: 0.9052 (m-40) cc_final: 0.8609 (t0) REVERT: C 1199 GLU cc_start: 0.8147 (mm-30) cc_final: 0.7909 (mm-30) REVERT: C 1216 PHE cc_start: 0.7614 (m-10) cc_final: 0.7408 (m-80) outliers start: 38 outliers final: 14 residues processed: 561 average time/residue: 0.1920 time to fit residues: 169.5166 Evaluate side-chains 489 residues out of total 3216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 473 time to evaluate : 1.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 405 SER Chi-restraints excluded: chain A residue 820 LEU Chi-restraints excluded: chain A residue 839 PHE Chi-restraints excluded: chain A residue 1003 LYS Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 321 ILE Chi-restraints excluded: chain B residue 785 SER Chi-restraints excluded: chain B residue 909 ASP Chi-restraints excluded: chain B residue 924 GLU Chi-restraints excluded: chain C residue 321 ILE Chi-restraints excluded: chain C residue 405 SER Chi-restraints excluded: chain C residue 781 ASP Chi-restraints excluded: chain C residue 1058 ILE 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 113 optimal weight: 2.9990 chunk 277 optimal weight: 4.9990 chunk 39 optimal weight: 7.9990 chunk 259 optimal weight: 4.9990 chunk 197 optimal weight: 2.9990 chunk 321 optimal weight: 4.9990 chunk 128 optimal weight: 6.9990 chunk 338 optimal weight: 1.9990 chunk 55 optimal weight: 8.9990 chunk 96 optimal weight: 0.0770 chunk 266 optimal weight: 0.9980 overall best weight: 1.8144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 607 ASN B 858 GLN C 364 HIS ** C 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 867 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.102117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.080815 restraints weight = 63913.541| |-----------------------------------------------------------------------------| r_work (start): 0.3111 rms_B_bonded: 3.86 r_work: 0.2932 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.2882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 30177 Z= 0.209 Angle : 0.618 10.775 41256 Z= 0.319 Chirality : 0.044 0.244 4842 Planarity : 0.004 0.060 5124 Dihedral : 4.563 23.746 3867 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 1.27 % Allowed : 12.00 % Favored : 86.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.62 (0.14), residues: 3573 helix: 1.69 (0.19), residues: 771 sheet: -0.15 (0.19), residues: 753 loop : -1.40 (0.13), residues: 2049 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 464 TYR 0.032 0.002 TYR C 713 PHE 0.019 0.001 PHE A 907 TRP 0.025 0.001 TRP B 257 HIS 0.006 0.001 HIS A 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00455 / 0.21 (30018) covalent geometry : angle 0.60141 / 0.31 (40851) SS BOND : bond 0.00449 / 0.28 ( 72) SS BOND : angle 1.34181 / 0.94 ( 144) hydrogen bonds : bond 0.04791 / 3.14 ( 1016) hydrogen bonds : angle 5.19532 / 3.47 ( 3102) link_BETA1-4 : bond 0.00510 / 0.30 ( 30) link_BETA1-4 : angle 1.60761 / 1.11 ( 90) link_NAG-ASN : bond 0.00361 / 0.20 ( 57) link_NAG-ASN : angle 1.69869 / 1.15 ( 171) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7146 Ramachandran restraints generated. 3573 Oldfield, 0 Emsley, 3573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7146 Ramachandran restraints generated. 3573 Oldfield, 0 Emsley, 3573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 543 residues out of total 3216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 502 time to evaluate : 1.079 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 SER cc_start: 0.8438 (m) cc_final: 0.8225 (t) REVERT: A 112 TYR cc_start: 0.8424 (m-80) cc_final: 0.8172 (m-80) REVERT: A 114 ASN cc_start: 0.9007 (m-40) cc_final: 0.8797 (m-40) REVERT: A 140 GLN cc_start: 0.7740 (tm-30) cc_final: 0.6794 (tm-30) REVERT: A 142 HIS cc_start: 0.8433 (m90) cc_final: 0.7118 (m90) REVERT: A 175 HIS cc_start: 0.8551 (p-80) cc_final: 0.8248 (p-80) REVERT: A 289 GLU cc_start: 0.8745 (mt-10) cc_final: 0.8314 (mm-30) REVERT: A 305 ASP cc_start: 0.8132 (p0) cc_final: 0.7731 (p0) REVERT: A 326 ASP cc_start: 0.7539 (t70) cc_final: 0.7136 (t0) REVERT: A 331 LYS cc_start: 0.8978 (mtpt) cc_final: 0.8683 (mtpp) REVERT: A 376 SER cc_start: 0.9091 (m) cc_final: 0.8690 (p) REVERT: A 384 LYS cc_start: 0.8815 (pttt) cc_final: 0.8576 (pttt) REVERT: A 397 ARG cc_start: 0.8831 (mmt180) cc_final: 0.8590 (mmm-85) REVERT: A 437 ASN cc_start: 0.8945 (t0) cc_final: 0.8545 (t0) REVERT: A 446 ARG cc_start: 0.8746 (ttm-80) cc_final: 0.7796 (mtm-85) REVERT: A 535 GLN cc_start: 0.8349 (pt0) cc_final: 0.8129 (pt0) REVERT: A 553 GLU cc_start: 0.8314 (mm-30) cc_final: 0.7890 (mm-30) REVERT: A 618 THR cc_start: 0.9258 (OUTLIER) cc_final: 0.9029 (m) REVERT: A 704 ASN cc_start: 0.7832 (p0) cc_final: 0.7609 (p0) REVERT: A 711 GLN cc_start: 0.8269 (pm20) cc_final: 0.7781 (mp10) REVERT: A 717 TYR cc_start: 0.8985 (t80) cc_final: 0.8664 (t80) REVERT: A 772 GLU cc_start: 0.8376 (mp0) cc_final: 0.8058 (mp0) REVERT: A 803 GLN cc_start: 0.8448 (tp40) cc_final: 0.8180 (tp-100) REVERT: A 842 ASN cc_start: 0.8928 (m-40) cc_final: 0.8659 (m-40) REVERT: A 844 ASN cc_start: 0.8951 (m-40) cc_final: 0.8026 (m-40) REVERT: A 848 ASP cc_start: 0.8543 (m-30) cc_final: 0.8122 (m-30) REVERT: A 858 GLN cc_start: 0.8724 (mm110) cc_final: 0.8393 (mm110) REVERT: A 874 ASN cc_start: 0.8818 (m-40) cc_final: 0.8358 (p0) REVERT: A 889 LYS cc_start: 0.9059 (ttpt) cc_final: 0.8732 (ttpp) REVERT: A 909 ASP cc_start: 0.8604 (m-30) cc_final: 0.8141 (m-30) REVERT: A 956 GLU cc_start: 0.7540 (pm20) cc_final: 0.7333 (pm20) REVERT: A 999 ASP cc_start: 0.8564 (t0) cc_final: 0.8079 (t0) REVERT: A 1054 LYS cc_start: 0.9170 (mttt) cc_final: 0.8958 (mmtm) REVERT: A 1095 GLN cc_start: 0.8725 (tm-30) cc_final: 0.8174 (tm-30) REVERT: A 1112 GLU cc_start: 0.8806 (tt0) cc_final: 0.8420 (tp30) REVERT: B 18 PHE cc_start: 0.8063 (t80) cc_final: 0.7767 (t80) REVERT: B 69 LYS cc_start: 0.9166 (tmtt) cc_final: 0.8878 (tmmt) REVERT: B 88 LEU cc_start: 0.9180 (mp) cc_final: 0.8848 (tp) REVERT: B 111 LEU cc_start: 0.8809 (mm) cc_final: 0.8350 (mt) REVERT: B 121 PHE cc_start: 0.8888 (p90) cc_final: 0.8493 (p90) REVERT: B 146 LEU cc_start: 0.8775 (mp) cc_final: 0.8441 (mp) REVERT: B 175 HIS cc_start: 0.8758 (p-80) cc_final: 0.8241 (p-80) REVERT: B 273 ARG cc_start: 0.8588 (OUTLIER) cc_final: 0.8257 (mtp-110) REVERT: B 326 ASP cc_start: 0.7455 (t70) cc_final: 0.6612 (t0) REVERT: B 328 ASP cc_start: 0.8093 (m-30) cc_final: 0.7590 (m-30) REVERT: B 331 LYS cc_start: 0.9080 (mttt) cc_final: 0.8638 (mtpp) REVERT: B 384 LYS cc_start: 0.8862 (pttt) cc_final: 0.8472 (pttp) REVERT: B 397 ARG cc_start: 0.8807 (mmt180) cc_final: 0.8231 (mmm-85) REVERT: B 400 ASP cc_start: 0.8391 (m-30) cc_final: 0.7839 (m-30) REVERT: B 411 SER cc_start: 0.9368 (t) cc_final: 0.8996 (p) REVERT: B 417 ASP cc_start: 0.8279 (t0) cc_final: 0.7997 (t0) REVERT: B 446 ARG cc_start: 0.8817 (ttm110) cc_final: 0.8530 (ttm110) REVERT: B 448 TYR cc_start: 0.8801 (m-80) cc_final: 0.8491 (m-10) REVERT: B 450 PHE cc_start: 0.8443 (t80) cc_final: 0.8163 (t80) REVERT: B 607 ASN cc_start: 0.8137 (t0) cc_final: 0.7710 (t0) REVERT: B 704 ASN cc_start: 0.7311 (p0) cc_final: 0.7060 (p0) REVERT: B 711 GLN cc_start: 0.8093 (pm20) cc_final: 0.7647 (mp10) REVERT: B 772 GLU cc_start: 0.8175 (mp0) cc_final: 0.7974 (mp0) REVERT: B 781 ASP cc_start: 0.8077 (t0) cc_final: 0.7776 (t0) REVERT: B 792 ILE cc_start: 0.9138 (tt) cc_final: 0.8799 (pt) REVERT: B 832 LEU cc_start: 0.8903 (mt) cc_final: 0.8402 (mm) REVERT: B 842 ASN cc_start: 0.8917 (m-40) cc_final: 0.8518 (m-40) REVERT: B 848 ASP cc_start: 0.8751 (m-30) cc_final: 0.8245 (m-30) REVERT: B 849 GLU cc_start: 0.8368 (pp20) cc_final: 0.8155 (tm-30) REVERT: B 855 ASP cc_start: 0.8331 (m-30) cc_final: 0.8038 (m-30) REVERT: B 874 ASN cc_start: 0.8758 (m-40) cc_final: 0.8164 (p0) REVERT: B 887 ASN cc_start: 0.8866 (OUTLIER) cc_final: 0.8655 (t0) REVERT: B 914 LYS cc_start: 0.9280 (mmmt) cc_final: 0.9059 (mmmm) REVERT: B 916 LYS cc_start: 0.8688 (pttt) cc_final: 0.8318 (ptmm) REVERT: B 924 GLU cc_start: 0.8568 (tm-30) cc_final: 0.8182 (tm-30) REVERT: B 999 ASP cc_start: 0.8491 (t0) cc_final: 0.8236 (t0) REVERT: B 1006 LYS cc_start: 0.9272 (mmmm) cc_final: 0.9002 (mmmm) REVERT: B 1010 THR cc_start: 0.9220 (m) cc_final: 0.8942 (p) REVERT: B 1042 GLN cc_start: 0.9052 (mt0) cc_final: 0.8708 (tm-30) REVERT: B 1054 LYS cc_start: 0.9125 (mttt) cc_final: 0.8821 (mmmm) REVERT: B 1070 ASP cc_start: 0.7440 (p0) cc_final: 0.7225 (p0) REVERT: B 1075 GLN cc_start: 0.8610 (mm-40) cc_final: 0.7987 (mm-40) REVERT: B 1079 ASP cc_start: 0.8692 (m-30) cc_final: 0.8398 (m-30) REVERT: B 1095 GLN cc_start: 0.8682 (tm-30) cc_final: 0.7650 (tm-30) REVERT: B 1099 ASP cc_start: 0.8808 (m-30) cc_final: 0.7923 (m-30) REVERT: B 1112 GLU cc_start: 0.8670 (tp30) cc_final: 0.8410 (tp30) REVERT: B 1177 LYS cc_start: 0.8445 (mmmm) cc_final: 0.8104 (mmmt) REVERT: B 1199 GLU cc_start: 0.8117 (mm-30) cc_final: 0.7892 (mm-30) REVERT: C 18 PHE cc_start: 0.8064 (t80) cc_final: 0.7560 (t80) REVERT: C 52 LEU cc_start: 0.8751 (pt) cc_final: 0.8471 (pp) REVERT: C 53 ASP cc_start: 0.8484 (m-30) cc_final: 0.7992 (m-30) REVERT: C 84 LYS cc_start: 0.8730 (mmmm) cc_final: 0.8452 (mmmt) REVERT: C 92 LYS cc_start: 0.9153 (mttt) cc_final: 0.8770 (mtpp) REVERT: C 147 GLU cc_start: 0.8296 (pp20) cc_final: 0.7991 (pp20) REVERT: C 205 GLU cc_start: 0.8243 (tp30) cc_final: 0.7556 (tp30) REVERT: C 206 ARG cc_start: 0.8839 (ptp-110) cc_final: 0.8293 (ptp90) REVERT: C 218 MET cc_start: 0.8693 (OUTLIER) cc_final: 0.8465 (mtp) REVERT: C 262 SER cc_start: 0.8245 (t) cc_final: 0.7854 (p) REVERT: C 288 SER cc_start: 0.8921 (m) cc_final: 0.8471 (t) REVERT: C 289 GLU cc_start: 0.8753 (mt-10) cc_final: 0.8486 (tm-30) REVERT: C 293 LYS cc_start: 0.9001 (ttpt) cc_final: 0.8751 (ttpt) REVERT: C 330 ASP cc_start: 0.8306 (p0) cc_final: 0.7953 (p0) REVERT: C 331 LYS cc_start: 0.9064 (mttt) cc_final: 0.8464 (mtpp) REVERT: C 384 LYS cc_start: 0.8927 (pttt) cc_final: 0.8467 (pttt) REVERT: C 397 ARG cc_start: 0.8805 (mmt180) cc_final: 0.8501 (mmm-85) REVERT: C 437 ASN cc_start: 0.8726 (t0) cc_final: 0.8393 (t0) REVERT: C 439 TYR cc_start: 0.8242 (t80) cc_final: 0.7981 (t80) REVERT: C 446 ARG cc_start: 0.8673 (tpp80) cc_final: 0.7891 (mtm-85) REVERT: C 460 VAL cc_start: 0.9169 (t) cc_final: 0.8847 (p) REVERT: C 481 PHE cc_start: 0.6814 (t80) cc_final: 0.6517 (t80) REVERT: C 500 ASN cc_start: 0.7790 (m-40) cc_final: 0.7490 (m-40) REVERT: C 574 PHE cc_start: 0.8613 (m-80) cc_final: 0.8273 (m-80) REVERT: C 704 ASN cc_start: 0.7352 (p0) cc_final: 0.7069 (p0) REVERT: C 772 GLU cc_start: 0.8134 (mp0) cc_final: 0.7908 (mp0) REVERT: C 832 LEU cc_start: 0.9117 (mt) cc_final: 0.8689 (mm) REVERT: C 842 ASN cc_start: 0.8802 (m-40) cc_final: 0.8540 (m-40) REVERT: C 848 ASP cc_start: 0.8731 (m-30) cc_final: 0.8176 (m-30) REVERT: C 873 SER cc_start: 0.8965 (m) cc_final: 0.8713 (p) REVERT: C 874 ASN cc_start: 0.8732 (m-40) cc_final: 0.8153 (p0) REVERT: C 889 LYS cc_start: 0.9268 (ttpt) cc_final: 0.8956 (ttpp) REVERT: C 909 ASP cc_start: 0.8448 (m-30) cc_final: 0.7911 (m-30) REVERT: C 998 MET cc_start: 0.9045 (tpp) cc_final: 0.8113 (tpp) REVERT: C 999 ASP cc_start: 0.8249 (t70) cc_final: 0.7886 (t0) REVERT: C 1045 ASN cc_start: 0.9282 (t0) cc_final: 0.9053 (t0) REVERT: C 1075 GLN cc_start: 0.8617 (mm-40) cc_final: 0.7712 (mm-40) REVERT: C 1079 ASP cc_start: 0.8600 (m-30) cc_final: 0.8224 (m-30) REVERT: C 1095 GLN cc_start: 0.8707 (tm-30) cc_final: 0.7586 (tm-30) REVERT: C 1099 ASP cc_start: 0.8814 (m-30) cc_final: 0.7619 (m-30) REVERT: C 1105 LEU cc_start: 0.9024 (mt) cc_final: 0.8818 (tt) REVERT: C 1112 GLU cc_start: 0.8683 (tp30) cc_final: 0.8263 (tp30) REVERT: C 1126 ASN cc_start: 0.9032 (m-40) cc_final: 0.8430 (t0) REVERT: C 1199 GLU cc_start: 0.8115 (mm-30) cc_final: 0.7803 (mm-30) REVERT: C 1209 MET cc_start: 0.8284 (mpp) cc_final: 0.7583 (mpp) REVERT: C 1216 PHE cc_start: 0.7989 (m-10) cc_final: 0.7713 (m-80) outliers start: 41 outliers final: 14 residues processed: 521 average time/residue: 0.1912 time to fit residues: 155.8671 Evaluate side-chains 482 residues out of total 3216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 464 time to evaluate : 1.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 405 SER Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 780 ASN Chi-restraints excluded: chain A residue 1007 LEU Chi-restraints excluded: chain A residue 1102 LEU Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 273 ARG Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 405 SER Chi-restraints excluded: chain B residue 887 ASN Chi-restraints excluded: chain C residue 69 LYS Chi-restraints excluded: chain C residue 218 MET Chi-restraints excluded: chain C residue 405 SER Chi-restraints excluded: chain C residue 1172 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 46 optimal weight: 0.9990 chunk 209 optimal weight: 1.9990 chunk 173 optimal weight: 9.9990 chunk 51 optimal weight: 0.0040 chunk 207 optimal weight: 0.9980 chunk 256 optimal weight: 3.9990 chunk 42 optimal weight: 5.9990 chunk 269 optimal weight: 3.9990 chunk 88 optimal weight: 2.9990 chunk 238 optimal weight: 0.5980 chunk 84 optimal weight: 0.8980 overall best weight: 0.6994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 364 HIS ** B 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 600 ASN B 858 GLN C 364 HIS ** C 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 958 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.105471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.084873 restraints weight = 63328.226| |-----------------------------------------------------------------------------| r_work (start): 0.3153 rms_B_bonded: 3.79 r_work: 0.2970 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.3093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 30177 Z= 0.117 Angle : 0.569 10.297 41256 Z= 0.290 Chirality : 0.043 0.248 4842 Planarity : 0.004 0.057 5124 Dihedral : 4.320 24.856 3867 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 1.24 % Allowed : 13.84 % Favored : 84.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.46 (0.14), residues: 3573 helix: 1.89 (0.19), residues: 771 sheet: -0.12 (0.18), residues: 774 loop : -1.31 (0.13), residues: 2028 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 587 TYR 0.030 0.001 TYR C 713 PHE 0.028 0.001 PHE C 888 TRP 0.010 0.001 TRP C 174 HIS 0.004 0.001 HIS B 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.12 (30018) covalent geometry : angle 0.55364 / 0.29 (40851) SS BOND : bond 0.00330 / 0.20 ( 72) SS BOND : angle 1.30170 / 0.87 ( 144) hydrogen bonds : bond 0.04006 / 2.63 ( 1016) hydrogen bonds : angle 4.96584 / 3.32 ( 3102) link_BETA1-4 : bond 0.00409 / 0.26 ( 30) link_BETA1-4 : angle 1.51537 / 1.04 ( 90) link_NAG-ASN : bond 0.00314 / 0.20 ( 57) link_NAG-ASN : angle 1.51930 / 1.01 ( 171) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7146 Ramachandran restraints generated. 3573 Oldfield, 0 Emsley, 3573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7146 Ramachandran restraints generated. 3573 Oldfield, 0 Emsley, 3573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 533 residues out of total 3216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 493 time to evaluate : 1.096 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 SER cc_start: 0.8448 (m) cc_final: 0.8219 (t) REVERT: A 112 TYR cc_start: 0.8420 (m-80) cc_final: 0.8181 (m-80) REVERT: A 114 ASN cc_start: 0.9060 (m-40) cc_final: 0.8837 (m-40) REVERT: A 137 ILE cc_start: 0.9002 (mt) cc_final: 0.8793 (tt) REVERT: A 140 GLN cc_start: 0.7692 (tm-30) cc_final: 0.6739 (tm-30) REVERT: A 142 HIS cc_start: 0.8426 (m90) cc_final: 0.7069 (m90) REVERT: A 175 HIS cc_start: 0.8558 (p-80) cc_final: 0.8261 (p-80) REVERT: A 186 LYS cc_start: 0.8643 (ttpp) cc_final: 0.8440 (ptpp) REVERT: A 288 SER cc_start: 0.8767 (m) cc_final: 0.8402 (p) REVERT: A 305 ASP cc_start: 0.8180 (p0) cc_final: 0.7795 (p0) REVERT: A 331 LYS cc_start: 0.8967 (mtpt) cc_final: 0.8668 (mtpp) REVERT: A 376 SER cc_start: 0.9067 (m) cc_final: 0.8657 (p) REVERT: A 384 LYS cc_start: 0.8794 (pttt) cc_final: 0.8512 (pttt) REVERT: A 397 ARG cc_start: 0.8814 (mmt180) cc_final: 0.8576 (mmm-85) REVERT: A 417 ASP cc_start: 0.8395 (t0) cc_final: 0.8053 (t0) REVERT: A 437 ASN cc_start: 0.8893 (t0) cc_final: 0.8487 (t0) REVERT: A 535 GLN cc_start: 0.8322 (pt0) cc_final: 0.8106 (pt0) REVERT: A 553 GLU cc_start: 0.8314 (mm-30) cc_final: 0.7900 (mm-30) REVERT: A 711 GLN cc_start: 0.8312 (pm20) cc_final: 0.7845 (mp10) REVERT: A 717 TYR cc_start: 0.8982 (t80) cc_final: 0.8646 (t80) REVERT: A 772 GLU cc_start: 0.8401 (mp0) cc_final: 0.7953 (mp0) REVERT: A 784 GLU cc_start: 0.8342 (mm-30) cc_final: 0.8109 (mp0) REVERT: A 792 ILE cc_start: 0.9181 (tp) cc_final: 0.8770 (pt) REVERT: A 803 GLN cc_start: 0.8493 (tp40) cc_final: 0.7824 (tp-100) REVERT: A 804 GLU cc_start: 0.7944 (pp20) cc_final: 0.7530 (pm20) REVERT: A 842 ASN cc_start: 0.8933 (m-40) cc_final: 0.8667 (m-40) REVERT: A 844 ASN cc_start: 0.8901 (m-40) cc_final: 0.7979 (m-40) REVERT: A 848 ASP cc_start: 0.8536 (m-30) cc_final: 0.8095 (m-30) REVERT: A 858 GLN cc_start: 0.8720 (mm110) cc_final: 0.8326 (mm110) REVERT: A 874 ASN cc_start: 0.8786 (m-40) cc_final: 0.8361 (p0) REVERT: A 889 LYS cc_start: 0.9036 (ttpt) cc_final: 0.8712 (ttpp) REVERT: A 909 ASP cc_start: 0.8507 (m-30) cc_final: 0.7821 (m-30) REVERT: A 956 GLU cc_start: 0.7504 (pm20) cc_final: 0.7293 (pm20) REVERT: A 999 ASP cc_start: 0.8587 (t0) cc_final: 0.8075 (t0) REVERT: A 1054 LYS cc_start: 0.9135 (mttt) cc_final: 0.8880 (mmmm) REVERT: A 1079 ASP cc_start: 0.8706 (m-30) cc_final: 0.8235 (m-30) REVERT: A 1095 GLN cc_start: 0.8679 (tm-30) cc_final: 0.7214 (tm-30) REVERT: A 1099 ASP cc_start: 0.8792 (m-30) cc_final: 0.7484 (m-30) REVERT: A 1112 GLU cc_start: 0.8794 (tt0) cc_final: 0.8402 (tp30) REVERT: A 1126 ASN cc_start: 0.8827 (m-40) cc_final: 0.8255 (t0) REVERT: A 1153 LYS cc_start: 0.8796 (tppt) cc_final: 0.8555 (tptp) REVERT: A 1177 LYS cc_start: 0.8541 (tppt) cc_final: 0.7988 (mptt) REVERT: B 18 PHE cc_start: 0.8004 (t80) cc_final: 0.7758 (t80) REVERT: B 69 LYS cc_start: 0.9183 (tmtt) cc_final: 0.8858 (tmmt) REVERT: B 88 LEU cc_start: 0.9131 (mp) cc_final: 0.8799 (tp) REVERT: B 111 LEU cc_start: 0.8851 (mm) cc_final: 0.8337 (mt) REVERT: B 131 ILE cc_start: 0.9009 (mp) cc_final: 0.8790 (tp) REVERT: B 175 HIS cc_start: 0.8757 (p-80) cc_final: 0.8269 (p-80) REVERT: B 273 ARG cc_start: 0.8609 (OUTLIER) cc_final: 0.8307 (mtp-110) REVERT: B 326 ASP cc_start: 0.7417 (t70) cc_final: 0.6762 (t70) REVERT: B 328 ASP cc_start: 0.8106 (m-30) cc_final: 0.7600 (m-30) REVERT: B 331 LYS cc_start: 0.9084 (mttt) cc_final: 0.8649 (mtpp) REVERT: B 384 LYS cc_start: 0.8820 (pttt) cc_final: 0.8454 (pttp) REVERT: B 397 ARG cc_start: 0.8790 (mmt180) cc_final: 0.8118 (mmm-85) REVERT: B 400 ASP cc_start: 0.8498 (m-30) cc_final: 0.7873 (m-30) REVERT: B 411 SER cc_start: 0.9369 (t) cc_final: 0.8972 (p) REVERT: B 417 ASP cc_start: 0.8295 (t0) cc_final: 0.7971 (t0) REVERT: B 446 ARG cc_start: 0.8759 (ttm110) cc_final: 0.8494 (ttm110) REVERT: B 448 TYR cc_start: 0.8813 (m-80) cc_final: 0.8529 (m-10) REVERT: B 450 PHE cc_start: 0.8368 (t80) cc_final: 0.8118 (t80) REVERT: B 587 ARG cc_start: 0.8270 (mtp85) cc_final: 0.8006 (mtp85) REVERT: B 607 ASN cc_start: 0.8199 (t0) cc_final: 0.7534 (t0) REVERT: B 711 GLN cc_start: 0.8133 (pm20) cc_final: 0.7709 (mp10) REVERT: B 772 GLU cc_start: 0.8176 (mp0) cc_final: 0.7925 (mp0) REVERT: B 781 ASP cc_start: 0.8070 (t0) cc_final: 0.7720 (t0) REVERT: B 792 ILE cc_start: 0.9169 (tt) cc_final: 0.8847 (pt) REVERT: B 832 LEU cc_start: 0.8919 (mt) cc_final: 0.8425 (mm) REVERT: B 842 ASN cc_start: 0.8867 (m-40) cc_final: 0.8474 (m-40) REVERT: B 848 ASP cc_start: 0.8700 (m-30) cc_final: 0.8222 (m-30) REVERT: B 849 GLU cc_start: 0.8375 (pp20) cc_final: 0.8172 (tm-30) REVERT: B 855 ASP cc_start: 0.8358 (m-30) cc_final: 0.8068 (m-30) REVERT: B 874 ASN cc_start: 0.8688 (m-40) cc_final: 0.8139 (p0) REVERT: B 889 LYS cc_start: 0.9081 (ttpt) cc_final: 0.8753 (ttmm) REVERT: B 914 LYS cc_start: 0.9239 (mmmt) cc_final: 0.9023 (mmmm) REVERT: B 916 LYS cc_start: 0.8727 (pttt) cc_final: 0.8354 (ptmm) REVERT: B 924 GLU cc_start: 0.8561 (OUTLIER) cc_final: 0.8259 (tm-30) REVERT: B 999 ASP cc_start: 0.8473 (t0) cc_final: 0.8180 (t0) REVERT: B 1006 LYS cc_start: 0.9256 (mmmm) cc_final: 0.9035 (mmmm) REVERT: B 1010 THR cc_start: 0.9200 (m) cc_final: 0.8913 (p) REVERT: B 1042 GLN cc_start: 0.9164 (OUTLIER) cc_final: 0.8748 (tm-30) REVERT: B 1054 LYS cc_start: 0.9120 (mttt) cc_final: 0.8793 (mmmm) REVERT: B 1070 ASP cc_start: 0.7348 (p0) cc_final: 0.7062 (p0) REVERT: B 1075 GLN cc_start: 0.8575 (mm-40) cc_final: 0.7868 (mm-40) REVERT: B 1079 ASP cc_start: 0.8688 (m-30) cc_final: 0.8373 (m-30) REVERT: B 1095 GLN cc_start: 0.8677 (tm-30) cc_final: 0.7363 (tm-30) REVERT: B 1099 ASP cc_start: 0.8849 (m-30) cc_final: 0.7647 (m-30) REVERT: B 1112 GLU cc_start: 0.8684 (tp30) cc_final: 0.8330 (tp30) REVERT: B 1177 LYS cc_start: 0.8463 (mmmm) cc_final: 0.8127 (mmmt) REVERT: B 1208 PHE cc_start: 0.9132 (m-80) cc_final: 0.8801 (m-80) REVERT: C 18 PHE cc_start: 0.8022 (t80) cc_final: 0.7403 (t80) REVERT: C 53 ASP cc_start: 0.8457 (m-30) cc_final: 0.8127 (m-30) REVERT: C 84 LYS cc_start: 0.8705 (mmmm) cc_final: 0.8420 (mmmt) REVERT: C 147 GLU cc_start: 0.8308 (pp20) cc_final: 0.8003 (pp20) REVERT: C 262 SER cc_start: 0.8237 (t) cc_final: 0.7831 (p) REVERT: C 288 SER cc_start: 0.8899 (m) cc_final: 0.8386 (t) REVERT: C 289 GLU cc_start: 0.8722 (mt-10) cc_final: 0.8452 (tm-30) REVERT: C 293 LYS cc_start: 0.9040 (ttpt) cc_final: 0.8755 (ttpt) REVERT: C 330 ASP cc_start: 0.8245 (p0) cc_final: 0.7863 (p0) REVERT: C 331 LYS cc_start: 0.9054 (mttt) cc_final: 0.8435 (mtpp) REVERT: C 384 LYS cc_start: 0.8884 (pttt) cc_final: 0.8530 (pttt) REVERT: C 397 ARG cc_start: 0.8844 (mmt180) cc_final: 0.8532 (mmm-85) REVERT: C 448 TYR cc_start: 0.8798 (m-80) cc_final: 0.8564 (m-80) REVERT: C 460 VAL cc_start: 0.9133 (t) cc_final: 0.8863 (p) REVERT: C 481 PHE cc_start: 0.6789 (t80) cc_final: 0.6478 (t80) REVERT: C 500 ASN cc_start: 0.7771 (m-40) cc_final: 0.7469 (m-40) REVERT: C 537 LYS cc_start: 0.8328 (tppt) cc_final: 0.8125 (tppt) REVERT: C 574 PHE cc_start: 0.8612 (m-80) cc_final: 0.8333 (m-80) REVERT: C 678 ARG cc_start: 0.7567 (ttm-80) cc_final: 0.7102 (ttm-80) REVERT: C 739 MET cc_start: 0.9134 (mmm) cc_final: 0.8810 (mmt) REVERT: C 772 GLU cc_start: 0.8186 (mp0) cc_final: 0.7907 (mp0) REVERT: C 792 ILE cc_start: 0.8985 (tp) cc_final: 0.8575 (pt) REVERT: C 832 LEU cc_start: 0.9146 (mt) cc_final: 0.8559 (mm) REVERT: C 842 ASN cc_start: 0.8792 (m-40) cc_final: 0.8449 (m-40) REVERT: C 848 ASP cc_start: 0.8713 (m-30) cc_final: 0.8304 (m-30) REVERT: C 874 ASN cc_start: 0.8748 (m-40) cc_final: 0.8162 (p0) REVERT: C 882 ASP cc_start: 0.8013 (OUTLIER) cc_final: 0.7756 (t70) REVERT: C 888 PHE cc_start: 0.8221 (m-80) cc_final: 0.7789 (m-80) REVERT: C 889 LYS cc_start: 0.9256 (ttpt) cc_final: 0.8949 (ttpp) REVERT: C 909 ASP cc_start: 0.8401 (m-30) cc_final: 0.8007 (m-30) REVERT: C 956 GLU cc_start: 0.7537 (mm-30) cc_final: 0.7282 (mm-30) REVERT: C 998 MET cc_start: 0.8878 (tpp) cc_final: 0.8284 (tpp) REVERT: C 999 ASP cc_start: 0.8248 (t70) cc_final: 0.7871 (t0) REVERT: C 1010 THR cc_start: 0.9112 (m) cc_final: 0.8739 (p) REVERT: C 1045 ASN cc_start: 0.9267 (t0) cc_final: 0.9034 (t0) REVERT: C 1075 GLN cc_start: 0.8540 (mm110) cc_final: 0.7597 (mm-40) REVERT: C 1079 ASP cc_start: 0.8570 (m-30) cc_final: 0.8167 (m-30) REVERT: C 1095 GLN cc_start: 0.8678 (tm-30) cc_final: 0.7556 (tm-30) REVERT: C 1099 ASP cc_start: 0.8820 (m-30) cc_final: 0.7600 (m-30) REVERT: C 1104 LYS cc_start: 0.8941 (tptp) cc_final: 0.8629 (ttmm) REVERT: C 1105 LEU cc_start: 0.8969 (mt) cc_final: 0.8753 (tt) REVERT: C 1112 GLU cc_start: 0.8705 (tp30) cc_final: 0.8240 (tp30) REVERT: C 1126 ASN cc_start: 0.9020 (m-40) cc_final: 0.8804 (t0) REVERT: C 1209 MET cc_start: 0.8317 (mpp) cc_final: 0.7625 (mpp) REVERT: C 1216 PHE cc_start: 0.7975 (m-10) cc_final: 0.7675 (m-80) outliers start: 40 outliers final: 16 residues processed: 515 average time/residue: 0.2115 time to fit residues: 169.6575 Evaluate side-chains 475 residues out of total 3216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 455 time to evaluate : 1.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 405 SER Chi-restraints excluded: chain A residue 820 LEU Chi-restraints excluded: chain A residue 1102 LEU Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 273 ARG Chi-restraints excluded: chain B residue 405 SER Chi-restraints excluded: chain B residue 924 GLU Chi-restraints excluded: chain B residue 940 CYS Chi-restraints excluded: chain B residue 1017 LEU Chi-restraints excluded: chain B residue 1032 LYS Chi-restraints excluded: chain B residue 1042 GLN Chi-restraints excluded: chain C residue 699 CYS Chi-restraints excluded: chain C residue 839 PHE Chi-restraints excluded: chain C residue 882 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 318 optimal weight: 4.9990 chunk 197 optimal weight: 3.9990 chunk 335 optimal weight: 4.9990 chunk 256 optimal weight: 4.9990 chunk 65 optimal weight: 5.9990 chunk 44 optimal weight: 4.9990 chunk 46 optimal weight: 0.3980 chunk 255 optimal weight: 3.9990 chunk 245 optimal weight: 4.9990 chunk 254 optimal weight: 4.9990 chunk 60 optimal weight: 5.9990 overall best weight: 3.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 945 ASN B 372 ASN ** B 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 858 GLN C 395 ASN ** C 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 586 ASN C 858 GLN C1184 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.097842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.076658 restraints weight = 64156.852| |-----------------------------------------------------------------------------| r_work (start): 0.3029 rms_B_bonded: 3.80 r_work: 0.2849 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.2849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 moved from start: 0.3874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.120 30177 Z= 0.396 Angle : 0.738 11.863 41256 Z= 0.379 Chirality : 0.048 0.257 4842 Planarity : 0.005 0.066 5124 Dihedral : 4.965 26.388 3867 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 2.24 % Allowed : 14.61 % Favored : 83.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.65 (0.14), residues: 3573 helix: 1.73 (0.20), residues: 759 sheet: -0.37 (0.18), residues: 789 loop : -1.35 (0.13), residues: 2025 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 587 TYR 0.032 0.002 TYR C 713 PHE 0.023 0.002 PHE B 591 TRP 0.014 0.002 TRP B 257 HIS 0.008 0.001 HIS B 234 Details of bonding type rmsd/Z covalent geometry : bond 0.00859 / 0.40 (30018) covalent geometry : angle 0.71891 / 0.37 (40851) SS BOND : bond 0.00699 / 0.48 ( 72) SS BOND : angle 1.74403 / 1.21 ( 144) hydrogen bonds : bond 0.05615 / 3.69 ( 1016) hydrogen bonds : angle 5.18225 / 3.45 ( 3102) link_BETA1-4 : bond 0.00341 / 0.22 ( 30) link_BETA1-4 : angle 1.74833 / 1.21 ( 90) link_NAG-ASN : bond 0.00575 / 0.34 ( 57) link_NAG-ASN : angle 1.92479 / 1.26 ( 171) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7146 Ramachandran restraints generated. 3573 Oldfield, 0 Emsley, 3573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7146 Ramachandran restraints generated. 3573 Oldfield, 0 Emsley, 3573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 570 residues out of total 3216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 498 time to evaluate : 1.149 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 SER cc_start: 0.8727 (m) cc_final: 0.8527 (t) REVERT: A 114 ASN cc_start: 0.9082 (m-40) cc_final: 0.8744 (p0) REVERT: A 140 GLN cc_start: 0.7789 (tm-30) cc_final: 0.7163 (tm-30) REVERT: A 331 LYS cc_start: 0.9152 (mtpt) cc_final: 0.8884 (mtpp) REVERT: A 336 PHE cc_start: 0.8368 (m-10) cc_final: 0.7912 (m-80) REVERT: A 376 SER cc_start: 0.9111 (m) cc_final: 0.8728 (p) REVERT: A 384 LYS cc_start: 0.8831 (pttt) cc_final: 0.8565 (pttt) REVERT: A 400 ASP cc_start: 0.8655 (m-30) cc_final: 0.8102 (t0) REVERT: A 417 ASP cc_start: 0.8450 (t0) cc_final: 0.8218 (t0) REVERT: A 446 ARG cc_start: 0.8784 (ttm-80) cc_final: 0.7976 (mtm-85) REVERT: A 553 GLU cc_start: 0.8474 (mm-30) cc_final: 0.7940 (mm-30) REVERT: A 618 THR cc_start: 0.9304 (OUTLIER) cc_final: 0.9039 (m) REVERT: A 711 GLN cc_start: 0.8379 (pm20) cc_final: 0.7837 (mp10) REVERT: A 717 TYR cc_start: 0.9048 (t80) cc_final: 0.8782 (t80) REVERT: A 772 GLU cc_start: 0.8444 (mp0) cc_final: 0.8047 (mp0) REVERT: A 781 ASP cc_start: 0.8292 (m-30) cc_final: 0.7412 (m-30) REVERT: A 803 GLN cc_start: 0.8519 (tp40) cc_final: 0.8161 (tp-100) REVERT: A 842 ASN cc_start: 0.8940 (m-40) cc_final: 0.8690 (m-40) REVERT: A 844 ASN cc_start: 0.9026 (m-40) cc_final: 0.8201 (m-40) REVERT: A 848 ASP cc_start: 0.8606 (m-30) cc_final: 0.8160 (m-30) REVERT: A 858 GLN cc_start: 0.8752 (mm110) cc_final: 0.8392 (mm110) REVERT: A 867 GLN cc_start: 0.8097 (mm-40) cc_final: 0.7847 (mm110) REVERT: A 873 SER cc_start: 0.8993 (m) cc_final: 0.8760 (p) REVERT: A 874 ASN cc_start: 0.8924 (m-40) cc_final: 0.8591 (p0) REVERT: A 889 LYS cc_start: 0.9132 (ttpt) cc_final: 0.8790 (ttpp) REVERT: A 909 ASP cc_start: 0.8670 (m-30) cc_final: 0.7876 (m-30) REVERT: A 956 GLU cc_start: 0.7636 (pm20) cc_final: 0.7330 (pm20) REVERT: A 999 ASP cc_start: 0.8708 (t0) cc_final: 0.8185 (t0) REVERT: A 1042 GLN cc_start: 0.8749 (tp-100) cc_final: 0.8489 (tp-100) REVERT: A 1054 LYS cc_start: 0.9151 (mttt) cc_final: 0.8759 (mtpp) REVERT: A 1064 GLU cc_start: 0.8494 (tp30) cc_final: 0.8134 (tp30) REVERT: A 1095 GLN cc_start: 0.8780 (tm-30) cc_final: 0.7358 (tm-30) REVERT: A 1099 ASP cc_start: 0.8805 (m-30) cc_final: 0.7622 (m-30) REVERT: A 1112 GLU cc_start: 0.8779 (tt0) cc_final: 0.8414 (tp30) REVERT: A 1153 LYS cc_start: 0.8808 (tppt) cc_final: 0.8602 (tptp) REVERT: A 1177 LYS cc_start: 0.8752 (tppt) cc_final: 0.8293 (tppt) REVERT: B 69 LYS cc_start: 0.9188 (tmtt) cc_final: 0.8852 (tmmt) REVERT: B 88 LEU cc_start: 0.9196 (mp) cc_final: 0.8833 (tp) REVERT: B 92 LYS cc_start: 0.9012 (mtmm) cc_final: 0.8776 (mtpp) REVERT: B 111 LEU cc_start: 0.8901 (mm) cc_final: 0.8402 (mt) REVERT: B 175 HIS cc_start: 0.8783 (p-80) cc_final: 0.8191 (p-80) REVERT: B 273 ARG cc_start: 0.8606 (mtp-110) cc_final: 0.8310 (mtp-110) REVERT: B 326 ASP cc_start: 0.7467 (t70) cc_final: 0.6942 (t70) REVERT: B 328 ASP cc_start: 0.8233 (m-30) cc_final: 0.7942 (m-30) REVERT: B 331 LYS cc_start: 0.9173 (mttt) cc_final: 0.8833 (ttmm) REVERT: B 397 ARG cc_start: 0.8941 (mmt180) cc_final: 0.8338 (mmm-85) REVERT: B 400 ASP cc_start: 0.8574 (m-30) cc_final: 0.8047 (m-30) REVERT: B 411 SER cc_start: 0.9362 (t) cc_final: 0.8971 (p) REVERT: B 417 ASP cc_start: 0.8472 (t0) cc_final: 0.8207 (t0) REVERT: B 448 TYR cc_start: 0.8921 (m-80) cc_final: 0.8573 (m-10) REVERT: B 450 PHE cc_start: 0.8515 (t80) cc_final: 0.8171 (t80) REVERT: B 587 ARG cc_start: 0.8409 (mtp85) cc_final: 0.7833 (ttm-80) REVERT: B 607 ASN cc_start: 0.8074 (t0) cc_final: 0.7340 (t0) REVERT: B 711 GLN cc_start: 0.8170 (pm20) cc_final: 0.7678 (mp10) REVERT: B 781 ASP cc_start: 0.8149 (t0) cc_final: 0.7646 (m-30) REVERT: B 792 ILE cc_start: 0.9151 (tt) cc_final: 0.8772 (pt) REVERT: B 832 LEU cc_start: 0.8928 (mt) cc_final: 0.8444 (mm) REVERT: B 842 ASN cc_start: 0.8909 (m-40) cc_final: 0.8589 (m-40) REVERT: B 848 ASP cc_start: 0.8765 (m-30) cc_final: 0.8307 (m-30) REVERT: B 855 ASP cc_start: 0.8326 (m-30) cc_final: 0.8071 (m-30) REVERT: B 873 SER cc_start: 0.8872 (m) cc_final: 0.8563 (p) REVERT: B 874 ASN cc_start: 0.9033 (m-40) cc_final: 0.8559 (p0) REVERT: B 889 LYS cc_start: 0.9231 (ttpt) cc_final: 0.8930 (ttmm) REVERT: B 914 LYS cc_start: 0.9258 (mmmt) cc_final: 0.8987 (mmmm) REVERT: B 916 LYS cc_start: 0.8834 (pttt) cc_final: 0.8501 (ptmm) REVERT: B 924 GLU cc_start: 0.8551 (OUTLIER) cc_final: 0.8317 (tm-30) REVERT: B 998 MET cc_start: 0.8819 (mmt) cc_final: 0.8512 (tpp) REVERT: B 999 ASP cc_start: 0.8530 (t0) cc_final: 0.8113 (t0) REVERT: B 1004 ASN cc_start: 0.8629 (m-40) cc_final: 0.8271 (m-40) REVERT: B 1042 GLN cc_start: 0.9098 (OUTLIER) cc_final: 0.8828 (tm-30) REVERT: B 1054 LYS cc_start: 0.9200 (mttt) cc_final: 0.8978 (mmmm) REVERT: B 1075 GLN cc_start: 0.8814 (mm-40) cc_final: 0.8088 (mm-40) REVERT: B 1079 ASP cc_start: 0.8763 (m-30) cc_final: 0.8435 (m-30) REVERT: B 1095 GLN cc_start: 0.8799 (tm-30) cc_final: 0.7737 (tm-30) REVERT: B 1099 ASP cc_start: 0.8872 (m-30) cc_final: 0.7545 (m-30) REVERT: B 1112 GLU cc_start: 0.8725 (tp30) cc_final: 0.8386 (tp30) REVERT: B 1158 LYS cc_start: 0.8466 (tttm) cc_final: 0.8189 (tttt) REVERT: C 15 ILE cc_start: 0.9204 (pt) cc_final: 0.8970 (pt) REVERT: C 17 ASP cc_start: 0.7615 (p0) cc_final: 0.7224 (p0) REVERT: C 53 ASP cc_start: 0.8583 (m-30) cc_final: 0.8231 (t0) REVERT: C 60 THR cc_start: 0.9185 (OUTLIER) cc_final: 0.8897 (p) REVERT: C 76 ASP cc_start: 0.8067 (t0) cc_final: 0.7857 (t0) REVERT: C 84 LYS cc_start: 0.8759 (mmmm) cc_final: 0.8257 (tptt) REVERT: C 147 GLU cc_start: 0.8378 (pp20) cc_final: 0.8163 (pp20) REVERT: C 218 MET cc_start: 0.8749 (OUTLIER) cc_final: 0.8443 (mmm) REVERT: C 288 SER cc_start: 0.8925 (m) cc_final: 0.8441 (t) REVERT: C 289 GLU cc_start: 0.8740 (mt-10) cc_final: 0.8301 (mm-30) REVERT: C 330 ASP cc_start: 0.8390 (p0) cc_final: 0.8070 (p0) REVERT: C 331 LYS cc_start: 0.9126 (mttt) cc_final: 0.8698 (ttmm) REVERT: C 384 LYS cc_start: 0.8967 (pttt) cc_final: 0.8616 (pttt) REVERT: C 397 ARG cc_start: 0.8944 (mmt180) cc_final: 0.8647 (mmm-85) REVERT: C 446 ARG cc_start: 0.8527 (ttm110) cc_final: 0.8299 (ttm110) REVERT: C 481 PHE cc_start: 0.6979 (t80) cc_final: 0.6675 (t80) REVERT: C 500 ASN cc_start: 0.7828 (m-40) cc_final: 0.7521 (m-40) REVERT: C 537 LYS cc_start: 0.8405 (tppt) cc_final: 0.8185 (tppt) REVERT: C 772 GLU cc_start: 0.8245 (mp0) cc_final: 0.7943 (mp0) REVERT: C 832 LEU cc_start: 0.9134 (mt) cc_final: 0.8627 (mm) REVERT: C 842 ASN cc_start: 0.8752 (m-40) cc_final: 0.8478 (m-40) REVERT: C 848 ASP cc_start: 0.8798 (m-30) cc_final: 0.8248 (m-30) REVERT: C 849 GLU cc_start: 0.8265 (pp20) cc_final: 0.8038 (pp20) REVERT: C 855 ASP cc_start: 0.8257 (m-30) cc_final: 0.7933 (m-30) REVERT: C 858 GLN cc_start: 0.8796 (OUTLIER) cc_final: 0.8469 (mm110) REVERT: C 873 SER cc_start: 0.9111 (m) cc_final: 0.8760 (p) REVERT: C 874 ASN cc_start: 0.8940 (m-40) cc_final: 0.8726 (p0) REVERT: C 889 LYS cc_start: 0.9298 (ttpt) cc_final: 0.8989 (ttpp) REVERT: C 909 ASP cc_start: 0.8430 (m-30) cc_final: 0.7664 (m-30) REVERT: C 956 GLU cc_start: 0.8014 (mm-30) cc_final: 0.7635 (mm-30) REVERT: C 998 MET cc_start: 0.9095 (tpp) cc_final: 0.8179 (tpp) REVERT: C 999 ASP cc_start: 0.8370 (t70) cc_final: 0.7954 (t0) REVERT: C 1045 ASN cc_start: 0.9269 (t0) cc_final: 0.9036 (t0) REVERT: C 1075 GLN cc_start: 0.8712 (mm110) cc_final: 0.7980 (mm-40) REVERT: C 1079 ASP cc_start: 0.8639 (m-30) cc_final: 0.8310 (m-30) REVERT: C 1095 GLN cc_start: 0.8775 (tm-30) cc_final: 0.7659 (tm-30) REVERT: C 1099 ASP cc_start: 0.8883 (m-30) cc_final: 0.7603 (m-30) REVERT: C 1112 GLU cc_start: 0.8688 (tp30) cc_final: 0.8258 (tp30) REVERT: C 1199 GLU cc_start: 0.7940 (mm-30) cc_final: 0.7606 (mm-30) REVERT: C 1204 LYS cc_start: 0.8872 (mttp) cc_final: 0.8636 (mttt) REVERT: C 1209 MET cc_start: 0.8321 (mpp) cc_final: 0.7652 (mpp) REVERT: C 1216 PHE cc_start: 0.8486 (m-10) cc_final: 0.8137 (m-80) outliers start: 72 outliers final: 35 residues processed: 538 average time/residue: 0.2080 time to fit residues: 175.9619 Evaluate side-chains 499 residues out of total 3216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 458 time to evaluate : 1.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 293 LYS Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 444 TRP Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 820 LEU Chi-restraints excluded: chain A residue 850 VAL Chi-restraints excluded: chain A residue 1007 LEU Chi-restraints excluded: chain A residue 1102 LEU Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 293 LYS Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 405 SER Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain B residue 866 MET Chi-restraints excluded: chain B residue 924 GLU Chi-restraints excluded: chain B residue 940 CYS Chi-restraints excluded: chain B residue 1017 LEU Chi-restraints excluded: chain B residue 1032 LYS Chi-restraints excluded: chain B residue 1042 GLN Chi-restraints excluded: chain B residue 1102 LEU Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 69 LYS Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 131 ILE Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 218 MET Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 776 VAL Chi-restraints excluded: chain C residue 858 GLN Chi-restraints excluded: chain C residue 1167 CYS Chi-restraints excluded: chain C residue 1184 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 111 optimal weight: 0.9980 chunk 34 optimal weight: 0.9980 chunk 44 optimal weight: 3.9990 chunk 31 optimal weight: 0.1980 chunk 246 optimal weight: 0.7980 chunk 292 optimal weight: 20.0000 chunk 213 optimal weight: 0.9980 chunk 30 optimal weight: 3.9990 chunk 332 optimal weight: 1.9990 chunk 198 optimal weight: 0.6980 chunk 346 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 395 ASN ** A 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 160 HIS ** B 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1184 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.101333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.079920 restraints weight = 62986.009| |-----------------------------------------------------------------------------| r_work (start): 0.3103 rms_B_bonded: 3.84 r_work: 0.2926 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.3894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 30177 Z= 0.129 Angle : 0.613 10.349 41256 Z= 0.314 Chirality : 0.043 0.281 4842 Planarity : 0.004 0.059 5124 Dihedral : 4.602 32.536 3867 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 1.46 % Allowed : 16.42 % Favored : 82.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.50 (0.14), residues: 3573 helix: 2.03 (0.19), residues: 759 sheet: -0.10 (0.18), residues: 744 loop : -1.40 (0.13), residues: 2070 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 446 TYR 0.037 0.001 TYR C 713 PHE 0.029 0.001 PHE A 473 TRP 0.012 0.001 TRP C 174 HIS 0.011 0.001 HIS C1184 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.13 (30018) covalent geometry : angle 0.59611 / 0.31 (40851) SS BOND : bond 0.00421 / 0.27 ( 72) SS BOND : angle 1.61487 / 1.19 ( 144) hydrogen bonds : bond 0.04382 / 2.88 ( 1016) hydrogen bonds : angle 4.96167 / 3.31 ( 3102) link_BETA1-4 : bond 0.00377 / 0.24 ( 30) link_BETA1-4 : angle 1.54540 / 1.06 ( 90) link_NAG-ASN : bond 0.00245 / 0.15 ( 57) link_NAG-ASN : angle 1.50744 / 1.00 ( 171) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7146 Ramachandran restraints generated. 3573 Oldfield, 0 Emsley, 3573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7146 Ramachandran restraints generated. 3573 Oldfield, 0 Emsley, 3573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 523 residues out of total 3216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 476 time to evaluate : 1.134 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 SER cc_start: 0.8661 (m) cc_final: 0.8432 (t) REVERT: A 140 GLN cc_start: 0.7743 (tm-30) cc_final: 0.7092 (tm-30) REVERT: A 186 LYS cc_start: 0.8757 (ptpp) cc_final: 0.8172 (mppt) REVERT: A 218 MET cc_start: 0.8641 (mtm) cc_final: 0.8439 (mtp) REVERT: A 273 ARG cc_start: 0.8558 (tpp80) cc_final: 0.8344 (mpp80) REVERT: A 288 SER cc_start: 0.8845 (m) cc_final: 0.8424 (t) REVERT: A 319 ARG cc_start: 0.8599 (mmm160) cc_final: 0.8270 (mmm-85) REVERT: A 331 LYS cc_start: 0.9047 (mtpt) cc_final: 0.8781 (mtpp) REVERT: A 336 PHE cc_start: 0.8304 (m-10) cc_final: 0.7898 (m-80) REVERT: A 376 SER cc_start: 0.9052 (m) cc_final: 0.8662 (p) REVERT: A 384 LYS cc_start: 0.8785 (pttt) cc_final: 0.8550 (pttt) REVERT: A 411 SER cc_start: 0.9154 (t) cc_final: 0.8864 (p) REVERT: A 437 ASN cc_start: 0.8726 (t0) cc_final: 0.8403 (t0) REVERT: A 553 GLU cc_start: 0.8403 (mm-30) cc_final: 0.7891 (mm-30) REVERT: A 618 THR cc_start: 0.9292 (OUTLIER) cc_final: 0.9027 (m) REVERT: A 711 GLN cc_start: 0.8430 (pm20) cc_final: 0.7935 (mp10) REVERT: A 717 TYR cc_start: 0.9010 (t80) cc_final: 0.8731 (t80) REVERT: A 772 GLU cc_start: 0.8388 (mp0) cc_final: 0.7983 (mp0) REVERT: A 781 ASP cc_start: 0.8165 (m-30) cc_final: 0.7412 (m-30) REVERT: A 792 ILE cc_start: 0.9174 (tp) cc_final: 0.8831 (pt) REVERT: A 842 ASN cc_start: 0.8915 (m-40) cc_final: 0.8601 (m-40) REVERT: A 844 ASN cc_start: 0.8946 (m-40) cc_final: 0.8265 (m-40) REVERT: A 848 ASP cc_start: 0.8543 (m-30) cc_final: 0.8204 (m-30) REVERT: A 858 GLN cc_start: 0.8742 (mm110) cc_final: 0.8327 (mm110) REVERT: A 867 GLN cc_start: 0.8101 (mm-40) cc_final: 0.7827 (mm110) REVERT: A 874 ASN cc_start: 0.8765 (m-40) cc_final: 0.8391 (p0) REVERT: A 889 LYS cc_start: 0.9030 (ttpt) cc_final: 0.8729 (ttpp) REVERT: A 909 ASP cc_start: 0.8551 (m-30) cc_final: 0.7854 (m-30) REVERT: A 956 GLU cc_start: 0.7608 (pm20) cc_final: 0.7359 (pm20) REVERT: A 999 ASP cc_start: 0.8600 (t0) cc_final: 0.8040 (t0) REVERT: A 1075 GLN cc_start: 0.8657 (mm-40) cc_final: 0.8429 (mm-40) REVERT: A 1095 GLN cc_start: 0.8682 (tm-30) cc_final: 0.7265 (tm-30) REVERT: A 1099 ASP cc_start: 0.8747 (m-30) cc_final: 0.7496 (m-30) REVERT: A 1112 GLU cc_start: 0.8768 (tt0) cc_final: 0.8374 (tp30) REVERT: A 1153 LYS cc_start: 0.8773 (tppt) cc_final: 0.8521 (tptp) REVERT: B 69 LYS cc_start: 0.9176 (tmtt) cc_final: 0.8780 (tmmt) REVERT: B 88 LEU cc_start: 0.9094 (mp) cc_final: 0.8741 (tp) REVERT: B 92 LYS cc_start: 0.8964 (mtmm) cc_final: 0.8717 (mtpp) REVERT: B 111 LEU cc_start: 0.8919 (mm) cc_final: 0.8354 (mt) REVERT: B 175 HIS cc_start: 0.8762 (p-80) cc_final: 0.8255 (p-80) REVERT: B 271 ASP cc_start: 0.7801 (p0) cc_final: 0.7428 (p0) REVERT: B 273 ARG cc_start: 0.8633 (OUTLIER) cc_final: 0.8398 (mtp-110) REVERT: B 326 ASP cc_start: 0.7405 (t70) cc_final: 0.6762 (t0) REVERT: B 331 LYS cc_start: 0.9098 (mttt) cc_final: 0.8745 (ttmm) REVERT: B 397 ARG cc_start: 0.8865 (mmt180) cc_final: 0.8384 (mmm-85) REVERT: B 398 ARG cc_start: 0.8702 (tpt-90) cc_final: 0.8499 (tpp80) REVERT: B 400 ASP cc_start: 0.8532 (m-30) cc_final: 0.8190 (m-30) REVERT: B 411 SER cc_start: 0.9350 (t) cc_final: 0.8971 (p) REVERT: B 417 ASP cc_start: 0.8414 (t0) cc_final: 0.8149 (t0) REVERT: B 448 TYR cc_start: 0.8916 (m-80) cc_final: 0.8617 (m-10) REVERT: B 450 PHE cc_start: 0.8322 (t80) cc_final: 0.8089 (t80) REVERT: B 464 ARG cc_start: 0.8665 (tpp80) cc_final: 0.8391 (tpp80) REVERT: B 529 ASP cc_start: 0.8325 (t70) cc_final: 0.7664 (t0) REVERT: B 536 LYS cc_start: 0.8301 (mmtp) cc_final: 0.7978 (mmtt) REVERT: B 587 ARG cc_start: 0.8476 (mtp85) cc_final: 0.7995 (ttm-80) REVERT: B 711 GLN cc_start: 0.8209 (pm20) cc_final: 0.7689 (mp10) REVERT: B 781 ASP cc_start: 0.8157 (t0) cc_final: 0.7852 (m-30) REVERT: B 792 ILE cc_start: 0.9173 (tt) cc_final: 0.8884 (pt) REVERT: B 832 LEU cc_start: 0.8893 (mt) cc_final: 0.8212 (mm) REVERT: B 842 ASN cc_start: 0.8897 (m-40) cc_final: 0.8571 (m-40) REVERT: B 848 ASP cc_start: 0.8728 (m-30) cc_final: 0.8278 (m-30) REVERT: B 849 GLU cc_start: 0.8521 (tm-30) cc_final: 0.8146 (pp20) REVERT: B 855 ASP cc_start: 0.8282 (m-30) cc_final: 0.8006 (m-30) REVERT: B 873 SER cc_start: 0.8760 (m) cc_final: 0.8439 (p) REVERT: B 874 ASN cc_start: 0.8968 (m-40) cc_final: 0.8533 (p0) REVERT: B 889 LYS cc_start: 0.9166 (ttpt) cc_final: 0.8822 (ttmm) REVERT: B 914 LYS cc_start: 0.9226 (mmmt) cc_final: 0.8996 (mmmm) REVERT: B 916 LYS cc_start: 0.8815 (pttt) cc_final: 0.8450 (ptmm) REVERT: B 924 GLU cc_start: 0.8531 (OUTLIER) cc_final: 0.8116 (tm-30) REVERT: B 998 MET cc_start: 0.8842 (mmt) cc_final: 0.8529 (tpp) REVERT: B 999 ASP cc_start: 0.8456 (t0) cc_final: 0.8042 (t0) REVERT: B 1004 ASN cc_start: 0.8484 (m-40) cc_final: 0.8176 (m-40) REVERT: B 1042 GLN cc_start: 0.9174 (OUTLIER) cc_final: 0.8882 (tm-30) REVERT: B 1054 LYS cc_start: 0.9164 (mttt) cc_final: 0.8912 (mmmm) REVERT: B 1075 GLN cc_start: 0.8710 (mm-40) cc_final: 0.7922 (mm-40) REVERT: B 1079 ASP cc_start: 0.8682 (m-30) cc_final: 0.8311 (m-30) REVERT: B 1095 GLN cc_start: 0.8710 (tm-30) cc_final: 0.7495 (tm-30) REVERT: B 1099 ASP cc_start: 0.8833 (m-30) cc_final: 0.7422 (m-30) REVERT: B 1112 GLU cc_start: 0.8723 (tp30) cc_final: 0.8302 (tp30) REVERT: B 1158 LYS cc_start: 0.8436 (tttm) cc_final: 0.8156 (tttt) REVERT: B 1204 LYS cc_start: 0.9030 (mtpt) cc_final: 0.8781 (mtpp) REVERT: C 15 ILE cc_start: 0.9083 (pt) cc_final: 0.8847 (pt) REVERT: C 17 ASP cc_start: 0.7459 (p0) cc_final: 0.7064 (p0) REVERT: C 53 ASP cc_start: 0.8532 (m-30) cc_final: 0.8200 (t0) REVERT: C 76 ASP cc_start: 0.7999 (t0) cc_final: 0.7728 (t0) REVERT: C 84 LYS cc_start: 0.8726 (mmmm) cc_final: 0.8216 (tptt) REVERT: C 147 GLU cc_start: 0.8401 (pp20) cc_final: 0.8115 (pp20) REVERT: C 288 SER cc_start: 0.8894 (m) cc_final: 0.8373 (t) REVERT: C 289 GLU cc_start: 0.8688 (mt-10) cc_final: 0.8486 (tm-30) REVERT: C 330 ASP cc_start: 0.8309 (p0) cc_final: 0.7951 (p0) REVERT: C 331 LYS cc_start: 0.9089 (mttt) cc_final: 0.8651 (ttmm) REVERT: C 345 GLU cc_start: 0.8183 (tp30) cc_final: 0.7785 (tp30) REVERT: C 384 LYS cc_start: 0.8899 (pttt) cc_final: 0.8469 (pttt) REVERT: C 397 ARG cc_start: 0.8924 (mmt180) cc_final: 0.8692 (mmm-85) REVERT: C 481 PHE cc_start: 0.6903 (t80) cc_final: 0.6597 (t80) REVERT: C 500 ASN cc_start: 0.7840 (m-40) cc_final: 0.7527 (m-40) REVERT: C 678 ARG cc_start: 0.7712 (ttm170) cc_final: 0.7413 (ttm-80) REVERT: C 832 LEU cc_start: 0.9117 (mt) cc_final: 0.8514 (mm) REVERT: C 842 ASN cc_start: 0.8778 (m-40) cc_final: 0.8514 (m-40) REVERT: C 848 ASP cc_start: 0.8715 (m-30) cc_final: 0.8125 (m-30) REVERT: C 849 GLU cc_start: 0.8274 (pp20) cc_final: 0.7956 (pp20) REVERT: C 858 GLN cc_start: 0.8862 (mm-40) cc_final: 0.8498 (mm-40) REVERT: C 873 SER cc_start: 0.9048 (m) cc_final: 0.8767 (p) REVERT: C 874 ASN cc_start: 0.8910 (m-40) cc_final: 0.8623 (p0) REVERT: C 882 ASP cc_start: 0.7772 (t70) cc_final: 0.6945 (t0) REVERT: C 889 LYS cc_start: 0.9292 (ttpt) cc_final: 0.8962 (ttpp) REVERT: C 909 ASP cc_start: 0.8331 (m-30) cc_final: 0.7767 (m-30) REVERT: C 956 GLU cc_start: 0.7878 (mm-30) cc_final: 0.7590 (mm-30) REVERT: C 998 MET cc_start: 0.8889 (tpp) cc_final: 0.8225 (tpp) REVERT: C 999 ASP cc_start: 0.8282 (t70) cc_final: 0.8007 (t0) REVERT: C 1045 ASN cc_start: 0.9259 (t0) cc_final: 0.9026 (t0) REVERT: C 1075 GLN cc_start: 0.8571 (mm110) cc_final: 0.7682 (mm-40) REVERT: C 1079 ASP cc_start: 0.8593 (m-30) cc_final: 0.8221 (m-30) REVERT: C 1095 GLN cc_start: 0.8685 (tm-30) cc_final: 0.7537 (tm-30) REVERT: C 1099 ASP cc_start: 0.8786 (m-30) cc_final: 0.7563 (m-30) REVERT: C 1104 LYS cc_start: 0.8910 (tptp) cc_final: 0.8567 (ttmm) REVERT: C 1112 GLU cc_start: 0.8638 (tp30) cc_final: 0.8200 (tp30) REVERT: C 1199 GLU cc_start: 0.7964 (mm-30) cc_final: 0.7691 (mm-30) REVERT: C 1204 LYS cc_start: 0.8795 (mttp) cc_final: 0.8531 (mttt) REVERT: C 1208 PHE cc_start: 0.8872 (m-10) cc_final: 0.8436 (m-80) REVERT: C 1209 MET cc_start: 0.8314 (mpp) cc_final: 0.7671 (mpp) outliers start: 47 outliers final: 29 residues processed: 508 average time/residue: 0.2161 time to fit residues: 171.0086 Evaluate side-chains 497 residues out of total 3216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 464 time to evaluate : 1.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 LYS Chi-restraints excluded: chain A residue 97 ASP Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 293 LYS Chi-restraints excluded: chain A residue 405 SER Chi-restraints excluded: chain A residue 444 TRP Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 703 LEU Chi-restraints excluded: chain A residue 820 LEU Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 1097 LEU Chi-restraints excluded: chain A residue 1102 LEU Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 273 ARG Chi-restraints excluded: chain B residue 293 LYS Chi-restraints excluded: chain B residue 405 SER Chi-restraints excluded: chain B residue 525 ILE Chi-restraints excluded: chain B residue 588 CYS Chi-restraints excluded: chain B residue 866 MET Chi-restraints excluded: chain B residue 924 GLU Chi-restraints excluded: chain B residue 1017 LEU Chi-restraints excluded: chain B residue 1032 LYS Chi-restraints excluded: chain B residue 1042 GLN Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 186 LYS Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 769 VAL Chi-restraints excluded: chain C residue 776 VAL Chi-restraints excluded: chain C residue 850 VAL Chi-restraints excluded: chain C residue 950 LEU Chi-restraints excluded: chain C residue 1167 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 14 optimal weight: 10.0000 chunk 336 optimal weight: 2.9990 chunk 253 optimal weight: 10.0000 chunk 257 optimal weight: 0.9990 chunk 170 optimal weight: 0.0970 chunk 259 optimal weight: 0.7980 chunk 188 optimal weight: 0.9990 chunk 55 optimal weight: 7.9990 chunk 144 optimal weight: 4.9990 chunk 239 optimal weight: 7.9990 chunk 106 optimal weight: 0.7980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 160 HIS ** A 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 364 HIS ** C 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 858 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.100391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.078909 restraints weight = 63246.228| |-----------------------------------------------------------------------------| r_work (start): 0.3109 rms_B_bonded: 3.89 r_work: 0.2932 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.3965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 30177 Z= 0.124 Angle : 0.595 9.721 41256 Z= 0.304 Chirality : 0.043 0.222 4842 Planarity : 0.004 0.057 5124 Dihedral : 4.397 29.357 3867 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 1.65 % Allowed : 17.07 % Favored : 81.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.39 (0.14), residues: 3573 helix: 2.18 (0.19), residues: 756 sheet: -0.09 (0.18), residues: 777 loop : -1.34 (0.13), residues: 2040 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 206 TYR 0.039 0.001 TYR C 713 PHE 0.023 0.001 PHE A 473 TRP 0.011 0.001 TRP C 646 HIS 0.004 0.001 HIS C 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.12 (30018) covalent geometry : angle 0.58103 / 0.30 (40851) SS BOND : bond 0.00402 / 0.24 ( 72) SS BOND : angle 1.38977 / 1.03 ( 144) hydrogen bonds : bond 0.04055 / 2.67 ( 1016) hydrogen bonds : angle 4.80752 / 3.21 ( 3102) link_BETA1-4 : bond 0.00400 / 0.26 ( 30) link_BETA1-4 : angle 1.52901 / 1.05 ( 90) link_NAG-ASN : bond 0.00242 / 0.15 ( 57) link_NAG-ASN : angle 1.39540 / 0.94 ( 171) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7146 Ramachandran restraints generated. 3573 Oldfield, 0 Emsley, 3573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7146 Ramachandran restraints generated. 3573 Oldfield, 0 Emsley, 3573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 543 residues out of total 3216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 490 time to evaluate : 1.136 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 TYR cc_start: 0.9184 (m-80) cc_final: 0.8947 (m-80) REVERT: A 140 GLN cc_start: 0.7733 (tm-30) cc_final: 0.6769 (tm-30) REVERT: A 142 HIS cc_start: 0.8335 (m90) cc_final: 0.6908 (m90) REVERT: A 218 MET cc_start: 0.8592 (mtm) cc_final: 0.8361 (mtp) REVERT: A 273 ARG cc_start: 0.8545 (tpp80) cc_final: 0.8338 (mpp80) REVERT: A 288 SER cc_start: 0.8840 (m) cc_final: 0.8410 (t) REVERT: A 305 ASP cc_start: 0.8134 (p0) cc_final: 0.7760 (p0) REVERT: A 319 ARG cc_start: 0.8600 (mmm160) cc_final: 0.8283 (mmm-85) REVERT: A 331 LYS cc_start: 0.9041 (mtpt) cc_final: 0.8771 (mtpp) REVERT: A 376 SER cc_start: 0.9049 (m) cc_final: 0.8645 (p) REVERT: A 384 LYS cc_start: 0.8773 (pttt) cc_final: 0.8520 (pttt) REVERT: A 388 LEU cc_start: 0.9109 (OUTLIER) cc_final: 0.8889 (mt) REVERT: A 398 ARG cc_start: 0.8996 (tpt-90) cc_final: 0.8768 (tpt90) REVERT: A 402 GLN cc_start: 0.8780 (tp-100) cc_final: 0.8501 (tp-100) REVERT: A 411 SER cc_start: 0.9159 (t) cc_final: 0.8926 (p) REVERT: A 417 ASP cc_start: 0.8448 (t0) cc_final: 0.8156 (t0) REVERT: A 437 ASN cc_start: 0.8710 (t0) cc_final: 0.8372 (t0) REVERT: A 446 ARG cc_start: 0.8542 (ttm-80) cc_final: 0.7840 (mtm-85) REVERT: A 553 GLU cc_start: 0.8344 (mm-30) cc_final: 0.7860 (mm-30) REVERT: A 618 THR cc_start: 0.9259 (OUTLIER) cc_final: 0.9032 (m) REVERT: A 711 GLN cc_start: 0.8488 (pm20) cc_final: 0.7927 (mp10) REVERT: A 717 TYR cc_start: 0.8993 (t80) cc_final: 0.8741 (t80) REVERT: A 772 GLU cc_start: 0.8452 (mp0) cc_final: 0.8061 (mp0) REVERT: A 781 ASP cc_start: 0.8126 (m-30) cc_final: 0.7388 (m-30) REVERT: A 784 GLU cc_start: 0.8299 (mm-30) cc_final: 0.7986 (mp0) REVERT: A 792 ILE cc_start: 0.9155 (tp) cc_final: 0.8826 (pt) REVERT: A 805 GLU cc_start: 0.8028 (tm-30) cc_final: 0.7725 (tm-30) REVERT: A 842 ASN cc_start: 0.8941 (m-40) cc_final: 0.8681 (m-40) REVERT: A 844 ASN cc_start: 0.8971 (m-40) cc_final: 0.7986 (m-40) REVERT: A 848 ASP cc_start: 0.8562 (m-30) cc_final: 0.8078 (m-30) REVERT: A 858 GLN cc_start: 0.8755 (mm110) cc_final: 0.8280 (mm110) REVERT: A 867 GLN cc_start: 0.8141 (mm-40) cc_final: 0.7852 (mm110) REVERT: A 874 ASN cc_start: 0.8772 (m-40) cc_final: 0.8455 (p0) REVERT: A 889 LYS cc_start: 0.9043 (ttpt) cc_final: 0.8755 (ttpp) REVERT: A 909 ASP cc_start: 0.8530 (m-30) cc_final: 0.8001 (m-30) REVERT: A 956 GLU cc_start: 0.7694 (pm20) cc_final: 0.7382 (pm20) REVERT: A 999 ASP cc_start: 0.8592 (t0) cc_final: 0.8022 (t0) REVERT: A 1075 GLN cc_start: 0.8657 (mm-40) cc_final: 0.7763 (mm-40) REVERT: A 1079 ASP cc_start: 0.8753 (m-30) cc_final: 0.8269 (m-30) REVERT: A 1095 GLN cc_start: 0.8645 (tm-30) cc_final: 0.7153 (tm-30) REVERT: A 1099 ASP cc_start: 0.8792 (m-30) cc_final: 0.7473 (m-30) REVERT: A 1112 GLU cc_start: 0.8756 (tt0) cc_final: 0.8361 (tp30) REVERT: A 1153 LYS cc_start: 0.8783 (tppt) cc_final: 0.8494 (tptp) REVERT: A 1177 LYS cc_start: 0.8686 (tppt) cc_final: 0.8241 (tppt) REVERT: B 69 LYS cc_start: 0.9194 (tmtt) cc_final: 0.8779 (tmmt) REVERT: B 88 LEU cc_start: 0.9055 (mp) cc_final: 0.8722 (tp) REVERT: B 92 LYS cc_start: 0.8964 (mtmm) cc_final: 0.8725 (mtpp) REVERT: B 111 LEU cc_start: 0.8944 (mm) cc_final: 0.8395 (mt) REVERT: B 175 HIS cc_start: 0.8738 (p-80) cc_final: 0.8219 (p-80) REVERT: B 326 ASP cc_start: 0.7115 (t70) cc_final: 0.6847 (t0) REVERT: B 331 LYS cc_start: 0.9244 (mttt) cc_final: 0.8778 (ttmm) REVERT: B 384 LYS cc_start: 0.8769 (pttt) cc_final: 0.8322 (pttp) REVERT: B 397 ARG cc_start: 0.8914 (mmt180) cc_final: 0.8483 (mmm-85) REVERT: B 400 ASP cc_start: 0.8530 (m-30) cc_final: 0.8125 (m-30) REVERT: B 411 SER cc_start: 0.9351 (t) cc_final: 0.8961 (p) REVERT: B 417 ASP cc_start: 0.8446 (t0) cc_final: 0.8082 (t0) REVERT: B 446 ARG cc_start: 0.8787 (ttm110) cc_final: 0.8261 (ttm110) REVERT: B 448 TYR cc_start: 0.8930 (m-80) cc_final: 0.8675 (m-10) REVERT: B 450 PHE cc_start: 0.8289 (t80) cc_final: 0.8015 (t80) REVERT: B 464 ARG cc_start: 0.8643 (tpp80) cc_final: 0.8387 (tpp80) REVERT: B 529 ASP cc_start: 0.8321 (t70) cc_final: 0.7672 (t0) REVERT: B 536 LYS cc_start: 0.8369 (mmtp) cc_final: 0.8056 (mptt) REVERT: B 711 GLN cc_start: 0.8239 (pm20) cc_final: 0.7706 (mp10) REVERT: B 781 ASP cc_start: 0.8178 (t0) cc_final: 0.7912 (m-30) REVERT: B 792 ILE cc_start: 0.9190 (tt) cc_final: 0.8915 (pt) REVERT: B 832 LEU cc_start: 0.8927 (mt) cc_final: 0.8399 (mm) REVERT: B 842 ASN cc_start: 0.8839 (m-40) cc_final: 0.8442 (m-40) REVERT: B 848 ASP cc_start: 0.8728 (m-30) cc_final: 0.8224 (m-30) REVERT: B 855 ASP cc_start: 0.8317 (m-30) cc_final: 0.7888 (m-30) REVERT: B 858 GLN cc_start: 0.8972 (mm-40) cc_final: 0.8740 (mm110) REVERT: B 873 SER cc_start: 0.8760 (m) cc_final: 0.8429 (p) REVERT: B 874 ASN cc_start: 0.8958 (m-40) cc_final: 0.8596 (p0) REVERT: B 889 LYS cc_start: 0.9150 (ttpt) cc_final: 0.8776 (ttmm) REVERT: B 914 LYS cc_start: 0.9318 (mmmt) cc_final: 0.9029 (mmmm) REVERT: B 916 LYS cc_start: 0.8831 (pttt) cc_final: 0.8461 (ptmm) REVERT: B 924 GLU cc_start: 0.8565 (OUTLIER) cc_final: 0.8280 (tm-30) REVERT: B 998 MET cc_start: 0.8869 (mmt) cc_final: 0.8626 (tpp) REVERT: B 999 ASP cc_start: 0.8464 (t0) cc_final: 0.8062 (t0) REVERT: B 1004 ASN cc_start: 0.8469 (m-40) cc_final: 0.8152 (m-40) REVERT: B 1042 GLN cc_start: 0.9162 (OUTLIER) cc_final: 0.8872 (tm-30) REVERT: B 1054 LYS cc_start: 0.9146 (mttt) cc_final: 0.8896 (mmmm) REVERT: B 1075 GLN cc_start: 0.8714 (mm-40) cc_final: 0.7980 (mm-40) REVERT: B 1079 ASP cc_start: 0.8695 (m-30) cc_final: 0.8359 (m-30) REVERT: B 1095 GLN cc_start: 0.8717 (tm-30) cc_final: 0.7481 (tm-30) REVERT: B 1099 ASP cc_start: 0.8823 (m-30) cc_final: 0.7429 (m-30) REVERT: B 1112 GLU cc_start: 0.8726 (tp30) cc_final: 0.8275 (tp30) REVERT: B 1158 LYS cc_start: 0.8444 (tttm) cc_final: 0.8146 (tttt) REVERT: B 1218 LYS cc_start: 0.8539 (mtpp) cc_final: 0.8248 (mmmm) REVERT: C 15 ILE cc_start: 0.9058 (pt) cc_final: 0.8845 (pt) REVERT: C 17 ASP cc_start: 0.7478 (p0) cc_final: 0.7153 (p0) REVERT: C 18 PHE cc_start: 0.8173 (t80) cc_final: 0.7797 (t80) REVERT: C 53 ASP cc_start: 0.8537 (m-30) cc_final: 0.8223 (t0) REVERT: C 60 THR cc_start: 0.9178 (OUTLIER) cc_final: 0.8853 (p) REVERT: C 76 ASP cc_start: 0.7983 (t0) cc_final: 0.7710 (t0) REVERT: C 84 LYS cc_start: 0.8705 (mmmm) cc_final: 0.8208 (tptt) REVERT: C 147 GLU cc_start: 0.8393 (pp20) cc_final: 0.8106 (pp20) REVERT: C 288 SER cc_start: 0.8892 (m) cc_final: 0.8358 (t) REVERT: C 330 ASP cc_start: 0.8290 (p0) cc_final: 0.7955 (m-30) REVERT: C 331 LYS cc_start: 0.9059 (mttt) cc_final: 0.8663 (ttmm) REVERT: C 345 GLU cc_start: 0.8262 (tp30) cc_final: 0.7939 (tp30) REVERT: C 384 LYS cc_start: 0.8929 (pttt) cc_final: 0.8541 (pttt) REVERT: C 397 ARG cc_start: 0.8956 (mmt180) cc_final: 0.8708 (mmm-85) REVERT: C 481 PHE cc_start: 0.6870 (t80) cc_final: 0.6568 (t80) REVERT: C 500 ASN cc_start: 0.7810 (m-40) cc_final: 0.7500 (m-40) REVERT: C 537 LYS cc_start: 0.8265 (tppt) cc_final: 0.7896 (tptt) REVERT: C 772 GLU cc_start: 0.8203 (mp0) cc_final: 0.7959 (mp0) REVERT: C 832 LEU cc_start: 0.9103 (mt) cc_final: 0.8485 (mm) REVERT: C 842 ASN cc_start: 0.8784 (m-40) cc_final: 0.8439 (m-40) REVERT: C 849 GLU cc_start: 0.8290 (pp20) cc_final: 0.8004 (pp20) REVERT: C 855 ASP cc_start: 0.8299 (m-30) cc_final: 0.7909 (m-30) REVERT: C 858 GLN cc_start: 0.8810 (OUTLIER) cc_final: 0.8329 (mm110) REVERT: C 873 SER cc_start: 0.9054 (m) cc_final: 0.8784 (p) REVERT: C 874 ASN cc_start: 0.8920 (m-40) cc_final: 0.8646 (p0) REVERT: C 882 ASP cc_start: 0.7854 (t70) cc_final: 0.7107 (t0) REVERT: C 888 PHE cc_start: 0.8344 (m-10) cc_final: 0.7651 (m-80) REVERT: C 889 LYS cc_start: 0.9194 (ttpt) cc_final: 0.8855 (ttpp) REVERT: C 909 ASP cc_start: 0.8342 (m-30) cc_final: 0.7708 (m-30) REVERT: C 999 ASP cc_start: 0.8264 (t70) cc_final: 0.8034 (t0) REVERT: C 1045 ASN cc_start: 0.9251 (t0) cc_final: 0.9026 (t0) REVERT: C 1075 GLN cc_start: 0.8593 (mm110) cc_final: 0.7691 (mm-40) REVERT: C 1079 ASP cc_start: 0.8595 (m-30) cc_final: 0.8214 (m-30) REVERT: C 1095 GLN cc_start: 0.8684 (tm-30) cc_final: 0.7532 (tm-30) REVERT: C 1099 ASP cc_start: 0.8806 (m-30) cc_final: 0.7577 (m-30) REVERT: C 1104 LYS cc_start: 0.8960 (tptp) cc_final: 0.8590 (ttmm) REVERT: C 1112 GLU cc_start: 0.8697 (tp30) cc_final: 0.8287 (tp30) REVERT: C 1204 LYS cc_start: 0.8785 (mttp) cc_final: 0.8478 (mtpt) REVERT: C 1208 PHE cc_start: 0.8859 (m-10) cc_final: 0.8578 (m-80) REVERT: C 1209 MET cc_start: 0.8303 (mpp) cc_final: 0.8100 (mmm) outliers start: 53 outliers final: 31 residues processed: 525 average time/residue: 0.2144 time to fit residues: 176.2666 Evaluate side-chains 515 residues out of total 3216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 478 time to evaluate : 1.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 LYS Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 293 LYS Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 820 LEU Chi-restraints excluded: chain A residue 850 VAL Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 1097 LEU Chi-restraints excluded: chain A residue 1102 LEU Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 293 LYS Chi-restraints excluded: chain B residue 525 ILE Chi-restraints excluded: chain B residue 535 GLN Chi-restraints excluded: chain B residue 575 LEU Chi-restraints excluded: chain B residue 588 CYS Chi-restraints excluded: chain B residue 924 GLU Chi-restraints excluded: chain B residue 940 CYS Chi-restraints excluded: chain B residue 1017 LEU Chi-restraints excluded: chain B residue 1042 GLN Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 588 CYS Chi-restraints excluded: chain C residue 776 VAL Chi-restraints excluded: chain C residue 839 PHE Chi-restraints excluded: chain C residue 850 VAL Chi-restraints excluded: chain C residue 858 GLN Chi-restraints excluded: chain C residue 1064 GLU Chi-restraints excluded: chain C residue 1167 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 127 optimal weight: 1.9990 chunk 90 optimal weight: 4.9990 chunk 134 optimal weight: 10.0000 chunk 24 optimal weight: 1.9990 chunk 186 optimal weight: 5.9990 chunk 47 optimal weight: 0.0470 chunk 260 optimal weight: 2.9990 chunk 38 optimal weight: 5.9990 chunk 253 optimal weight: 6.9990 chunk 86 optimal weight: 6.9990 chunk 52 optimal weight: 0.9980 overall best weight: 1.6084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 867 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 255 GLN ** C 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 867 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 880 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.099321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.077918 restraints weight = 63599.763| |-----------------------------------------------------------------------------| r_work (start): 0.3085 rms_B_bonded: 3.88 r_work: 0.2907 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.4110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 30177 Z= 0.187 Angle : 0.632 12.640 41256 Z= 0.322 Chirality : 0.044 0.450 4842 Planarity : 0.004 0.079 5124 Dihedral : 4.467 28.247 3867 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 1.49 % Allowed : 17.41 % Favored : 81.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.43 (0.14), residues: 3573 helix: 2.08 (0.20), residues: 762 sheet: -0.13 (0.18), residues: 780 loop : -1.34 (0.13), residues: 2031 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 678 TYR 0.037 0.001 TYR C 713 PHE 0.043 0.001 PHE C 888 TRP 0.010 0.001 TRP C 646 HIS 0.005 0.001 HIS A 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00416 / 0.19 (30018) covalent geometry : angle 0.60952 / 0.32 (40851) SS BOND : bond 0.00374 / 0.24 ( 72) SS BOND : angle 1.65623 / 1.18 ( 144) hydrogen bonds : bond 0.04335 / 2.86 ( 1016) hydrogen bonds : angle 4.82211 / 3.22 ( 3102) link_BETA1-4 : bond 0.00376 / 0.25 ( 30) link_BETA1-4 : angle 1.62345 / 1.09 ( 90) link_NAG-ASN : bond 0.00446 / 0.31 ( 57) link_NAG-ASN : angle 1.94433 / 1.20 ( 171) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7146 Ramachandran restraints generated. 3573 Oldfield, 0 Emsley, 3573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7146 Ramachandran restraints generated. 3573 Oldfield, 0 Emsley, 3573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 543 residues out of total 3216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 495 time to evaluate : 1.131 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 TYR cc_start: 0.9223 (m-80) cc_final: 0.8934 (m-80) REVERT: A 140 GLN cc_start: 0.7734 (tm-30) cc_final: 0.7088 (tm-30) REVERT: A 175 HIS cc_start: 0.8673 (p-80) cc_final: 0.8296 (p-80) REVERT: A 273 ARG cc_start: 0.8573 (tpp80) cc_final: 0.8362 (mpp80) REVERT: A 288 SER cc_start: 0.8870 (m) cc_final: 0.8455 (t) REVERT: A 305 ASP cc_start: 0.8208 (p0) cc_final: 0.7849 (p0) REVERT: A 319 ARG cc_start: 0.8619 (mmm160) cc_final: 0.8306 (mmm-85) REVERT: A 331 LYS cc_start: 0.9061 (mtpt) cc_final: 0.8807 (mtpp) REVERT: A 336 PHE cc_start: 0.8296 (m-10) cc_final: 0.7883 (m-80) REVERT: A 376 SER cc_start: 0.9054 (m) cc_final: 0.8662 (p) REVERT: A 384 LYS cc_start: 0.8822 (pttt) cc_final: 0.8589 (pttt) REVERT: A 388 LEU cc_start: 0.9125 (OUTLIER) cc_final: 0.8918 (mt) REVERT: A 411 SER cc_start: 0.9175 (t) cc_final: 0.8944 (p) REVERT: A 417 ASP cc_start: 0.8463 (t0) cc_final: 0.8190 (t0) REVERT: A 446 ARG cc_start: 0.8676 (ttm-80) cc_final: 0.8222 (mtm-85) REVERT: A 553 GLU cc_start: 0.8376 (mm-30) cc_final: 0.7858 (mm-30) REVERT: A 618 THR cc_start: 0.9278 (OUTLIER) cc_final: 0.9026 (m) REVERT: A 711 GLN cc_start: 0.8498 (pm20) cc_final: 0.7936 (mp10) REVERT: A 717 TYR cc_start: 0.9017 (t80) cc_final: 0.8761 (t80) REVERT: A 772 GLU cc_start: 0.8438 (mp0) cc_final: 0.7915 (mp0) REVERT: A 781 ASP cc_start: 0.8090 (m-30) cc_final: 0.7326 (m-30) REVERT: A 792 ILE cc_start: 0.9157 (tp) cc_final: 0.8826 (pt) REVERT: A 805 GLU cc_start: 0.8002 (tm-30) cc_final: 0.7694 (tm-30) REVERT: A 842 ASN cc_start: 0.8951 (m-40) cc_final: 0.8691 (m-40) REVERT: A 844 ASN cc_start: 0.8993 (m-40) cc_final: 0.8011 (m-40) REVERT: A 848 ASP cc_start: 0.8592 (m-30) cc_final: 0.8126 (m-30) REVERT: A 858 GLN cc_start: 0.8771 (mm110) cc_final: 0.8287 (mm110) REVERT: A 867 GLN cc_start: 0.8189 (mm-40) cc_final: 0.7881 (mm110) REVERT: A 874 ASN cc_start: 0.8859 (m-40) cc_final: 0.8540 (p0) REVERT: A 889 LYS cc_start: 0.9071 (ttpt) cc_final: 0.8772 (ttpp) REVERT: A 909 ASP cc_start: 0.8508 (m-30) cc_final: 0.8004 (m-30) REVERT: A 956 GLU cc_start: 0.7712 (pm20) cc_final: 0.7366 (pm20) REVERT: A 999 ASP cc_start: 0.8616 (t0) cc_final: 0.8081 (t0) REVERT: A 1075 GLN cc_start: 0.8697 (mm-40) cc_final: 0.7830 (mm-40) REVERT: A 1079 ASP cc_start: 0.8751 (m-30) cc_final: 0.8280 (m-30) REVERT: A 1095 GLN cc_start: 0.8680 (tm-30) cc_final: 0.7198 (tm-30) REVERT: A 1099 ASP cc_start: 0.8767 (m-30) cc_final: 0.7501 (m-30) REVERT: A 1112 GLU cc_start: 0.8742 (tt0) cc_final: 0.8351 (tp30) REVERT: A 1153 LYS cc_start: 0.8782 (tppt) cc_final: 0.8556 (tptp) REVERT: A 1177 LYS cc_start: 0.8668 (tppt) cc_final: 0.8165 (tppt) REVERT: B 69 LYS cc_start: 0.9210 (tmtt) cc_final: 0.8812 (tmmt) REVERT: B 88 LEU cc_start: 0.9075 (mp) cc_final: 0.8755 (tp) REVERT: B 92 LYS cc_start: 0.8966 (mtmm) cc_final: 0.8727 (mtpp) REVERT: B 111 LEU cc_start: 0.8964 (mm) cc_final: 0.8435 (mt) REVERT: B 175 HIS cc_start: 0.8736 (p-80) cc_final: 0.8180 (p-80) REVERT: B 218 MET cc_start: 0.8401 (mmm) cc_final: 0.7971 (tpp) REVERT: B 273 ARG cc_start: 0.8635 (mtp-110) cc_final: 0.8301 (mtp-110) REVERT: B 319 ARG cc_start: 0.8946 (mmm-85) cc_final: 0.8667 (mmm-85) REVERT: B 326 ASP cc_start: 0.7080 (t70) cc_final: 0.6816 (t0) REVERT: B 331 LYS cc_start: 0.9261 (mttt) cc_final: 0.8781 (ttmm) REVERT: B 384 LYS cc_start: 0.8784 (pttt) cc_final: 0.8335 (pttp) REVERT: B 397 ARG cc_start: 0.8912 (mmt180) cc_final: 0.8488 (mmm-85) REVERT: B 400 ASP cc_start: 0.8477 (m-30) cc_final: 0.8072 (m-30) REVERT: B 411 SER cc_start: 0.9345 (t) cc_final: 0.8963 (p) REVERT: B 417 ASP cc_start: 0.8500 (t0) cc_final: 0.8218 (t0) REVERT: B 446 ARG cc_start: 0.8752 (ttm110) cc_final: 0.8314 (ttm110) REVERT: B 448 TYR cc_start: 0.8933 (m-80) cc_final: 0.8646 (m-10) REVERT: B 529 ASP cc_start: 0.8347 (t70) cc_final: 0.7732 (t0) REVERT: B 536 LYS cc_start: 0.8397 (mmtp) cc_final: 0.8086 (mptt) REVERT: B 587 ARG cc_start: 0.8440 (mtp85) cc_final: 0.8185 (ttm-80) REVERT: B 711 GLN cc_start: 0.8246 (pm20) cc_final: 0.7697 (mp10) REVERT: B 781 ASP cc_start: 0.8159 (t0) cc_final: 0.7917 (m-30) REVERT: B 792 ILE cc_start: 0.9188 (tt) cc_final: 0.8916 (pt) REVERT: B 832 LEU cc_start: 0.8886 (mt) cc_final: 0.8082 (mm) REVERT: B 842 ASN cc_start: 0.8829 (m-40) cc_final: 0.8444 (m-40) REVERT: B 848 ASP cc_start: 0.8719 (m-30) cc_final: 0.8249 (m-30) REVERT: B 849 GLU cc_start: 0.8531 (tm-30) cc_final: 0.8123 (pp20) REVERT: B 855 ASP cc_start: 0.8334 (m-30) cc_final: 0.7913 (m-30) REVERT: B 873 SER cc_start: 0.8855 (m) cc_final: 0.8513 (p) REVERT: B 874 ASN cc_start: 0.8999 (m-40) cc_final: 0.8589 (p0) REVERT: B 889 LYS cc_start: 0.9174 (ttpt) cc_final: 0.8805 (ttmm) REVERT: B 914 LYS cc_start: 0.9271 (mmmt) cc_final: 0.9028 (mmmm) REVERT: B 916 LYS cc_start: 0.8850 (pttt) cc_final: 0.8493 (ptmm) REVERT: B 924 GLU cc_start: 0.8570 (OUTLIER) cc_final: 0.8290 (tm-30) REVERT: B 998 MET cc_start: 0.8830 (mmt) cc_final: 0.8533 (tpp) REVERT: B 999 ASP cc_start: 0.8479 (t0) cc_final: 0.8064 (t0) REVERT: B 1004 ASN cc_start: 0.8492 (m-40) cc_final: 0.8180 (m-40) REVERT: B 1030 LEU cc_start: 0.8924 (mt) cc_final: 0.8715 (mm) REVERT: B 1042 GLN cc_start: 0.9123 (mt0) cc_final: 0.8842 (tm-30) REVERT: B 1054 LYS cc_start: 0.9167 (mttt) cc_final: 0.8940 (mmmm) REVERT: B 1075 GLN cc_start: 0.8745 (mm-40) cc_final: 0.7843 (mm-40) REVERT: B 1079 ASP cc_start: 0.8703 (m-30) cc_final: 0.8345 (m-30) REVERT: B 1095 GLN cc_start: 0.8712 (tm-30) cc_final: 0.7462 (tm-30) REVERT: B 1099 ASP cc_start: 0.8768 (m-30) cc_final: 0.7419 (m-30) REVERT: B 1112 GLU cc_start: 0.8737 (tp30) cc_final: 0.8288 (tp30) REVERT: B 1158 LYS cc_start: 0.8451 (tttm) cc_final: 0.8161 (tttt) REVERT: B 1218 LYS cc_start: 0.8568 (mtpp) cc_final: 0.8242 (mmmm) REVERT: C 15 ILE cc_start: 0.9092 (pt) cc_final: 0.8879 (pt) REVERT: C 17 ASP cc_start: 0.7567 (p0) cc_final: 0.7211 (p0) REVERT: C 53 ASP cc_start: 0.8563 (m-30) cc_final: 0.8221 (t0) REVERT: C 60 THR cc_start: 0.9187 (OUTLIER) cc_final: 0.8858 (p) REVERT: C 76 ASP cc_start: 0.8003 (t0) cc_final: 0.7735 (t0) REVERT: C 84 LYS cc_start: 0.8723 (mmmm) cc_final: 0.8235 (tptt) REVERT: C 147 GLU cc_start: 0.8419 (pp20) cc_final: 0.8163 (pp20) REVERT: C 288 SER cc_start: 0.8865 (m) cc_final: 0.8372 (t) REVERT: C 293 LYS cc_start: 0.8940 (ttpt) cc_final: 0.8662 (ptpp) REVERT: C 330 ASP cc_start: 0.8311 (p0) cc_final: 0.7978 (m-30) REVERT: C 331 LYS cc_start: 0.9096 (mttt) cc_final: 0.8686 (ttmm) REVERT: C 345 GLU cc_start: 0.8281 (tp30) cc_final: 0.8068 (tp30) REVERT: C 384 LYS cc_start: 0.8936 (pttt) cc_final: 0.8572 (pttt) REVERT: C 397 ARG cc_start: 0.8948 (mmt180) cc_final: 0.8653 (mmm-85) REVERT: C 481 PHE cc_start: 0.6972 (t80) cc_final: 0.6663 (t80) REVERT: C 500 ASN cc_start: 0.7864 (m-40) cc_final: 0.7548 (m-40) REVERT: C 537 LYS cc_start: 0.8263 (tppt) cc_final: 0.7886 (tppt) REVERT: C 772 GLU cc_start: 0.8232 (mp0) cc_final: 0.7854 (mp0) REVERT: C 832 LEU cc_start: 0.9099 (mt) cc_final: 0.8463 (mm) REVERT: C 842 ASN cc_start: 0.8795 (m-40) cc_final: 0.8462 (m-40) REVERT: C 849 GLU cc_start: 0.8291 (pp20) cc_final: 0.7916 (pp20) REVERT: C 855 ASP cc_start: 0.8303 (m-30) cc_final: 0.7930 (m-30) REVERT: C 858 GLN cc_start: 0.8834 (mt0) cc_final: 0.8628 (mm-40) REVERT: C 873 SER cc_start: 0.9072 (m) cc_final: 0.8783 (p) REVERT: C 874 ASN cc_start: 0.8927 (m-40) cc_final: 0.8691 (p0) REVERT: C 882 ASP cc_start: 0.7806 (t70) cc_final: 0.7064 (t0) REVERT: C 888 PHE cc_start: 0.7941 (m-80) cc_final: 0.7696 (m-10) REVERT: C 889 LYS cc_start: 0.9209 (ttpt) cc_final: 0.8859 (ttpp) REVERT: C 909 ASP cc_start: 0.8319 (m-30) cc_final: 0.7726 (m-30) REVERT: C 999 ASP cc_start: 0.8255 (t70) cc_final: 0.7895 (t0) REVERT: C 1045 ASN cc_start: 0.9242 (t0) cc_final: 0.9022 (t0) REVERT: C 1075 GLN cc_start: 0.8617 (mm110) cc_final: 0.7752 (mm-40) REVERT: C 1079 ASP cc_start: 0.8623 (m-30) cc_final: 0.8242 (m-30) REVERT: C 1095 GLN cc_start: 0.8709 (tm-30) cc_final: 0.7556 (tm-30) REVERT: C 1099 ASP cc_start: 0.8815 (m-30) cc_final: 0.7599 (m-30) REVERT: C 1112 GLU cc_start: 0.8700 (tp30) cc_final: 0.8362 (tp30) REVERT: C 1116 GLU cc_start: 0.8242 (mm-30) cc_final: 0.7961 (mm-30) REVERT: C 1204 LYS cc_start: 0.8830 (mttp) cc_final: 0.8516 (mtpt) REVERT: C 1208 PHE cc_start: 0.8869 (m-10) cc_final: 0.8440 (m-80) REVERT: C 1209 MET cc_start: 0.8278 (mpp) cc_final: 0.7644 (mpp) outliers start: 48 outliers final: 37 residues processed: 527 average time/residue: 0.2117 time to fit residues: 175.0970 Evaluate side-chains 518 residues out of total 3216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 477 time to evaluate : 1.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 LYS Chi-restraints excluded: chain A residue 97 ASP Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 293 LYS Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 589 ASN Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 703 LEU Chi-restraints excluded: chain A residue 820 LEU Chi-restraints excluded: chain A residue 850 VAL Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 1097 LEU Chi-restraints excluded: chain A residue 1102 LEU Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 293 LYS Chi-restraints excluded: chain B residue 535 GLN Chi-restraints excluded: chain B residue 575 LEU Chi-restraints excluded: chain B residue 588 CYS Chi-restraints excluded: chain B residue 924 GLU Chi-restraints excluded: chain B residue 940 CYS Chi-restraints excluded: chain B residue 1017 LEU Chi-restraints excluded: chain B residue 1212 CYS Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 69 LYS Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 588 CYS Chi-restraints excluded: chain C residue 776 VAL Chi-restraints excluded: chain C residue 850 VAL Chi-restraints excluded: chain C residue 950 LEU Chi-restraints excluded: chain C residue 1064 GLU Chi-restraints excluded: chain C residue 1167 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 33 optimal weight: 5.9990 chunk 55 optimal weight: 20.0000 chunk 233 optimal weight: 0.0870 chunk 282 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 264 optimal weight: 0.9990 chunk 266 optimal weight: 2.9990 chunk 124 optimal weight: 0.7980 chunk 348 optimal weight: 5.9990 chunk 163 optimal weight: 3.9990 chunk 305 optimal weight: 0.0770 overall best weight: 0.9920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 160 HIS ** A 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 160 HIS ** B 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 748 ASN ** C 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 867 GLN ** C 880 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.101433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.080064 restraints weight = 63022.196| |-----------------------------------------------------------------------------| r_work (start): 0.3103 rms_B_bonded: 3.83 r_work: 0.2925 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.4189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 30177 Z= 0.141 Angle : 0.625 11.053 41256 Z= 0.319 Chirality : 0.044 0.410 4842 Planarity : 0.004 0.056 5124 Dihedral : 4.437 28.893 3867 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 1.55 % Allowed : 17.60 % Favored : 80.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.45 (0.14), residues: 3573 helix: 2.01 (0.19), residues: 768 sheet: -0.09 (0.18), residues: 777 loop : -1.35 (0.13), residues: 2028 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 206 TYR 0.037 0.001 TYR C 713 PHE 0.023 0.001 PHE B 714 TRP 0.011 0.001 TRP C 646 HIS 0.004 0.001 HIS A 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.14 (30018) covalent geometry : angle 0.60375 / 0.31 (40851) SS BOND : bond 0.00360 / 0.23 ( 72) SS BOND : angle 1.73794 / 1.24 ( 144) hydrogen bonds : bond 0.04065 / 2.66 ( 1016) hydrogen bonds : angle 4.80353 / 3.21 ( 3102) link_BETA1-4 : bond 0.00411 / 0.26 ( 30) link_BETA1-4 : angle 1.53790 / 1.04 ( 90) link_NAG-ASN : bond 0.00483 / 0.36 ( 57) link_NAG-ASN : angle 1.80340 / 1.12 ( 171) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7146 Ramachandran restraints generated. 3573 Oldfield, 0 Emsley, 3573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7146 Ramachandran restraints generated. 3573 Oldfield, 0 Emsley, 3573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 540 residues out of total 3216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 490 time to evaluate : 1.130 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 TYR cc_start: 0.9220 (m-80) cc_final: 0.8952 (m-80) REVERT: A 140 GLN cc_start: 0.7720 (tm-30) cc_final: 0.6825 (tm-30) REVERT: A 142 HIS cc_start: 0.8315 (m90) cc_final: 0.6921 (m90) REVERT: A 175 HIS cc_start: 0.8655 (p-80) cc_final: 0.8304 (p-80) REVERT: A 218 MET cc_start: 0.8456 (mmm) cc_final: 0.7975 (mmm) REVERT: A 273 ARG cc_start: 0.8568 (tpp80) cc_final: 0.8363 (mpp80) REVERT: A 288 SER cc_start: 0.8867 (m) cc_final: 0.8459 (t) REVERT: A 305 ASP cc_start: 0.8149 (p0) cc_final: 0.7809 (p0) REVERT: A 319 ARG cc_start: 0.8603 (mmm160) cc_final: 0.8170 (mmm-85) REVERT: A 331 LYS cc_start: 0.9050 (mtpt) cc_final: 0.8778 (mtpp) REVERT: A 336 PHE cc_start: 0.8289 (m-10) cc_final: 0.7885 (m-80) REVERT: A 376 SER cc_start: 0.9046 (m) cc_final: 0.8645 (p) REVERT: A 384 LYS cc_start: 0.8779 (pttt) cc_final: 0.8524 (pttt) REVERT: A 388 LEU cc_start: 0.9123 (OUTLIER) cc_final: 0.8914 (mt) REVERT: A 411 SER cc_start: 0.9149 (t) cc_final: 0.8938 (p) REVERT: A 437 ASN cc_start: 0.8684 (t0) cc_final: 0.8354 (t0) REVERT: A 446 ARG cc_start: 0.8596 (ttm-80) cc_final: 0.8178 (mtm-85) REVERT: A 553 GLU cc_start: 0.8317 (mm-30) cc_final: 0.7781 (mm-30) REVERT: A 611 GLN cc_start: 0.8794 (mp10) cc_final: 0.8528 (mp10) REVERT: A 618 THR cc_start: 0.9252 (OUTLIER) cc_final: 0.9024 (m) REVERT: A 711 GLN cc_start: 0.8500 (pm20) cc_final: 0.7940 (mp10) REVERT: A 717 TYR cc_start: 0.9007 (t80) cc_final: 0.8746 (t80) REVERT: A 772 GLU cc_start: 0.8436 (mp0) cc_final: 0.7948 (mp0) REVERT: A 781 ASP cc_start: 0.8056 (m-30) cc_final: 0.7292 (m-30) REVERT: A 792 ILE cc_start: 0.9145 (tp) cc_final: 0.8841 (pt) REVERT: A 805 GLU cc_start: 0.7986 (tm-30) cc_final: 0.7695 (tm-30) REVERT: A 842 ASN cc_start: 0.8929 (m-40) cc_final: 0.8673 (m-40) REVERT: A 844 ASN cc_start: 0.8977 (m-40) cc_final: 0.7994 (m-40) REVERT: A 848 ASP cc_start: 0.8577 (m-30) cc_final: 0.8159 (m-30) REVERT: A 867 GLN cc_start: 0.8173 (mm-40) cc_final: 0.7868 (mm110) REVERT: A 871 LEU cc_start: 0.9047 (OUTLIER) cc_final: 0.8793 (mp) REVERT: A 874 ASN cc_start: 0.8839 (m-40) cc_final: 0.8536 (p0) REVERT: A 889 LYS cc_start: 0.9047 (ttpt) cc_final: 0.8768 (ttpp) REVERT: A 909 ASP cc_start: 0.8514 (m-30) cc_final: 0.7893 (m-30) REVERT: A 999 ASP cc_start: 0.8582 (t0) cc_final: 0.8037 (t0) REVERT: A 1054 LYS cc_start: 0.9136 (mttt) cc_final: 0.8731 (mtpp) REVERT: A 1075 GLN cc_start: 0.8677 (mm-40) cc_final: 0.7793 (mm-40) REVERT: A 1079 ASP cc_start: 0.8736 (m-30) cc_final: 0.8270 (m-30) REVERT: A 1095 GLN cc_start: 0.8644 (tm-30) cc_final: 0.7133 (tm-30) REVERT: A 1099 ASP cc_start: 0.8756 (m-30) cc_final: 0.7365 (m-30) REVERT: A 1112 GLU cc_start: 0.8710 (tt0) cc_final: 0.8345 (tp30) REVERT: A 1153 LYS cc_start: 0.8761 (tppt) cc_final: 0.8528 (tptp) REVERT: A 1177 LYS cc_start: 0.8708 (tppt) cc_final: 0.8257 (tppt) REVERT: A 1178 GLN cc_start: 0.8708 (tt0) cc_final: 0.8436 (tt0) REVERT: B 69 LYS cc_start: 0.9210 (tmtt) cc_final: 0.8800 (tmmt) REVERT: B 88 LEU cc_start: 0.9029 (mp) cc_final: 0.8697 (tp) REVERT: B 92 LYS cc_start: 0.8939 (mtmm) cc_final: 0.8697 (mtpp) REVERT: B 111 LEU cc_start: 0.8929 (mm) cc_final: 0.8394 (mt) REVERT: B 175 HIS cc_start: 0.8729 (p-80) cc_final: 0.8200 (p-80) REVERT: B 271 ASP cc_start: 0.7766 (p0) cc_final: 0.7454 (p0) REVERT: B 273 ARG cc_start: 0.8649 (OUTLIER) cc_final: 0.8408 (mtp-110) REVERT: B 319 ARG cc_start: 0.8909 (mmm-85) cc_final: 0.8675 (mmm-85) REVERT: B 326 ASP cc_start: 0.7015 (t70) cc_final: 0.6759 (t0) REVERT: B 331 LYS cc_start: 0.9269 (mttt) cc_final: 0.8822 (ttmm) REVERT: B 384 LYS cc_start: 0.8754 (pttt) cc_final: 0.8299 (pttp) REVERT: B 397 ARG cc_start: 0.8879 (mmt180) cc_final: 0.8446 (mmm-85) REVERT: B 400 ASP cc_start: 0.8426 (m-30) cc_final: 0.8029 (m-30) REVERT: B 411 SER cc_start: 0.9311 (t) cc_final: 0.8941 (p) REVERT: B 417 ASP cc_start: 0.8486 (t0) cc_final: 0.8210 (t0) REVERT: B 446 ARG cc_start: 0.8720 (ttm110) cc_final: 0.8318 (ttm110) REVERT: B 448 TYR cc_start: 0.8908 (m-80) cc_final: 0.8651 (m-10) REVERT: B 529 ASP cc_start: 0.8337 (t70) cc_final: 0.7698 (t0) REVERT: B 536 LYS cc_start: 0.8424 (mmtp) cc_final: 0.8130 (mptt) REVERT: B 587 ARG cc_start: 0.8398 (mtp85) cc_final: 0.8076 (ttm-80) REVERT: B 711 GLN cc_start: 0.8274 (pm20) cc_final: 0.7718 (mp10) REVERT: B 792 ILE cc_start: 0.9206 (tt) cc_final: 0.8947 (pt) REVERT: B 832 LEU cc_start: 0.8928 (mt) cc_final: 0.8055 (mm) REVERT: B 842 ASN cc_start: 0.8806 (m-40) cc_final: 0.8496 (m-40) REVERT: B 848 ASP cc_start: 0.8709 (m-30) cc_final: 0.8232 (m-30) REVERT: B 849 GLU cc_start: 0.8478 (tm-30) cc_final: 0.8064 (pp20) REVERT: B 855 ASP cc_start: 0.8326 (m-30) cc_final: 0.7901 (m-30) REVERT: B 873 SER cc_start: 0.8835 (m) cc_final: 0.8481 (p) REVERT: B 889 LYS cc_start: 0.9156 (ttpt) cc_final: 0.8759 (ttmm) REVERT: B 914 LYS cc_start: 0.9359 (mmmt) cc_final: 0.9046 (mmmm) REVERT: B 916 LYS cc_start: 0.8852 (pttt) cc_final: 0.8497 (ptmm) REVERT: B 924 GLU cc_start: 0.8561 (OUTLIER) cc_final: 0.8276 (tm-30) REVERT: B 998 MET cc_start: 0.8805 (mmt) cc_final: 0.8557 (tpp) REVERT: B 999 ASP cc_start: 0.8443 (t0) cc_final: 0.8026 (t0) REVERT: B 1003 LYS cc_start: 0.9016 (ttpp) cc_final: 0.8776 (ttpp) REVERT: B 1004 ASN cc_start: 0.8469 (m-40) cc_final: 0.8059 (m-40) REVERT: B 1042 GLN cc_start: 0.9112 (mt0) cc_final: 0.8823 (tm-30) REVERT: B 1054 LYS cc_start: 0.9146 (mttt) cc_final: 0.8926 (mmmm) REVERT: B 1075 GLN cc_start: 0.8691 (mm-40) cc_final: 0.7789 (mm-40) REVERT: B 1079 ASP cc_start: 0.8669 (m-30) cc_final: 0.8306 (m-30) REVERT: B 1095 GLN cc_start: 0.8670 (tm-30) cc_final: 0.7397 (tm-30) REVERT: B 1099 ASP cc_start: 0.8747 (m-30) cc_final: 0.7407 (m-30) REVERT: B 1112 GLU cc_start: 0.8673 (tp30) cc_final: 0.8227 (tp30) REVERT: B 1158 LYS cc_start: 0.8467 (tttm) cc_final: 0.8177 (tttt) REVERT: B 1218 LYS cc_start: 0.8565 (mtpp) cc_final: 0.8230 (mmmm) REVERT: C 15 ILE cc_start: 0.9094 (pt) cc_final: 0.8885 (pt) REVERT: C 17 ASP cc_start: 0.7516 (p0) cc_final: 0.7165 (p0) REVERT: C 18 PHE cc_start: 0.8193 (t80) cc_final: 0.7724 (t80) REVERT: C 53 ASP cc_start: 0.8546 (m-30) cc_final: 0.8170 (t0) REVERT: C 60 THR cc_start: 0.9175 (OUTLIER) cc_final: 0.8845 (p) REVERT: C 76 ASP cc_start: 0.7945 (t0) cc_final: 0.7708 (t0) REVERT: C 84 LYS cc_start: 0.8721 (mmmm) cc_final: 0.8245 (tptt) REVERT: C 147 GLU cc_start: 0.8438 (pp20) cc_final: 0.8231 (pp20) REVERT: C 288 SER cc_start: 0.8889 (m) cc_final: 0.8415 (t) REVERT: C 293 LYS cc_start: 0.8969 (ttpt) cc_final: 0.8602 (ptpp) REVERT: C 330 ASP cc_start: 0.8297 (p0) cc_final: 0.7957 (m-30) REVERT: C 331 LYS cc_start: 0.9087 (mttt) cc_final: 0.8703 (ttmm) REVERT: C 384 LYS cc_start: 0.8922 (pttt) cc_final: 0.8550 (pttt) REVERT: C 397 ARG cc_start: 0.8930 (mmt180) cc_final: 0.8633 (mmm-85) REVERT: C 481 PHE cc_start: 0.7006 (t80) cc_final: 0.6680 (t80) REVERT: C 500 ASN cc_start: 0.7874 (m-40) cc_final: 0.7559 (m-40) REVERT: C 529 ASP cc_start: 0.8223 (t70) cc_final: 0.7617 (t0) REVERT: C 537 LYS cc_start: 0.8344 (tppt) cc_final: 0.8007 (tptt) REVERT: C 772 GLU cc_start: 0.8211 (mp0) cc_final: 0.7812 (mp0) REVERT: C 832 LEU cc_start: 0.9094 (mt) cc_final: 0.8438 (mm) REVERT: C 842 ASN cc_start: 0.8791 (m-40) cc_final: 0.8448 (m-40) REVERT: C 849 GLU cc_start: 0.8290 (pp20) cc_final: 0.7894 (pp20) REVERT: C 855 ASP cc_start: 0.8294 (m-30) cc_final: 0.7925 (m-30) REVERT: C 858 GLN cc_start: 0.8792 (mt0) cc_final: 0.8427 (mm110) REVERT: C 867 GLN cc_start: 0.7684 (OUTLIER) cc_final: 0.7473 (mm-40) REVERT: C 873 SER cc_start: 0.9043 (m) cc_final: 0.8767 (p) REVERT: C 889 LYS cc_start: 0.9188 (ttpt) cc_final: 0.8853 (ttpp) REVERT: C 909 ASP cc_start: 0.8287 (m-30) cc_final: 0.7697 (m-30) REVERT: C 999 ASP cc_start: 0.8220 (t70) cc_final: 0.7871 (t0) REVERT: C 1045 ASN cc_start: 0.9233 (t0) cc_final: 0.9002 (t0) REVERT: C 1075 GLN cc_start: 0.8600 (mm110) cc_final: 0.7649 (mm-40) REVERT: C 1079 ASP cc_start: 0.8580 (m-30) cc_final: 0.8208 (m-30) REVERT: C 1095 GLN cc_start: 0.8689 (tm-30) cc_final: 0.7513 (tm-30) REVERT: C 1099 ASP cc_start: 0.8788 (m-30) cc_final: 0.7534 (m-30) REVERT: C 1112 GLU cc_start: 0.8622 (tp30) cc_final: 0.8369 (tp30) REVERT: C 1116 GLU cc_start: 0.8309 (mm-30) cc_final: 0.7939 (mm-30) REVERT: C 1204 LYS cc_start: 0.8807 (mttp) cc_final: 0.8492 (mtpt) REVERT: C 1208 PHE cc_start: 0.8872 (m-10) cc_final: 0.8452 (m-80) REVERT: C 1209 MET cc_start: 0.8236 (mpp) cc_final: 0.7602 (mpp) outliers start: 50 outliers final: 34 residues processed: 524 average time/residue: 0.2088 time to fit residues: 172.0488 Evaluate side-chains 524 residues out of total 3216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 483 time to evaluate : 1.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 LYS Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 293 LYS Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 820 LEU Chi-restraints excluded: chain A residue 850 VAL Chi-restraints excluded: chain A residue 871 LEU Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 1097 LEU Chi-restraints excluded: chain A residue 1102 LEU Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 273 ARG Chi-restraints excluded: chain B residue 293 LYS Chi-restraints excluded: chain B residue 535 GLN Chi-restraints excluded: chain B residue 575 LEU Chi-restraints excluded: chain B residue 924 GLU Chi-restraints excluded: chain B residue 981 ILE Chi-restraints excluded: chain B residue 1017 LEU Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 588 CYS Chi-restraints excluded: chain C residue 589 ASN Chi-restraints excluded: chain C residue 610 LEU Chi-restraints excluded: chain C residue 621 CYS Chi-restraints excluded: chain C residue 699 CYS Chi-restraints excluded: chain C residue 776 VAL Chi-restraints excluded: chain C residue 850 VAL Chi-restraints excluded: chain C residue 867 GLN Chi-restraints excluded: chain C residue 950 LEU Chi-restraints excluded: chain C residue 1064 GLU Chi-restraints excluded: chain C residue 1167 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 167 optimal weight: 0.0980 chunk 249 optimal weight: 4.9990 chunk 54 optimal weight: 20.0000 chunk 331 optimal weight: 3.9990 chunk 269 optimal weight: 0.9990 chunk 312 optimal weight: 1.9990 chunk 267 optimal weight: 0.5980 chunk 63 optimal weight: 2.9990 chunk 166 optimal weight: 5.9990 chunk 162 optimal weight: 3.9990 chunk 198 optimal weight: 0.6980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 748 ASN ** C 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 867 GLN ** C 880 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.101539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.080147 restraints weight = 62970.926| |-----------------------------------------------------------------------------| r_work (start): 0.3106 rms_B_bonded: 3.83 r_work: 0.2929 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.4252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 30177 Z= 0.136 Angle : 0.630 11.327 41256 Z= 0.323 Chirality : 0.044 0.382 4842 Planarity : 0.004 0.056 5124 Dihedral : 4.424 28.615 3867 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 1.31 % Allowed : 18.22 % Favored : 80.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.43 (0.14), residues: 3573 helix: 1.98 (0.19), residues: 768 sheet: -0.04 (0.18), residues: 777 loop : -1.34 (0.13), residues: 2028 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 904 TYR 0.038 0.001 TYR C 713 PHE 0.035 0.001 PHE C 888 TRP 0.015 0.001 TRP C 174 HIS 0.004 0.001 HIS A1184 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.14 (30018) covalent geometry : angle 0.61053 / 0.32 (40851) SS BOND : bond 0.00324 / 0.20 ( 72) SS BOND : angle 1.68899 / 1.21 ( 144) hydrogen bonds : bond 0.03979 / 2.61 ( 1016) hydrogen bonds : angle 4.76474 / 3.19 ( 3102) link_BETA1-4 : bond 0.00396 / 0.25 ( 30) link_BETA1-4 : angle 1.51699 / 1.02 ( 90) link_NAG-ASN : bond 0.00422 / 0.31 ( 57) link_NAG-ASN : angle 1.78108 / 1.11 ( 171) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7146 Ramachandran restraints generated. 3573 Oldfield, 0 Emsley, 3573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7146 Ramachandran restraints generated. 3573 Oldfield, 0 Emsley, 3573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 530 residues out of total 3216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 488 time to evaluate : 1.152 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 TYR cc_start: 0.9211 (m-80) cc_final: 0.8959 (m-80) REVERT: A 140 GLN cc_start: 0.7722 (tm-30) cc_final: 0.6822 (tm-30) REVERT: A 142 HIS cc_start: 0.8306 (m90) cc_final: 0.6902 (m90) REVERT: A 175 HIS cc_start: 0.8674 (p-80) cc_final: 0.8296 (p-80) REVERT: A 218 MET cc_start: 0.8471 (mmm) cc_final: 0.8003 (mmm) REVERT: A 273 ARG cc_start: 0.8544 (tpp80) cc_final: 0.8343 (mpp80) REVERT: A 288 SER cc_start: 0.8826 (m) cc_final: 0.8420 (t) REVERT: A 319 ARG cc_start: 0.8605 (mmm160) cc_final: 0.8182 (mmm-85) REVERT: A 336 PHE cc_start: 0.8300 (m-10) cc_final: 0.7900 (m-80) REVERT: A 376 SER cc_start: 0.9049 (m) cc_final: 0.8650 (p) REVERT: A 384 LYS cc_start: 0.8780 (pttt) cc_final: 0.8498 (pttt) REVERT: A 388 LEU cc_start: 0.9120 (OUTLIER) cc_final: 0.8905 (mt) REVERT: A 411 SER cc_start: 0.9154 (t) cc_final: 0.8936 (p) REVERT: A 415 LYS cc_start: 0.8871 (tmtt) cc_final: 0.8633 (tmtt) REVERT: A 446 ARG cc_start: 0.8578 (ttm-80) cc_final: 0.8166 (mtm-85) REVERT: A 553 GLU cc_start: 0.8313 (mm-30) cc_final: 0.7791 (mm-30) REVERT: A 610 LEU cc_start: 0.9025 (tp) cc_final: 0.8810 (tp) REVERT: A 611 GLN cc_start: 0.8795 (mp10) cc_final: 0.8344 (mp10) REVERT: A 618 THR cc_start: 0.9243 (OUTLIER) cc_final: 0.9018 (m) REVERT: A 703 LEU cc_start: 0.8984 (tp) cc_final: 0.8711 (mm) REVERT: A 711 GLN cc_start: 0.8509 (pm20) cc_final: 0.7943 (mp10) REVERT: A 717 TYR cc_start: 0.8994 (t80) cc_final: 0.8766 (t80) REVERT: A 772 GLU cc_start: 0.8437 (mp0) cc_final: 0.7943 (mp0) REVERT: A 792 ILE cc_start: 0.9137 (tp) cc_final: 0.8842 (pt) REVERT: A 842 ASN cc_start: 0.8927 (m-40) cc_final: 0.8669 (m-40) REVERT: A 844 ASN cc_start: 0.8973 (m-40) cc_final: 0.7997 (m-40) REVERT: A 848 ASP cc_start: 0.8607 (m-30) cc_final: 0.8167 (m-30) REVERT: A 858 GLN cc_start: 0.8836 (mm110) cc_final: 0.8498 (mm110) REVERT: A 867 GLN cc_start: 0.8160 (mm-40) cc_final: 0.7852 (mm110) REVERT: A 871 LEU cc_start: 0.9049 (OUTLIER) cc_final: 0.8788 (mp) REVERT: A 874 ASN cc_start: 0.8832 (m-40) cc_final: 0.8507 (p0) REVERT: A 889 LYS cc_start: 0.9038 (ttpt) cc_final: 0.8733 (ttpp) REVERT: A 909 ASP cc_start: 0.8464 (m-30) cc_final: 0.7887 (m-30) REVERT: A 999 ASP cc_start: 0.8593 (t0) cc_final: 0.8107 (t0) REVERT: A 1064 GLU cc_start: 0.8532 (tp30) cc_final: 0.7871 (tp30) REVERT: A 1075 GLN cc_start: 0.8670 (mm-40) cc_final: 0.7775 (mm-40) REVERT: A 1079 ASP cc_start: 0.8712 (m-30) cc_final: 0.8243 (m-30) REVERT: A 1095 GLN cc_start: 0.8630 (tm-30) cc_final: 0.7151 (tm-30) REVERT: A 1099 ASP cc_start: 0.8768 (m-30) cc_final: 0.7364 (m-30) REVERT: A 1112 GLU cc_start: 0.8695 (tt0) cc_final: 0.8330 (tp30) REVERT: A 1153 LYS cc_start: 0.8765 (tppt) cc_final: 0.8522 (tptp) REVERT: A 1177 LYS cc_start: 0.8640 (tppt) cc_final: 0.8121 (tppt) REVERT: A 1178 GLN cc_start: 0.8720 (tt0) cc_final: 0.8449 (tt0) REVERT: A 1199 GLU cc_start: 0.7855 (mm-30) cc_final: 0.7634 (mm-30) REVERT: B 69 LYS cc_start: 0.9221 (tmtt) cc_final: 0.8824 (tmmt) REVERT: B 88 LEU cc_start: 0.9012 (mp) cc_final: 0.8672 (tp) REVERT: B 92 LYS cc_start: 0.8945 (mtmm) cc_final: 0.8708 (mtpp) REVERT: B 111 LEU cc_start: 0.8965 (mm) cc_final: 0.8402 (mt) REVERT: B 147 GLU cc_start: 0.8175 (pp20) cc_final: 0.7928 (pp20) REVERT: B 175 HIS cc_start: 0.8727 (p-80) cc_final: 0.8192 (p-80) REVERT: B 218 MET cc_start: 0.8120 (mmm) cc_final: 0.7816 (tpt) REVERT: B 319 ARG cc_start: 0.8921 (mmm-85) cc_final: 0.8691 (mmm-85) REVERT: B 326 ASP cc_start: 0.7021 (t70) cc_final: 0.6795 (t0) REVERT: B 328 ASP cc_start: 0.8094 (m-30) cc_final: 0.7810 (m-30) REVERT: B 331 LYS cc_start: 0.9259 (mttt) cc_final: 0.8805 (ttmm) REVERT: B 384 LYS cc_start: 0.8740 (pttt) cc_final: 0.8346 (pttt) REVERT: B 397 ARG cc_start: 0.8897 (mmt180) cc_final: 0.8476 (mmm-85) REVERT: B 400 ASP cc_start: 0.8424 (m-30) cc_final: 0.8018 (m-30) REVERT: B 411 SER cc_start: 0.9308 (t) cc_final: 0.8927 (p) REVERT: B 417 ASP cc_start: 0.8489 (t0) cc_final: 0.8217 (t0) REVERT: B 446 ARG cc_start: 0.8741 (ttm110) cc_final: 0.8350 (ttm110) REVERT: B 448 TYR cc_start: 0.8907 (m-80) cc_final: 0.8692 (m-10) REVERT: B 529 ASP cc_start: 0.8354 (t70) cc_final: 0.7691 (t0) REVERT: B 536 LYS cc_start: 0.8397 (mmtp) cc_final: 0.8106 (mptt) REVERT: B 544 GLU cc_start: 0.8107 (tp30) cc_final: 0.7900 (tp30) REVERT: B 587 ARG cc_start: 0.8435 (mtp85) cc_final: 0.8115 (ttm-80) REVERT: B 711 GLN cc_start: 0.8282 (pm20) cc_final: 0.7724 (mp10) REVERT: B 832 LEU cc_start: 0.8916 (mt) cc_final: 0.8658 (mm) REVERT: B 842 ASN cc_start: 0.8787 (m-40) cc_final: 0.8398 (m-40) REVERT: B 848 ASP cc_start: 0.8715 (m-30) cc_final: 0.8212 (m-30) REVERT: B 849 GLU cc_start: 0.8459 (tm-30) cc_final: 0.8054 (pp20) REVERT: B 855 ASP cc_start: 0.8293 (m-30) cc_final: 0.7863 (m-30) REVERT: B 867 GLN cc_start: 0.7637 (mm110) cc_final: 0.7300 (mp10) REVERT: B 873 SER cc_start: 0.8866 (m) cc_final: 0.8458 (p) REVERT: B 889 LYS cc_start: 0.9125 (ttpt) cc_final: 0.8741 (ttmm) REVERT: B 914 LYS cc_start: 0.9290 (mmmt) cc_final: 0.9012 (mmmm) REVERT: B 916 LYS cc_start: 0.8840 (pttt) cc_final: 0.8491 (ptmm) REVERT: B 924 GLU cc_start: 0.8548 (OUTLIER) cc_final: 0.8275 (tm-30) REVERT: B 998 MET cc_start: 0.8822 (mmt) cc_final: 0.8590 (tpp) REVERT: B 999 ASP cc_start: 0.8444 (t0) cc_final: 0.8048 (t0) REVERT: B 1004 ASN cc_start: 0.8455 (m-40) cc_final: 0.8085 (m-40) REVERT: B 1042 GLN cc_start: 0.9123 (mt0) cc_final: 0.8792 (tm-30) REVERT: B 1054 LYS cc_start: 0.9144 (mttt) cc_final: 0.8924 (mmmm) REVERT: B 1079 ASP cc_start: 0.8679 (m-30) cc_final: 0.8369 (m-30) REVERT: B 1095 GLN cc_start: 0.8666 (tm-30) cc_final: 0.7388 (tm-30) REVERT: B 1099 ASP cc_start: 0.8742 (m-30) cc_final: 0.7381 (m-30) REVERT: B 1112 GLU cc_start: 0.8671 (tp30) cc_final: 0.8236 (tp30) REVERT: B 1158 LYS cc_start: 0.8460 (tttm) cc_final: 0.8164 (tttt) REVERT: B 1209 MET cc_start: 0.8403 (mmm) cc_final: 0.8076 (tpp) REVERT: B 1218 LYS cc_start: 0.8557 (mtpp) cc_final: 0.8175 (mmmm) REVERT: C 15 ILE cc_start: 0.9103 (pt) cc_final: 0.8892 (pt) REVERT: C 17 ASP cc_start: 0.7491 (p0) cc_final: 0.7141 (p0) REVERT: C 18 PHE cc_start: 0.8047 (t80) cc_final: 0.7702 (t80) REVERT: C 53 ASP cc_start: 0.8527 (m-30) cc_final: 0.8160 (t0) REVERT: C 60 THR cc_start: 0.9188 (OUTLIER) cc_final: 0.8854 (p) REVERT: C 84 LYS cc_start: 0.8706 (mmmm) cc_final: 0.8239 (tptt) REVERT: C 288 SER cc_start: 0.8897 (m) cc_final: 0.8411 (t) REVERT: C 330 ASP cc_start: 0.8336 (p0) cc_final: 0.7987 (m-30) REVERT: C 331 LYS cc_start: 0.9093 (mttt) cc_final: 0.8709 (ttmm) REVERT: C 345 GLU cc_start: 0.8273 (tp30) cc_final: 0.8064 (tp30) REVERT: C 384 LYS cc_start: 0.8914 (pttt) cc_final: 0.8468 (pttp) REVERT: C 397 ARG cc_start: 0.8942 (mmt180) cc_final: 0.8666 (mmm-85) REVERT: C 481 PHE cc_start: 0.6992 (t80) cc_final: 0.6683 (t80) REVERT: C 500 ASN cc_start: 0.7838 (m-40) cc_final: 0.7527 (m-40) REVERT: C 529 ASP cc_start: 0.8223 (t70) cc_final: 0.7620 (t0) REVERT: C 537 LYS cc_start: 0.8390 (tppt) cc_final: 0.8117 (tptt) REVERT: C 772 GLU cc_start: 0.8220 (mp0) cc_final: 0.7826 (mp0) REVERT: C 792 ILE cc_start: 0.8988 (tp) cc_final: 0.8705 (pt) REVERT: C 832 LEU cc_start: 0.9092 (mt) cc_final: 0.8428 (mm) REVERT: C 842 ASN cc_start: 0.8765 (m-40) cc_final: 0.8439 (m-40) REVERT: C 849 GLU cc_start: 0.8271 (pp20) cc_final: 0.7942 (pp20) REVERT: C 858 GLN cc_start: 0.8780 (mt0) cc_final: 0.8423 (mm110) REVERT: C 873 SER cc_start: 0.9130 (m) cc_final: 0.8794 (p) REVERT: C 889 LYS cc_start: 0.9159 (ttpt) cc_final: 0.8807 (ttpp) REVERT: C 999 ASP cc_start: 0.8213 (t70) cc_final: 0.7865 (t0) REVERT: C 1045 ASN cc_start: 0.9231 (t0) cc_final: 0.9003 (t0) REVERT: C 1075 GLN cc_start: 0.8599 (mm110) cc_final: 0.7639 (mm-40) REVERT: C 1079 ASP cc_start: 0.8555 (m-30) cc_final: 0.8171 (m-30) REVERT: C 1095 GLN cc_start: 0.8678 (tm-30) cc_final: 0.7529 (tm-30) REVERT: C 1099 ASP cc_start: 0.8793 (m-30) cc_final: 0.7520 (m-30) REVERT: C 1104 LYS cc_start: 0.9009 (tptt) cc_final: 0.8596 (ttmm) REVERT: C 1112 GLU cc_start: 0.8605 (tp30) cc_final: 0.8344 (tp30) REVERT: C 1116 GLU cc_start: 0.8329 (mm-30) cc_final: 0.7921 (mm-30) REVERT: C 1204 LYS cc_start: 0.8790 (mttp) cc_final: 0.8464 (mtpt) REVERT: C 1208 PHE cc_start: 0.8868 (m-10) cc_final: 0.8448 (m-80) REVERT: C 1209 MET cc_start: 0.8261 (mpp) cc_final: 0.7613 (mpp) outliers start: 42 outliers final: 33 residues processed: 515 average time/residue: 0.2141 time to fit residues: 172.8188 Evaluate side-chains 513 residues out of total 3216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 475 time to evaluate : 1.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 LYS Chi-restraints excluded: chain A residue 293 LYS Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 820 LEU Chi-restraints excluded: chain A residue 850 VAL Chi-restraints excluded: chain A residue 871 LEU Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 1097 LEU Chi-restraints excluded: chain A residue 1102 LEU Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 293 LYS Chi-restraints excluded: chain B residue 535 GLN Chi-restraints excluded: chain B residue 575 LEU Chi-restraints excluded: chain B residue 924 GLU Chi-restraints excluded: chain B residue 981 ILE Chi-restraints excluded: chain B residue 1017 LEU Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 388 LEU Chi-restraints excluded: chain C residue 589 ASN Chi-restraints excluded: chain C residue 610 LEU Chi-restraints excluded: chain C residue 621 CYS Chi-restraints excluded: chain C residue 699 CYS Chi-restraints excluded: chain C residue 776 VAL Chi-restraints excluded: chain C residue 850 VAL Chi-restraints excluded: chain C residue 950 LEU Chi-restraints excluded: chain C residue 1064 GLU Chi-restraints excluded: chain C residue 1167 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 26 optimal weight: 0.5980 chunk 102 optimal weight: 0.7980 chunk 62 optimal weight: 1.9990 chunk 239 optimal weight: 20.0000 chunk 251 optimal weight: 7.9990 chunk 66 optimal weight: 5.9990 chunk 153 optimal weight: 3.9990 chunk 115 optimal weight: 2.9990 chunk 172 optimal weight: 10.0000 chunk 121 optimal weight: 2.9990 chunk 354 optimal weight: 0.0060 overall best weight: 1.2800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 160 HIS ** A 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 748 ASN ** B 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 364 HIS ** C 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 867 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.101044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.079676 restraints weight = 63512.443| |-----------------------------------------------------------------------------| r_work (start): 0.3098 rms_B_bonded: 3.84 r_work: 0.2918 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.4354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 30177 Z= 0.163 Angle : 0.640 11.355 41256 Z= 0.329 Chirality : 0.044 0.382 4842 Planarity : 0.004 0.057 5124 Dihedral : 4.455 28.699 3867 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 1.46 % Allowed : 18.35 % Favored : 80.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.45 (0.14), residues: 3573 helix: 1.98 (0.19), residues: 768 sheet: -0.05 (0.18), residues: 801 loop : -1.37 (0.14), residues: 2004 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 464 TYR 0.036 0.001 TYR B 675 PHE 0.034 0.001 PHE C 888 TRP 0.013 0.001 TRP C 174 HIS 0.006 0.001 HIS C 880 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.16 (30018) covalent geometry : angle 0.62007 / 0.32 (40851) SS BOND : bond 0.00357 / 0.21 ( 72) SS BOND : angle 1.70019 / 1.22 ( 144) hydrogen bonds : bond 0.04129 / 2.71 ( 1016) hydrogen bonds : angle 4.77290 / 3.19 ( 3102) link_BETA1-4 : bond 0.00400 / 0.26 ( 30) link_BETA1-4 : angle 1.52943 / 1.03 ( 90) link_NAG-ASN : bond 0.00419 / 0.31 ( 57) link_NAG-ASN : angle 1.80307 / 1.13 ( 171) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6890.84 seconds wall clock time: 119 minutes 30.43 seconds (7170.43 seconds total)