Starting phenix.real_space_refine on Wed Jun 25 15:03:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ohn_16882/06_2025/8ohn_16882.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ohn_16882/06_2025/8ohn_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8ohn_16882/06_2025/8ohn_16882.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ohn_16882/06_2025/8ohn_16882.map" model { file = "/net/cci-nas-00/data/ceres_data/8ohn_16882/06_2025/8ohn_16882.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ohn_16882/06_2025/8ohn_16882.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.020 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): 0.47s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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 dihedrals: 30 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 dihedrals: 30 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 dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Time building chain proxies: 17.75, per 1000 atoms: 0.61 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: 7.88 Conformation dependent library (CDL) restraints added in 3.6 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: 4.40 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: 13.58 Time building geometry restraints manager: 9.23 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 - 21.88: 17522 21.88 - 43.76: 1205 43.76 - 65.64: 167 65.64 - 87.53: 38 87.53 - 109.41: 19 Dihedral angle restraints: 18951 sinusoidal: 8418 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 18948 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: 0.10 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: 2.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.170 Check model and map are aligned: 0.210 Set scattering table: 0.250 Process input model: 69.990 Find NCS groups from input model: 1.890 Set up NCS constraints: 0.210 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:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 78.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 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 : 14.339 109.407 11973 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 3.94 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.013 0.001 TRP C 444 HIS 0.005 0.001 HIS B 201 PHE 0.026 0.001 PHE A 176 TYR 0.038 0.001 TYR C 266 ARG 0.002 0.000 ARG B 346 Details of bonding type rmsd link_NAG-ASN : bond 0.00373 ( 57) link_NAG-ASN : angle 2.04442 ( 171) link_BETA1-4 : bond 0.00832 ( 30) link_BETA1-4 : angle 2.12967 ( 90) hydrogen bonds : bond 0.21456 ( 1016) hydrogen bonds : angle 8.15339 ( 3102) SS BOND : bond 0.00320 ( 72) SS BOND : angle 1.00057 ( 144) covalent geometry : bond 0.00419 (30018) covalent geometry : angle 0.70027 (40851) *********************** 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 : 3.537 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 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: 0.6663 (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: 0.7850 (p-80) REVERT: A 186 LYS cc_start: 0.8085 (ttmt) cc_final: 0.7826 (ttmm) REVERT: A 206 ARG cc_start: 0.8309 (mtm110) cc_final: 0.7971 (ptp-110) REVERT: A 262 SER cc_start: 0.7690 (t) cc_final: 0.7268 (p) REVERT: A 316 THR cc_start: 0.8891 (m) cc_final: 0.8391 (p) REVERT: A 326 ASP cc_start: 0.7211 (t70) cc_final: 0.6422 (t0) REVERT: A 328 ASP cc_start: 0.7587 (m-30) cc_final: 0.7175 (m-30) REVERT: A 397 ARG cc_start: 0.8446 (mmt180) cc_final: 0.8206 (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: 0.8358 (p0) REVERT: A 553 GLU cc_start: 0.8386 (mm-30) cc_final: 0.7640 (mp0) REVERT: A 574 PHE cc_start: 0.8415 (m-80) cc_final: 0.7816 (m-80) REVERT: A 711 GLN cc_start: 0.7366 (pm20) cc_final: 0.6999 (mp10) REVERT: A 717 TYR cc_start: 0.8608 (t80) cc_final: 0.8381 (t80) REVERT: A 725 ASP cc_start: 0.7792 (p0) cc_final: 0.7489 (p0) REVERT: A 779 VAL cc_start: 0.8602 (t) cc_final: 0.7837 (m) REVERT: A 792 ILE cc_start: 0.8997 (tt) cc_final: 0.8538 (pt) REVERT: A 832 LEU cc_start: 0.8932 (mt) cc_final: 0.7897 (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: 0.7506 (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: 0.7570 (m-30) REVERT: A 874 ASN cc_start: 0.8409 (m-40) cc_final: 0.7740 (p0) REVERT: A 887 ASN cc_start: 0.8967 (m-40) cc_final: 0.8551 (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: 0.8334 (mt) REVERT: A 999 ASP cc_start: 0.8080 (t0) cc_final: 0.7621 (t0) REVERT: A 1005 GLN cc_start: 0.8484 (tm-30) cc_final: 0.8080 (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: 0.8560 (mmmm) REVERT: A 1079 ASP cc_start: 0.8305 (m-30) cc_final: 0.7696 (m-30) REVERT: A 1083 ASN cc_start: 0.8560 (m-40) cc_final: 0.8337 (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: 0.7618 (m100) REVERT: B 316 THR cc_start: 0.8762 (m) cc_final: 0.8126 (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: 0.8104 (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: 0.8013 (m-10) REVERT: B 450 PHE cc_start: 0.8419 (t80) cc_final: 0.7989 (t80) REVERT: B 462 TYR cc_start: 0.8109 (p90) cc_final: 0.7844 (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: 0.7580 (p0) REVERT: B 711 GLN cc_start: 0.7309 (pm20) cc_final: 0.7012 (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: 0.8197 (m-40) REVERT: B 848 ASP cc_start: 0.8154 (m-30) cc_final: 0.7713 (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: 0.7692 (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: 0.8661 (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: 0.7763 (t0) REVERT: B 1003 LYS cc_start: 0.8928 (mtpt) cc_final: 0.8503 (mtpp) REVERT: B 1004 ASN cc_start: 0.8036 (m-40) cc_final: 0.6342 (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: 0.8427 (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: 0.7244 (mm-40) REVERT: B 1079 ASP cc_start: 0.8165 (m-30) cc_final: 0.7747 (m-30) REVERT: B 1095 GLN cc_start: 0.7941 (tm-30) cc_final: 0.6490 (tm-30) REVERT: B 1099 ASP cc_start: 0.8219 (m-30) cc_final: 0.7138 (m-30) REVERT: B 1177 LYS cc_start: 0.8308 (ttmm) cc_final: 0.7949 (mmmm) REVERT: B 1210 ASN cc_start: 0.8957 (t0) cc_final: 0.8752 (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: 0.7314 (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: 0.8661 (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: 0.7829 (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: 0.6791 (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: 0.8229 (p) REVERT: C 331 LYS cc_start: 0.8451 (mttt) cc_final: 0.8145 (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: 0.8041 (p0) REVERT: C 439 TYR cc_start: 0.8164 (t80) cc_final: 0.7875 (t80) REVERT: C 448 TYR cc_start: 0.8718 (m-80) cc_final: 0.8380 (m-80) REVERT: C 460 VAL cc_start: 0.8550 (t) cc_final: 0.8343 (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: 0.7319 (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: 0.8321 (mm) REVERT: C 842 ASN cc_start: 0.8599 (m-40) cc_final: 0.8356 (m-40) REVERT: C 848 ASP cc_start: 0.8080 (m-30) cc_final: 0.7644 (m-30) REVERT: C 849 GLU cc_start: 0.7800 (mm-30) cc_final: 0.7441 (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: 0.8836 (mt) REVERT: C 998 MET cc_start: 0.8861 (tpp) cc_final: 0.8127 (mmm) REVERT: C 999 ASP cc_start: 0.8059 (t70) cc_final: 0.7543 (t0) REVERT: C 1010 THR cc_start: 0.8834 (m) cc_final: 0.8473 (p) REVERT: C 1045 ASN cc_start: 0.8882 (t0) cc_final: 0.8624 (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: 0.6869 (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: 0.8188 (t0) outliers start: 0 outliers final: 0 residues processed: 696 average time/residue: 0.4872 time to fit residues: 528.0915 Evaluate side-chains 498 residues out of total 3216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 498 time to evaluate : 3.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 301 optimal weight: 3.9990 chunk 270 optimal weight: 0.0570 chunk 150 optimal weight: 0.8980 chunk 92 optimal weight: 3.9990 chunk 182 optimal weight: 3.9990 chunk 144 optimal weight: 3.9990 chunk 279 optimal weight: 3.9990 chunk 108 optimal weight: 2.9990 chunk 170 optimal weight: 0.0970 chunk 208 optimal weight: 2.9990 chunk 324 optimal weight: 1.9990 overall best weight: 1.2100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 ASN ** 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 586 ASN A 685 GLN A 867 GLN ** B 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 364 HIS B 413 ASN ** B 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 586 ASN ** B 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 685 GLN B 858 GLN B 867 GLN B 945 ASN ** C 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 586 ASN ** C 867 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.106953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.086602 restraints weight = 63948.112| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 3.82 r_work: 0.3012 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.1997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 30177 Z= 0.165 Angle : 0.624 11.032 41256 Z= 0.319 Chirality : 0.044 0.227 4842 Planarity : 0.005 0.085 5124 Dihedral : 8.301 70.146 5688 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 1.12 % Allowed : 8.30 % Favored : 90.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.14), residues: 3573 helix: 1.50 (0.19), residues: 765 sheet: -0.26 (0.18), residues: 756 loop : -1.48 (0.13), residues: 2052 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 257 HIS 0.006 0.001 HIS C 175 PHE 0.021 0.002 PHE A 176 TYR 0.025 0.001 TYR A 713 ARG 0.008 0.001 ARG C 446 Details of bonding type rmsd link_NAG-ASN : bond 0.00366 ( 57) link_NAG-ASN : angle 1.71131 ( 171) link_BETA1-4 : bond 0.00467 ( 30) link_BETA1-4 : angle 1.83643 ( 90) hydrogen bonds : bond 0.04954 ( 1016) hydrogen bonds : angle 5.67202 ( 3102) SS BOND : bond 0.00266 ( 72) SS BOND : angle 1.23300 ( 144) covalent geometry : bond 0.00361 (30018) covalent geometry : angle 0.60703 (40851) *********************** 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 573 residues out of total 3216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 537 time to evaluate : 3.202 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: 0.8194 (m) cc_final: 0.7949 (t) REVERT: A 140 GLN cc_start: 0.7656 (tm-30) cc_final: 0.6706 (tm-30) REVERT: A 142 HIS cc_start: 0.8103 (m90) cc_final: 0.7426 (m90) REVERT: A 175 HIS cc_start: 0.8529 (p-80) cc_final: 0.8308 (p-80) REVERT: A 262 SER cc_start: 0.8088 (t) cc_final: 0.7723 (p) REVERT: A 289 GLU cc_start: 0.8747 (mt-10) cc_final: 0.8243 (mm-30) REVERT: A 326 ASP cc_start: 0.7505 (t70) cc_final: 0.6785 (t0) REVERT: A 331 LYS cc_start: 0.8744 (mtpt) cc_final: 0.8494 (mtpp) REVERT: A 376 SER cc_start: 0.9093 (m) cc_final: 0.8682 (p) REVERT: A 384 LYS cc_start: 0.8685 (pttp) cc_final: 0.8428 (pttt) REVERT: A 397 ARG cc_start: 0.8875 (mmt180) cc_final: 0.8588 (mmm-85) REVERT: A 417 ASP cc_start: 0.8399 (t70) cc_final: 0.8186 (t0) REVERT: A 437 ASN cc_start: 0.8993 (t0) cc_final: 0.8689 (t0) REVERT: A 446 ARG cc_start: 0.8789 (ttm-80) cc_final: 0.8235 (mtm-85) REVERT: A 481 PHE cc_start: 0.6577 (t80) cc_final: 0.6314 (t80) REVERT: A 535 GLN cc_start: 0.8323 (pt0) cc_final: 0.7719 (pt0) REVERT: A 536 LYS cc_start: 0.8620 (ptpp) cc_final: 0.8391 (mtmm) REVERT: A 553 GLU cc_start: 0.8368 (mm-30) cc_final: 0.7752 (mp0) REVERT: A 580 ASP cc_start: 0.8496 (t0) cc_final: 0.8009 (t0) REVERT: A 704 ASN cc_start: 0.7901 (p0) cc_final: 0.7576 (p0) REVERT: A 711 GLN cc_start: 0.8014 (pm20) cc_final: 0.7560 (mp10) REVERT: A 803 GLN cc_start: 0.8326 (tp40) cc_final: 0.8063 (tp-100) REVERT: A 842 ASN cc_start: 0.8875 (m-40) cc_final: 0.8566 (m-40) REVERT: A 844 ASN cc_start: 0.8827 (m-40) cc_final: 0.7972 (m-40) REVERT: A 848 ASP cc_start: 0.8491 (m-30) cc_final: 0.8046 (m-30) REVERT: A 858 GLN cc_start: 0.8684 (mm110) cc_final: 0.8355 (mm110) REVERT: A 867 GLN cc_start: 0.7777 (mm110) cc_final: 0.7519 (mm-40) REVERT: A 874 ASN cc_start: 0.8761 (m-40) cc_final: 0.8212 (p0) REVERT: A 889 LYS cc_start: 0.9042 (ttpt) cc_final: 0.8709 (ttpp) REVERT: A 909 ASP cc_start: 0.8532 (m-30) cc_final: 0.7836 (m-30) REVERT: A 999 ASP cc_start: 0.8527 (t0) cc_final: 0.8011 (t0) REVERT: A 1010 THR cc_start: 0.9234 (m) cc_final: 0.8892 (p) REVERT: A 1054 LYS cc_start: 0.9163 (mttt) cc_final: 0.8885 (mtpp) REVERT: A 1079 ASP cc_start: 0.8802 (m-30) cc_final: 0.8189 (m-30) REVERT: A 1095 GLN cc_start: 0.8687 (tm-30) cc_final: 0.8182 (tm-30) REVERT: A 1112 GLU cc_start: 0.8737 (tt0) cc_final: 0.8362 (tp30) REVERT: A 1177 LYS cc_start: 0.8340 (tppt) cc_final: 0.8050 (tppt) REVERT: A 1189 MET cc_start: 0.8255 (mtt) cc_final: 0.7915 (mtt) REVERT: A 1209 MET cc_start: 0.8374 (mtt) cc_final: 0.8006 (mtt) REVERT: B 69 LYS cc_start: 0.9100 (tmtt) cc_final: 0.8748 (ttpp) REVERT: B 88 LEU cc_start: 0.9156 (mp) cc_final: 0.8877 (tp) REVERT: B 107 LYS cc_start: 0.8519 (tttt) cc_final: 0.7998 (ttmt) REVERT: B 131 ILE cc_start: 0.9054 (mp) cc_final: 0.8801 (tp) REVERT: B 133 ASN cc_start: 0.8514 (p0) cc_final: 0.8180 (p0) REVERT: B 142 HIS cc_start: 0.8235 (m-70) cc_final: 0.7444 (m-70) REVERT: B 175 HIS cc_start: 0.8679 (p-80) cc_final: 0.8184 (p-80) REVERT: B 197 TRP cc_start: 0.8335 (m100) cc_final: 0.7776 (m100) REVERT: B 206 ARG cc_start: 0.8897 (ptp90) cc_final: 0.8675 (ptp90) REVERT: B 293 LYS cc_start: 0.8882 (OUTLIER) cc_final: 0.8669 (pttp) REVERT: B 326 ASP cc_start: 0.7455 (t70) cc_final: 0.6609 (t0) REVERT: B 328 ASP cc_start: 0.8074 (m-30) cc_final: 0.7373 (m-30) REVERT: B 331 LYS cc_start: 0.8973 (mttt) cc_final: 0.8540 (mtpp) REVERT: B 397 ARG cc_start: 0.8823 (mmt180) cc_final: 0.8242 (mmm-85) REVERT: B 400 ASP cc_start: 0.8316 (m-30) cc_final: 0.7821 (m-30) REVERT: B 411 SER cc_start: 0.9364 (t) cc_final: 0.8957 (p) REVERT: B 448 TYR cc_start: 0.8742 (m-80) cc_final: 0.8418 (m-10) REVERT: B 607 ASN cc_start: 0.8202 (t0) cc_final: 0.7977 (t0) REVERT: B 615 GLU cc_start: 0.7760 (tm-30) cc_final: 0.7403 (tm-30) REVERT: B 636 LYS cc_start: 0.8823 (mttt) cc_final: 0.8607 (mtmt) REVERT: B 646 TRP cc_start: 0.8355 (p90) cc_final: 0.8098 (p90) REVERT: B 653 PHE cc_start: 0.8607 (p90) cc_final: 0.8360 (p90) REVERT: B 678 ARG cc_start: 0.7677 (ttp-170) cc_final: 0.7426 (ttm-80) REVERT: B 711 GLN cc_start: 0.7921 (pm20) cc_final: 0.7525 (mp10) REVERT: B 772 GLU cc_start: 0.8036 (mp0) cc_final: 0.7668 (mp0) REVERT: B 792 ILE cc_start: 0.9150 (tt) cc_final: 0.8814 (pt) REVERT: B 842 ASN cc_start: 0.8853 (m-40) cc_final: 0.8534 (m-40) REVERT: B 848 ASP cc_start: 0.8653 (m-30) cc_final: 0.8249 (m-30) REVERT: B 855 ASP cc_start: 0.8238 (m-30) cc_final: 0.8014 (m-30) REVERT: B 867 GLN cc_start: 0.7587 (mm110) cc_final: 0.7380 (mm-40) REVERT: B 874 ASN cc_start: 0.8566 (m-40) cc_final: 0.7987 (p0) REVERT: B 887 ASN cc_start: 0.8787 (m-40) cc_final: 0.8563 (t0) REVERT: B 889 LYS cc_start: 0.9084 (ttpt) cc_final: 0.8751 (ttmm) REVERT: B 916 LYS cc_start: 0.8598 (pttt) cc_final: 0.8226 (ptmm) REVERT: B 924 GLU cc_start: 0.8478 (OUTLIER) cc_final: 0.8211 (tm-30) REVERT: B 999 ASP cc_start: 0.8461 (t0) cc_final: 0.8055 (t0) REVERT: B 1003 LYS cc_start: 0.9116 (mtpt) cc_final: 0.8712 (mtpp) REVERT: B 1004 ASN cc_start: 0.8389 (m-40) cc_final: 0.6655 (t0) REVERT: B 1006 LYS cc_start: 0.9252 (mmmm) cc_final: 0.8888 (mmmm) REVERT: B 1010 THR cc_start: 0.9160 (m) cc_final: 0.8865 (p) REVERT: B 1045 ASN cc_start: 0.9093 (t0) cc_final: 0.8862 (t0) REVERT: B 1054 LYS cc_start: 0.9098 (mttt) cc_final: 0.8789 (mmmm) REVERT: B 1075 GLN cc_start: 0.8451 (mm-40) cc_final: 0.7757 (mm-40) REVERT: B 1079 ASP cc_start: 0.8643 (m-30) cc_final: 0.8344 (m-30) REVERT: B 1095 GLN cc_start: 0.8622 (tm-30) cc_final: 0.7516 (tm-30) REVERT: B 1099 ASP cc_start: 0.8850 (m-30) cc_final: 0.7908 (m-30) REVERT: B 1208 PHE cc_start: 0.9116 (m-10) cc_final: 0.8720 (m-80) REVERT: B 1209 MET cc_start: 0.8440 (mmm) cc_final: 0.8227 (mpp) REVERT: B 1216 PHE cc_start: 0.7901 (m-10) cc_final: 0.7504 (m-80) REVERT: C 53 ASP cc_start: 0.8422 (m-30) cc_final: 0.7971 (m-30) REVERT: C 92 LYS cc_start: 0.9141 (mttt) cc_final: 0.8726 (mtpp) REVERT: C 140 GLN cc_start: 0.7856 (tm-30) cc_final: 0.7437 (tm-30) REVERT: C 262 SER cc_start: 0.7977 (t) cc_final: 0.7607 (p) REVERT: C 288 SER cc_start: 0.8942 (m) cc_final: 0.8427 (t) REVERT: C 289 GLU cc_start: 0.8732 (mt-10) cc_final: 0.8430 (tm-30) REVERT: C 293 LYS cc_start: 0.8974 (ttpt) cc_final: 0.8695 (ttpt) REVERT: C 330 ASP cc_start: 0.8191 (p0) cc_final: 0.7935 (p0) REVERT: C 331 LYS cc_start: 0.8960 (mttt) cc_final: 0.8407 (mtpp) REVERT: C 397 ARG cc_start: 0.8862 (mmt180) cc_final: 0.8498 (mmm-85) REVERT: C 437 ASN cc_start: 0.8734 (t0) cc_final: 0.8414 (t0) REVERT: C 439 TYR cc_start: 0.8448 (t80) cc_final: 0.8133 (t80) REVERT: C 460 VAL cc_start: 0.9043 (t) cc_final: 0.8762 (p) REVERT: C 481 PHE cc_start: 0.6762 (t80) cc_final: 0.6464 (t80) REVERT: C 500 ASN cc_start: 0.7825 (m-40) cc_final: 0.7559 (m-40) REVERT: C 579 TYR cc_start: 0.8583 (p90) cc_final: 0.8308 (p90) REVERT: C 580 ASP cc_start: 0.8207 (t0) cc_final: 0.7994 (t0) REVERT: C 587 ARG cc_start: 0.8533 (mtp85) cc_final: 0.8306 (mtp85) REVERT: C 632 GLN cc_start: 0.8736 (pt0) cc_final: 0.8414 (pp30) REVERT: C 678 ARG cc_start: 0.7343 (ttm-80) cc_final: 0.7056 (ttm170) REVERT: C 704 ASN cc_start: 0.7561 (p0) cc_final: 0.7256 (p0) REVERT: C 772 GLU cc_start: 0.7977 (mp0) cc_final: 0.7538 (mp0) REVERT: C 832 LEU cc_start: 0.9146 (mt) cc_final: 0.8871 (mm) REVERT: C 842 ASN cc_start: 0.8867 (m-40) cc_final: 0.8620 (m-40) REVERT: C 848 ASP cc_start: 0.8651 (m-30) cc_final: 0.8256 (m-30) REVERT: C 873 SER cc_start: 0.8863 (m) cc_final: 0.8643 (p) REVERT: C 874 ASN cc_start: 0.8683 (m-40) cc_final: 0.8033 (p0) REVERT: C 888 PHE cc_start: 0.8368 (m-10) cc_final: 0.7932 (m-10) REVERT: C 889 LYS cc_start: 0.9236 (ttpt) cc_final: 0.8947 (ttpp) REVERT: C 909 ASP cc_start: 0.8517 (m-30) cc_final: 0.7879 (m-30) REVERT: C 971 MET cc_start: 0.8106 (ttt) cc_final: 0.7905 (ttt) REVERT: C 998 MET cc_start: 0.8968 (tpp) cc_final: 0.8350 (tpp) REVERT: C 999 ASP cc_start: 0.8275 (t70) cc_final: 0.7775 (t0) REVERT: C 1010 THR cc_start: 0.9072 (m) cc_final: 0.8704 (p) REVERT: C 1045 ASN cc_start: 0.9263 (t0) cc_final: 0.9045 (t0) REVERT: C 1075 GLN cc_start: 0.8495 (mm-40) cc_final: 0.7466 (mm-40) REVERT: C 1079 ASP cc_start: 0.8633 (m-30) cc_final: 0.8306 (m-30) REVERT: C 1095 GLN cc_start: 0.8633 (tm-30) cc_final: 0.7555 (tm-30) REVERT: C 1099 ASP cc_start: 0.8822 (m-30) cc_final: 0.7489 (m-30) REVERT: C 1104 LYS cc_start: 0.8993 (tptt) cc_final: 0.8767 (tptp) REVERT: C 1105 LEU cc_start: 0.9025 (mt) cc_final: 0.8731 (tt) REVERT: C 1112 GLU cc_start: 0.8650 (tp30) cc_final: 0.8267 (tp30) REVERT: C 1126 ASN cc_start: 0.9035 (m-40) cc_final: 0.8609 (t0) REVERT: C 1216 PHE cc_start: 0.7631 (m-80) cc_final: 0.7377 (m-80) outliers start: 36 outliers final: 14 residues processed: 556 average time/residue: 0.4538 time to fit residues: 393.0735 Evaluate side-chains 495 residues out of total 3216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 479 time to evaluate : 3.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 ASN 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 293 LYS Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 321 ILE 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 1159 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 343 optimal weight: 4.9990 chunk 74 optimal weight: 3.9990 chunk 261 optimal weight: 8.9990 chunk 130 optimal weight: 0.6980 chunk 94 optimal weight: 0.0570 chunk 176 optimal weight: 1.9990 chunk 173 optimal weight: 0.0570 chunk 66 optimal weight: 10.0000 chunk 172 optimal weight: 0.8980 chunk 100 optimal weight: 0.8980 chunk 33 optimal weight: 0.7980 overall best weight: 0.5016 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 611 GLN ** B 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 364 HIS ** B 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 607 ASN B1042 GLN C 364 HIS ** C 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 887 ASN C1139 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.107532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.087189 restraints weight = 63361.091| |-----------------------------------------------------------------------------| r_work (start): 0.3199 rms_B_bonded: 3.81 r_work: 0.3019 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.2501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 30177 Z= 0.114 Angle : 0.585 10.139 41256 Z= 0.298 Chirality : 0.043 0.210 4842 Planarity : 0.004 0.064 5124 Dihedral : 7.215 59.839 5688 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 1.12 % Allowed : 11.16 % Favored : 87.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.14), residues: 3573 helix: 1.71 (0.19), residues: 768 sheet: -0.12 (0.18), residues: 753 loop : -1.45 (0.13), residues: 2052 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP B 257 HIS 0.013 0.001 HIS B 142 PHE 0.017 0.001 PHE A 907 TYR 0.027 0.001 TYR C 713 ARG 0.004 0.000 ARG C 464 Details of bonding type rmsd link_NAG-ASN : bond 0.00378 ( 57) link_NAG-ASN : angle 1.61505 ( 171) link_BETA1-4 : bond 0.00460 ( 30) link_BETA1-4 : angle 1.74221 ( 90) hydrogen bonds : bond 0.04142 ( 1016) hydrogen bonds : angle 5.21990 ( 3102) SS BOND : bond 0.00365 ( 72) SS BOND : angle 1.15101 ( 144) covalent geometry : bond 0.00254 (30018) covalent geometry : angle 0.56880 (40851) *********************** 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 540 residues out of total 3216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 504 time to evaluate : 3.218 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: 0.8169 (m) cc_final: 0.7924 (t) REVERT: A 114 ASN cc_start: 0.8584 (m-40) cc_final: 0.8139 (p0) REVERT: A 133 ASN cc_start: 0.8734 (p0) cc_final: 0.8516 (p0) REVERT: A 140 GLN cc_start: 0.7668 (tm-30) cc_final: 0.6740 (tm-30) REVERT: A 142 HIS cc_start: 0.8356 (m90) cc_final: 0.7313 (m90) REVERT: A 175 HIS cc_start: 0.8522 (p-80) cc_final: 0.8269 (p-80) REVERT: A 262 SER cc_start: 0.8217 (t) cc_final: 0.7832 (p) REVERT: A 288 SER cc_start: 0.8764 (m) cc_final: 0.8379 (p) REVERT: A 289 GLU cc_start: 0.8707 (mt-10) cc_final: 0.8249 (mm-30) REVERT: A 326 ASP cc_start: 0.7512 (t70) cc_final: 0.7100 (t0) REVERT: A 331 LYS cc_start: 0.8858 (mtpt) cc_final: 0.8538 (mtpp) REVERT: A 376 SER cc_start: 0.9068 (m) cc_final: 0.8674 (p) REVERT: A 384 LYS cc_start: 0.8709 (pttp) cc_final: 0.8402 (pttt) REVERT: A 397 ARG cc_start: 0.8834 (mmt180) cc_final: 0.8537 (mmm-85) REVERT: A 437 ASN cc_start: 0.8967 (t0) cc_final: 0.8632 (t0) REVERT: A 446 ARG cc_start: 0.8658 (ttm-80) cc_final: 0.7906 (mtm-85) REVERT: A 553 GLU cc_start: 0.8337 (mm-30) cc_final: 0.8002 (mm-30) REVERT: A 618 THR cc_start: 0.9203 (OUTLIER) cc_final: 0.8938 (m) REVERT: A 704 ASN cc_start: 0.7807 (p0) cc_final: 0.7580 (p0) REVERT: A 711 GLN cc_start: 0.8120 (pm20) cc_final: 0.7669 (mp10) REVERT: A 772 GLU cc_start: 0.8300 (mp0) cc_final: 0.8027 (mp0) REVERT: A 803 GLN cc_start: 0.8413 (tp40) cc_final: 0.8122 (tp-100) REVERT: A 842 ASN cc_start: 0.8937 (m-40) cc_final: 0.8649 (m-40) REVERT: A 844 ASN cc_start: 0.8798 (m-40) cc_final: 0.7936 (m-40) REVERT: A 848 ASP cc_start: 0.8478 (m-30) cc_final: 0.8033 (m-30) REVERT: A 858 GLN cc_start: 0.8695 (mm110) cc_final: 0.8335 (mm110) REVERT: A 874 ASN cc_start: 0.8718 (m-40) cc_final: 0.8205 (p0) REVERT: A 889 LYS cc_start: 0.8996 (ttpt) cc_final: 0.8674 (ttpp) REVERT: A 909 ASP cc_start: 0.8590 (m-30) cc_final: 0.7929 (m-30) REVERT: A 924 GLU cc_start: 0.8432 (OUTLIER) cc_final: 0.8181 (tm-30) REVERT: A 999 ASP cc_start: 0.8487 (t0) cc_final: 0.8019 (t0) REVERT: A 1010 THR cc_start: 0.9248 (m) cc_final: 0.8903 (p) REVERT: A 1054 LYS cc_start: 0.9170 (mttt) cc_final: 0.8883 (mtpp) REVERT: A 1095 GLN cc_start: 0.8678 (tm-30) cc_final: 0.8150 (tm-30) REVERT: A 1112 GLU cc_start: 0.8820 (tt0) cc_final: 0.8370 (tp30) REVERT: A 1177 LYS cc_start: 0.8375 (tppt) cc_final: 0.8095 (tppt) REVERT: A 1209 MET cc_start: 0.8368 (mtt) cc_final: 0.8114 (mtt) REVERT: B 69 LYS cc_start: 0.9126 (tmtt) cc_final: 0.8837 (tmmt) REVERT: B 88 LEU cc_start: 0.9101 (mp) cc_final: 0.8779 (tp) REVERT: B 111 LEU cc_start: 0.8670 (mm) cc_final: 0.8238 (mt) REVERT: B 133 ASN cc_start: 0.8455 (p0) cc_final: 0.8103 (p0) REVERT: B 146 LEU cc_start: 0.8731 (mp) cc_final: 0.8499 (mt) REVERT: B 175 HIS cc_start: 0.8678 (p-80) cc_final: 0.8174 (p-80) REVERT: B 236 TYR cc_start: 0.8190 (t80) cc_final: 0.7901 (t80) REVERT: B 273 ARG cc_start: 0.8544 (OUTLIER) cc_final: 0.8198 (mtp-110) REVERT: B 326 ASP cc_start: 0.7413 (t70) cc_final: 0.6586 (t0) REVERT: B 328 ASP cc_start: 0.8060 (m-30) cc_final: 0.7483 (m-30) REVERT: B 331 LYS cc_start: 0.9020 (mttt) cc_final: 0.8590 (mtpp) REVERT: B 397 ARG cc_start: 0.8791 (mmt180) cc_final: 0.8226 (mmm-85) REVERT: B 400 ASP cc_start: 0.8366 (m-30) cc_final: 0.7888 (m-30) REVERT: B 411 SER cc_start: 0.9374 (t) cc_final: 0.8979 (p) REVERT: B 417 ASP cc_start: 0.8233 (t0) cc_final: 0.7977 (t0) REVERT: B 446 ARG cc_start: 0.8830 (ttm110) cc_final: 0.8294 (ttm110) REVERT: B 448 TYR cc_start: 0.8766 (m-80) cc_final: 0.8475 (m-10) REVERT: B 607 ASN cc_start: 0.8236 (t0) cc_final: 0.7896 (t0) REVERT: B 704 ASN cc_start: 0.7180 (p0) cc_final: 0.6978 (p0) REVERT: B 711 GLN cc_start: 0.8002 (pm20) cc_final: 0.7617 (mp10) REVERT: B 792 ILE cc_start: 0.9153 (tt) cc_final: 0.8832 (pt) REVERT: B 842 ASN cc_start: 0.8875 (m-40) cc_final: 0.8561 (m-40) REVERT: B 848 ASP cc_start: 0.8687 (m-30) cc_final: 0.8278 (m-30) REVERT: B 855 ASP cc_start: 0.8261 (m-30) cc_final: 0.7953 (m-30) REVERT: B 874 ASN cc_start: 0.8600 (m-40) cc_final: 0.8038 (p0) REVERT: B 889 LYS cc_start: 0.9012 (ttpt) cc_final: 0.8675 (ttmm) REVERT: B 914 LYS cc_start: 0.9295 (mmmt) cc_final: 0.9078 (mmmm) REVERT: B 916 LYS cc_start: 0.8571 (pttt) cc_final: 0.8201 (ptmm) REVERT: B 924 GLU cc_start: 0.8490 (tm-30) cc_final: 0.8103 (tm-30) REVERT: B 998 MET cc_start: 0.8982 (tpp) cc_final: 0.8420 (mmm) REVERT: B 999 ASP cc_start: 0.8455 (t0) cc_final: 0.8071 (t0) REVERT: B 1006 LYS cc_start: 0.9249 (mmmm) cc_final: 0.8863 (mmmm) REVERT: B 1010 THR cc_start: 0.9175 (m) cc_final: 0.8878 (p) REVERT: B 1032 LYS cc_start: 0.8805 (mtpt) cc_final: 0.8600 (mtpt) REVERT: B 1045 ASN cc_start: 0.9114 (t0) cc_final: 0.8895 (t0) REVERT: B 1054 LYS cc_start: 0.9073 (mttt) cc_final: 0.8769 (mmmm) REVERT: B 1075 GLN cc_start: 0.8410 (mm-40) cc_final: 0.7702 (mm-40) REVERT: B 1079 ASP cc_start: 0.8624 (m-30) cc_final: 0.8313 (m-30) REVERT: B 1095 GLN cc_start: 0.8577 (tm-30) cc_final: 0.7487 (tm-30) REVERT: B 1099 ASP cc_start: 0.8801 (m-30) cc_final: 0.7850 (m-30) REVERT: B 1112 GLU cc_start: 0.8614 (tp30) cc_final: 0.8298 (tp30) REVERT: B 1177 LYS cc_start: 0.8427 (mmmm) cc_final: 0.8053 (mmmt) REVERT: B 1208 PHE cc_start: 0.9035 (m-80) cc_final: 0.8730 (m-80) REVERT: B 1209 MET cc_start: 0.8505 (mmm) cc_final: 0.8289 (mpp) REVERT: B 1216 PHE cc_start: 0.7832 (m-10) cc_final: 0.7381 (m-80) REVERT: C 18 PHE cc_start: 0.7878 (t80) cc_final: 0.7499 (t80) REVERT: C 53 ASP cc_start: 0.8382 (m-30) cc_final: 0.7931 (m-30) REVERT: C 92 LYS cc_start: 0.9179 (mttt) cc_final: 0.8775 (mtpp) REVERT: C 120 GLU cc_start: 0.7749 (pm20) cc_final: 0.7447 (pm20) REVERT: C 147 GLU cc_start: 0.8140 (pp20) cc_final: 0.7869 (pp20) REVERT: C 205 GLU cc_start: 0.8089 (tp30) cc_final: 0.7845 (tp30) REVERT: C 206 ARG cc_start: 0.8801 (ptp-110) cc_final: 0.8547 (ptp90) REVERT: C 218 MET cc_start: 0.8609 (OUTLIER) cc_final: 0.8364 (mtp) REVERT: C 262 SER cc_start: 0.8078 (t) cc_final: 0.7705 (p) REVERT: C 288 SER cc_start: 0.8842 (m) cc_final: 0.8334 (t) REVERT: C 289 GLU cc_start: 0.8730 (mt-10) cc_final: 0.8441 (tm-30) REVERT: C 293 LYS cc_start: 0.9002 (ttpt) cc_final: 0.8708 (ttpt) REVERT: C 330 ASP cc_start: 0.8213 (p0) cc_final: 0.7898 (p0) REVERT: C 331 LYS cc_start: 0.8976 (mttt) cc_final: 0.8414 (mtpp) REVERT: C 384 LYS cc_start: 0.8821 (OUTLIER) cc_final: 0.8517 (pttt) REVERT: C 397 ARG cc_start: 0.8822 (mmt180) cc_final: 0.8477 (mmm-85) REVERT: C 437 ASN cc_start: 0.8711 (t0) cc_final: 0.8374 (t0) REVERT: C 446 ARG cc_start: 0.8828 (tpp80) cc_final: 0.8048 (mtm-85) REVERT: C 460 VAL cc_start: 0.9068 (t) cc_final: 0.8771 (p) REVERT: C 481 PHE cc_start: 0.6701 (t80) cc_final: 0.6401 (t80) REVERT: C 500 ASN cc_start: 0.7768 (m-40) cc_final: 0.7498 (m-40) REVERT: C 579 TYR cc_start: 0.8587 (p90) cc_final: 0.8329 (p90) REVERT: C 587 ARG cc_start: 0.8421 (mtp85) cc_final: 0.8219 (ttt90) REVERT: C 632 GLN cc_start: 0.8722 (pt0) cc_final: 0.8350 (pp30) REVERT: C 678 ARG cc_start: 0.7359 (ttm-80) cc_final: 0.6970 (ttm-80) REVERT: C 704 ASN cc_start: 0.7385 (p0) cc_final: 0.7112 (p0) REVERT: C 772 GLU cc_start: 0.8054 (mp0) cc_final: 0.7828 (mp0) REVERT: C 832 LEU cc_start: 0.9083 (mt) cc_final: 0.8614 (mm) REVERT: C 842 ASN cc_start: 0.8826 (m-40) cc_final: 0.8581 (m-40) REVERT: C 848 ASP cc_start: 0.8642 (m-30) cc_final: 0.8275 (m-30) REVERT: C 858 GLN cc_start: 0.8664 (mt0) cc_final: 0.8446 (mm110) REVERT: C 874 ASN cc_start: 0.8672 (m-40) cc_final: 0.8131 (p0) REVERT: C 881 PHE cc_start: 0.7959 (p90) cc_final: 0.7667 (p90) REVERT: C 889 LYS cc_start: 0.9198 (ttpt) cc_final: 0.8912 (ttpp) REVERT: C 909 ASP cc_start: 0.8438 (m-30) cc_final: 0.7794 (m-30) REVERT: C 998 MET cc_start: 0.8978 (tpp) cc_final: 0.8250 (tpp) REVERT: C 999 ASP cc_start: 0.8262 (t70) cc_final: 0.7781 (t0) REVERT: C 1010 THR cc_start: 0.9070 (m) cc_final: 0.8705 (p) REVERT: C 1045 ASN cc_start: 0.9279 (t0) cc_final: 0.9063 (t0) REVERT: C 1075 GLN cc_start: 0.8498 (mm-40) cc_final: 0.7667 (mm-40) REVERT: C 1079 ASP cc_start: 0.8615 (m-30) cc_final: 0.8219 (m-30) REVERT: C 1095 GLN cc_start: 0.8669 (tm-30) cc_final: 0.7568 (tm-30) REVERT: C 1099 ASP cc_start: 0.8838 (m-30) cc_final: 0.7635 (m-30) REVERT: C 1104 LYS cc_start: 0.9024 (tptt) cc_final: 0.8820 (tptp) REVERT: C 1105 LEU cc_start: 0.9002 (mt) cc_final: 0.8792 (tt) REVERT: C 1112 GLU cc_start: 0.8656 (tp30) cc_final: 0.8211 (tp30) REVERT: C 1126 ASN cc_start: 0.9029 (m-40) cc_final: 0.8564 (t0) REVERT: C 1199 GLU cc_start: 0.8303 (mp0) cc_final: 0.7836 (mp0) REVERT: C 1209 MET cc_start: 0.8292 (mpp) cc_final: 0.7430 (mpp) REVERT: C 1216 PHE cc_start: 0.7670 (m-10) cc_final: 0.7411 (m-80) outliers start: 36 outliers final: 10 residues processed: 524 average time/residue: 0.4512 time to fit residues: 366.5996 Evaluate side-chains 486 residues out of total 3216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 471 time to evaluate : 3.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 405 SER Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 632 GLN Chi-restraints excluded: chain A residue 780 ASN Chi-restraints excluded: chain A residue 839 PHE Chi-restraints excluded: chain A residue 924 GLU Chi-restraints excluded: chain A residue 1102 LEU Chi-restraints excluded: chain B residue 273 ARG Chi-restraints excluded: chain B residue 321 ILE Chi-restraints excluded: chain C residue 218 MET Chi-restraints excluded: chain C residue 321 ILE Chi-restraints excluded: chain C residue 384 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 193 optimal weight: 3.9990 chunk 6 optimal weight: 7.9990 chunk 212 optimal weight: 0.8980 chunk 316 optimal weight: 3.9990 chunk 341 optimal weight: 3.9990 chunk 143 optimal weight: 5.9990 chunk 177 optimal weight: 5.9990 chunk 324 optimal weight: 4.9990 chunk 327 optimal weight: 4.9990 chunk 107 optimal weight: 1.9990 chunk 66 optimal weight: 5.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 ASN ** A 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 945 ASN ** B 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 402 GLN ** C 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 858 GLN ** 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 = 0.3466 r_free = 0.3466 target = 0.099371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.078062 restraints weight = 64021.421| |-----------------------------------------------------------------------------| r_work (start): 0.3048 rms_B_bonded: 3.82 r_work: 0.2869 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.3530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.113 30177 Z= 0.335 Angle : 0.718 11.738 41256 Z= 0.371 Chirality : 0.047 0.252 4842 Planarity : 0.005 0.066 5124 Dihedral : 6.716 59.734 5688 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 1.62 % Allowed : 13.28 % Favored : 85.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.14), residues: 3573 helix: 1.72 (0.20), residues: 759 sheet: -0.29 (0.18), residues: 789 loop : -1.35 (0.13), residues: 2025 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 257 HIS 0.014 0.002 HIS C1184 PHE 0.023 0.002 PHE B 591 TYR 0.033 0.002 TYR C 713 ARG 0.005 0.001 ARG A 54 Details of bonding type rmsd link_NAG-ASN : bond 0.00575 ( 57) link_NAG-ASN : angle 1.96364 ( 171) link_BETA1-4 : bond 0.00394 ( 30) link_BETA1-4 : angle 1.71338 ( 90) hydrogen bonds : bond 0.05594 ( 1016) hydrogen bonds : angle 5.24042 ( 3102) SS BOND : bond 0.00514 ( 72) SS BOND : angle 1.52260 ( 144) covalent geometry : bond 0.00729 (30018) covalent geometry : angle 0.69980 (40851) *********************** 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 561 residues out of total 3216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 509 time to evaluate : 3.055 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: symmetry clash REVERT: A 112 TYR cc_start: 0.8337 (m-80) cc_final: 0.8061 (m-80) REVERT: A 140 GLN cc_start: 0.7732 (tm-30) cc_final: 0.7129 (tm-30) REVERT: A 175 HIS cc_start: 0.8630 (p-80) cc_final: 0.8278 (p-80) REVERT: A 180 GLU cc_start: 0.8312 (tp30) cc_final: 0.7995 (tp30) REVERT: A 186 LYS cc_start: 0.8710 (ttpp) cc_final: 0.8478 (ptmm) REVERT: A 305 ASP cc_start: 0.8186 (p0) cc_final: 0.7772 (p0) REVERT: A 331 LYS cc_start: 0.9102 (mtpt) cc_final: 0.8891 (ttmm) REVERT: A 376 SER cc_start: 0.9101 (m) cc_final: 0.8732 (p) REVERT: A 384 LYS cc_start: 0.8686 (pttp) cc_final: 0.8422 (pttt) REVERT: A 400 ASP cc_start: 0.8570 (m-30) cc_final: 0.8024 (t0) REVERT: A 417 ASP cc_start: 0.8347 (t0) cc_final: 0.8082 (t0) REVERT: A 537 LYS cc_start: 0.8638 (tppt) cc_final: 0.8435 (tppt) REVERT: A 553 GLU cc_start: 0.8448 (mm-30) cc_final: 0.7919 (mm-30) REVERT: A 704 ASN cc_start: 0.7752 (p0) cc_final: 0.7548 (p0) REVERT: A 711 GLN cc_start: 0.8355 (pm20) cc_final: 0.7859 (mp10) REVERT: A 772 GLU cc_start: 0.8252 (mp0) cc_final: 0.7986 (mp0) REVERT: A 781 ASP cc_start: 0.7692 (p0) cc_final: 0.7413 (p0) REVERT: A 784 GLU cc_start: 0.8354 (mm-30) cc_final: 0.8038 (mp0) REVERT: A 792 ILE cc_start: 0.9194 (tp) cc_final: 0.8751 (pt) REVERT: A 803 GLN cc_start: 0.8538 (tp40) cc_final: 0.8195 (tp-100) REVERT: A 805 GLU cc_start: 0.8278 (tm-30) cc_final: 0.8019 (tm-30) REVERT: A 839 PHE cc_start: 0.8613 (OUTLIER) cc_final: 0.8390 (m-80) REVERT: A 842 ASN cc_start: 0.8937 (m-40) cc_final: 0.8616 (m-40) REVERT: A 844 ASN cc_start: 0.9028 (m-40) cc_final: 0.8200 (m-40) REVERT: A 848 ASP cc_start: 0.8571 (m-30) cc_final: 0.8173 (m-30) REVERT: A 849 GLU cc_start: 0.8198 (pp20) cc_final: 0.7989 (pp20) REVERT: A 867 GLN cc_start: 0.8145 (mm-40) cc_final: 0.7919 (mm110) REVERT: A 889 LYS cc_start: 0.9119 (ttpt) cc_final: 0.8789 (ttpp) REVERT: A 909 ASP cc_start: 0.8653 (m-30) cc_final: 0.7981 (m-30) REVERT: A 924 GLU cc_start: 0.8495 (OUTLIER) cc_final: 0.8268 (tm-30) REVERT: A 956 GLU cc_start: 0.7570 (pm20) cc_final: 0.7278 (pm20) REVERT: A 999 ASP cc_start: 0.8700 (t0) cc_final: 0.8176 (t0) REVERT: A 1054 LYS cc_start: 0.9132 (mttt) cc_final: 0.8742 (mtpp) REVERT: A 1064 GLU cc_start: 0.8485 (tp30) cc_final: 0.8169 (tp30) REVERT: A 1095 GLN cc_start: 0.8792 (tm-30) cc_final: 0.7355 (tm-30) REVERT: A 1099 ASP cc_start: 0.8785 (m-30) cc_final: 0.7617 (m-30) REVERT: A 1112 GLU cc_start: 0.8794 (tt0) cc_final: 0.8413 (tp30) REVERT: A 1153 LYS cc_start: 0.8834 (tppt) cc_final: 0.8566 (tptp) REVERT: B 18 PHE cc_start: 0.8274 (t80) cc_final: 0.7969 (t80) REVERT: B 69 LYS cc_start: 0.9186 (tmtt) cc_final: 0.8847 (tmmt) REVERT: B 88 LEU cc_start: 0.9252 (mp) cc_final: 0.8870 (tp) REVERT: B 92 LYS cc_start: 0.9012 (mtmm) cc_final: 0.8775 (mtpp) REVERT: B 111 LEU cc_start: 0.8852 (mm) cc_final: 0.8368 (mt) REVERT: B 146 LEU cc_start: 0.8788 (mp) cc_final: 0.8560 (mp) REVERT: B 175 HIS cc_start: 0.8804 (p-80) cc_final: 0.8235 (p-80) REVERT: B 271 ASP cc_start: 0.7900 (p0) cc_final: 0.7649 (p0) REVERT: B 273 ARG cc_start: 0.8734 (OUTLIER) cc_final: 0.8430 (mtp-110) REVERT: B 293 LYS cc_start: 0.9013 (OUTLIER) cc_final: 0.8749 (pttm) REVERT: B 326 ASP cc_start: 0.7453 (t70) cc_final: 0.6868 (t70) REVERT: B 328 ASP cc_start: 0.8198 (m-30) cc_final: 0.7836 (m-30) REVERT: B 331 LYS cc_start: 0.9144 (mttt) cc_final: 0.8801 (ttmm) REVERT: B 384 LYS cc_start: 0.8785 (pttt) cc_final: 0.8501 (pttp) REVERT: B 397 ARG cc_start: 0.8879 (mmt180) cc_final: 0.8347 (mmm-85) REVERT: B 400 ASP cc_start: 0.8457 (m-30) cc_final: 0.7980 (m-30) REVERT: B 411 SER cc_start: 0.9375 (t) cc_final: 0.9001 (p) REVERT: B 417 ASP cc_start: 0.8397 (t0) cc_final: 0.8123 (t0) REVERT: B 448 TYR cc_start: 0.8913 (m-80) cc_final: 0.8555 (m-10) REVERT: B 544 GLU cc_start: 0.7868 (mp0) cc_final: 0.7661 (mp0) REVERT: B 587 ARG cc_start: 0.8341 (mtp85) cc_final: 0.7208 (ttm-80) REVERT: B 607 ASN cc_start: 0.8114 (t0) cc_final: 0.7428 (t0) REVERT: B 711 GLN cc_start: 0.8185 (pm20) cc_final: 0.7700 (mp10) REVERT: B 772 GLU cc_start: 0.8293 (mp0) cc_final: 0.8013 (mp0) REVERT: B 781 ASP cc_start: 0.8010 (p0) cc_final: 0.7738 (t0) REVERT: B 792 ILE cc_start: 0.9176 (tt) cc_final: 0.8905 (pt) REVERT: B 805 GLU cc_start: 0.8245 (tm-30) cc_final: 0.8014 (tm-30) REVERT: B 832 LEU cc_start: 0.8883 (mt) cc_final: 0.8683 (mm) REVERT: B 842 ASN cc_start: 0.8877 (m-40) cc_final: 0.8580 (m-40) REVERT: B 848 ASP cc_start: 0.8761 (m-30) cc_final: 0.8270 (m-30) REVERT: B 855 ASP cc_start: 0.8305 (m-30) cc_final: 0.8054 (m-30) REVERT: B 873 SER cc_start: 0.8777 (m) cc_final: 0.8504 (p) REVERT: B 874 ASN cc_start: 0.8932 (m-40) cc_final: 0.8499 (p0) REVERT: B 914 LYS cc_start: 0.9261 (mmmt) cc_final: 0.9032 (mmmm) REVERT: B 916 LYS cc_start: 0.8815 (pttt) cc_final: 0.8449 (ptmm) REVERT: B 924 GLU cc_start: 0.8503 (OUTLIER) cc_final: 0.8235 (tm-30) REVERT: B 999 ASP cc_start: 0.8547 (t0) cc_final: 0.8246 (t0) REVERT: B 1004 ASN cc_start: 0.8669 (m-40) cc_final: 0.8277 (m-40) REVERT: B 1042 GLN cc_start: 0.9002 (OUTLIER) cc_final: 0.8792 (tm-30) REVERT: B 1054 LYS cc_start: 0.9160 (mttt) cc_final: 0.8852 (mmmm) REVERT: B 1079 ASP cc_start: 0.8744 (m-30) cc_final: 0.8452 (m-30) REVERT: B 1095 GLN cc_start: 0.8769 (tm-30) cc_final: 0.7581 (tm-30) REVERT: B 1099 ASP cc_start: 0.8873 (m-30) cc_final: 0.7571 (m-30) REVERT: B 1112 GLU cc_start: 0.8725 (tp30) cc_final: 0.8315 (tp30) REVERT: B 1126 ASN cc_start: 0.8581 (t0) cc_final: 0.8291 (t0) REVERT: B 1158 LYS cc_start: 0.8475 (tttm) cc_final: 0.8194 (tttt) REVERT: B 1218 LYS cc_start: 0.8506 (mmmm) cc_final: 0.7991 (mmmm) REVERT: C 53 ASP cc_start: 0.8600 (m-30) cc_final: 0.8284 (t0) REVERT: C 76 ASP cc_start: 0.8036 (t0) cc_final: 0.7785 (t0) REVERT: C 84 LYS cc_start: 0.8753 (mmmm) cc_final: 0.8476 (mmmt) REVERT: C 109 THR cc_start: 0.8780 (m) cc_final: 0.7333 (p) REVERT: C 120 GLU cc_start: 0.7813 (pm20) cc_final: 0.7128 (pm20) REVERT: C 205 GLU cc_start: 0.8174 (tp30) cc_final: 0.7881 (tp30) REVERT: C 206 ARG cc_start: 0.8750 (ptp-110) cc_final: 0.8482 (ptp90) REVERT: C 288 SER cc_start: 0.8909 (m) cc_final: 0.8433 (t) REVERT: C 289 GLU cc_start: 0.8739 (mt-10) cc_final: 0.8460 (tm-30) REVERT: C 293 LYS cc_start: 0.9036 (ttpt) cc_final: 0.8750 (ttpt) REVERT: C 330 ASP cc_start: 0.8358 (p0) cc_final: 0.8007 (p0) REVERT: C 331 LYS cc_start: 0.9166 (mttt) cc_final: 0.8756 (ttmm) REVERT: C 345 GLU cc_start: 0.8362 (tp30) cc_final: 0.8041 (tp30) REVERT: C 384 LYS cc_start: 0.8844 (OUTLIER) cc_final: 0.8511 (pttp) REVERT: C 397 ARG cc_start: 0.8893 (mmt180) cc_final: 0.8671 (mmm-85) REVERT: C 448 TYR cc_start: 0.8929 (m-80) cc_final: 0.8574 (m-10) REVERT: C 481 PHE cc_start: 0.6968 (t80) cc_final: 0.6656 (t80) REVERT: C 500 ASN cc_start: 0.7858 (m-40) cc_final: 0.7560 (m-40) REVERT: C 537 LYS cc_start: 0.8463 (tppt) cc_final: 0.8241 (tppt) REVERT: C 587 ARG cc_start: 0.8431 (mtp85) cc_final: 0.8065 (ttt-90) REVERT: C 772 GLU cc_start: 0.8160 (mp0) cc_final: 0.7848 (mp0) REVERT: C 832 LEU cc_start: 0.9100 (mt) cc_final: 0.8611 (mm) REVERT: C 842 ASN cc_start: 0.8776 (m-40) cc_final: 0.8504 (m-40) REVERT: C 848 ASP cc_start: 0.8756 (m-30) cc_final: 0.8164 (m-30) REVERT: C 855 ASP cc_start: 0.8282 (m-30) cc_final: 0.7927 (m-30) REVERT: C 858 GLN cc_start: 0.8682 (mt0) cc_final: 0.8470 (mm110) REVERT: C 873 SER cc_start: 0.9057 (m) cc_final: 0.8698 (p) REVERT: C 874 ASN cc_start: 0.8851 (m-40) cc_final: 0.8497 (p0) REVERT: C 881 PHE cc_start: 0.7960 (p90) cc_final: 0.6705 (p90) REVERT: C 882 ASP cc_start: 0.7911 (m-30) cc_final: 0.7630 (t0) REVERT: C 889 LYS cc_start: 0.9277 (ttpt) cc_final: 0.8737 (ttmm) REVERT: C 909 ASP cc_start: 0.8444 (m-30) cc_final: 0.7829 (m-30) REVERT: C 998 MET cc_start: 0.9032 (tpp) cc_final: 0.8362 (tpp) REVERT: C 999 ASP cc_start: 0.8352 (t70) cc_final: 0.7889 (t0) REVERT: C 1003 LYS cc_start: 0.9117 (ttpp) cc_final: 0.8853 (ttpp) REVERT: C 1045 ASN cc_start: 0.9281 (t0) cc_final: 0.9052 (t0) REVERT: C 1075 GLN cc_start: 0.8649 (mm110) cc_final: 0.7929 (mm-40) REVERT: C 1079 ASP cc_start: 0.8649 (m-30) cc_final: 0.8309 (m-30) REVERT: C 1095 GLN cc_start: 0.8732 (tm-30) cc_final: 0.7646 (tm-30) REVERT: C 1099 ASP cc_start: 0.8840 (m-30) cc_final: 0.7545 (m-30) REVERT: C 1104 LYS cc_start: 0.9060 (tptt) cc_final: 0.8729 (tppt) REVERT: C 1105 LEU cc_start: 0.9002 (mt) cc_final: 0.8787 (tt) REVERT: C 1112 GLU cc_start: 0.8703 (tp30) cc_final: 0.8286 (tp30) REVERT: C 1199 GLU cc_start: 0.8033 (mp0) cc_final: 0.7546 (mm-30) REVERT: C 1209 MET cc_start: 0.8297 (mpp) cc_final: 0.7507 (mpp) REVERT: C 1216 PHE cc_start: 0.8288 (m-10) cc_final: 0.7940 (m-80) outliers start: 52 outliers final: 27 residues processed: 539 average time/residue: 0.4452 time to fit residues: 368.2079 Evaluate side-chains 504 residues out of total 3216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 470 time to evaluate : 3.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 405 SER Chi-restraints excluded: chain A residue 538 SER Chi-restraints excluded: chain A residue 703 LEU Chi-restraints excluded: chain A residue 780 ASN Chi-restraints excluded: chain A residue 820 LEU Chi-restraints excluded: chain A residue 839 PHE Chi-restraints excluded: chain A residue 850 VAL Chi-restraints excluded: chain A residue 924 GLU Chi-restraints excluded: chain A residue 1003 LYS 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 231 LEU Chi-restraints excluded: chain B residue 273 ARG 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 619 ASP Chi-restraints excluded: chain B residue 924 GLU Chi-restraints excluded: chain B residue 940 CYS Chi-restraints excluded: chain B residue 1042 GLN Chi-restraints excluded: chain B residue 1102 LEU Chi-restraints excluded: chain B residue 1189 MET Chi-restraints excluded: chain C residue 69 LYS Chi-restraints excluded: chain C residue 131 ILE Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 384 LYS Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 703 LEU Chi-restraints excluded: chain C residue 885 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 302 optimal weight: 0.6980 chunk 209 optimal weight: 4.9990 chunk 59 optimal weight: 1.9990 chunk 201 optimal weight: 0.7980 chunk 333 optimal weight: 0.9980 chunk 246 optimal weight: 0.6980 chunk 80 optimal weight: 2.9990 chunk 235 optimal weight: 0.0980 chunk 319 optimal weight: 0.9980 chunk 33 optimal weight: 0.6980 chunk 160 optimal weight: 0.9980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 ASN ** A 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 395 ASN ** A 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 858 GLN ** C 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 395 ASN ** C 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 858 GLN ** 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 = 0.3506 r_free = 0.3506 target = 0.100039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.078800 restraints weight = 63215.815| |-----------------------------------------------------------------------------| r_work (start): 0.3107 rms_B_bonded: 3.84 r_work: 0.2935 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.3596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 30177 Z= 0.123 Angle : 0.606 13.506 41256 Z= 0.306 Chirality : 0.043 0.297 4842 Planarity : 0.004 0.058 5124 Dihedral : 6.279 59.779 5688 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.67 % Favored : 96.31 % Rotamer: Outliers : 1.55 % Allowed : 15.17 % Favored : 83.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.14), residues: 3573 helix: 1.78 (0.19), residues: 789 sheet: -0.13 (0.18), residues: 777 loop : -1.33 (0.13), residues: 2007 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 174 HIS 0.005 0.001 HIS B 234 PHE 0.017 0.001 PHE C 336 TYR 0.034 0.001 TYR C 713 ARG 0.005 0.000 ARG C 678 Details of bonding type rmsd link_NAG-ASN : bond 0.00268 ( 57) link_NAG-ASN : angle 2.08324 ( 171) link_BETA1-4 : bond 0.00381 ( 30) link_BETA1-4 : angle 1.53271 ( 90) hydrogen bonds : bond 0.04268 ( 1016) hydrogen bonds : angle 4.97811 ( 3102) SS BOND : bond 0.00343 ( 72) SS BOND : angle 1.36892 ( 144) covalent geometry : bond 0.00275 (30018) covalent geometry : angle 0.58374 (40851) *********************** 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 547 residues out of total 3216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 497 time to evaluate : 3.415 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: A 112 TYR cc_start: 0.8343 (m-80) cc_final: 0.8071 (m-80) REVERT: A 140 GLN cc_start: 0.7741 (tm-30) cc_final: 0.6752 (tm-30) REVERT: A 142 HIS cc_start: 0.8415 (m90) cc_final: 0.7048 (m90) REVERT: A 175 HIS cc_start: 0.8599 (p-80) cc_final: 0.8295 (p-80) REVERT: A 273 ARG cc_start: 0.8579 (tpp80) cc_final: 0.8370 (mpp80) REVERT: A 288 SER cc_start: 0.8854 (m) cc_final: 0.8419 (t) REVERT: A 289 GLU cc_start: 0.8721 (mt-10) cc_final: 0.8261 (mm-30) REVERT: A 305 ASP cc_start: 0.8134 (p0) cc_final: 0.7743 (p0) REVERT: A 331 LYS cc_start: 0.9031 (mtpt) cc_final: 0.8823 (ttmm) REVERT: A 376 SER cc_start: 0.9061 (m) cc_final: 0.8641 (p) REVERT: A 384 LYS cc_start: 0.8692 (pttp) cc_final: 0.8484 (pttt) REVERT: A 411 SER cc_start: 0.9138 (t) cc_final: 0.8841 (p) REVERT: A 417 ASP cc_start: 0.8353 (t0) cc_final: 0.8046 (t0) REVERT: A 437 ASN cc_start: 0.8760 (t0) cc_final: 0.8434 (t0) REVERT: A 446 ARG cc_start: 0.8746 (ttm-80) cc_final: 0.8531 (ttm-80) REVERT: A 537 LYS cc_start: 0.8660 (tppt) cc_final: 0.8427 (tppt) REVERT: A 553 GLU cc_start: 0.8364 (mm-30) cc_final: 0.7923 (mm-30) REVERT: A 618 THR cc_start: 0.9262 (OUTLIER) cc_final: 0.9034 (m) REVERT: A 711 GLN cc_start: 0.8373 (pm20) cc_final: 0.7902 (mp10) REVERT: A 772 GLU cc_start: 0.8261 (mp0) cc_final: 0.7997 (mp0) REVERT: A 784 GLU cc_start: 0.8330 (mm-30) cc_final: 0.8051 (mp0) REVERT: A 792 ILE cc_start: 0.9170 (tp) cc_final: 0.8820 (pt) REVERT: A 842 ASN cc_start: 0.8932 (m-40) cc_final: 0.8670 (m-40) REVERT: A 844 ASN cc_start: 0.8960 (m-40) cc_final: 0.8010 (m-40) REVERT: A 848 ASP cc_start: 0.8517 (m-30) cc_final: 0.8112 (m-30) REVERT: A 849 GLU cc_start: 0.8182 (pp20) cc_final: 0.7958 (pp20) REVERT: A 858 GLN cc_start: 0.8613 (mm110) cc_final: 0.8357 (mm110) REVERT: A 867 GLN cc_start: 0.8066 (mm-40) cc_final: 0.7851 (mm-40) REVERT: A 889 LYS cc_start: 0.9021 (ttpt) cc_final: 0.8693 (ttpp) REVERT: A 909 ASP cc_start: 0.8539 (m-30) cc_final: 0.7985 (m-30) REVERT: A 924 GLU cc_start: 0.8431 (OUTLIER) cc_final: 0.8192 (tm-30) REVERT: A 956 GLU cc_start: 0.7531 (pm20) cc_final: 0.7246 (pm20) REVERT: A 999 ASP cc_start: 0.8637 (t0) cc_final: 0.8029 (t0) REVERT: A 1054 LYS cc_start: 0.9149 (mttt) cc_final: 0.8641 (mtpp) REVERT: A 1075 GLN cc_start: 0.8624 (mm-40) cc_final: 0.7821 (mm-40) REVERT: A 1079 ASP cc_start: 0.8705 (m-30) cc_final: 0.8235 (m-30) REVERT: A 1095 GLN cc_start: 0.8665 (tm-30) cc_final: 0.7247 (tm-30) REVERT: A 1099 ASP cc_start: 0.8768 (m-30) cc_final: 0.7485 (m-30) REVERT: A 1112 GLU cc_start: 0.8736 (tt0) cc_final: 0.8356 (tp30) REVERT: A 1153 LYS cc_start: 0.8767 (tppt) cc_final: 0.8516 (tptp) REVERT: A 1177 LYS cc_start: 0.8666 (tppt) cc_final: 0.8144 (mptt) REVERT: A 1178 GLN cc_start: 0.8696 (tt0) cc_final: 0.8388 (tt0) REVERT: A 1189 MET cc_start: 0.8328 (mtt) cc_final: 0.7795 (mtt) REVERT: B 18 PHE cc_start: 0.8158 (t80) cc_final: 0.7888 (t80) REVERT: B 69 LYS cc_start: 0.9193 (tmtt) cc_final: 0.8805 (tmmt) REVERT: B 88 LEU cc_start: 0.9145 (mp) cc_final: 0.8793 (tp) REVERT: B 92 LYS cc_start: 0.8962 (mtmm) cc_final: 0.8721 (mtpp) REVERT: B 111 LEU cc_start: 0.8919 (mm) cc_final: 0.8404 (mt) REVERT: B 131 ILE cc_start: 0.9090 (mp) cc_final: 0.8879 (tp) REVERT: B 147 GLU cc_start: 0.8242 (pp20) cc_final: 0.7894 (pp20) REVERT: B 175 HIS cc_start: 0.8787 (p-80) cc_final: 0.8251 (p-80) REVERT: B 218 MET cc_start: 0.8433 (OUTLIER) cc_final: 0.8190 (mmm) REVERT: B 271 ASP cc_start: 0.7850 (p0) cc_final: 0.7606 (p0) REVERT: B 273 ARG cc_start: 0.8625 (OUTLIER) cc_final: 0.8316 (mtp-110) REVERT: B 293 LYS cc_start: 0.9021 (tttm) cc_final: 0.8817 (tmmt) REVERT: B 326 ASP cc_start: 0.7418 (t70) cc_final: 0.6755 (t0) REVERT: B 331 LYS cc_start: 0.9095 (mttt) cc_final: 0.8759 (ttmm) REVERT: B 397 ARG cc_start: 0.8804 (mmt180) cc_final: 0.8253 (mmm-85) REVERT: B 400 ASP cc_start: 0.8509 (m-30) cc_final: 0.7991 (m-30) REVERT: B 411 SER cc_start: 0.9358 (t) cc_final: 0.8975 (p) REVERT: B 417 ASP cc_start: 0.8339 (t0) cc_final: 0.7984 (t0) REVERT: B 446 ARG cc_start: 0.8691 (ttm110) cc_final: 0.8347 (ttm110) REVERT: B 448 TYR cc_start: 0.8853 (m-80) cc_final: 0.8543 (m-10) REVERT: B 536 LYS cc_start: 0.8288 (mmtp) cc_final: 0.7943 (mmtt) REVERT: B 587 ARG cc_start: 0.8392 (mtp85) cc_final: 0.7970 (ttm-80) REVERT: B 711 GLN cc_start: 0.8224 (pm20) cc_final: 0.7706 (mp10) REVERT: B 792 ILE cc_start: 0.9164 (tt) cc_final: 0.8936 (pt) REVERT: B 805 GLU cc_start: 0.8414 (tm-30) cc_final: 0.8016 (tm-30) REVERT: B 832 LEU cc_start: 0.8940 (mt) cc_final: 0.8402 (mm) REVERT: B 842 ASN cc_start: 0.8888 (m-40) cc_final: 0.8604 (m-40) REVERT: B 848 ASP cc_start: 0.8725 (m-30) cc_final: 0.8248 (m-30) REVERT: B 849 GLU cc_start: 0.8528 (tm-30) cc_final: 0.8152 (pp20) REVERT: B 855 ASP cc_start: 0.8284 (m-30) cc_final: 0.8006 (m-30) REVERT: B 867 GLN cc_start: 0.7849 (mm-40) cc_final: 0.7625 (mm110) REVERT: B 874 ASN cc_start: 0.8855 (m-40) cc_final: 0.8508 (p0) REVERT: B 889 LYS cc_start: 0.9130 (ttpt) cc_final: 0.8779 (ttmm) REVERT: B 914 LYS cc_start: 0.9240 (mmmt) cc_final: 0.9021 (mmmm) REVERT: B 916 LYS cc_start: 0.8762 (pttt) cc_final: 0.8393 (ptmm) REVERT: B 924 GLU cc_start: 0.8529 (OUTLIER) cc_final: 0.8118 (tm-30) REVERT: B 999 ASP cc_start: 0.8523 (t0) cc_final: 0.8227 (t0) REVERT: B 1004 ASN cc_start: 0.8450 (m-40) cc_final: 0.8078 (m-40) REVERT: B 1034 GLN cc_start: 0.8972 (OUTLIER) cc_final: 0.8612 (mp10) REVERT: B 1042 GLN cc_start: 0.9035 (OUTLIER) cc_final: 0.8737 (tm-30) REVERT: B 1054 LYS cc_start: 0.9131 (mttt) cc_final: 0.8810 (mmmm) REVERT: B 1070 ASP cc_start: 0.7632 (p0) cc_final: 0.7273 (p0) REVERT: B 1075 GLN cc_start: 0.8664 (mm-40) cc_final: 0.7965 (mm-40) REVERT: B 1079 ASP cc_start: 0.8697 (m-30) cc_final: 0.8364 (m-30) REVERT: B 1095 GLN cc_start: 0.8733 (tm-30) cc_final: 0.7508 (tm-30) REVERT: B 1099 ASP cc_start: 0.8852 (m-30) cc_final: 0.7425 (m-30) REVERT: B 1112 GLU cc_start: 0.8711 (tp30) cc_final: 0.8484 (tp30) REVERT: B 1126 ASN cc_start: 0.8557 (t0) cc_final: 0.8277 (t0) REVERT: B 1218 LYS cc_start: 0.8456 (mmmm) cc_final: 0.7879 (mmmm) REVERT: C 18 PHE cc_start: 0.8125 (t80) cc_final: 0.7634 (t80) REVERT: C 53 ASP cc_start: 0.8528 (m-30) cc_final: 0.8239 (t0) REVERT: C 60 THR cc_start: 0.9159 (OUTLIER) cc_final: 0.8814 (p) REVERT: C 76 ASP cc_start: 0.8028 (t0) cc_final: 0.7576 (t0) REVERT: C 84 LYS cc_start: 0.8753 (mmmm) cc_final: 0.8459 (mmmt) REVERT: C 120 GLU cc_start: 0.7729 (pm20) cc_final: 0.7412 (pm20) REVERT: C 288 SER cc_start: 0.8891 (m) cc_final: 0.8364 (t) REVERT: C 289 GLU cc_start: 0.8701 (mt-10) cc_final: 0.8473 (tm-30) REVERT: C 293 LYS cc_start: 0.9023 (ttpt) cc_final: 0.8740 (ttpt) REVERT: C 331 LYS cc_start: 0.9096 (mttt) cc_final: 0.8712 (ttmm) REVERT: C 384 LYS cc_start: 0.8831 (OUTLIER) cc_final: 0.8369 (pttp) REVERT: C 397 ARG cc_start: 0.8933 (mmt180) cc_final: 0.8581 (mmm-85) REVERT: C 460 VAL cc_start: 0.9128 (t) cc_final: 0.8825 (p) REVERT: C 481 PHE cc_start: 0.6902 (t80) cc_final: 0.6578 (t80) REVERT: C 500 ASN cc_start: 0.7818 (m-40) cc_final: 0.7526 (m-40) REVERT: C 587 ARG cc_start: 0.8394 (mtp85) cc_final: 0.8062 (ttm-80) REVERT: C 772 GLU cc_start: 0.8162 (mp0) cc_final: 0.7841 (mp0) REVERT: C 832 LEU cc_start: 0.9114 (mt) cc_final: 0.8519 (mm) REVERT: C 842 ASN cc_start: 0.8808 (m-40) cc_final: 0.8542 (m-40) REVERT: C 848 ASP cc_start: 0.8713 (m-30) cc_final: 0.8130 (m-30) REVERT: C 849 GLU cc_start: 0.8278 (pp20) cc_final: 0.8039 (pp20) REVERT: C 873 SER cc_start: 0.8977 (m) cc_final: 0.8644 (p) REVERT: C 874 ASN cc_start: 0.8902 (m-40) cc_final: 0.8594 (p0) REVERT: C 881 PHE cc_start: 0.7817 (p90) cc_final: 0.7524 (p90) REVERT: C 882 ASP cc_start: 0.7865 (m-30) cc_final: 0.7425 (t0) REVERT: C 889 LYS cc_start: 0.9295 (ttpt) cc_final: 0.8999 (ttpp) REVERT: C 909 ASP cc_start: 0.8408 (m-30) cc_final: 0.7805 (m-30) REVERT: C 956 GLU cc_start: 0.7738 (mm-30) cc_final: 0.7487 (mm-30) REVERT: C 999 ASP cc_start: 0.8271 (t70) cc_final: 0.7773 (t0) REVERT: C 1045 ASN cc_start: 0.9262 (t0) cc_final: 0.9028 (t0) REVERT: C 1075 GLN cc_start: 0.8565 (mm110) cc_final: 0.7647 (mm-40) REVERT: C 1079 ASP cc_start: 0.8613 (m-30) cc_final: 0.8240 (m-30) REVERT: C 1095 GLN cc_start: 0.8700 (tm-30) cc_final: 0.7573 (tm-30) REVERT: C 1099 ASP cc_start: 0.8815 (m-30) cc_final: 0.7601 (m-30) REVERT: C 1104 LYS cc_start: 0.9029 (tptt) cc_final: 0.8786 (tptp) REVERT: C 1112 GLU cc_start: 0.8662 (tp30) cc_final: 0.8218 (tp30) REVERT: C 1199 GLU cc_start: 0.8149 (mp0) cc_final: 0.7715 (mm-30) REVERT: C 1209 MET cc_start: 0.8278 (mpp) cc_final: 0.7592 (mpp) REVERT: C 1218 LYS cc_start: 0.8431 (mmmm) cc_final: 0.8037 (mmmm) outliers start: 50 outliers final: 23 residues processed: 530 average time/residue: 0.6394 time to fit residues: 526.5011 Evaluate side-chains 511 residues out of total 3216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 479 time to evaluate : 4.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 193 VAL 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 618 THR Chi-restraints excluded: chain A residue 703 LEU Chi-restraints excluded: chain A residue 820 LEU Chi-restraints excluded: chain A residue 924 GLU Chi-restraints excluded: chain A residue 1102 LEU Chi-restraints excluded: chain B residue 218 MET 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 535 GLN Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain B residue 588 CYS Chi-restraints excluded: chain B residue 924 GLU Chi-restraints excluded: chain B residue 1034 GLN Chi-restraints excluded: chain B residue 1042 GLN Chi-restraints excluded: chain B residue 1189 MET Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 384 LYS Chi-restraints excluded: chain C residue 699 CYS Chi-restraints excluded: chain C residue 776 VAL Chi-restraints excluded: chain C residue 839 PHE Chi-restraints excluded: chain C residue 885 ASN Chi-restraints excluded: chain C residue 1017 LEU Chi-restraints excluded: chain C residue 1167 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 200 optimal weight: 5.9990 chunk 66 optimal weight: 5.9990 chunk 124 optimal weight: 4.9990 chunk 223 optimal weight: 6.9990 chunk 339 optimal weight: 2.9990 chunk 326 optimal weight: 0.9990 chunk 82 optimal weight: 4.9990 chunk 127 optimal weight: 5.9990 chunk 314 optimal weight: 0.8980 chunk 15 optimal weight: 4.9990 chunk 68 optimal weight: 2.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 HIS ** A 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 372 ASN ** B 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 858 GLN ** C 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 445 ASN ** 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 = 0.3470 r_free = 0.3470 target = 0.099631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.078370 restraints weight = 63527.126| |-----------------------------------------------------------------------------| r_work (start): 0.3055 rms_B_bonded: 3.80 r_work: 0.2877 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.3985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.090 30177 Z= 0.280 Angle : 0.662 10.810 41256 Z= 0.340 Chirality : 0.045 0.236 4842 Planarity : 0.004 0.062 5124 Dihedral : 6.070 59.205 5688 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 1.83 % Allowed : 16.39 % Favored : 81.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.14), residues: 3573 helix: 1.76 (0.19), residues: 777 sheet: -0.28 (0.18), residues: 792 loop : -1.35 (0.13), residues: 2004 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 174 HIS 0.007 0.001 HIS A 201 PHE 0.024 0.002 PHE A 473 TYR 0.036 0.002 TYR C 713 ARG 0.013 0.001 ARG A 904 Details of bonding type rmsd link_NAG-ASN : bond 0.00398 ( 57) link_NAG-ASN : angle 1.83483 ( 171) link_BETA1-4 : bond 0.00380 ( 30) link_BETA1-4 : angle 1.60517 ( 90) hydrogen bonds : bond 0.05019 ( 1016) hydrogen bonds : angle 4.98799 ( 3102) SS BOND : bond 0.00507 ( 72) SS BOND : angle 1.45337 ( 144) covalent geometry : bond 0.00612 (30018) covalent geometry : angle 0.64400 (40851) *********************** 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 548 residues out of total 3216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 489 time to evaluate : 4.366 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 112 TYR cc_start: 0.8326 (m-80) cc_final: 0.8040 (m-80) REVERT: A 140 GLN cc_start: 0.7776 (tm-30) cc_final: 0.6850 (tm-30) REVERT: A 142 HIS cc_start: 0.8351 (m90) cc_final: 0.6937 (m90) REVERT: A 273 ARG cc_start: 0.8595 (tpp80) cc_final: 0.8372 (mpp80) REVERT: A 289 GLU cc_start: 0.8693 (mt-10) cc_final: 0.8201 (mm-30) REVERT: A 305 ASP cc_start: 0.8310 (p0) cc_final: 0.7925 (p0) REVERT: A 331 LYS cc_start: 0.9093 (mtpt) cc_final: 0.8834 (mtpp) REVERT: A 376 SER cc_start: 0.9084 (m) cc_final: 0.8714 (p) REVERT: A 384 LYS cc_start: 0.8743 (pttp) cc_final: 0.8444 (pttt) REVERT: A 400 ASP cc_start: 0.8618 (m-30) cc_final: 0.8281 (m-30) REVERT: A 411 SER cc_start: 0.9204 (t) cc_final: 0.8904 (p) REVERT: A 417 ASP cc_start: 0.8427 (t0) cc_final: 0.8127 (t0) REVERT: A 446 ARG cc_start: 0.8712 (ttm-80) cc_final: 0.8448 (ttm-80) REVERT: A 553 GLU cc_start: 0.8471 (mm-30) cc_final: 0.7973 (mm-30) REVERT: A 618 THR cc_start: 0.9301 (OUTLIER) cc_final: 0.9030 (m) REVERT: A 711 GLN cc_start: 0.8387 (pm20) cc_final: 0.7829 (mp10) REVERT: A 772 GLU cc_start: 0.8261 (mp0) cc_final: 0.7877 (mp0) REVERT: A 792 ILE cc_start: 0.9210 (tp) cc_final: 0.8838 (pt) REVERT: A 803 GLN cc_start: 0.8556 (tp-100) cc_final: 0.8349 (tp-100) REVERT: A 842 ASN cc_start: 0.8932 (m-40) cc_final: 0.8635 (m-40) REVERT: A 844 ASN cc_start: 0.9009 (m-40) cc_final: 0.8161 (m-40) REVERT: A 848 ASP cc_start: 0.8573 (m-30) cc_final: 0.8175 (m-30) REVERT: A 849 GLU cc_start: 0.8187 (pp20) cc_final: 0.7950 (pp20) REVERT: A 867 GLN cc_start: 0.8221 (mm-40) cc_final: 0.7967 (mm110) REVERT: A 889 LYS cc_start: 0.9099 (ttpt) cc_final: 0.8778 (ttpp) REVERT: A 909 ASP cc_start: 0.8554 (m-30) cc_final: 0.7971 (m-30) REVERT: A 924 GLU cc_start: 0.8449 (OUTLIER) cc_final: 0.8207 (tm-30) REVERT: A 956 GLU cc_start: 0.7571 (pm20) cc_final: 0.7303 (pm20) REVERT: A 999 ASP cc_start: 0.8675 (t0) cc_final: 0.8101 (t0) REVERT: A 1054 LYS cc_start: 0.9123 (mttt) cc_final: 0.8742 (mtpp) REVERT: A 1075 GLN cc_start: 0.8758 (mm-40) cc_final: 0.8009 (mm-40) REVERT: A 1079 ASP cc_start: 0.8733 (m-30) cc_final: 0.8291 (m-30) REVERT: A 1095 GLN cc_start: 0.8682 (tm-30) cc_final: 0.7243 (tm-30) REVERT: A 1099 ASP cc_start: 0.8814 (m-30) cc_final: 0.7587 (m-30) REVERT: A 1112 GLU cc_start: 0.8766 (tt0) cc_final: 0.8441 (tp30) REVERT: A 1153 LYS cc_start: 0.8771 (tppt) cc_final: 0.8556 (tptp) REVERT: A 1177 LYS cc_start: 0.8705 (tppt) cc_final: 0.8251 (tppt) REVERT: A 1189 MET cc_start: 0.8356 (mtt) cc_final: 0.8000 (mtt) REVERT: B 18 PHE cc_start: 0.8273 (t80) cc_final: 0.7732 (t80) REVERT: B 60 THR cc_start: 0.9096 (OUTLIER) cc_final: 0.8801 (p) REVERT: B 69 LYS cc_start: 0.9194 (tmtt) cc_final: 0.8824 (tmmt) REVERT: B 88 LEU cc_start: 0.9151 (mp) cc_final: 0.8779 (tp) REVERT: B 92 LYS cc_start: 0.8975 (mtmm) cc_final: 0.8729 (mtpp) REVERT: B 111 LEU cc_start: 0.8945 (mm) cc_final: 0.8436 (mt) REVERT: B 147 GLU cc_start: 0.8281 (pp20) cc_final: 0.7982 (pp20) REVERT: B 175 HIS cc_start: 0.8773 (p-80) cc_final: 0.8229 (p-80) REVERT: B 218 MET cc_start: 0.8452 (tpp) cc_final: 0.8217 (mmm) REVERT: B 271 ASP cc_start: 0.7814 (p0) cc_final: 0.7564 (p0) REVERT: B 273 ARG cc_start: 0.8599 (OUTLIER) cc_final: 0.8341 (mtp-110) REVERT: B 326 ASP cc_start: 0.7182 (t70) cc_final: 0.6919 (t0) REVERT: B 331 LYS cc_start: 0.9302 (mttt) cc_final: 0.8835 (ttmm) REVERT: B 397 ARG cc_start: 0.8916 (mmt180) cc_final: 0.8314 (mmm-85) REVERT: B 400 ASP cc_start: 0.8544 (m-30) cc_final: 0.8025 (m-30) REVERT: B 411 SER cc_start: 0.9353 (t) cc_final: 0.8960 (p) REVERT: B 417 ASP cc_start: 0.8428 (t0) cc_final: 0.8164 (t0) REVERT: B 446 ARG cc_start: 0.8767 (ttm110) cc_final: 0.8424 (ttm110) REVERT: B 448 TYR cc_start: 0.8943 (m-80) cc_final: 0.8578 (m-10) REVERT: B 536 LYS cc_start: 0.8382 (mmtp) cc_final: 0.8025 (mmtt) REVERT: B 537 LYS cc_start: 0.8525 (tppt) cc_final: 0.8234 (tppt) REVERT: B 587 ARG cc_start: 0.8342 (mtp85) cc_final: 0.7186 (ttm-80) REVERT: B 711 GLN cc_start: 0.8172 (pm20) cc_final: 0.7660 (mp10) REVERT: B 781 ASP cc_start: 0.7686 (p0) cc_final: 0.7325 (p0) REVERT: B 805 GLU cc_start: 0.8344 (tm-30) cc_final: 0.8025 (tm-30) REVERT: B 832 LEU cc_start: 0.8919 (mt) cc_final: 0.8340 (mm) REVERT: B 842 ASN cc_start: 0.8888 (m-40) cc_final: 0.8561 (m-40) REVERT: B 848 ASP cc_start: 0.8751 (m-30) cc_final: 0.8296 (m-30) REVERT: B 855 ASP cc_start: 0.8284 (m-30) cc_final: 0.7923 (m-30) REVERT: B 867 GLN cc_start: 0.7991 (mm-40) cc_final: 0.7781 (mm110) REVERT: B 873 SER cc_start: 0.8888 (m) cc_final: 0.8564 (p) REVERT: B 874 ASN cc_start: 0.9005 (m-40) cc_final: 0.8591 (p0) REVERT: B 889 LYS cc_start: 0.9208 (ttpt) cc_final: 0.8861 (ttmm) REVERT: B 914 LYS cc_start: 0.9260 (mmmt) cc_final: 0.8977 (mmmm) REVERT: B 916 LYS cc_start: 0.8807 (pttt) cc_final: 0.8288 (ptmm) REVERT: B 924 GLU cc_start: 0.8520 (OUTLIER) cc_final: 0.8302 (tm-30) REVERT: B 999 ASP cc_start: 0.8544 (t0) cc_final: 0.8128 (t0) REVERT: B 1004 ASN cc_start: 0.8583 (m-40) cc_final: 0.8199 (m-40) REVERT: B 1034 GLN cc_start: 0.8995 (OUTLIER) cc_final: 0.8584 (mp10) REVERT: B 1042 GLN cc_start: 0.9034 (mt0) cc_final: 0.8792 (tm-30) REVERT: B 1054 LYS cc_start: 0.9189 (mttt) cc_final: 0.8960 (mmmm) REVERT: B 1073 GLU cc_start: 0.7813 (pm20) cc_final: 0.7581 (pm20) REVERT: B 1075 GLN cc_start: 0.8756 (mm-40) cc_final: 0.8012 (mm-40) REVERT: B 1079 ASP cc_start: 0.8714 (m-30) cc_final: 0.8390 (m-30) REVERT: B 1095 GLN cc_start: 0.8772 (tm-30) cc_final: 0.7576 (tm-30) REVERT: B 1099 ASP cc_start: 0.8854 (m-30) cc_final: 0.7499 (m-30) REVERT: B 1111 MET cc_start: 0.9033 (mtm) cc_final: 0.8802 (mtm) REVERT: B 1112 GLU cc_start: 0.8723 (tp30) cc_final: 0.8389 (tp30) REVERT: B 1126 ASN cc_start: 0.8613 (t0) cc_final: 0.8203 (t0) REVERT: B 1208 PHE cc_start: 0.9070 (m-80) cc_final: 0.8597 (m-80) REVERT: B 1209 MET cc_start: 0.8458 (mmm) cc_final: 0.8005 (mpp) REVERT: C 17 ASP cc_start: 0.7573 (p0) cc_final: 0.7162 (p0) REVERT: C 53 ASP cc_start: 0.8570 (m-30) cc_final: 0.8216 (t0) REVERT: C 76 ASP cc_start: 0.8074 (t0) cc_final: 0.7855 (t0) REVERT: C 84 LYS cc_start: 0.8781 (mmmm) cc_final: 0.8448 (mmmt) REVERT: C 206 ARG cc_start: 0.8820 (ptp-110) cc_final: 0.8590 (ptp-110) REVERT: C 288 SER cc_start: 0.8914 (m) cc_final: 0.8434 (t) REVERT: C 289 GLU cc_start: 0.8708 (mt-10) cc_final: 0.8490 (tm-30) REVERT: C 293 LYS cc_start: 0.9035 (ttpt) cc_final: 0.8748 (ttpt) REVERT: C 330 ASP cc_start: 0.8377 (p0) cc_final: 0.8027 (p0) REVERT: C 331 LYS cc_start: 0.9166 (mttt) cc_final: 0.8778 (ttmm) REVERT: C 345 GLU cc_start: 0.8255 (tp30) cc_final: 0.7951 (tp30) REVERT: C 384 LYS cc_start: 0.8888 (OUTLIER) cc_final: 0.8602 (pttt) REVERT: C 397 ARG cc_start: 0.8932 (mmt180) cc_final: 0.8648 (mmm-85) REVERT: C 481 PHE cc_start: 0.6899 (t80) cc_final: 0.6602 (t80) REVERT: C 500 ASN cc_start: 0.7920 (m-40) cc_final: 0.7609 (m-40) REVERT: C 537 LYS cc_start: 0.8396 (tppt) cc_final: 0.8189 (tppt) REVERT: C 587 ARG cc_start: 0.8455 (mtp85) cc_final: 0.8215 (ttm-80) REVERT: C 772 GLU cc_start: 0.8253 (mp0) cc_final: 0.7934 (mp0) REVERT: C 832 LEU cc_start: 0.9125 (mt) cc_final: 0.8560 (mm) REVERT: C 842 ASN cc_start: 0.8784 (m-40) cc_final: 0.8535 (m-40) REVERT: C 848 ASP cc_start: 0.8744 (m-30) cc_final: 0.8175 (m-30) REVERT: C 849 GLU cc_start: 0.8286 (pp20) cc_final: 0.7978 (pp20) REVERT: C 850 VAL cc_start: 0.9391 (OUTLIER) cc_final: 0.9066 (p) REVERT: C 855 ASP cc_start: 0.8315 (m-30) cc_final: 0.7973 (m-30) REVERT: C 858 GLN cc_start: 0.8856 (mm110) cc_final: 0.8577 (mm110) REVERT: C 873 SER cc_start: 0.9088 (m) cc_final: 0.8790 (p) REVERT: C 874 ASN cc_start: 0.8997 (m-40) cc_final: 0.8538 (p0) REVERT: C 882 ASP cc_start: 0.7726 (m-30) cc_final: 0.7369 (m-30) REVERT: C 889 LYS cc_start: 0.9322 (ttpt) cc_final: 0.9022 (ttpp) REVERT: C 909 ASP cc_start: 0.8382 (m-30) cc_final: 0.7823 (m-30) REVERT: C 999 ASP cc_start: 0.8223 (t70) cc_final: 0.7771 (t0) REVERT: C 1045 ASN cc_start: 0.9279 (t0) cc_final: 0.9054 (t0) REVERT: C 1075 GLN cc_start: 0.8658 (mm110) cc_final: 0.7802 (mm-40) REVERT: C 1079 ASP cc_start: 0.8618 (m-30) cc_final: 0.8260 (m-30) REVERT: C 1095 GLN cc_start: 0.8722 (tm-30) cc_final: 0.7605 (tm-30) REVERT: C 1099 ASP cc_start: 0.8837 (m-30) cc_final: 0.7539 (m-30) REVERT: C 1104 LYS cc_start: 0.9020 (tptt) cc_final: 0.8664 (tppt) REVERT: C 1112 GLU cc_start: 0.8680 (tp30) cc_final: 0.8244 (tp30) REVERT: C 1199 GLU cc_start: 0.8071 (OUTLIER) cc_final: 0.7538 (mm-30) REVERT: C 1209 MET cc_start: 0.8268 (mpp) cc_final: 0.7582 (mpp) outliers start: 59 outliers final: 34 residues processed: 525 average time/residue: 0.6666 time to fit residues: 552.4953 Evaluate side-chains 518 residues out of total 3216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 475 time to evaluate : 5.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 LYS Chi-restraints excluded: chain A residue 114 ASN Chi-restraints excluded: chain A residue 193 VAL 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 444 TRP Chi-restraints excluded: chain A residue 525 ILE 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 924 GLU Chi-restraints excluded: chain A residue 1102 LEU Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 248 ASN Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 273 ARG Chi-restraints excluded: chain B residue 405 SER Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain B residue 589 ASN Chi-restraints excluded: chain B residue 924 GLU Chi-restraints excluded: chain B residue 940 CYS Chi-restraints excluded: chain B residue 1034 GLN Chi-restraints excluded: chain B residue 1158 LYS Chi-restraints excluded: chain B residue 1189 MET 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 311 VAL Chi-restraints excluded: chain C residue 384 LYS Chi-restraints excluded: chain C residue 399 SER 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 1003 LYS Chi-restraints excluded: chain C residue 1167 CYS Chi-restraints excluded: chain C residue 1199 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 57 optimal weight: 4.9990 chunk 319 optimal weight: 5.9990 chunk 109 optimal weight: 1.9990 chunk 271 optimal weight: 1.9990 chunk 203 optimal weight: 3.9990 chunk 238 optimal weight: 5.9990 chunk 87 optimal weight: 2.9990 chunk 47 optimal weight: 9.9990 chunk 17 optimal weight: 2.9990 chunk 30 optimal weight: 0.0470 chunk 193 optimal weight: 0.5980 overall best weight: 1.5284 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 HIS ** A 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 160 HIS B 858 GLN ** C 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 445 ASN ** 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 = 0.3490 r_free = 0.3490 target = 0.100599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.079041 restraints weight = 63002.423| |-----------------------------------------------------------------------------| r_work (start): 0.3072 rms_B_bonded: 3.93 r_work: 0.2889 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.4058 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= 0.182 Angle : 0.619 10.303 41256 Z= 0.318 Chirality : 0.044 0.223 4842 Planarity : 0.004 0.059 5124 Dihedral : 5.812 58.932 5688 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 2.02 % Allowed : 16.76 % Favored : 81.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.14), residues: 3573 helix: 1.86 (0.19), residues: 774 sheet: -0.15 (0.18), residues: 747 loop : -1.38 (0.13), residues: 2052 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 174 HIS 0.004 0.001 HIS B 234 PHE 0.024 0.001 PHE B 714 TYR 0.037 0.001 TYR C 713 ARG 0.009 0.000 ARG A 904 Details of bonding type rmsd link_NAG-ASN : bond 0.00264 ( 57) link_NAG-ASN : angle 1.73533 ( 171) link_BETA1-4 : bond 0.00381 ( 30) link_BETA1-4 : angle 1.52235 ( 90) hydrogen bonds : bond 0.04512 ( 1016) hydrogen bonds : angle 4.91935 ( 3102) SS BOND : bond 0.00349 ( 72) SS BOND : angle 1.49871 ( 144) covalent geometry : bond 0.00404 (30018) covalent geometry : angle 0.60096 (40851) *********************** 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 563 residues out of total 3216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 498 time to evaluate : 2.867 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 140 GLN cc_start: 0.7711 (tm-30) cc_final: 0.6780 (tm-30) REVERT: A 142 HIS cc_start: 0.8295 (m90) cc_final: 0.6907 (m90) REVERT: A 175 HIS cc_start: 0.8692 (p-80) cc_final: 0.8290 (p-80) REVERT: A 273 ARG cc_start: 0.8616 (tpp80) cc_final: 0.8374 (mpp80) REVERT: A 288 SER cc_start: 0.8824 (m) cc_final: 0.8353 (t) REVERT: A 289 GLU cc_start: 0.8733 (mt-10) cc_final: 0.8224 (mm-30) REVERT: A 319 ARG cc_start: 0.8602 (mmm160) cc_final: 0.8254 (mmm-85) REVERT: A 331 LYS cc_start: 0.9094 (mtpt) cc_final: 0.8827 (mtpp) REVERT: A 336 PHE cc_start: 0.8333 (m-10) cc_final: 0.7884 (m-80) REVERT: A 376 SER cc_start: 0.9079 (m) cc_final: 0.8679 (p) REVERT: A 384 LYS cc_start: 0.8744 (pttp) cc_final: 0.8400 (pttt) REVERT: A 398 ARG cc_start: 0.9031 (tpt-90) cc_final: 0.8795 (tpt90) REVERT: A 411 SER cc_start: 0.9200 (t) cc_final: 0.8922 (p) REVERT: A 417 ASP cc_start: 0.8482 (t0) cc_final: 0.8115 (t0) REVERT: A 437 ASN cc_start: 0.8672 (t0) cc_final: 0.8334 (t0) REVERT: A 446 ARG cc_start: 0.8632 (ttm-80) cc_final: 0.8381 (ttm-80) REVERT: A 553 GLU cc_start: 0.8486 (mm-30) cc_final: 0.7942 (mm-30) REVERT: A 618 THR cc_start: 0.9286 (OUTLIER) cc_final: 0.9012 (m) REVERT: A 711 GLN cc_start: 0.8451 (pm20) cc_final: 0.7859 (mp10) REVERT: A 772 GLU cc_start: 0.8307 (mp0) cc_final: 0.7845 (mp0) REVERT: A 784 GLU cc_start: 0.8358 (mm-30) cc_final: 0.8028 (mp0) REVERT: A 792 ILE cc_start: 0.9171 (tp) cc_final: 0.8837 (pt) REVERT: A 842 ASN cc_start: 0.8944 (m-40) cc_final: 0.8639 (m-40) REVERT: A 844 ASN cc_start: 0.9005 (m-40) cc_final: 0.8070 (m-40) REVERT: A 848 ASP cc_start: 0.8592 (m-30) cc_final: 0.8167 (m-30) REVERT: A 849 GLU cc_start: 0.8225 (pp20) cc_final: 0.7948 (pp20) REVERT: A 867 GLN cc_start: 0.8213 (mm-40) cc_final: 0.7934 (mm110) REVERT: A 889 LYS cc_start: 0.9077 (ttpt) cc_final: 0.8757 (ttpp) REVERT: A 909 ASP cc_start: 0.8623 (m-30) cc_final: 0.7911 (m-30) REVERT: A 924 GLU cc_start: 0.8436 (OUTLIER) cc_final: 0.8187 (tm-30) REVERT: A 956 GLU cc_start: 0.7632 (pm20) cc_final: 0.7360 (pm20) REVERT: A 998 MET cc_start: 0.9064 (tpp) cc_final: 0.8354 (tpp) REVERT: A 999 ASP cc_start: 0.8674 (t0) cc_final: 0.8089 (t0) REVERT: A 1054 LYS cc_start: 0.9179 (mttt) cc_final: 0.8704 (mtpp) REVERT: A 1075 GLN cc_start: 0.8698 (mm-40) cc_final: 0.7907 (mm-40) REVERT: A 1079 ASP cc_start: 0.8774 (m-30) cc_final: 0.8297 (m-30) REVERT: A 1095 GLN cc_start: 0.8675 (tm-30) cc_final: 0.7252 (tm-30) REVERT: A 1099 ASP cc_start: 0.8826 (m-30) cc_final: 0.7561 (m-30) REVERT: A 1112 GLU cc_start: 0.8800 (tt0) cc_final: 0.8398 (tp30) REVERT: A 1153 LYS cc_start: 0.8760 (tppt) cc_final: 0.8476 (tptp) REVERT: A 1177 LYS cc_start: 0.8678 (tppt) cc_final: 0.8188 (tppt) REVERT: A 1178 GLN cc_start: 0.8810 (tt0) cc_final: 0.8502 (tt0) REVERT: A 1189 MET cc_start: 0.8371 (mtt) cc_final: 0.7898 (mtt) REVERT: B 18 PHE cc_start: 0.8253 (t80) cc_final: 0.8052 (t80) REVERT: B 60 THR cc_start: 0.9099 (OUTLIER) cc_final: 0.8816 (p) REVERT: B 69 LYS cc_start: 0.9200 (tmtt) cc_final: 0.8748 (tmmt) REVERT: B 88 LEU cc_start: 0.9111 (mp) cc_final: 0.8728 (tp) REVERT: B 92 LYS cc_start: 0.9006 (mtmm) cc_final: 0.8759 (mtpp) REVERT: B 111 LEU cc_start: 0.8935 (mm) cc_final: 0.8392 (mt) REVERT: B 147 GLU cc_start: 0.8389 (pp20) cc_final: 0.8066 (pp20) REVERT: B 175 HIS cc_start: 0.8764 (p-80) cc_final: 0.8189 (p-80) REVERT: B 218 MET cc_start: 0.8508 (OUTLIER) cc_final: 0.8189 (mmm) REVERT: B 271 ASP cc_start: 0.7798 (p0) cc_final: 0.7558 (p0) REVERT: B 273 ARG cc_start: 0.8594 (OUTLIER) cc_final: 0.8305 (mtp-110) REVERT: B 326 ASP cc_start: 0.7109 (t70) cc_final: 0.6856 (t0) REVERT: B 331 LYS cc_start: 0.9267 (mttt) cc_final: 0.8789 (ttmm) REVERT: B 384 LYS cc_start: 0.8745 (pttt) cc_final: 0.8307 (pttp) REVERT: B 397 ARG cc_start: 0.8946 (mmt180) cc_final: 0.8413 (mmm-85) REVERT: B 398 ARG cc_start: 0.8768 (tpt-90) cc_final: 0.8513 (tpp80) REVERT: B 400 ASP cc_start: 0.8595 (m-30) cc_final: 0.8257 (m-30) REVERT: B 411 SER cc_start: 0.9348 (t) cc_final: 0.8937 (p) REVERT: B 417 ASP cc_start: 0.8518 (t0) cc_final: 0.8208 (t0) REVERT: B 446 ARG cc_start: 0.8793 (ttm110) cc_final: 0.8419 (ttm110) REVERT: B 448 TYR cc_start: 0.8930 (m-80) cc_final: 0.8576 (m-10) REVERT: B 466 CYS cc_start: 0.4730 (m) cc_final: 0.4354 (m) REVERT: B 529 ASP cc_start: 0.8338 (t70) cc_final: 0.7686 (t0) REVERT: B 536 LYS cc_start: 0.8335 (mmtp) cc_final: 0.7969 (mmtt) REVERT: B 587 ARG cc_start: 0.8392 (mtp85) cc_final: 0.8082 (ttm-80) REVERT: B 711 GLN cc_start: 0.8230 (pm20) cc_final: 0.7675 (mp10) REVERT: B 781 ASP cc_start: 0.7752 (p0) cc_final: 0.7356 (p0) REVERT: B 805 GLU cc_start: 0.8426 (tm-30) cc_final: 0.8029 (tm-30) REVERT: B 832 LEU cc_start: 0.8896 (mt) cc_final: 0.8230 (mm) REVERT: B 842 ASN cc_start: 0.8911 (m-40) cc_final: 0.8581 (m-40) REVERT: B 848 ASP cc_start: 0.8735 (m-30) cc_final: 0.8276 (m-30) REVERT: B 849 GLU cc_start: 0.8610 (tm-30) cc_final: 0.8217 (pp20) REVERT: B 855 ASP cc_start: 0.8308 (m-30) cc_final: 0.7928 (m-30) REVERT: B 867 GLN cc_start: 0.7945 (mm-40) cc_final: 0.7711 (mm110) REVERT: B 873 SER cc_start: 0.8851 (m) cc_final: 0.8541 (p) REVERT: B 874 ASN cc_start: 0.9012 (m-40) cc_final: 0.8575 (p0) REVERT: B 883 VAL cc_start: 0.8573 (OUTLIER) cc_final: 0.8357 (p) REVERT: B 889 LYS cc_start: 0.9215 (ttpt) cc_final: 0.8825 (ttmm) REVERT: B 914 LYS cc_start: 0.9256 (mmmt) cc_final: 0.8957 (mmmm) REVERT: B 916 LYS cc_start: 0.8844 (pttt) cc_final: 0.8475 (ptmm) REVERT: B 924 GLU cc_start: 0.8529 (OUTLIER) cc_final: 0.8251 (tm-30) REVERT: B 999 ASP cc_start: 0.8522 (t0) cc_final: 0.8081 (t0) REVERT: B 1004 ASN cc_start: 0.8502 (m-40) cc_final: 0.8187 (m-40) REVERT: B 1034 GLN cc_start: 0.8998 (OUTLIER) cc_final: 0.8598 (mp10) REVERT: B 1042 GLN cc_start: 0.9064 (OUTLIER) cc_final: 0.8785 (tm-30) REVERT: B 1054 LYS cc_start: 0.9201 (mttt) cc_final: 0.8934 (mmmm) REVERT: B 1075 GLN cc_start: 0.8749 (mm-40) cc_final: 0.8445 (mm-40) REVERT: B 1095 GLN cc_start: 0.8719 (tm-30) cc_final: 0.7493 (tm-30) REVERT: B 1099 ASP cc_start: 0.8816 (m-30) cc_final: 0.7480 (m-30) REVERT: B 1111 MET cc_start: 0.9001 (mtm) cc_final: 0.8768 (mtm) REVERT: B 1112 GLU cc_start: 0.8768 (tp30) cc_final: 0.8364 (tp30) REVERT: B 1126 ASN cc_start: 0.8639 (t0) cc_final: 0.8192 (t0) REVERT: B 1204 LYS cc_start: 0.9011 (mtpt) cc_final: 0.8787 (mtpp) REVERT: C 15 ILE cc_start: 0.9098 (pt) cc_final: 0.8863 (pt) REVERT: C 17 ASP cc_start: 0.7656 (p0) cc_final: 0.7352 (p0) REVERT: C 53 ASP cc_start: 0.8643 (m-30) cc_final: 0.8209 (t0) REVERT: C 60 THR cc_start: 0.9223 (OUTLIER) cc_final: 0.8925 (p) REVERT: C 76 ASP cc_start: 0.8109 (t0) cc_final: 0.7908 (t0) REVERT: C 84 LYS cc_start: 0.8752 (mmmm) cc_final: 0.8196 (tptt) REVERT: C 288 SER cc_start: 0.8875 (m) cc_final: 0.8358 (t) REVERT: C 289 GLU cc_start: 0.8719 (mt-10) cc_final: 0.8438 (tm-30) REVERT: C 293 LYS cc_start: 0.9067 (ttpt) cc_final: 0.8742 (ttpt) REVERT: C 330 ASP cc_start: 0.8368 (p0) cc_final: 0.8015 (p0) REVERT: C 331 LYS cc_start: 0.9206 (mttt) cc_final: 0.8816 (ttmm) REVERT: C 384 LYS cc_start: 0.8846 (OUTLIER) cc_final: 0.8410 (pttp) REVERT: C 397 ARG cc_start: 0.8985 (mmt180) cc_final: 0.8654 (mmm-85) REVERT: C 481 PHE cc_start: 0.6795 (t80) cc_final: 0.6503 (t80) REVERT: C 500 ASN cc_start: 0.7752 (m-40) cc_final: 0.7444 (m-40) REVERT: C 772 GLU cc_start: 0.8309 (mp0) cc_final: 0.7953 (mp0) REVERT: C 832 LEU cc_start: 0.9070 (mt) cc_final: 0.8450 (mm) REVERT: C 842 ASN cc_start: 0.8847 (m-40) cc_final: 0.8565 (m-40) REVERT: C 848 ASP cc_start: 0.8749 (m-30) cc_final: 0.8157 (m-30) REVERT: C 849 GLU cc_start: 0.8316 (pp20) cc_final: 0.7983 (pp20) REVERT: C 850 VAL cc_start: 0.9350 (OUTLIER) cc_final: 0.9008 (p) REVERT: C 855 ASP cc_start: 0.8330 (m-30) cc_final: 0.7969 (m-30) REVERT: C 858 GLN cc_start: 0.8843 (mm110) cc_final: 0.8446 (mm110) REVERT: C 873 SER cc_start: 0.9080 (m) cc_final: 0.8791 (p) REVERT: C 874 ASN cc_start: 0.9016 (m-40) cc_final: 0.8493 (p0) REVERT: C 882 ASP cc_start: 0.7750 (m-30) cc_final: 0.7452 (t0) REVERT: C 888 PHE cc_start: 0.8509 (m-80) cc_final: 0.8159 (m-80) REVERT: C 909 ASP cc_start: 0.8412 (m-30) cc_final: 0.7836 (m-30) REVERT: C 956 GLU cc_start: 0.7903 (mm-30) cc_final: 0.7598 (mm-30) REVERT: C 999 ASP cc_start: 0.8257 (t70) cc_final: 0.7788 (t0) REVERT: C 1045 ASN cc_start: 0.9265 (t0) cc_final: 0.9053 (t0) REVERT: C 1075 GLN cc_start: 0.8636 (mm110) cc_final: 0.7693 (mm-40) REVERT: C 1079 ASP cc_start: 0.8656 (m-30) cc_final: 0.8260 (m-30) REVERT: C 1095 GLN cc_start: 0.8705 (tm-30) cc_final: 0.7572 (tm-30) REVERT: C 1099 ASP cc_start: 0.8831 (m-30) cc_final: 0.7634 (m-30) REVERT: C 1104 LYS cc_start: 0.8967 (tptt) cc_final: 0.8576 (tppt) REVERT: C 1112 GLU cc_start: 0.8736 (tp30) cc_final: 0.8304 (tp30) REVERT: C 1116 GLU cc_start: 0.8260 (mm-30) cc_final: 0.7990 (mm-30) REVERT: C 1199 GLU cc_start: 0.8098 (OUTLIER) cc_final: 0.7636 (mm-30) REVERT: C 1209 MET cc_start: 0.8323 (mpp) cc_final: 0.7617 (mpp) outliers start: 65 outliers final: 39 residues processed: 538 average time/residue: 0.4625 time to fit residues: 388.8049 Evaluate side-chains 533 residues out of total 3216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 481 time to evaluate : 3.328 ------------------------------------------------------------------------------- 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 114 ASN Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 193 VAL 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 444 TRP Chi-restraints excluded: chain A residue 525 ILE Chi-restraints excluded: chain A residue 583 VAL 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 924 GLU 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 60 THR Chi-restraints excluded: chain B residue 218 MET 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 535 GLN Chi-restraints excluded: chain B residue 575 LEU Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain B residue 588 CYS Chi-restraints excluded: chain B residue 589 ASN Chi-restraints excluded: chain B residue 883 VAL Chi-restraints excluded: chain B residue 924 GLU Chi-restraints excluded: chain B residue 940 CYS Chi-restraints excluded: chain B residue 1034 GLN Chi-restraints excluded: chain B residue 1042 GLN Chi-restraints excluded: chain B residue 1189 MET Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 384 LYS Chi-restraints excluded: chain C residue 699 CYS 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 1199 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 246 optimal weight: 1.9990 chunk 73 optimal weight: 0.9990 chunk 282 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 12 optimal weight: 7.9990 chunk 190 optimal weight: 5.9990 chunk 158 optimal weight: 6.9990 chunk 243 optimal weight: 0.6980 chunk 221 optimal weight: 2.9990 chunk 28 optimal weight: 0.6980 chunk 256 optimal weight: 0.9980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 HIS ** A 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 858 GLN ** C 142 HIS ** 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** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.098836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.077402 restraints weight = 63308.204| |-----------------------------------------------------------------------------| r_work (start): 0.3088 rms_B_bonded: 3.84 r_work: 0.2912 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.4123 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= 0.147 Angle : 0.612 9.895 41256 Z= 0.314 Chirality : 0.043 0.220 4842 Planarity : 0.004 0.058 5124 Dihedral : 5.578 57.340 5688 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 1.90 % Allowed : 17.29 % Favored : 80.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.14), residues: 3573 helix: 2.02 (0.20), residues: 762 sheet: -0.14 (0.18), residues: 771 loop : -1.36 (0.13), residues: 2040 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 646 HIS 0.004 0.001 HIS B 201 PHE 0.028 0.001 PHE B 714 TYR 0.040 0.001 TYR C 713 ARG 0.007 0.000 ARG A 904 Details of bonding type rmsd link_NAG-ASN : bond 0.00252 ( 57) link_NAG-ASN : angle 1.62015 ( 171) link_BETA1-4 : bond 0.00395 ( 30) link_BETA1-4 : angle 1.50437 ( 90) hydrogen bonds : bond 0.04254 ( 1016) hydrogen bonds : angle 4.82967 ( 3102) SS BOND : bond 0.00378 ( 72) SS BOND : angle 1.35652 ( 144) covalent geometry : bond 0.00333 (30018) covalent geometry : angle 0.59625 (40851) *********************** 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 568 residues out of total 3216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 507 time to evaluate : 4.436 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 73 ASN cc_start: 0.8977 (p0) cc_final: 0.8722 (p0) REVERT: A 114 ASN cc_start: 0.8747 (OUTLIER) cc_final: 0.8439 (p0) REVERT: A 140 GLN cc_start: 0.7733 (tm-30) cc_final: 0.6795 (tm-30) REVERT: A 142 HIS cc_start: 0.8305 (m90) cc_final: 0.6916 (m90) REVERT: A 175 HIS cc_start: 0.8656 (p-80) cc_final: 0.8306 (p-80) REVERT: A 273 ARG cc_start: 0.8570 (tpp80) cc_final: 0.8345 (mpp80) REVERT: A 288 SER cc_start: 0.8873 (m) cc_final: 0.8461 (t) REVERT: A 319 ARG cc_start: 0.8591 (mmm160) cc_final: 0.8151 (mmm-85) REVERT: A 331 LYS cc_start: 0.9054 (mtpt) cc_final: 0.8793 (mtpp) REVERT: A 336 PHE cc_start: 0.8290 (m-10) cc_final: 0.7895 (m-80) REVERT: A 376 SER cc_start: 0.9047 (m) cc_final: 0.8658 (p) REVERT: A 384 LYS cc_start: 0.8728 (pttp) cc_final: 0.8395 (pttt) REVERT: A 411 SER cc_start: 0.9170 (t) cc_final: 0.8943 (p) REVERT: A 437 ASN cc_start: 0.8685 (t0) cc_final: 0.8353 (t0) REVERT: A 446 ARG cc_start: 0.8637 (ttm-80) cc_final: 0.8369 (ttm-80) REVERT: A 553 GLU cc_start: 0.8345 (mm-30) cc_final: 0.7866 (mm-30) REVERT: A 618 THR cc_start: 0.9281 (OUTLIER) cc_final: 0.9025 (m) REVERT: A 711 GLN cc_start: 0.8473 (pm20) cc_final: 0.7920 (mp10) REVERT: A 772 GLU cc_start: 0.8280 (mp0) cc_final: 0.7876 (mp0) REVERT: A 784 GLU cc_start: 0.8319 (mm-30) cc_final: 0.8048 (mp0) REVERT: A 792 ILE cc_start: 0.9165 (tp) cc_final: 0.8853 (pt) REVERT: A 805 GLU cc_start: 0.7970 (tm-30) cc_final: 0.7688 (tm-30) REVERT: A 842 ASN cc_start: 0.8928 (m-40) cc_final: 0.8668 (m-40) REVERT: A 844 ASN cc_start: 0.8982 (m-40) cc_final: 0.7989 (m-40) REVERT: A 848 ASP cc_start: 0.8565 (m-30) cc_final: 0.8157 (m-30) REVERT: A 849 GLU cc_start: 0.8186 (pp20) cc_final: 0.7929 (pp20) REVERT: A 867 GLN cc_start: 0.8189 (mm-40) cc_final: 0.7934 (mm110) REVERT: A 889 LYS cc_start: 0.9043 (ttpt) cc_final: 0.8739 (ttpp) REVERT: A 909 ASP cc_start: 0.8518 (m-30) cc_final: 0.8022 (m-30) REVERT: A 924 GLU cc_start: 0.8347 (OUTLIER) cc_final: 0.8070 (pp20) REVERT: A 956 GLU cc_start: 0.7635 (pm20) cc_final: 0.7327 (pm20) REVERT: A 998 MET cc_start: 0.9037 (tpp) cc_final: 0.8367 (tpp) REVERT: A 999 ASP cc_start: 0.8647 (t0) cc_final: 0.8104 (t0) REVERT: A 1075 GLN cc_start: 0.8684 (mm-40) cc_final: 0.8479 (mm-40) REVERT: A 1095 GLN cc_start: 0.8652 (tm-30) cc_final: 0.7201 (tm-30) REVERT: A 1099 ASP cc_start: 0.8772 (m-30) cc_final: 0.7497 (m-30) REVERT: A 1112 GLU cc_start: 0.8680 (tt0) cc_final: 0.8320 (tp30) REVERT: A 1153 LYS cc_start: 0.8756 (tppt) cc_final: 0.8514 (tptp) REVERT: A 1177 LYS cc_start: 0.8719 (tppt) cc_final: 0.8261 (tppt) REVERT: A 1178 GLN cc_start: 0.8766 (tt0) cc_final: 0.8496 (tt0) REVERT: B 69 LYS cc_start: 0.9203 (tmtt) cc_final: 0.8792 (tmmt) REVERT: B 88 LEU cc_start: 0.9090 (mp) cc_final: 0.8748 (tp) REVERT: B 92 LYS cc_start: 0.8977 (mtmm) cc_final: 0.8731 (mtpp) REVERT: B 111 LEU cc_start: 0.8996 (mm) cc_final: 0.8442 (mt) REVERT: B 147 GLU cc_start: 0.8391 (pp20) cc_final: 0.8064 (pp20) REVERT: B 175 HIS cc_start: 0.8767 (p-80) cc_final: 0.8191 (p-80) REVERT: B 218 MET cc_start: 0.8444 (tpp) cc_final: 0.8199 (mmm) REVERT: B 271 ASP cc_start: 0.7659 (p0) cc_final: 0.7443 (p0) REVERT: B 273 ARG cc_start: 0.8508 (OUTLIER) cc_final: 0.8208 (mtp-110) REVERT: B 326 ASP cc_start: 0.7062 (t70) cc_final: 0.6794 (t0) REVERT: B 331 LYS cc_start: 0.9257 (mttt) cc_final: 0.8790 (ttmm) REVERT: B 384 LYS cc_start: 0.8720 (pttt) cc_final: 0.8316 (pttp) REVERT: B 388 LEU cc_start: 0.8925 (OUTLIER) cc_final: 0.8638 (mp) REVERT: B 397 ARG cc_start: 0.8881 (mmt180) cc_final: 0.8471 (mmm-85) REVERT: B 398 ARG cc_start: 0.8707 (tpt-90) cc_final: 0.8504 (tpp80) REVERT: B 400 ASP cc_start: 0.8444 (m-30) cc_final: 0.8032 (m-30) REVERT: B 411 SER cc_start: 0.9331 (t) cc_final: 0.8957 (p) REVERT: B 417 ASP cc_start: 0.8446 (t0) cc_final: 0.8171 (t0) REVERT: B 446 ARG cc_start: 0.8751 (ttm110) cc_final: 0.8463 (ttm-80) REVERT: B 448 TYR cc_start: 0.8913 (m-80) cc_final: 0.8597 (m-10) REVERT: B 464 ARG cc_start: 0.8597 (tpp80) cc_final: 0.8119 (tpp80) REVERT: B 466 CYS cc_start: 0.4783 (m) cc_final: 0.4438 (m) REVERT: B 529 ASP cc_start: 0.8375 (t70) cc_final: 0.7709 (t0) REVERT: B 536 LYS cc_start: 0.8408 (mmtp) cc_final: 0.8094 (mptt) REVERT: B 587 ARG cc_start: 0.8383 (mtp85) cc_final: 0.8064 (ttm-80) REVERT: B 711 GLN cc_start: 0.8286 (pm20) cc_final: 0.7733 (mp10) REVERT: B 781 ASP cc_start: 0.7804 (p0) cc_final: 0.7393 (p0) REVERT: B 805 GLU cc_start: 0.8342 (tm-30) cc_final: 0.8113 (tm-30) REVERT: B 832 LEU cc_start: 0.8927 (mt) cc_final: 0.8024 (mm) REVERT: B 842 ASN cc_start: 0.8832 (m-40) cc_final: 0.8523 (m-40) REVERT: B 848 ASP cc_start: 0.8703 (m-30) cc_final: 0.8241 (m-30) REVERT: B 849 GLU cc_start: 0.8541 (tm-30) cc_final: 0.8194 (pp20) REVERT: B 855 ASP cc_start: 0.8264 (m-30) cc_final: 0.7886 (m-30) REVERT: B 867 GLN cc_start: 0.7935 (mm-40) cc_final: 0.7712 (mm110) REVERT: B 873 SER cc_start: 0.8851 (m) cc_final: 0.8515 (p) REVERT: B 874 ASN cc_start: 0.8966 (m-40) cc_final: 0.8598 (p0) REVERT: B 881 PHE cc_start: 0.7798 (p90) cc_final: 0.7024 (p90) REVERT: B 882 ASP cc_start: 0.8194 (m-30) cc_final: 0.7637 (m-30) REVERT: B 883 VAL cc_start: 0.8571 (OUTLIER) cc_final: 0.8353 (p) REVERT: B 888 PHE cc_start: 0.8328 (m-10) cc_final: 0.8104 (m-10) REVERT: B 889 LYS cc_start: 0.9169 (ttpt) cc_final: 0.8682 (ttmm) REVERT: B 914 LYS cc_start: 0.9275 (mmmt) cc_final: 0.9002 (mmmm) REVERT: B 916 LYS cc_start: 0.8815 (pttt) cc_final: 0.8467 (ptmm) REVERT: B 924 GLU cc_start: 0.8513 (OUTLIER) cc_final: 0.8128 (tm-30) REVERT: B 999 ASP cc_start: 0.8489 (t0) cc_final: 0.8034 (t0) REVERT: B 1004 ASN cc_start: 0.8514 (m-40) cc_final: 0.8176 (m-40) REVERT: B 1034 GLN cc_start: 0.8963 (OUTLIER) cc_final: 0.8590 (mp10) REVERT: B 1042 GLN cc_start: 0.9046 (mt0) cc_final: 0.8803 (tm-30) REVERT: B 1054 LYS cc_start: 0.9167 (mttt) cc_final: 0.8939 (mmmm) REVERT: B 1075 GLN cc_start: 0.8695 (mm-40) cc_final: 0.7817 (mm-40) REVERT: B 1079 ASP cc_start: 0.8662 (m-30) cc_final: 0.8284 (m-30) REVERT: B 1095 GLN cc_start: 0.8695 (tm-30) cc_final: 0.7423 (tm-30) REVERT: B 1099 ASP cc_start: 0.8741 (m-30) cc_final: 0.7375 (m-30) REVERT: B 1112 GLU cc_start: 0.8727 (tp30) cc_final: 0.8242 (tp30) REVERT: B 1126 ASN cc_start: 0.8634 (t0) cc_final: 0.8271 (t0) REVERT: B 1202 SER cc_start: 0.8894 (t) cc_final: 0.8606 (p) REVERT: B 1209 MET cc_start: 0.8526 (tpp) cc_final: 0.8057 (mpp) REVERT: C 15 ILE cc_start: 0.9083 (pt) cc_final: 0.8857 (pt) REVERT: C 17 ASP cc_start: 0.7523 (p0) cc_final: 0.7166 (p0) REVERT: C 18 PHE cc_start: 0.8222 (t80) cc_final: 0.7902 (t80) REVERT: C 53 ASP cc_start: 0.8524 (m-30) cc_final: 0.8184 (t0) REVERT: C 60 THR cc_start: 0.9188 (OUTLIER) cc_final: 0.8860 (p) REVERT: C 76 ASP cc_start: 0.7994 (t0) cc_final: 0.7749 (t0) REVERT: C 84 LYS cc_start: 0.8754 (mmmm) cc_final: 0.8238 (tptt) REVERT: C 288 SER cc_start: 0.8895 (m) cc_final: 0.8378 (t) REVERT: C 289 GLU cc_start: 0.8706 (mt-10) cc_final: 0.8475 (tm-30) REVERT: C 293 LYS cc_start: 0.9033 (ttpt) cc_final: 0.8759 (ttpt) REVERT: C 330 ASP cc_start: 0.8348 (p0) cc_final: 0.7997 (p0) REVERT: C 331 LYS cc_start: 0.9186 (mttt) cc_final: 0.8793 (ttmm) REVERT: C 384 LYS cc_start: 0.8824 (OUTLIER) cc_final: 0.8384 (pttp) REVERT: C 397 ARG cc_start: 0.8942 (mmt180) cc_final: 0.8656 (mmm-85) REVERT: C 481 PHE cc_start: 0.6872 (t80) cc_final: 0.6570 (t80) REVERT: C 500 ASN cc_start: 0.7842 (m-40) cc_final: 0.7527 (m-40) REVERT: C 529 ASP cc_start: 0.8220 (t70) cc_final: 0.7632 (t0) REVERT: C 772 GLU cc_start: 0.8303 (mp0) cc_final: 0.7968 (mp0) REVERT: C 832 LEU cc_start: 0.9105 (mt) cc_final: 0.8476 (mm) REVERT: C 842 ASN cc_start: 0.8771 (m-40) cc_final: 0.8506 (m-40) REVERT: C 848 ASP cc_start: 0.8722 (m-30) cc_final: 0.8137 (m-30) REVERT: C 849 GLU cc_start: 0.8287 (pp20) cc_final: 0.7952 (pp20) REVERT: C 855 ASP cc_start: 0.8277 (m-30) cc_final: 0.7929 (m-30) REVERT: C 858 GLN cc_start: 0.8817 (mm110) cc_final: 0.8574 (mm110) REVERT: C 873 SER cc_start: 0.9076 (m) cc_final: 0.8799 (p) REVERT: C 874 ASN cc_start: 0.8958 (m-40) cc_final: 0.8607 (p0) REVERT: C 888 PHE cc_start: 0.8241 (m-80) cc_final: 0.7975 (m-80) REVERT: C 889 LYS cc_start: 0.9258 (ttpt) cc_final: 0.8950 (ttpp) REVERT: C 909 ASP cc_start: 0.8329 (m-30) cc_final: 0.7715 (m-30) REVERT: C 956 GLU cc_start: 0.7864 (mm-30) cc_final: 0.7624 (mm-30) REVERT: C 999 ASP cc_start: 0.8265 (t70) cc_final: 0.7965 (t0) REVERT: C 1045 ASN cc_start: 0.9250 (t0) cc_final: 0.9029 (t0) REVERT: C 1075 GLN cc_start: 0.8612 (mm110) cc_final: 0.7732 (mm-40) REVERT: C 1079 ASP cc_start: 0.8577 (m-30) cc_final: 0.8220 (m-30) REVERT: C 1095 GLN cc_start: 0.8690 (tm-30) cc_final: 0.7525 (tm-30) REVERT: C 1099 ASP cc_start: 0.8788 (m-30) cc_final: 0.7552 (m-30) REVERT: C 1104 LYS cc_start: 0.9010 (tptt) cc_final: 0.8652 (tppt) REVERT: C 1112 GLU cc_start: 0.8662 (tp30) cc_final: 0.8396 (tp30) REVERT: C 1116 GLU cc_start: 0.8258 (mm-30) cc_final: 0.7891 (mm-30) REVERT: C 1189 MET cc_start: 0.8710 (mtt) cc_final: 0.8303 (mtt) REVERT: C 1199 GLU cc_start: 0.8074 (OUTLIER) cc_final: 0.7564 (mm-30) REVERT: C 1209 MET cc_start: 0.8304 (mpp) cc_final: 0.7645 (mpp) outliers start: 61 outliers final: 36 residues processed: 547 average time/residue: 0.4367 time to fit residues: 371.6031 Evaluate side-chains 536 residues out of total 3216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 489 time to evaluate : 3.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 LYS Chi-restraints excluded: chain A residue 114 ASN Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 193 VAL 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 444 TRP Chi-restraints excluded: chain A residue 525 ILE Chi-restraints excluded: chain A residue 583 VAL 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 924 GLU 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 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 388 LEU Chi-restraints excluded: chain B residue 405 SER Chi-restraints excluded: chain B residue 535 GLN Chi-restraints excluded: chain B residue 589 ASN Chi-restraints excluded: chain B residue 883 VAL Chi-restraints excluded: chain B residue 924 GLU Chi-restraints excluded: chain B residue 1034 GLN Chi-restraints excluded: chain B residue 1036 VAL Chi-restraints excluded: chain B residue 1189 MET Chi-restraints excluded: chain C residue 52 LEU 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 384 LYS 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 1167 CYS Chi-restraints excluded: chain C residue 1199 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 82 optimal weight: 1.9990 chunk 353 optimal weight: 0.7980 chunk 248 optimal weight: 10.0000 chunk 166 optimal weight: 2.9990 chunk 156 optimal weight: 0.7980 chunk 70 optimal weight: 1.9990 chunk 130 optimal weight: 5.9990 chunk 275 optimal weight: 4.9990 chunk 71 optimal weight: 0.1980 chunk 153 optimal weight: 0.6980 chunk 349 optimal weight: 2.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 HIS ** A 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 858 GLN ** 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 858 GLN B1021 ASN ** C 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 445 ASN ** 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 = 0.3504 r_free = 0.3504 target = 0.101619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.080318 restraints weight = 62682.484| |-----------------------------------------------------------------------------| r_work (start): 0.3095 rms_B_bonded: 3.80 r_work: 0.2916 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.4198 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= 0.137 Angle : 0.619 13.011 41256 Z= 0.316 Chirality : 0.043 0.387 4842 Planarity : 0.004 0.057 5124 Dihedral : 5.474 55.444 5688 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 1.62 % Allowed : 17.85 % Favored : 80.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.14), residues: 3573 helix: 1.97 (0.19), residues: 768 sheet: -0.08 (0.18), residues: 771 loop : -1.36 (0.13), residues: 2034 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 646 HIS 0.004 0.001 HIS B 201 PHE 0.029 0.001 PHE B 714 TYR 0.039 0.001 TYR C 713 ARG 0.007 0.001 ARG B 206 Details of bonding type rmsd link_NAG-ASN : bond 0.00526 ( 57) link_NAG-ASN : angle 1.98630 ( 171) link_BETA1-4 : bond 0.00412 ( 30) link_BETA1-4 : angle 1.54116 ( 90) hydrogen bonds : bond 0.04113 ( 1016) hydrogen bonds : angle 4.78268 ( 3102) SS BOND : bond 0.00352 ( 72) SS BOND : angle 1.30798 ( 144) covalent geometry : bond 0.00311 (30018) covalent geometry : angle 0.59930 (40851) *********************** 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 553 residues out of total 3216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 501 time to evaluate : 3.161 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: A 73 ASN cc_start: 0.8989 (p0) cc_final: 0.8713 (p0) REVERT: A 114 ASN cc_start: 0.8762 (OUTLIER) cc_final: 0.8444 (p0) REVERT: A 135 TYR cc_start: 0.9159 (m-80) cc_final: 0.8880 (m-80) REVERT: A 140 GLN cc_start: 0.7717 (tm-30) cc_final: 0.6780 (tm-30) REVERT: A 142 HIS cc_start: 0.8303 (m90) cc_final: 0.6912 (m90) REVERT: A 175 HIS cc_start: 0.8651 (p-80) cc_final: 0.8282 (p-80) REVERT: A 273 ARG cc_start: 0.8560 (tpp80) cc_final: 0.8337 (mpp80) REVERT: A 288 SER cc_start: 0.8875 (m) cc_final: 0.8466 (t) REVERT: A 305 ASP cc_start: 0.8119 (p0) cc_final: 0.7630 (p0) REVERT: A 319 ARG cc_start: 0.8586 (mmm160) cc_final: 0.8146 (mmm-85) REVERT: A 331 LYS cc_start: 0.9051 (mtpt) cc_final: 0.8795 (mtpp) REVERT: A 336 PHE cc_start: 0.8291 (m-10) cc_final: 0.7888 (m-80) REVERT: A 376 SER cc_start: 0.9041 (m) cc_final: 0.8644 (p) REVERT: A 384 LYS cc_start: 0.8723 (pttp) cc_final: 0.8504 (pttt) REVERT: A 411 SER cc_start: 0.9160 (t) cc_final: 0.8924 (p) REVERT: A 417 ASP cc_start: 0.8424 (t0) cc_final: 0.8137 (t0) REVERT: A 446 ARG cc_start: 0.8594 (ttm-80) cc_final: 0.8336 (ttm-80) REVERT: A 553 GLU cc_start: 0.8366 (mm-30) cc_final: 0.7895 (mm-30) REVERT: A 587 ARG cc_start: 0.8374 (mtp85) cc_final: 0.7868 (ttt90) REVERT: A 618 THR cc_start: 0.9255 (OUTLIER) cc_final: 0.9028 (m) REVERT: A 711 GLN cc_start: 0.8476 (pm20) cc_final: 0.7917 (mp10) REVERT: A 772 GLU cc_start: 0.8290 (mp0) cc_final: 0.7886 (mp0) REVERT: A 792 ILE cc_start: 0.9144 (tp) cc_final: 0.8830 (pt) REVERT: A 805 GLU cc_start: 0.7967 (tm-30) cc_final: 0.7683 (tm-30) REVERT: A 842 ASN cc_start: 0.8933 (m-40) cc_final: 0.8670 (m-40) REVERT: A 844 ASN cc_start: 0.8983 (m-40) cc_final: 0.7993 (m-40) REVERT: A 848 ASP cc_start: 0.8569 (m-30) cc_final: 0.8149 (m-30) REVERT: A 849 GLU cc_start: 0.8168 (pp20) cc_final: 0.7920 (pp20) REVERT: A 867 GLN cc_start: 0.8185 (mm-40) cc_final: 0.7914 (mm110) REVERT: A 889 LYS cc_start: 0.9027 (ttpt) cc_final: 0.8735 (ttpp) REVERT: A 909 ASP cc_start: 0.8481 (m-30) cc_final: 0.7911 (m-30) REVERT: A 998 MET cc_start: 0.9043 (tpp) cc_final: 0.8365 (tpp) REVERT: A 999 ASP cc_start: 0.8630 (t0) cc_final: 0.8094 (t0) REVERT: A 1075 GLN cc_start: 0.8677 (mm-40) cc_final: 0.7898 (mm-40) REVERT: A 1079 ASP cc_start: 0.8716 (m-30) cc_final: 0.8263 (m-30) REVERT: A 1095 GLN cc_start: 0.8648 (tm-30) cc_final: 0.7185 (tm-30) REVERT: A 1099 ASP cc_start: 0.8772 (m-30) cc_final: 0.7464 (m-30) REVERT: A 1112 GLU cc_start: 0.8673 (tt0) cc_final: 0.8405 (tp30) REVERT: A 1153 LYS cc_start: 0.8756 (tppt) cc_final: 0.8497 (tptp) REVERT: A 1177 LYS cc_start: 0.8703 (tppt) cc_final: 0.8232 (tppt) REVERT: A 1178 GLN cc_start: 0.8745 (tt0) cc_final: 0.8473 (tt0) REVERT: B 69 LYS cc_start: 0.9215 (tmtt) cc_final: 0.8795 (tmmt) REVERT: B 88 LEU cc_start: 0.9058 (mp) cc_final: 0.8728 (tp) REVERT: B 92 LYS cc_start: 0.8959 (mtmm) cc_final: 0.8713 (mtpp) REVERT: B 111 LEU cc_start: 0.8971 (mm) cc_final: 0.8421 (mt) REVERT: B 147 GLU cc_start: 0.8413 (pp20) cc_final: 0.8161 (pp20) REVERT: B 175 HIS cc_start: 0.8751 (p-80) cc_final: 0.8170 (p-80) REVERT: B 218 MET cc_start: 0.8433 (tpp) cc_final: 0.8206 (mmm) REVERT: B 271 ASP cc_start: 0.7650 (p0) cc_final: 0.7433 (p0) REVERT: B 273 ARG cc_start: 0.8496 (OUTLIER) cc_final: 0.8197 (mtp-110) REVERT: B 319 ARG cc_start: 0.8896 (mmm-85) cc_final: 0.8691 (mmm-85) REVERT: B 326 ASP cc_start: 0.7061 (t70) cc_final: 0.6795 (t0) REVERT: B 331 LYS cc_start: 0.9282 (mttt) cc_final: 0.8824 (ttmm) REVERT: B 388 LEU cc_start: 0.8930 (OUTLIER) cc_final: 0.8641 (mp) REVERT: B 397 ARG cc_start: 0.8883 (mmt180) cc_final: 0.8456 (mmm-85) REVERT: B 400 ASP cc_start: 0.8424 (m-30) cc_final: 0.8003 (m-30) REVERT: B 411 SER cc_start: 0.9331 (t) cc_final: 0.8959 (p) REVERT: B 417 ASP cc_start: 0.8447 (t0) cc_final: 0.8160 (t0) REVERT: B 446 ARG cc_start: 0.8718 (ttm110) cc_final: 0.8458 (ttm-80) REVERT: B 448 TYR cc_start: 0.8931 (m-80) cc_final: 0.8563 (m-10) REVERT: B 466 CYS cc_start: 0.4679 (m) cc_final: 0.4406 (m) REVERT: B 529 ASP cc_start: 0.8361 (t70) cc_final: 0.7676 (t0) REVERT: B 536 LYS cc_start: 0.8441 (mmtp) cc_final: 0.8068 (mmtt) REVERT: B 587 ARG cc_start: 0.8424 (mtp85) cc_final: 0.7957 (ttm-80) REVERT: B 711 GLN cc_start: 0.8286 (pm20) cc_final: 0.7721 (mp10) REVERT: B 781 ASP cc_start: 0.7801 (p0) cc_final: 0.7402 (p0) REVERT: B 805 GLU cc_start: 0.8375 (tm-30) cc_final: 0.8133 (tm-30) REVERT: B 832 LEU cc_start: 0.8922 (mt) cc_final: 0.8025 (mm) REVERT: B 842 ASN cc_start: 0.8812 (m-40) cc_final: 0.8501 (m-40) REVERT: B 848 ASP cc_start: 0.8714 (m-30) cc_final: 0.8332 (m-30) REVERT: B 849 GLU cc_start: 0.8543 (tm-30) cc_final: 0.8193 (pp20) REVERT: B 855 ASP cc_start: 0.8259 (m-30) cc_final: 0.7871 (m-30) REVERT: B 867 GLN cc_start: 0.7925 (mm-40) cc_final: 0.7694 (mm110) REVERT: B 873 SER cc_start: 0.8824 (m) cc_final: 0.8480 (p) REVERT: B 874 ASN cc_start: 0.8940 (m-40) cc_final: 0.8666 (p0) REVERT: B 881 PHE cc_start: 0.7780 (p90) cc_final: 0.6934 (p90) REVERT: B 882 ASP cc_start: 0.8233 (m-30) cc_final: 0.7616 (m-30) REVERT: B 883 VAL cc_start: 0.8608 (OUTLIER) cc_final: 0.8387 (p) REVERT: B 889 LYS cc_start: 0.9140 (ttpt) cc_final: 0.8641 (ttmm) REVERT: B 914 LYS cc_start: 0.9361 (mmmt) cc_final: 0.9110 (mmmm) REVERT: B 916 LYS cc_start: 0.8825 (pttt) cc_final: 0.8471 (ptmm) REVERT: B 924 GLU cc_start: 0.8533 (OUTLIER) cc_final: 0.8142 (tm-30) REVERT: B 998 MET cc_start: 0.8721 (tpp) cc_final: 0.8518 (mmm) REVERT: B 999 ASP cc_start: 0.8477 (t0) cc_final: 0.8018 (t0) REVERT: B 1004 ASN cc_start: 0.8471 (m-40) cc_final: 0.8086 (m-40) REVERT: B 1034 GLN cc_start: 0.8950 (OUTLIER) cc_final: 0.8585 (mp10) REVERT: B 1042 GLN cc_start: 0.9074 (mt0) cc_final: 0.8817 (tm-30) REVERT: B 1054 LYS cc_start: 0.9156 (mttt) cc_final: 0.8935 (mmmm) REVERT: B 1075 GLN cc_start: 0.8679 (mm-40) cc_final: 0.7817 (mm-40) REVERT: B 1079 ASP cc_start: 0.8632 (m-30) cc_final: 0.8277 (m-30) REVERT: B 1095 GLN cc_start: 0.8658 (tm-30) cc_final: 0.7376 (tm-30) REVERT: B 1099 ASP cc_start: 0.8761 (m-30) cc_final: 0.7380 (m-30) REVERT: B 1112 GLU cc_start: 0.8700 (tp30) cc_final: 0.8194 (tp30) REVERT: B 1126 ASN cc_start: 0.8624 (t0) cc_final: 0.8232 (t0) REVERT: B 1177 LYS cc_start: 0.8492 (mmmm) cc_final: 0.7908 (mmmm) REVERT: B 1202 SER cc_start: 0.8854 (t) cc_final: 0.8562 (p) REVERT: C 15 ILE cc_start: 0.9067 (pt) cc_final: 0.8845 (pt) REVERT: C 17 ASP cc_start: 0.7532 (p0) cc_final: 0.7195 (p0) REVERT: C 18 PHE cc_start: 0.8201 (t80) cc_final: 0.7878 (t80) REVERT: C 53 ASP cc_start: 0.8508 (m-30) cc_final: 0.8139 (t0) REVERT: C 60 THR cc_start: 0.9195 (OUTLIER) cc_final: 0.8863 (p) REVERT: C 76 ASP cc_start: 0.7977 (t0) cc_final: 0.7732 (t0) REVERT: C 84 LYS cc_start: 0.8748 (mmmm) cc_final: 0.8229 (tptt) REVERT: C 288 SER cc_start: 0.8898 (m) cc_final: 0.8376 (t) REVERT: C 293 LYS cc_start: 0.9030 (ttpt) cc_final: 0.8772 (ttpt) REVERT: C 330 ASP cc_start: 0.8353 (p0) cc_final: 0.7996 (p0) REVERT: C 331 LYS cc_start: 0.9166 (mttt) cc_final: 0.8769 (ttmm) REVERT: C 384 LYS cc_start: 0.8798 (OUTLIER) cc_final: 0.8430 (pttt) REVERT: C 397 ARG cc_start: 0.8938 (mmt180) cc_final: 0.8644 (mmm-85) REVERT: C 415 LYS cc_start: 0.8944 (tmtt) cc_final: 0.8690 (tmtt) REVERT: C 446 ARG cc_start: 0.8577 (tpp80) cc_final: 0.8330 (ttm110) REVERT: C 481 PHE cc_start: 0.6885 (t80) cc_final: 0.6578 (t80) REVERT: C 500 ASN cc_start: 0.7827 (m-40) cc_final: 0.7510 (m-40) REVERT: C 529 ASP cc_start: 0.8222 (t70) cc_final: 0.7637 (t0) REVERT: C 675 TYR cc_start: 0.8332 (t80) cc_final: 0.7947 (t80) REVERT: C 832 LEU cc_start: 0.9100 (mt) cc_final: 0.8457 (mm) REVERT: C 842 ASN cc_start: 0.8781 (m-40) cc_final: 0.8458 (m-40) REVERT: C 848 ASP cc_start: 0.8730 (m-30) cc_final: 0.8336 (m-30) REVERT: C 849 GLU cc_start: 0.8266 (pp20) cc_final: 0.7962 (pp20) REVERT: C 858 GLN cc_start: 0.8802 (mm110) cc_final: 0.8539 (mm110) REVERT: C 873 SER cc_start: 0.9070 (m) cc_final: 0.8809 (p) REVERT: C 874 ASN cc_start: 0.8925 (m-40) cc_final: 0.8665 (p0) REVERT: C 889 LYS cc_start: 0.9205 (ttpt) cc_final: 0.8887 (ttpp) REVERT: C 909 ASP cc_start: 0.8336 (m-30) cc_final: 0.7808 (m-30) REVERT: C 956 GLU cc_start: 0.7848 (mm-30) cc_final: 0.7635 (mm-30) REVERT: C 999 ASP cc_start: 0.8276 (t70) cc_final: 0.7995 (t0) REVERT: C 1045 ASN cc_start: 0.9251 (t0) cc_final: 0.9025 (t0) REVERT: C 1075 GLN cc_start: 0.8559 (mm110) cc_final: 0.7625 (mm-40) REVERT: C 1079 ASP cc_start: 0.8571 (m-30) cc_final: 0.8202 (m-30) REVERT: C 1095 GLN cc_start: 0.8666 (tm-30) cc_final: 0.7521 (tm-30) REVERT: C 1099 ASP cc_start: 0.8794 (m-30) cc_final: 0.7528 (m-30) REVERT: C 1104 LYS cc_start: 0.9022 (tptt) cc_final: 0.8675 (tppt) REVERT: C 1112 GLU cc_start: 0.8678 (tp30) cc_final: 0.8404 (tp30) REVERT: C 1116 GLU cc_start: 0.8262 (mm-30) cc_final: 0.7856 (mm-30) REVERT: C 1199 GLU cc_start: 0.8075 (OUTLIER) cc_final: 0.7553 (mm-30) REVERT: C 1209 MET cc_start: 0.8304 (mpp) cc_final: 0.7618 (mpp) outliers start: 52 outliers final: 34 residues processed: 531 average time/residue: 0.4203 time to fit residues: 347.8239 Evaluate side-chains 536 residues out of total 3216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 492 time to evaluate : 3.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 LYS Chi-restraints excluded: chain A residue 114 ASN Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 317 VAL 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 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 388 LEU Chi-restraints excluded: chain B residue 405 SER Chi-restraints excluded: chain B residue 535 GLN Chi-restraints excluded: chain B residue 575 LEU Chi-restraints excluded: chain B residue 883 VAL Chi-restraints excluded: chain B residue 909 ASP Chi-restraints excluded: chain B residue 924 GLU Chi-restraints excluded: chain B residue 1034 GLN Chi-restraints excluded: chain B residue 1189 MET Chi-restraints excluded: chain C residue 52 LEU 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 384 LYS Chi-restraints excluded: chain C residue 405 SER Chi-restraints excluded: chain C residue 610 LEU 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 1167 CYS Chi-restraints excluded: chain C residue 1199 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 344 optimal weight: 0.9990 chunk 237 optimal weight: 5.9990 chunk 257 optimal weight: 0.9980 chunk 83 optimal weight: 1.9990 chunk 9 optimal weight: 6.9990 chunk 317 optimal weight: 3.9990 chunk 272 optimal weight: 0.5980 chunk 259 optimal weight: 0.8980 chunk 246 optimal weight: 1.9990 chunk 214 optimal weight: 0.9980 chunk 149 optimal weight: 0.0000 overall best weight: 0.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 858 GLN ** B 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 858 GLN ** C 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 842 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.102315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.080796 restraints weight = 62858.089| |-----------------------------------------------------------------------------| r_work (start): 0.3111 rms_B_bonded: 3.89 r_work: 0.2932 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.4257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 30177 Z= 0.127 Angle : 0.623 11.576 41256 Z= 0.319 Chirality : 0.043 0.374 4842 Planarity : 0.004 0.057 5124 Dihedral : 5.314 55.812 5688 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.95 % Favored : 96.03 % Rotamer: Outliers : 1.49 % Allowed : 18.03 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.14), residues: 3573 helix: 1.98 (0.20), residues: 771 sheet: -0.02 (0.18), residues: 795 loop : -1.36 (0.14), residues: 2007 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 646 HIS 0.005 0.001 HIS B 201 PHE 0.032 0.001 PHE B 714 TYR 0.039 0.001 TYR C 713 ARG 0.011 0.001 ARG B 206 Details of bonding type rmsd link_NAG-ASN : bond 0.00441 ( 57) link_NAG-ASN : angle 1.87836 ( 171) link_BETA1-4 : bond 0.00440 ( 30) link_BETA1-4 : angle 1.49304 ( 90) hydrogen bonds : bond 0.03922 ( 1016) hydrogen bonds : angle 4.73308 ( 3102) SS BOND : bond 0.00321 ( 72) SS BOND : angle 1.22661 ( 144) covalent geometry : bond 0.00292 (30018) covalent geometry : angle 0.60555 (40851) ********************** 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 562 residues out of total 3216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 514 time to evaluate : 3.155 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: symmetry clash REVERT: A 73 ASN cc_start: 0.8980 (p0) cc_final: 0.8716 (p0) REVERT: A 114 ASN cc_start: 0.8788 (OUTLIER) cc_final: 0.8453 (p0) REVERT: A 135 TYR cc_start: 0.9146 (m-80) cc_final: 0.8916 (m-80) REVERT: A 140 GLN cc_start: 0.7717 (tm-30) cc_final: 0.6820 (tm-30) REVERT: A 142 HIS cc_start: 0.8298 (m90) cc_final: 0.6930 (m90) REVERT: A 175 HIS cc_start: 0.8684 (p-80) cc_final: 0.8292 (p-80) REVERT: A 273 ARG cc_start: 0.8565 (tpp80) cc_final: 0.8328 (mpp80) REVERT: A 288 SER cc_start: 0.8880 (m) cc_final: 0.8402 (t) REVERT: A 305 ASP cc_start: 0.8158 (p0) cc_final: 0.7685 (p0) REVERT: A 319 ARG cc_start: 0.8576 (mmm160) cc_final: 0.8133 (mmm-85) REVERT: A 376 SER cc_start: 0.9038 (m) cc_final: 0.8633 (p) REVERT: A 384 LYS cc_start: 0.8692 (pttp) cc_final: 0.8440 (pttt) REVERT: A 411 SER cc_start: 0.9161 (t) cc_final: 0.8917 (p) REVERT: A 417 ASP cc_start: 0.8418 (t0) cc_final: 0.8122 (t0) REVERT: A 446 ARG cc_start: 0.8542 (ttm-80) cc_final: 0.8304 (ttm-80) REVERT: A 553 GLU cc_start: 0.8345 (mm-30) cc_final: 0.7884 (mm-30) REVERT: A 587 ARG cc_start: 0.8368 (mtp85) cc_final: 0.7854 (ttt90) REVERT: A 610 LEU cc_start: 0.9042 (tp) cc_final: 0.8808 (tp) REVERT: A 618 THR cc_start: 0.9264 (OUTLIER) cc_final: 0.8981 (m) REVERT: A 620 VAL cc_start: 0.8209 (OUTLIER) cc_final: 0.8006 (m) REVERT: A 711 GLN cc_start: 0.8508 (pm20) cc_final: 0.7938 (mp10) REVERT: A 772 GLU cc_start: 0.8292 (mp0) cc_final: 0.7875 (mp0) REVERT: A 805 GLU cc_start: 0.7981 (tm-30) cc_final: 0.7691 (tm-30) REVERT: A 842 ASN cc_start: 0.8946 (m-40) cc_final: 0.8678 (m-40) REVERT: A 844 ASN cc_start: 0.8996 (m-40) cc_final: 0.8008 (m-40) REVERT: A 848 ASP cc_start: 0.8597 (m-30) cc_final: 0.8164 (m-30) REVERT: A 849 GLU cc_start: 0.8181 (pp20) cc_final: 0.7927 (pp20) REVERT: A 867 GLN cc_start: 0.8186 (mm-40) cc_final: 0.7904 (mm110) REVERT: A 871 LEU cc_start: 0.9102 (OUTLIER) cc_final: 0.8817 (mp) REVERT: A 889 LYS cc_start: 0.9033 (ttpt) cc_final: 0.8737 (ttpp) REVERT: A 909 ASP cc_start: 0.8492 (m-30) cc_final: 0.8033 (m-30) REVERT: A 998 MET cc_start: 0.9042 (tpp) cc_final: 0.8314 (tpp) REVERT: A 999 ASP cc_start: 0.8642 (t0) cc_final: 0.8114 (t0) REVERT: A 1019 ILE cc_start: 0.9358 (tt) cc_final: 0.9105 (tt) REVERT: A 1075 GLN cc_start: 0.8641 (mm-40) cc_final: 0.7864 (mm-40) REVERT: A 1079 ASP cc_start: 0.8713 (m-30) cc_final: 0.8256 (m-30) REVERT: A 1095 GLN cc_start: 0.8636 (tm-30) cc_final: 0.7159 (tm-30) REVERT: A 1099 ASP cc_start: 0.8796 (m-30) cc_final: 0.7399 (m-30) REVERT: A 1112 GLU cc_start: 0.8685 (tt0) cc_final: 0.8382 (tp30) REVERT: A 1153 LYS cc_start: 0.8784 (tppt) cc_final: 0.8507 (tptp) REVERT: A 1178 GLN cc_start: 0.8767 (tt0) cc_final: 0.8497 (tt0) REVERT: B 69 LYS cc_start: 0.9191 (tmtt) cc_final: 0.8764 (tmmt) REVERT: B 88 LEU cc_start: 0.9009 (mp) cc_final: 0.8663 (tp) REVERT: B 92 LYS cc_start: 0.8951 (mtmm) cc_final: 0.8699 (mtpp) REVERT: B 111 LEU cc_start: 0.8961 (mm) cc_final: 0.8379 (mt) REVERT: B 175 HIS cc_start: 0.8726 (p-80) cc_final: 0.8142 (p-80) REVERT: B 218 MET cc_start: 0.8390 (tpp) cc_final: 0.8163 (mmm) REVERT: B 271 ASP cc_start: 0.7632 (p0) cc_final: 0.7424 (p0) REVERT: B 273 ARG cc_start: 0.8496 (mtp-110) cc_final: 0.8191 (mtp-110) REVERT: B 319 ARG cc_start: 0.8913 (mmm-85) cc_final: 0.8708 (mmm-85) REVERT: B 326 ASP cc_start: 0.7054 (t70) cc_final: 0.6771 (t0) REVERT: B 331 LYS cc_start: 0.9269 (mttt) cc_final: 0.8835 (ttmm) REVERT: B 384 LYS cc_start: 0.8718 (pttt) cc_final: 0.8348 (pttt) REVERT: B 388 LEU cc_start: 0.8895 (OUTLIER) cc_final: 0.8609 (mp) REVERT: B 397 ARG cc_start: 0.8933 (mmt180) cc_final: 0.8374 (mmm-85) REVERT: B 400 ASP cc_start: 0.8470 (m-30) cc_final: 0.7958 (m-30) REVERT: B 411 SER cc_start: 0.9343 (t) cc_final: 0.8960 (p) REVERT: B 417 ASP cc_start: 0.8454 (t0) cc_final: 0.8165 (t0) REVERT: B 446 ARG cc_start: 0.8690 (ttm110) cc_final: 0.8419 (ttm-80) REVERT: B 448 TYR cc_start: 0.8941 (m-80) cc_final: 0.8600 (m-10) REVERT: B 466 CYS cc_start: 0.4683 (m) cc_final: 0.4407 (m) REVERT: B 529 ASP cc_start: 0.8358 (t70) cc_final: 0.7668 (t0) REVERT: B 536 LYS cc_start: 0.8412 (mmtp) cc_final: 0.8026 (mmtt) REVERT: B 587 ARG cc_start: 0.8412 (mtp85) cc_final: 0.8067 (ttm-80) REVERT: B 615 GLU cc_start: 0.7682 (tm-30) cc_final: 0.7429 (tm-30) REVERT: B 711 GLN cc_start: 0.8316 (pm20) cc_final: 0.7745 (mp10) REVERT: B 781 ASP cc_start: 0.7772 (p0) cc_final: 0.7437 (p0) REVERT: B 805 GLU cc_start: 0.8364 (tm-30) cc_final: 0.8130 (tm-30) REVERT: B 832 LEU cc_start: 0.8949 (mt) cc_final: 0.8043 (mm) REVERT: B 842 ASN cc_start: 0.8828 (m-40) cc_final: 0.8511 (m-40) REVERT: B 848 ASP cc_start: 0.8735 (m-30) cc_final: 0.8338 (m-30) REVERT: B 849 GLU cc_start: 0.8551 (tm-30) cc_final: 0.8207 (pp20) REVERT: B 855 ASP cc_start: 0.8265 (m-30) cc_final: 0.7853 (m-30) REVERT: B 867 GLN cc_start: 0.7941 (mm-40) cc_final: 0.7716 (mm-40) REVERT: B 881 PHE cc_start: 0.7741 (p90) cc_final: 0.7403 (p90) REVERT: B 882 ASP cc_start: 0.8238 (m-30) cc_final: 0.7880 (m-30) REVERT: B 889 LYS cc_start: 0.9124 (ttpt) cc_final: 0.8694 (ttmm) REVERT: B 914 LYS cc_start: 0.9293 (mmmt) cc_final: 0.9047 (mmmm) REVERT: B 916 LYS cc_start: 0.8836 (pttt) cc_final: 0.8482 (ptmm) REVERT: B 924 GLU cc_start: 0.8520 (OUTLIER) cc_final: 0.8250 (tm-30) REVERT: B 998 MET cc_start: 0.8733 (tpp) cc_final: 0.8520 (mmm) REVERT: B 999 ASP cc_start: 0.8494 (t0) cc_final: 0.8015 (t0) REVERT: B 1004 ASN cc_start: 0.8401 (m-40) cc_final: 0.8044 (m-40) REVERT: B 1034 GLN cc_start: 0.8967 (OUTLIER) cc_final: 0.8558 (mp10) REVERT: B 1042 GLN cc_start: 0.9057 (mt0) cc_final: 0.8793 (tm-30) REVERT: B 1054 LYS cc_start: 0.9148 (mttt) cc_final: 0.8907 (mmmm) REVERT: B 1075 GLN cc_start: 0.8647 (mm-40) cc_final: 0.7757 (mm-40) REVERT: B 1079 ASP cc_start: 0.8664 (m-30) cc_final: 0.8298 (m-30) REVERT: B 1095 GLN cc_start: 0.8680 (tm-30) cc_final: 0.7387 (tm-30) REVERT: B 1099 ASP cc_start: 0.8743 (m-30) cc_final: 0.7378 (m-30) REVERT: B 1112 GLU cc_start: 0.8739 (tp30) cc_final: 0.8207 (tp30) REVERT: B 1126 ASN cc_start: 0.8628 (t0) cc_final: 0.8220 (t0) REVERT: B 1177 LYS cc_start: 0.8487 (mmmm) cc_final: 0.7978 (mmmt) REVERT: B 1202 SER cc_start: 0.8802 (t) cc_final: 0.8586 (p) REVERT: B 1209 MET cc_start: 0.8577 (tpp) cc_final: 0.8148 (mpp) REVERT: C 15 ILE cc_start: 0.9052 (pt) cc_final: 0.8828 (pt) REVERT: C 17 ASP cc_start: 0.7514 (p0) cc_final: 0.7161 (p0) REVERT: C 18 PHE cc_start: 0.8049 (t80) cc_final: 0.7733 (t80) REVERT: C 53 ASP cc_start: 0.8524 (m-30) cc_final: 0.8135 (t0) REVERT: C 60 THR cc_start: 0.9193 (OUTLIER) cc_final: 0.8860 (p) REVERT: C 84 LYS cc_start: 0.8735 (mmmm) cc_final: 0.8225 (tptt) REVERT: C 288 SER cc_start: 0.8857 (m) cc_final: 0.8358 (t) REVERT: C 330 ASP cc_start: 0.8370 (p0) cc_final: 0.8012 (m-30) REVERT: C 331 LYS cc_start: 0.9166 (mttt) cc_final: 0.8751 (ttmm) REVERT: C 384 LYS cc_start: 0.8779 (OUTLIER) cc_final: 0.8402 (pttt) REVERT: C 397 ARG cc_start: 0.8975 (mmt180) cc_final: 0.8700 (mmm-85) REVERT: C 415 LYS cc_start: 0.8935 (tmtt) cc_final: 0.8641 (tmtt) REVERT: C 436 ILE cc_start: 0.8995 (OUTLIER) cc_final: 0.8736 (pt) REVERT: C 446 ARG cc_start: 0.8526 (tpp80) cc_final: 0.8276 (ttm110) REVERT: C 467 PHE cc_start: 0.8492 (m-80) cc_final: 0.7635 (m-80) REVERT: C 481 PHE cc_start: 0.6864 (t80) cc_final: 0.6561 (t80) REVERT: C 500 ASN cc_start: 0.7824 (m-40) cc_final: 0.7501 (m-40) REVERT: C 529 ASP cc_start: 0.8234 (t70) cc_final: 0.7750 (t0) REVERT: C 544 GLU cc_start: 0.8281 (pm20) cc_final: 0.7958 (pm20) REVERT: C 675 TYR cc_start: 0.8292 (t80) cc_final: 0.7886 (t80) REVERT: C 739 MET cc_start: 0.9279 (mmm) cc_final: 0.8867 (mmt) REVERT: C 792 ILE cc_start: 0.9037 (tp) cc_final: 0.8764 (pt) REVERT: C 832 LEU cc_start: 0.9094 (mt) cc_final: 0.8401 (mm) REVERT: C 842 ASN cc_start: 0.8758 (m110) cc_final: 0.8424 (m-40) REVERT: C 849 GLU cc_start: 0.8269 (pp20) cc_final: 0.8067 (pp20) REVERT: C 858 GLN cc_start: 0.8850 (mm110) cc_final: 0.8579 (mm110) REVERT: C 873 SER cc_start: 0.9045 (m) cc_final: 0.8782 (p) REVERT: C 874 ASN cc_start: 0.8923 (m-40) cc_final: 0.8701 (p0) REVERT: C 889 LYS cc_start: 0.9138 (ttpt) cc_final: 0.8806 (ttpp) REVERT: C 956 GLU cc_start: 0.7832 (mm-30) cc_final: 0.7609 (mm-30) REVERT: C 971 MET cc_start: 0.8450 (tpp) cc_final: 0.8023 (ttt) REVERT: C 999 ASP cc_start: 0.8320 (t70) cc_final: 0.8031 (t0) REVERT: C 1045 ASN cc_start: 0.9248 (t0) cc_final: 0.9027 (t0) REVERT: C 1075 GLN cc_start: 0.8565 (mm110) cc_final: 0.7689 (mm-40) REVERT: C 1079 ASP cc_start: 0.8587 (m-30) cc_final: 0.8157 (m-30) REVERT: C 1095 GLN cc_start: 0.8663 (tm-30) cc_final: 0.7521 (tm-30) REVERT: C 1099 ASP cc_start: 0.8803 (m-30) cc_final: 0.7531 (m-30) REVERT: C 1104 LYS cc_start: 0.9002 (tptt) cc_final: 0.8647 (tppt) REVERT: C 1112 GLU cc_start: 0.8676 (tp30) cc_final: 0.8404 (tp30) REVERT: C 1116 GLU cc_start: 0.8338 (mm-30) cc_final: 0.7858 (mm-30) REVERT: C 1199 GLU cc_start: 0.8092 (OUTLIER) cc_final: 0.7566 (mm-30) REVERT: C 1208 PHE cc_start: 0.8878 (m-10) cc_final: 0.8446 (m-80) REVERT: C 1209 MET cc_start: 0.8315 (mpp) cc_final: 0.7605 (mpp) outliers start: 48 outliers final: 29 residues processed: 542 average time/residue: 0.4382 time to fit residues: 369.4026 Evaluate side-chains 537 residues out of total 3216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 497 time to evaluate : 3.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 LYS Chi-restraints excluded: chain A residue 114 ASN Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 620 VAL 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 388 LEU Chi-restraints excluded: chain B residue 405 SER Chi-restraints excluded: chain B residue 535 GLN Chi-restraints excluded: chain B residue 575 LEU Chi-restraints excluded: chain B residue 589 ASN Chi-restraints excluded: chain B residue 924 GLU Chi-restraints excluded: chain B residue 1034 GLN Chi-restraints excluded: chain B residue 1189 MET Chi-restraints excluded: chain C residue 46 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 384 LYS Chi-restraints excluded: chain C residue 405 SER Chi-restraints excluded: chain C residue 436 ILE Chi-restraints excluded: chain C residue 610 LEU Chi-restraints excluded: chain C residue 699 CYS Chi-restraints excluded: chain C residue 950 LEU Chi-restraints excluded: chain C residue 1167 CYS Chi-restraints excluded: chain C residue 1199 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 207 optimal weight: 3.9990 chunk 159 optimal weight: 3.9990 chunk 88 optimal weight: 0.9990 chunk 38 optimal weight: 3.9990 chunk 299 optimal weight: 5.9990 chunk 273 optimal weight: 4.9990 chunk 169 optimal weight: 6.9990 chunk 345 optimal weight: 2.9990 chunk 163 optimal weight: 0.9990 chunk 4 optimal weight: 0.8980 chunk 314 optimal weight: 3.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 160 HIS ** B 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 748 ASN ** B 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 880 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 842 ASN ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.100218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.078860 restraints weight = 63019.655| |-----------------------------------------------------------------------------| r_work (start): 0.3071 rms_B_bonded: 3.84 r_work: 0.2889 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.4407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 30177 Z= 0.222 Angle : 0.664 11.970 41256 Z= 0.342 Chirality : 0.045 0.379 4842 Planarity : 0.004 0.068 5124 Dihedral : 5.391 56.368 5688 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 1.52 % Allowed : 18.41 % Favored : 80.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.14), residues: 3573 helix: 1.88 (0.19), residues: 771 sheet: -0.14 (0.18), residues: 804 loop : -1.37 (0.14), residues: 1998 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 646 HIS 0.006 0.001 HIS C 201 PHE 0.039 0.001 PHE B 714 TYR 0.037 0.002 TYR B 675 ARG 0.012 0.001 ARG B 206 Details of bonding type rmsd link_NAG-ASN : bond 0.00457 ( 57) link_NAG-ASN : angle 1.97269 ( 171) link_BETA1-4 : bond 0.00387 ( 30) link_BETA1-4 : angle 1.56658 ( 90) hydrogen bonds : bond 0.04486 ( 1016) hydrogen bonds : angle 4.83036 ( 3102) SS BOND : bond 0.00414 ( 72) SS BOND : angle 1.43508 ( 144) covalent geometry : bond 0.00492 (30018) covalent geometry : angle 0.64569 (40851) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15078.48 seconds wall clock time: 267 minutes 41.93 seconds (16061.93 seconds total)