Starting phenix.real_space_refine on Thu Mar 5 16:03:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6u7h_20668/03_2026/6u7h_20668.cif Found real_map, /net/cci-nas-00/data/ceres_data/6u7h_20668/03_2026/6u7h_20668.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6u7h_20668/03_2026/6u7h_20668.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6u7h_20668/03_2026/6u7h_20668.map" model { file = "/net/cci-nas-00/data/ceres_data/6u7h_20668/03_2026/6u7h_20668.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6u7h_20668/03_2026/6u7h_20668.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.088 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 111 5.16 5 C 14841 2.51 5 N 3741 2.21 5 O 4701 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 189 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 23394 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 7438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 965, 7438 Classifications: {'peptide': 965} Link IDs: {'PTRANS': 33, 'TRANS': 931} Chain breaks: 3 Chain: "B" Number of atoms: 7438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 965, 7438 Classifications: {'peptide': 965} Link IDs: {'PTRANS': 33, 'TRANS': 931} Chain breaks: 3 Chain: "C" Number of atoms: 7438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 965, 7438 Classifications: {'peptide': 965} Link IDs: {'PTRANS': 33, 'TRANS': 931} Chain breaks: 3 Chain: "D" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 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: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 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: 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: "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: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "R" Number of atoms: 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: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "B" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "C" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Time building chain proxies: 5.82, per 1000 atoms: 0.25 Number of scatterers: 23394 At special positions: 0 Unit cell: (129.32, 134.62, 148.4, 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 111 16.00 O 4701 8.00 N 3741 7.00 C 14841 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 Simple disulfide: pdb=" SG CYS A 81 " - pdb=" SG CYS A 105 " distance=2.04 Simple disulfide: pdb=" SG CYS A 145 " - pdb=" SG CYS A 168 " distance=2.04 Simple disulfide: pdb=" SG CYS A 255 " - pdb=" SG CYS A 264 " distance=1.99 Simple disulfide: pdb=" SG CYS A 317 " - pdb=" SG CYS A 320 " distance=2.03 Simple disulfide: pdb=" SG CYS A 340 " - pdb=" SG CYS A 386 " distance=2.02 Simple disulfide: pdb=" SG CYS A 369 " - pdb=" SG CYS A 396 " distance=2.01 Simple disulfide: pdb=" SG CYS A 446 " - pdb=" SG CYS A 497 " distance=2.03 Simple disulfide: pdb=" SG CYS A 543 " - pdb=" SG CYS A 556 " distance=2.04 Simple disulfide: pdb=" SG CYS A 608 " - pdb=" SG CYS A 630 " distance=2.04 Simple disulfide: pdb=" SG CYS A 613 " - pdb=" SG CYS A 619 " distance=2.01 Simple disulfide: pdb=" SG CYS A 715 " - pdb=" SG CYS A 726 " distance=2.03 Simple disulfide: pdb=" SG CYS A 917 " - pdb=" SG CYS A 928 " distance=1.99 Simple disulfide: pdb=" SG CYS A 967 " - pdb=" SG CYS A1014 " distance=2.03 Simple disulfide: pdb=" SG CYS B 81 " - pdb=" SG CYS B 105 " distance=2.04 Simple disulfide: pdb=" SG CYS B 145 " - pdb=" SG CYS B 168 " distance=2.04 Simple disulfide: pdb=" SG CYS B 255 " - pdb=" SG CYS B 264 " distance=1.99 Simple disulfide: pdb=" SG CYS B 317 " - pdb=" SG CYS B 320 " distance=2.03 Simple disulfide: pdb=" SG CYS B 340 " - pdb=" SG CYS B 386 " distance=2.03 Simple disulfide: pdb=" SG CYS B 369 " - pdb=" SG CYS B 396 " distance=2.01 Simple disulfide: pdb=" SG CYS B 446 " - pdb=" SG CYS B 497 " distance=2.03 Simple disulfide: pdb=" SG CYS B 543 " - pdb=" SG CYS B 556 " distance=2.03 Simple disulfide: pdb=" SG CYS B 608 " - pdb=" SG CYS B 630 " distance=2.04 Simple disulfide: pdb=" SG CYS B 613 " - pdb=" SG CYS B 619 " distance=2.01 Simple disulfide: pdb=" SG CYS B 715 " - pdb=" SG CYS B 726 " distance=2.03 Simple disulfide: pdb=" SG CYS B 917 " - pdb=" SG CYS B 928 " distance=1.99 Simple disulfide: pdb=" SG CYS B 967 " - pdb=" SG CYS B1014 " distance=2.03 Simple disulfide: pdb=" SG CYS C 81 " - pdb=" SG CYS C 105 " distance=2.04 Simple disulfide: pdb=" SG CYS C 145 " - pdb=" SG CYS C 168 " distance=2.04 Simple disulfide: pdb=" SG CYS C 255 " - pdb=" SG CYS C 264 " distance=1.99 Simple disulfide: pdb=" SG CYS C 317 " - pdb=" SG CYS C 320 " distance=2.03 Simple disulfide: pdb=" SG CYS C 340 " - pdb=" SG CYS C 386 " distance=2.02 Simple disulfide: pdb=" SG CYS C 369 " - pdb=" SG CYS C 396 " distance=2.01 Simple disulfide: pdb=" SG CYS C 446 " - pdb=" SG CYS C 497 " distance=2.03 Simple disulfide: pdb=" SG CYS C 543 " - pdb=" SG CYS C 556 " distance=2.03 Simple disulfide: pdb=" SG CYS C 608 " - pdb=" SG CYS C 630 " distance=2.04 Simple disulfide: pdb=" SG CYS C 613 " - pdb=" SG CYS C 619 " distance=2.01 Simple disulfide: pdb=" SG CYS C 715 " - pdb=" SG CYS C 726 " distance=2.03 Simple disulfide: pdb=" SG CYS C 917 " - pdb=" SG CYS C 928 " distance=1.99 Simple disulfide: pdb=" SG CYS C 967 " - pdb=" SG CYS C1014 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN D 4 " - " MAN D 5 " " MAN I 4 " - " MAN I 5 " " MAN N 4 " - " MAN N 5 " ALPHA1-3 " BMA D 3 " - " MAN D 4 " " MAN D 6 " - " MAN D 7 " " BMA I 3 " - " MAN I 4 " " MAN I 6 " - " MAN I 7 " " BMA N 3 " - " MAN N 4 " " MAN N 6 " - " MAN N 7 " ALPHA1-6 " BMA D 3 " - " MAN D 6 " " BMA I 3 " - " MAN I 6 " " BMA N 3 " - " MAN N 6 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG L 2 " - " BMA L 3 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " NAG-ASN " NAG A1210 " - " ASN A 147 " " NAG A1213 " - " ASN A 220 " " NAG A1217 " - " ASN A 326 " " NAG A1218 " - " ASN A 440 " " NAG A1219 " - " ASN A 464 " " NAG A1220 " - " ASN A 518 " " NAG A1223 " - " ASN A 542 " " NAG A1224 " - " ASN A 663 " " NAG A1225 " - " ASN A 671 " " NAG A1226 " - " ASN A 714 " " NAG A1227 " - " ASN A 930 " " NAG B1210 " - " ASN B 147 " " NAG B1213 " - " ASN B 220 " " NAG B1217 " - " ASN B 326 " " NAG B1218 " - " ASN B 440 " " NAG B1219 " - " ASN B 464 " " NAG B1220 " - " ASN B 518 " " NAG B1223 " - " ASN B 542 " " NAG B1224 " - " ASN B 663 " " NAG B1225 " - " ASN B 671 " " NAG B1226 " - " ASN B 714 " " NAG B1227 " - " ASN B 930 " " NAG C1210 " - " ASN C 147 " " NAG C1213 " - " ASN C 220 " " NAG C1217 " - " ASN C 326 " " NAG C1218 " - " ASN C 440 " " NAG C1219 " - " ASN C 464 " " NAG C1220 " - " ASN C 518 " " NAG C1223 " - " ASN C 542 " " NAG C1224 " - " ASN C 663 " " NAG C1225 " - " ASN C 671 " " NAG C1226 " - " ASN C 714 " " NAG C1227 " - " ASN C 930 " " NAG D 1 " - " ASN A 62 " " NAG E 1 " - " ASN A 98 " " NAG F 1 " - " ASN A 171 " " NAG G 1 " - " ASN A 243 " " NAG H 1 " - " ASN A 538 " " NAG I 1 " - " ASN B 62 " " NAG J 1 " - " ASN B 98 " " NAG K 1 " - " ASN B 171 " " NAG L 1 " - " ASN B 243 " " NAG M 1 " - " ASN B 538 " " NAG N 1 " - " ASN C 62 " " NAG O 1 " - " ASN C 98 " " NAG P 1 " - " ASN C 171 " " NAG Q 1 " - " ASN C 243 " " NAG R 1 " - " ASN C 538 " Time building additional restraints: 2.35 Conformation dependent library (CDL) restraints added in 950.8 milliseconds 5742 Ramachandran restraints generated. 2871 Oldfield, 0 Emsley, 2871 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5382 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 36 sheets defined 26.9% alpha, 36.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.94 Creating SS restraints... Processing helix chain 'A' and resid 257 through 265 Processing helix chain 'A' and resid 333 through 337 Processing helix chain 'A' and resid 374 through 378 Processing helix chain 'A' and resid 520 through 524 removed outlier: 3.957A pdb=" N GLY A 523 " --> pdb=" O THR A 520 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 614 Processing helix chain 'A' and resid 616 through 624 Processing helix chain 'A' and resid 628 through 652 Processing helix chain 'A' and resid 655 through 662 Processing helix chain 'A' and resid 663 through 667 Processing helix chain 'A' and resid 671 through 675 removed outlier: 4.262A pdb=" N SER A 674 " --> pdb=" O ASN A 671 " (cutoff:3.500A) Processing helix chain 'A' and resid 690 through 700 removed outlier: 3.564A pdb=" N ILE A 700 " --> pdb=" O LEU A 696 " (cutoff:3.500A) Processing helix chain 'A' and resid 711 through 715 removed outlier: 4.456A pdb=" N ASN A 714 " --> pdb=" O ASP A 711 " (cutoff:3.500A) Processing helix chain 'A' and resid 723 through 731 removed outlier: 3.551A pdb=" N ASN A 731 " --> pdb=" O ALA A 727 " (cutoff:3.500A) Processing helix chain 'A' and resid 741 through 755 Processing helix chain 'A' and resid 769 through 779 Processing helix chain 'A' and resid 787 through 811 Processing helix chain 'A' and resid 816 through 851 removed outlier: 4.656A pdb=" N ALA A 822 " --> pdb=" O GLN A 818 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N THR A 825 " --> pdb=" O GLN A 821 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU A 847 " --> pdb=" O SER A 843 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LEU A 851 " --> pdb=" O LEU A 847 " (cutoff:3.500A) Processing helix chain 'A' and resid 861 through 869 Processing helix chain 'A' and resid 870 through 918 removed outlier: 3.880A pdb=" N GLN A 876 " --> pdb=" O PRO A 872 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ARG A 880 " --> pdb=" O GLN A 876 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU A 881 " --> pdb=" O GLN A 877 " (cutoff:3.500A) Processing helix chain 'A' and resid 1024 through 1029 Processing helix chain 'B' and resid 257 through 265 Processing helix chain 'B' and resid 333 through 337 Processing helix chain 'B' and resid 374 through 378 Processing helix chain 'B' and resid 520 through 524 removed outlier: 3.956A pdb=" N GLY B 523 " --> pdb=" O THR B 520 " (cutoff:3.500A) Processing helix chain 'B' and resid 607 through 614 Processing helix chain 'B' and resid 616 through 624 Processing helix chain 'B' and resid 628 through 652 Processing helix chain 'B' and resid 655 through 662 Processing helix chain 'B' and resid 663 through 667 Processing helix chain 'B' and resid 671 through 675 removed outlier: 4.263A pdb=" N SER B 674 " --> pdb=" O ASN B 671 " (cutoff:3.500A) Processing helix chain 'B' and resid 690 through 700 removed outlier: 3.563A pdb=" N ILE B 700 " --> pdb=" O LEU B 696 " (cutoff:3.500A) Processing helix chain 'B' and resid 711 through 715 removed outlier: 4.455A pdb=" N ASN B 714 " --> pdb=" O ASP B 711 " (cutoff:3.500A) Processing helix chain 'B' and resid 723 through 731 removed outlier: 3.550A pdb=" N ASN B 731 " --> pdb=" O ALA B 727 " (cutoff:3.500A) Processing helix chain 'B' and resid 741 through 755 Processing helix chain 'B' and resid 769 through 779 Processing helix chain 'B' and resid 787 through 811 Processing helix chain 'B' and resid 816 through 851 removed outlier: 4.656A pdb=" N ALA B 822 " --> pdb=" O GLN B 818 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N THR B 825 " --> pdb=" O GLN B 821 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU B 847 " --> pdb=" O SER B 843 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LEU B 851 " --> pdb=" O LEU B 847 " (cutoff:3.500A) Processing helix chain 'B' and resid 861 through 869 Processing helix chain 'B' and resid 870 through 918 removed outlier: 3.879A pdb=" N GLN B 876 " --> pdb=" O PRO B 872 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ARG B 880 " --> pdb=" O GLN B 876 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU B 881 " --> pdb=" O GLN B 877 " (cutoff:3.500A) Processing helix chain 'B' and resid 1024 through 1029 Processing helix chain 'C' and resid 257 through 265 Processing helix chain 'C' and resid 333 through 337 Processing helix chain 'C' and resid 374 through 378 Processing helix chain 'C' and resid 520 through 524 removed outlier: 3.956A pdb=" N GLY C 523 " --> pdb=" O THR C 520 " (cutoff:3.500A) Processing helix chain 'C' and resid 607 through 614 Processing helix chain 'C' and resid 616 through 624 Processing helix chain 'C' and resid 628 through 652 Processing helix chain 'C' and resid 655 through 662 Processing helix chain 'C' and resid 663 through 667 Processing helix chain 'C' and resid 671 through 675 removed outlier: 4.262A pdb=" N SER C 674 " --> pdb=" O ASN C 671 " (cutoff:3.500A) Processing helix chain 'C' and resid 690 through 700 removed outlier: 3.564A pdb=" N ILE C 700 " --> pdb=" O LEU C 696 " (cutoff:3.500A) Processing helix chain 'C' and resid 711 through 715 removed outlier: 4.455A pdb=" N ASN C 714 " --> pdb=" O ASP C 711 " (cutoff:3.500A) Processing helix chain 'C' and resid 723 through 731 removed outlier: 3.550A pdb=" N ASN C 731 " --> pdb=" O ALA C 727 " (cutoff:3.500A) Processing helix chain 'C' and resid 741 through 755 Processing helix chain 'C' and resid 769 through 779 Processing helix chain 'C' and resid 787 through 811 Processing helix chain 'C' and resid 816 through 851 removed outlier: 4.657A pdb=" N ALA C 822 " --> pdb=" O GLN C 818 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N THR C 825 " --> pdb=" O GLN C 821 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU C 847 " --> pdb=" O SER C 843 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LEU C 851 " --> pdb=" O LEU C 847 " (cutoff:3.500A) Processing helix chain 'C' and resid 861 through 869 Processing helix chain 'C' and resid 870 through 918 removed outlier: 3.880A pdb=" N GLN C 876 " --> pdb=" O PRO C 872 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ARG C 880 " --> pdb=" O GLN C 876 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU C 881 " --> pdb=" O GLN C 877 " (cutoff:3.500A) Processing helix chain 'C' and resid 1024 through 1029 Processing sheet with id=AA1, first strand: chain 'A' and resid 65 through 66 removed outlier: 3.707A pdb=" N THR C 474 " --> pdb=" O SER A 65 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N TYR C 473 " --> pdb=" O LEU C 481 " (cutoff:3.500A) removed outlier: 5.344A pdb=" N LEU C 481 " --> pdb=" O ILE C 494 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N SER C 289 " --> pdb=" O ASN C 450 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 69 through 86 removed outlier: 3.721A pdb=" N LEU A 77 " --> pdb=" O SER A 236 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N SER A 236 " --> pdb=" O LEU A 77 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N LEU A 79 " --> pdb=" O LEU A 234 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N LEU A 234 " --> pdb=" O LEU A 79 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N CYS A 81 " --> pdb=" O VAL A 232 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N VAL A 232 " --> pdb=" O CYS A 81 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N TRP A 83 " --> pdb=" O PHE A 230 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N PHE A 230 " --> pdb=" O TRP A 83 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N HIS A 200 " --> pdb=" O SER A 196 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N PHE A 201 " --> pdb=" O TYR A 208 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 69 through 86 removed outlier: 3.721A pdb=" N LEU A 77 " --> pdb=" O SER A 236 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N SER A 236 " --> pdb=" O LEU A 77 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N LEU A 79 " --> pdb=" O LEU A 234 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N LEU A 234 " --> pdb=" O LEU A 79 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N CYS A 81 " --> pdb=" O VAL A 232 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N VAL A 232 " --> pdb=" O CYS A 81 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N TRP A 83 " --> pdb=" O PHE A 230 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N PHE A 230 " --> pdb=" O TRP A 83 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N ASP A 239 " --> pdb=" O TYR A 254 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N TYR A 254 " --> pdb=" O ASP A 239 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N LEU A 241 " --> pdb=" O ILE A 252 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N ILE A 252 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N ASN A 243 " --> pdb=" O ALA A 250 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 94 through 96 removed outlier: 6.751A pdb=" N LYS A 135 " --> pdb=" O GLU A 215 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N VAL A 217 " --> pdb=" O LEU A 133 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N LEU A 133 " --> pdb=" O VAL A 217 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N PHE A 219 " --> pdb=" O THR A 131 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N THR A 131 " --> pdb=" O PHE A 219 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N VAL A 140 " --> pdb=" O THR A 173 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLY A 184 " --> pdb=" O CYS A 168 " (cutoff:3.500A) removed outlier: 5.689A pdb=" N VAL A 170 " --> pdb=" O PHE A 182 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N PHE A 182 " --> pdb=" O VAL A 170 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N THR A 172 " --> pdb=" O SER A 180 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N SER A 180 " --> pdb=" O THR A 172 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N ILE A 174 " --> pdb=" O THR A 178 " (cutoff:3.500A) removed outlier: 5.124A pdb=" N THR A 178 " --> pdb=" O ILE A 174 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 274 through 278 removed outlier: 3.642A pdb=" N GLY A 512 " --> pdb=" O VAL A 504 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 288 through 291 removed outlier: 6.674A pdb=" N SER A 289 " --> pdb=" O ASN A 450 " (cutoff:3.500A) removed outlier: 5.344A pdb=" N LEU A 481 " --> pdb=" O ILE A 494 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N TYR A 473 " --> pdb=" O LEU A 481 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N THR A 472 " --> pdb=" O SER B 65 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 323 through 329 removed outlier: 4.397A pdb=" N VAL A 325 " --> pdb=" O ASP A 307 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N ASP A 307 " --> pdb=" O VAL A 325 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N ILE A 327 " --> pdb=" O TYR A 305 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N TYR A 305 " --> pdb=" O ILE A 327 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N LEU A 329 " --> pdb=" O VAL A 303 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N VAL A 303 " --> pdb=" O LEU A 329 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N SER A 384 " --> pdb=" O SER A 420 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N GLY A 422 " --> pdb=" O PHE A 382 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 323 through 329 removed outlier: 4.397A pdb=" N VAL A 325 " --> pdb=" O ASP A 307 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N ASP A 307 " --> pdb=" O VAL A 325 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N ILE A 327 " --> pdb=" O TYR A 305 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N TYR A 305 " --> pdb=" O ILE A 327 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N LEU A 329 " --> pdb=" O VAL A 303 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N VAL A 303 " --> pdb=" O LEU A 329 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N TYR A 409 " --> pdb=" O TRP A 404 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N TRP A 404 " --> pdb=" O TYR A 409 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N THR A 411 " --> pdb=" O ALA A 402 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N ALA A 402 " --> pdb=" O THR A 411 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 546 through 550 Processing sheet with id=AB1, first strand: chain 'A' and resid 583 through 598 removed outlier: 6.511A pdb=" N GLN A 956 " --> pdb=" O SER A 586 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N TRP A 588 " --> pdb=" O PRO A 954 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N ILE A 590 " --> pdb=" O LEU A 952 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N LEU A 952 " --> pdb=" O ILE A 590 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N VAL A 592 " --> pdb=" O THR A 950 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N THR A 950 " --> pdb=" O VAL A 592 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N VAL A 594 " --> pdb=" O LEU A 948 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N LEU A 948 " --> pdb=" O VAL A 594 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N TYR A 596 " --> pdb=" O VAL A 946 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N VAL A 946 " --> pdb=" O TYR A 596 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N GLN A 598 " --> pdb=" O GLY A 944 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N GLY A 944 " --> pdb=" O GLN A 598 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N PHE A 935 " --> pdb=" O THR A 950 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N LEU A 952 " --> pdb=" O HIS A 933 " (cutoff:3.500A) removed outlier: 5.916A pdb=" N HIS A 933 " --> pdb=" O LEU A 952 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 604 through 606 Processing sheet with id=AB3, first strand: chain 'A' and resid 1008 through 1011 Processing sheet with id=AB4, first strand: chain 'A' and resid 981 through 986 Processing sheet with id=AB5, first strand: chain 'B' and resid 69 through 86 removed outlier: 3.721A pdb=" N LEU B 77 " --> pdb=" O SER B 236 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N SER B 236 " --> pdb=" O LEU B 77 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N LEU B 79 " --> pdb=" O LEU B 234 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N LEU B 234 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N CYS B 81 " --> pdb=" O VAL B 232 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N VAL B 232 " --> pdb=" O CYS B 81 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N TRP B 83 " --> pdb=" O PHE B 230 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N PHE B 230 " --> pdb=" O TRP B 83 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N HIS B 200 " --> pdb=" O SER B 196 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N PHE B 201 " --> pdb=" O TYR B 208 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 69 through 86 removed outlier: 3.721A pdb=" N LEU B 77 " --> pdb=" O SER B 236 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N SER B 236 " --> pdb=" O LEU B 77 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N LEU B 79 " --> pdb=" O LEU B 234 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N LEU B 234 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N CYS B 81 " --> pdb=" O VAL B 232 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N VAL B 232 " --> pdb=" O CYS B 81 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N TRP B 83 " --> pdb=" O PHE B 230 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N PHE B 230 " --> pdb=" O TRP B 83 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N ASP B 239 " --> pdb=" O TYR B 254 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N TYR B 254 " --> pdb=" O ASP B 239 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N LEU B 241 " --> pdb=" O ILE B 252 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N ILE B 252 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N ASN B 243 " --> pdb=" O ALA B 250 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 94 through 96 removed outlier: 6.751A pdb=" N LYS B 135 " --> pdb=" O GLU B 215 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N VAL B 217 " --> pdb=" O LEU B 133 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N LEU B 133 " --> pdb=" O VAL B 217 " (cutoff:3.500A) removed outlier: 4.941A pdb=" N PHE B 219 " --> pdb=" O THR B 131 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N THR B 131 " --> pdb=" O PHE B 219 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N VAL B 140 " --> pdb=" O THR B 173 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLY B 184 " --> pdb=" O CYS B 168 " (cutoff:3.500A) removed outlier: 5.689A pdb=" N VAL B 170 " --> pdb=" O PHE B 182 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N PHE B 182 " --> pdb=" O VAL B 170 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N THR B 172 " --> pdb=" O SER B 180 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N SER B 180 " --> pdb=" O THR B 172 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N ILE B 174 " --> pdb=" O THR B 178 " (cutoff:3.500A) removed outlier: 5.124A pdb=" N THR B 178 " --> pdb=" O ILE B 174 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 274 through 278 removed outlier: 3.643A pdb=" N GLY B 512 " --> pdb=" O VAL B 504 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 288 through 291 removed outlier: 6.674A pdb=" N SER B 289 " --> pdb=" O ASN B 450 " (cutoff:3.500A) removed outlier: 5.344A pdb=" N LEU B 481 " --> pdb=" O ILE B 494 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N TYR B 473 " --> pdb=" O LEU B 481 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N THR B 472 " --> pdb=" O SER C 65 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 323 through 329 removed outlier: 4.397A pdb=" N VAL B 325 " --> pdb=" O ASP B 307 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N ASP B 307 " --> pdb=" O VAL B 325 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N ILE B 327 " --> pdb=" O TYR B 305 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N TYR B 305 " --> pdb=" O ILE B 327 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N LEU B 329 " --> pdb=" O VAL B 303 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N VAL B 303 " --> pdb=" O LEU B 329 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N SER B 384 " --> pdb=" O SER B 420 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N GLY B 422 " --> pdb=" O PHE B 382 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 323 through 329 removed outlier: 4.397A pdb=" N VAL B 325 " --> pdb=" O ASP B 307 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N ASP B 307 " --> pdb=" O VAL B 325 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N ILE B 327 " --> pdb=" O TYR B 305 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N TYR B 305 " --> pdb=" O ILE B 327 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N LEU B 329 " --> pdb=" O VAL B 303 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N VAL B 303 " --> pdb=" O LEU B 329 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N TYR B 409 " --> pdb=" O TRP B 404 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N TRP B 404 " --> pdb=" O TYR B 409 " (cutoff:3.500A) removed outlier: 5.069A pdb=" N THR B 411 " --> pdb=" O ALA B 402 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N ALA B 402 " --> pdb=" O THR B 411 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 546 through 550 Processing sheet with id=AC4, first strand: chain 'B' and resid 583 through 598 removed outlier: 6.511A pdb=" N GLN B 956 " --> pdb=" O SER B 586 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N TRP B 588 " --> pdb=" O PRO B 954 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N ILE B 590 " --> pdb=" O LEU B 952 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N LEU B 952 " --> pdb=" O ILE B 590 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N VAL B 592 " --> pdb=" O THR B 950 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N THR B 950 " --> pdb=" O VAL B 592 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N VAL B 594 " --> pdb=" O LEU B 948 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N LEU B 948 " --> pdb=" O VAL B 594 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N TYR B 596 " --> pdb=" O VAL B 946 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N VAL B 946 " --> pdb=" O TYR B 596 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N GLN B 598 " --> pdb=" O GLY B 944 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N GLY B 944 " --> pdb=" O GLN B 598 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N PHE B 935 " --> pdb=" O THR B 950 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N LEU B 952 " --> pdb=" O HIS B 933 " (cutoff:3.500A) removed outlier: 5.916A pdb=" N HIS B 933 " --> pdb=" O LEU B 952 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 604 through 606 Processing sheet with id=AC6, first strand: chain 'B' and resid 1008 through 1011 Processing sheet with id=AC7, first strand: chain 'B' and resid 981 through 986 Processing sheet with id=AC8, first strand: chain 'C' and resid 69 through 86 removed outlier: 3.721A pdb=" N LEU C 77 " --> pdb=" O SER C 236 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N SER C 236 " --> pdb=" O LEU C 77 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N LEU C 79 " --> pdb=" O LEU C 234 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N LEU C 234 " --> pdb=" O LEU C 79 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N CYS C 81 " --> pdb=" O VAL C 232 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N VAL C 232 " --> pdb=" O CYS C 81 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N TRP C 83 " --> pdb=" O PHE C 230 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N PHE C 230 " --> pdb=" O TRP C 83 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N HIS C 200 " --> pdb=" O SER C 196 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N PHE C 201 " --> pdb=" O TYR C 208 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 69 through 86 removed outlier: 3.721A pdb=" N LEU C 77 " --> pdb=" O SER C 236 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N SER C 236 " --> pdb=" O LEU C 77 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N LEU C 79 " --> pdb=" O LEU C 234 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N LEU C 234 " --> pdb=" O LEU C 79 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N CYS C 81 " --> pdb=" O VAL C 232 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N VAL C 232 " --> pdb=" O CYS C 81 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N TRP C 83 " --> pdb=" O PHE C 230 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N PHE C 230 " --> pdb=" O TRP C 83 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N ASP C 239 " --> pdb=" O TYR C 254 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N TYR C 254 " --> pdb=" O ASP C 239 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N LEU C 241 " --> pdb=" O ILE C 252 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N ILE C 252 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N ASN C 243 " --> pdb=" O ALA C 250 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 94 through 96 removed outlier: 6.751A pdb=" N LYS C 135 " --> pdb=" O GLU C 215 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N VAL C 217 " --> pdb=" O LEU C 133 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N LEU C 133 " --> pdb=" O VAL C 217 " (cutoff:3.500A) removed outlier: 4.941A pdb=" N PHE C 219 " --> pdb=" O THR C 131 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N THR C 131 " --> pdb=" O PHE C 219 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N VAL C 140 " --> pdb=" O THR C 173 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLY C 184 " --> pdb=" O CYS C 168 " (cutoff:3.500A) removed outlier: 5.689A pdb=" N VAL C 170 " --> pdb=" O PHE C 182 " (cutoff:3.500A) removed outlier: 5.465A pdb=" N PHE C 182 " --> pdb=" O VAL C 170 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N THR C 172 " --> pdb=" O SER C 180 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N SER C 180 " --> pdb=" O THR C 172 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N ILE C 174 " --> pdb=" O THR C 178 " (cutoff:3.500A) removed outlier: 5.124A pdb=" N THR C 178 " --> pdb=" O ILE C 174 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 274 through 278 removed outlier: 3.642A pdb=" N GLY C 512 " --> pdb=" O VAL C 504 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 323 through 329 removed outlier: 4.397A pdb=" N VAL C 325 " --> pdb=" O ASP C 307 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N ASP C 307 " --> pdb=" O VAL C 325 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N ILE C 327 " --> pdb=" O TYR C 305 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N TYR C 305 " --> pdb=" O ILE C 327 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N LEU C 329 " --> pdb=" O VAL C 303 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N VAL C 303 " --> pdb=" O LEU C 329 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N SER C 384 " --> pdb=" O SER C 420 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N GLY C 422 " --> pdb=" O PHE C 382 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 323 through 329 removed outlier: 4.397A pdb=" N VAL C 325 " --> pdb=" O ASP C 307 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N ASP C 307 " --> pdb=" O VAL C 325 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N ILE C 327 " --> pdb=" O TYR C 305 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N TYR C 305 " --> pdb=" O ILE C 327 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N LEU C 329 " --> pdb=" O VAL C 303 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N VAL C 303 " --> pdb=" O LEU C 329 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N TYR C 409 " --> pdb=" O TRP C 404 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N TRP C 404 " --> pdb=" O TYR C 409 " (cutoff:3.500A) removed outlier: 5.069A pdb=" N THR C 411 " --> pdb=" O ALA C 402 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N ALA C 402 " --> pdb=" O THR C 411 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 546 through 550 Processing sheet with id=AD6, first strand: chain 'C' and resid 583 through 598 removed outlier: 6.511A pdb=" N GLN C 956 " --> pdb=" O SER C 586 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N TRP C 588 " --> pdb=" O PRO C 954 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N ILE C 590 " --> pdb=" O LEU C 952 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N LEU C 952 " --> pdb=" O ILE C 590 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N VAL C 592 " --> pdb=" O THR C 950 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N THR C 950 " --> pdb=" O VAL C 592 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N VAL C 594 " --> pdb=" O LEU C 948 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N LEU C 948 " --> pdb=" O VAL C 594 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N TYR C 596 " --> pdb=" O VAL C 946 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N VAL C 946 " --> pdb=" O TYR C 596 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N GLN C 598 " --> pdb=" O GLY C 944 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N GLY C 944 " --> pdb=" O GLN C 598 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N PHE C 935 " --> pdb=" O THR C 950 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N LEU C 952 " --> pdb=" O HIS C 933 " (cutoff:3.500A) removed outlier: 5.916A pdb=" N HIS C 933 " --> pdb=" O LEU C 952 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 604 through 606 Processing sheet with id=AD8, first strand: chain 'C' and resid 1008 through 1011 Processing sheet with id=AD9, first strand: chain 'C' and resid 981 through 986 1000 hydrogen bonds defined for protein. 2700 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: 5.87 Time building geometry restraints manager: 3.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6459 1.33 - 1.45: 4544 1.45 - 1.57: 12715 1.57 - 1.69: 0 1.69 - 1.81: 144 Bond restraints: 23862 Sorted by residual: bond pdb=" CE1 HIS C 949 " pdb=" NE2 HIS C 949 " ideal model delta sigma weight residual 1.321 1.373 -0.052 1.00e-02 1.00e+04 2.70e+01 bond pdb=" CE1 HIS B 949 " pdb=" NE2 HIS B 949 " ideal model delta sigma weight residual 1.321 1.373 -0.052 1.00e-02 1.00e+04 2.68e+01 bond pdb=" CE1 HIS A 949 " pdb=" NE2 HIS A 949 " ideal model delta sigma weight residual 1.321 1.373 -0.052 1.00e-02 1.00e+04 2.68e+01 bond pdb=" C1 MAN I 5 " pdb=" O5 MAN I 5 " ideal model delta sigma weight residual 1.399 1.475 -0.076 2.00e-02 2.50e+03 1.45e+01 bond pdb=" C1 MAN N 5 " pdb=" O5 MAN N 5 " ideal model delta sigma weight residual 1.399 1.475 -0.076 2.00e-02 2.50e+03 1.44e+01 ... (remaining 23857 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.80: 23077 1.80 - 3.60: 7743 3.60 - 5.39: 1528 5.39 - 7.19: 130 7.19 - 8.99: 27 Bond angle restraints: 32505 Sorted by residual: angle pdb=" CA ASP A 635 " pdb=" CB ASP A 635 " pdb=" CG ASP A 635 " ideal model delta sigma weight residual 112.60 118.90 -6.30 1.00e+00 1.00e+00 3.98e+01 angle pdb=" CA ASP B 635 " pdb=" CB ASP B 635 " pdb=" CG ASP B 635 " ideal model delta sigma weight residual 112.60 118.89 -6.29 1.00e+00 1.00e+00 3.95e+01 angle pdb=" CA ASP C 635 " pdb=" CB ASP C 635 " pdb=" CG ASP C 635 " ideal model delta sigma weight residual 112.60 118.88 -6.28 1.00e+00 1.00e+00 3.94e+01 angle pdb=" CA ASP A 68 " pdb=" CB ASP A 68 " pdb=" CG ASP A 68 " ideal model delta sigma weight residual 112.60 118.83 -6.23 1.00e+00 1.00e+00 3.88e+01 angle pdb=" CA ASP B 68 " pdb=" CB ASP B 68 " pdb=" CG ASP B 68 " ideal model delta sigma weight residual 112.60 118.82 -6.22 1.00e+00 1.00e+00 3.87e+01 ... (remaining 32500 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.50: 14318 22.50 - 44.99: 634 44.99 - 67.49: 69 67.49 - 89.98: 84 89.98 - 112.48: 36 Dihedral angle restraints: 15141 sinusoidal: 6729 harmonic: 8412 Sorted by residual: dihedral pdb=" CA GLY B 539 " pdb=" C GLY B 539 " pdb=" N THR B 540 " pdb=" CA THR B 540 " ideal model delta harmonic sigma weight residual 180.00 150.71 29.29 0 5.00e+00 4.00e-02 3.43e+01 dihedral pdb=" CA GLY A 539 " pdb=" C GLY A 539 " pdb=" N THR A 540 " pdb=" CA THR A 540 " ideal model delta harmonic sigma weight residual 180.00 150.74 29.26 0 5.00e+00 4.00e-02 3.42e+01 dihedral pdb=" CA GLY C 539 " pdb=" C GLY C 539 " pdb=" N THR C 540 " pdb=" CA THR C 540 " ideal model delta harmonic sigma weight residual 180.00 150.74 29.26 0 5.00e+00 4.00e-02 3.42e+01 ... (remaining 15138 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.105: 2688 0.105 - 0.211: 1168 0.211 - 0.316: 125 0.316 - 0.421: 27 0.421 - 0.527: 18 Chirality restraints: 4026 Sorted by residual: chirality pdb=" C1 BMA L 3 " pdb=" O4 NAG L 2 " pdb=" C2 BMA L 3 " pdb=" O5 BMA L 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.57 0.17 2.00e-02 2.50e+03 7.38e+01 chirality pdb=" C1 NAG J 2 " pdb=" O4 NAG J 1 " pdb=" C2 NAG J 2 " pdb=" O5 NAG J 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.57 0.17 2.00e-02 2.50e+03 7.32e+01 chirality pdb=" C1 NAG O 2 " pdb=" O4 NAG O 1 " pdb=" C2 NAG O 2 " pdb=" O5 NAG O 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.57 0.17 2.00e-02 2.50e+03 7.29e+01 ... (remaining 4023 not shown) Planarity restraints: 4089 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1223 " 0.238 2.00e-02 2.50e+03 1.98e-01 4.89e+02 pdb=" C7 NAG B1223 " -0.063 2.00e-02 2.50e+03 pdb=" C8 NAG B1223 " 0.167 2.00e-02 2.50e+03 pdb=" N2 NAG B1223 " -0.327 2.00e-02 2.50e+03 pdb=" O7 NAG B1223 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C1223 " -0.238 2.00e-02 2.50e+03 1.98e-01 4.88e+02 pdb=" C7 NAG C1223 " 0.063 2.00e-02 2.50e+03 pdb=" C8 NAG C1223 " -0.167 2.00e-02 2.50e+03 pdb=" N2 NAG C1223 " 0.327 2.00e-02 2.50e+03 pdb=" O7 NAG C1223 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1223 " 0.238 2.00e-02 2.50e+03 1.98e-01 4.88e+02 pdb=" C7 NAG A1223 " -0.063 2.00e-02 2.50e+03 pdb=" C8 NAG A1223 " 0.167 2.00e-02 2.50e+03 pdb=" N2 NAG A1223 " -0.327 2.00e-02 2.50e+03 pdb=" O7 NAG A1223 " -0.015 2.00e-02 2.50e+03 ... (remaining 4086 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.81: 4597 2.81 - 3.33: 23641 3.33 - 3.85: 38048 3.85 - 4.38: 45244 4.38 - 4.90: 76650 Nonbonded interactions: 188180 Sorted by model distance: nonbonded pdb=" OG SER A 665 " pdb=" O6 NAG A1224 " model vdw 2.282 3.040 nonbonded pdb=" OG SER B 665 " pdb=" O6 NAG B1224 " model vdw 2.282 3.040 nonbonded pdb=" OG SER C 665 " pdb=" O6 NAG C1224 " model vdw 2.283 3.040 nonbonded pdb=" O4 NAG B1210 " pdb=" O6 NAG B1210 " model vdw 2.317 3.040 nonbonded pdb=" O4 NAG A1210 " pdb=" O6 NAG A1210 " model vdw 2.317 3.040 ... (remaining 188175 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'I' selection = chain 'N' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'H' selection = chain 'J' selection = chain 'K' selection = chain 'M' selection = chain 'O' selection = chain 'P' selection = chain 'R' } ncs_group { reference = chain 'G' selection = chain 'L' selection = chain 'Q' } 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: 2.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.370 Check model and map are aligned: 0.080 Set scattering table: 0.080 Process input model: 23.880 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.076 23982 Z= 0.771 Angle : 1.810 10.067 32826 Z= 1.171 Chirality : 0.112 0.527 4026 Planarity : 0.014 0.198 4041 Dihedral : 15.362 112.478 9642 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 0.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 0.24 % Allowed : 2.28 % Favored : 97.48 % Cbeta Deviations : 1.23 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.94 (0.14), residues: 2871 helix: -0.46 (0.18), residues: 657 sheet: 0.76 (0.20), residues: 564 loop : -1.21 (0.14), residues: 1650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.040 0.006 ARG B 261 TYR 0.098 0.016 TYR A 237 PHE 0.080 0.013 PHE A 809 TRP 0.053 0.011 TRP A 588 HIS 0.015 0.005 HIS A 846 Details of bonding type rmsd covalent geometry : bond 0.01327 (23862) covalent geometry : angle 1.78204 (32505) SS BOND : bond 0.01924 ( 39) SS BOND : angle 1.88897 ( 78) hydrogen bonds : bond 0.16488 ( 946) hydrogen bonds : angle 8.60239 ( 2700) link_ALPHA1-2 : bond 0.02266 ( 3) link_ALPHA1-2 : angle 5.06190 ( 9) link_ALPHA1-3 : bond 0.01494 ( 6) link_ALPHA1-3 : angle 4.70243 ( 18) link_ALPHA1-6 : bond 0.00573 ( 3) link_ALPHA1-6 : angle 5.08452 ( 9) link_BETA1-4 : bond 0.02067 ( 21) link_BETA1-4 : angle 3.75851 ( 63) link_NAG-ASN : bond 0.00725 ( 48) link_NAG-ASN : angle 3.94948 ( 144) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5742 Ramachandran restraints generated. 2871 Oldfield, 0 Emsley, 2871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5742 Ramachandran restraints generated. 2871 Oldfield, 0 Emsley, 2871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 244 time to evaluate : 0.759 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 802 MET cc_start: 0.9242 (mmm) cc_final: 0.8827 (tpp) REVERT: A 943 GLU cc_start: 0.7988 (mt-10) cc_final: 0.7728 (mt-10) REVERT: A 997 MET cc_start: 0.8312 (mmt) cc_final: 0.7997 (mpp) REVERT: B 644 GLU cc_start: 0.8220 (mm-30) cc_final: 0.7998 (mm-30) REVERT: B 943 GLU cc_start: 0.7989 (mt-10) cc_final: 0.7780 (mt-10) REVERT: C 300 MET cc_start: 0.8797 (ttm) cc_final: 0.8418 (ttm) REVERT: C 890 ASN cc_start: 0.8691 (m-40) cc_final: 0.8455 (m110) outliers start: 6 outliers final: 3 residues processed: 250 average time/residue: 0.1433 time to fit residues: 58.2100 Evaluate side-chains 142 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 139 time to evaluate : 1.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1019 VAL Chi-restraints excluded: chain B residue 1019 VAL Chi-restraints excluded: chain C residue 1019 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 197 optimal weight: 6.9990 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 0.7980 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 8.9990 chunk 183 optimal weight: 0.6980 chunk 111 optimal weight: 2.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 200 HIS A 266 GLN ** A 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 365 ASN A 731 ASN A 778 ASN A 824 GLN A 831 ASN A 850 GLN A 933 HIS A1020 ASN B 200 HIS ** B 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 365 ASN B 731 ASN B 778 ASN B 824 GLN B 831 ASN B 850 GLN B 933 HIS B1020 ASN C 200 HIS C 365 ASN C 731 ASN C 778 ASN C 831 ASN C 850 GLN C 933 HIS Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.096126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.060893 restraints weight = 61525.560| |-----------------------------------------------------------------------------| r_work (start): 0.2888 rms_B_bonded: 4.11 r_work: 0.2717 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.2717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.1901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 23982 Z= 0.162 Angle : 0.707 7.192 32826 Z= 0.374 Chirality : 0.050 0.239 4026 Planarity : 0.004 0.038 4041 Dihedral : 11.038 74.168 4794 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 1.24 % Allowed : 5.21 % Favored : 93.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.05 (0.15), residues: 2871 helix: 1.13 (0.20), residues: 663 sheet: 0.77 (0.20), residues: 597 loop : -0.72 (0.15), residues: 1611 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 72 TYR 0.026 0.002 TYR A 957 PHE 0.021 0.002 PHE C 379 TRP 0.016 0.002 TRP C 588 HIS 0.004 0.001 HIS C 345 Details of bonding type rmsd covalent geometry : bond 0.00345 (23862) covalent geometry : angle 0.68201 (32505) SS BOND : bond 0.00376 ( 39) SS BOND : angle 1.21976 ( 78) hydrogen bonds : bond 0.05361 ( 946) hydrogen bonds : angle 6.36925 ( 2700) link_ALPHA1-2 : bond 0.01541 ( 3) link_ALPHA1-2 : angle 2.65868 ( 9) link_ALPHA1-3 : bond 0.00614 ( 6) link_ALPHA1-3 : angle 2.99347 ( 18) link_ALPHA1-6 : bond 0.00229 ( 3) link_ALPHA1-6 : angle 1.49524 ( 9) link_BETA1-4 : bond 0.00549 ( 21) link_BETA1-4 : angle 2.18194 ( 63) link_NAG-ASN : bond 0.00368 ( 48) link_NAG-ASN : angle 2.10325 ( 144) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5742 Ramachandran restraints generated. 2871 Oldfield, 0 Emsley, 2871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5742 Ramachandran restraints generated. 2871 Oldfield, 0 Emsley, 2871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 164 time to evaluate : 0.661 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 381 LYS cc_start: 0.8690 (mtpp) cc_final: 0.8450 (mtpp) REVERT: A 890 ASN cc_start: 0.9436 (m-40) cc_final: 0.9168 (m110) REVERT: A 943 GLU cc_start: 0.8828 (mt-10) cc_final: 0.8374 (mt-10) REVERT: A 997 MET cc_start: 0.8542 (mmt) cc_final: 0.8176 (mmm) REVERT: B 644 GLU cc_start: 0.9040 (mm-30) cc_final: 0.8822 (tp30) REVERT: B 997 MET cc_start: 0.8569 (mpp) cc_final: 0.8144 (mmm) REVERT: C 265 ASP cc_start: 0.8975 (m-30) cc_final: 0.8743 (m-30) REVERT: C 890 ASN cc_start: 0.9445 (m-40) cc_final: 0.9029 (m110) REVERT: C 943 GLU cc_start: 0.8787 (mt-10) cc_final: 0.8549 (mt-10) REVERT: C 997 MET cc_start: 0.8595 (mpp) cc_final: 0.8239 (mmm) outliers start: 31 outliers final: 12 residues processed: 190 average time/residue: 0.1272 time to fit residues: 41.1676 Evaluate side-chains 127 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 115 time to evaluate : 0.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 645 SER Chi-restraints excluded: chain A residue 831 ASN Chi-restraints excluded: chain A residue 1019 VAL Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 831 ASN Chi-restraints excluded: chain B residue 1019 VAL Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 268 SER Chi-restraints excluded: chain C residue 392 ILE Chi-restraints excluded: chain C residue 831 ASN Chi-restraints excluded: chain C residue 1019 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 220 optimal weight: 3.9990 chunk 272 optimal weight: 2.9990 chunk 160 optimal weight: 6.9990 chunk 148 optimal weight: 20.0000 chunk 90 optimal weight: 50.0000 chunk 262 optimal weight: 10.0000 chunk 69 optimal weight: 6.9990 chunk 138 optimal weight: 3.9990 chunk 133 optimal weight: 0.2980 chunk 94 optimal weight: 20.0000 chunk 40 optimal weight: 0.6980 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 831 ASN A 956 GLN B 831 ASN B 956 GLN C 831 ASN C1020 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.094900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.059796 restraints weight = 61808.033| |-----------------------------------------------------------------------------| r_work (start): 0.2866 rms_B_bonded: 4.07 r_work: 0.2693 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.2693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.2376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 23982 Z= 0.205 Angle : 0.642 8.008 32826 Z= 0.335 Chirality : 0.048 0.249 4026 Planarity : 0.004 0.040 4041 Dihedral : 9.006 62.093 4794 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.20 % Allowed : 6.25 % Favored : 92.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.26 (0.16), residues: 2871 helix: 1.59 (0.20), residues: 654 sheet: 0.61 (0.19), residues: 690 loop : -0.66 (0.16), residues: 1527 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 72 TYR 0.021 0.001 TYR B 957 PHE 0.017 0.001 PHE A 382 TRP 0.008 0.001 TRP B 963 HIS 0.005 0.001 HIS B 846 Details of bonding type rmsd covalent geometry : bond 0.00457 (23862) covalent geometry : angle 0.62003 (32505) SS BOND : bond 0.00384 ( 39) SS BOND : angle 1.02440 ( 78) hydrogen bonds : bond 0.04844 ( 946) hydrogen bonds : angle 6.00126 ( 2700) link_ALPHA1-2 : bond 0.01563 ( 3) link_ALPHA1-2 : angle 2.87171 ( 9) link_ALPHA1-3 : bond 0.00508 ( 6) link_ALPHA1-3 : angle 2.81946 ( 18) link_ALPHA1-6 : bond 0.00176 ( 3) link_ALPHA1-6 : angle 1.70135 ( 9) link_BETA1-4 : bond 0.00353 ( 21) link_BETA1-4 : angle 1.89330 ( 63) link_NAG-ASN : bond 0.00358 ( 48) link_NAG-ASN : angle 1.84678 ( 144) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5742 Ramachandran restraints generated. 2871 Oldfield, 0 Emsley, 2871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5742 Ramachandran restraints generated. 2871 Oldfield, 0 Emsley, 2871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 130 time to evaluate : 0.772 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 381 LYS cc_start: 0.8936 (mtpp) cc_final: 0.8536 (mtpp) REVERT: A 802 MET cc_start: 0.9487 (tpp) cc_final: 0.9168 (tpp) REVERT: A 832 LYS cc_start: 0.9370 (tttm) cc_final: 0.9128 (ttmm) REVERT: A 943 GLU cc_start: 0.8973 (mt-10) cc_final: 0.8458 (mt-10) REVERT: A 990 TYR cc_start: 0.8519 (t80) cc_final: 0.8241 (t80) REVERT: A 997 MET cc_start: 0.8411 (mmt) cc_final: 0.8090 (mmm) REVERT: A 1005 MET cc_start: 0.3906 (mmm) cc_final: 0.3662 (mmm) REVERT: B 423 ASP cc_start: 0.9288 (OUTLIER) cc_final: 0.8952 (p0) REVERT: B 425 ILE cc_start: 0.9226 (mm) cc_final: 0.8894 (mt) REVERT: B 832 LYS cc_start: 0.9337 (ttmm) cc_final: 0.9061 (ttpp) REVERT: B 943 GLU cc_start: 0.8913 (mt-10) cc_final: 0.8598 (mt-10) REVERT: B 997 MET cc_start: 0.8265 (mpp) cc_final: 0.8060 (mmm) REVERT: C 265 ASP cc_start: 0.9050 (m-30) cc_final: 0.8779 (m-30) REVERT: C 300 MET cc_start: 0.8216 (ttm) cc_final: 0.7894 (ttm) REVERT: C 423 ASP cc_start: 0.9151 (p0) cc_final: 0.8768 (p0) REVERT: C 425 ILE cc_start: 0.9245 (mm) cc_final: 0.8955 (mt) REVERT: C 890 ASN cc_start: 0.9460 (m-40) cc_final: 0.9081 (m110) REVERT: C 943 GLU cc_start: 0.8844 (mt-10) cc_final: 0.8642 (mt-10) REVERT: C 997 MET cc_start: 0.8300 (mpp) cc_final: 0.8098 (mmm) outliers start: 30 outliers final: 14 residues processed: 154 average time/residue: 0.1351 time to fit residues: 34.7917 Evaluate side-chains 127 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 112 time to evaluate : 0.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 268 SER Chi-restraints excluded: chain A residue 645 SER Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 912 GLN Chi-restraints excluded: chain A residue 1019 VAL Chi-restraints excluded: chain B residue 268 SER Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 423 ASP Chi-restraints excluded: chain B residue 912 GLN Chi-restraints excluded: chain B residue 1019 VAL Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 268 SER Chi-restraints excluded: chain C residue 392 ILE Chi-restraints excluded: chain C residue 1019 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 177 optimal weight: 0.9980 chunk 83 optimal weight: 5.9990 chunk 274 optimal weight: 0.7980 chunk 120 optimal weight: 0.0470 chunk 47 optimal weight: 5.9990 chunk 107 optimal weight: 0.1980 chunk 134 optimal weight: 30.0000 chunk 35 optimal weight: 8.9990 chunk 206 optimal weight: 6.9990 chunk 171 optimal weight: 3.9990 chunk 98 optimal weight: 1.9990 overall best weight: 0.8080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 831 ASN ** B 498 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 831 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.096469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.061584 restraints weight = 61418.617| |-----------------------------------------------------------------------------| r_work (start): 0.2909 rms_B_bonded: 4.08 r_work: 0.2739 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.2739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.2761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 23982 Z= 0.117 Angle : 0.572 8.481 32826 Z= 0.298 Chirality : 0.046 0.219 4026 Planarity : 0.004 0.039 4041 Dihedral : 7.435 53.225 4794 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.24 % Allowed : 7.45 % Favored : 91.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.34 (0.16), residues: 2871 helix: 1.87 (0.21), residues: 663 sheet: 0.48 (0.19), residues: 681 loop : -0.62 (0.16), residues: 1527 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 72 TYR 0.019 0.001 TYR B 957 PHE 0.018 0.001 PHE A 769 TRP 0.006 0.001 TRP C 588 HIS 0.004 0.001 HIS B 297 Details of bonding type rmsd covalent geometry : bond 0.00242 (23862) covalent geometry : angle 0.55066 (32505) SS BOND : bond 0.00294 ( 39) SS BOND : angle 0.98067 ( 78) hydrogen bonds : bond 0.04201 ( 946) hydrogen bonds : angle 5.68825 ( 2700) link_ALPHA1-2 : bond 0.01879 ( 3) link_ALPHA1-2 : angle 2.47097 ( 9) link_ALPHA1-3 : bond 0.00838 ( 6) link_ALPHA1-3 : angle 2.78332 ( 18) link_ALPHA1-6 : bond 0.00363 ( 3) link_ALPHA1-6 : angle 1.33140 ( 9) link_BETA1-4 : bond 0.00459 ( 21) link_BETA1-4 : angle 1.78755 ( 63) link_NAG-ASN : bond 0.00201 ( 48) link_NAG-ASN : angle 1.63135 ( 144) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5742 Ramachandran restraints generated. 2871 Oldfield, 0 Emsley, 2871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5742 Ramachandran restraints generated. 2871 Oldfield, 0 Emsley, 2871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 139 time to evaluate : 0.683 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 381 LYS cc_start: 0.8971 (mtpp) cc_final: 0.8537 (mtpp) REVERT: A 635 ASP cc_start: 0.8845 (p0) cc_final: 0.8611 (p0) REVERT: A 802 MET cc_start: 0.9472 (tpp) cc_final: 0.9209 (tpp) REVERT: A 890 ASN cc_start: 0.9432 (m-40) cc_final: 0.9156 (m110) REVERT: A 943 GLU cc_start: 0.8968 (mt-10) cc_final: 0.8452 (mt-10) REVERT: A 997 MET cc_start: 0.8464 (mmt) cc_final: 0.8182 (mmm) REVERT: A 1005 MET cc_start: 0.4215 (mmm) cc_final: 0.3988 (mmm) REVERT: B 423 ASP cc_start: 0.9263 (OUTLIER) cc_final: 0.8955 (p0) REVERT: B 425 ILE cc_start: 0.9220 (mm) cc_final: 0.8838 (mt) REVERT: B 997 MET cc_start: 0.8280 (mpp) cc_final: 0.8057 (mmm) REVERT: B 1005 MET cc_start: 0.3946 (mmm) cc_final: 0.3721 (mmm) REVERT: C 265 ASP cc_start: 0.9041 (m-30) cc_final: 0.8760 (m-30) REVERT: C 300 MET cc_start: 0.8241 (ttm) cc_final: 0.7898 (ttm) REVERT: C 423 ASP cc_start: 0.9113 (OUTLIER) cc_final: 0.8716 (p0) REVERT: C 425 ILE cc_start: 0.9232 (mm) cc_final: 0.8944 (mt) REVERT: C 644 GLU cc_start: 0.9007 (tp30) cc_final: 0.8665 (tp30) REVERT: C 802 MET cc_start: 0.9347 (mmm) cc_final: 0.8964 (tpp) REVERT: C 890 ASN cc_start: 0.9424 (m-40) cc_final: 0.9037 (m-40) REVERT: C 943 GLU cc_start: 0.8867 (mt-10) cc_final: 0.8433 (mm-30) outliers start: 31 outliers final: 16 residues processed: 162 average time/residue: 0.1300 time to fit residues: 35.3808 Evaluate side-chains 137 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 119 time to evaluate : 0.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 317 CYS Chi-restraints excluded: chain A residue 466 THR Chi-restraints excluded: chain A residue 705 LEU Chi-restraints excluded: chain A residue 912 GLN Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 423 ASP Chi-restraints excluded: chain B residue 805 ILE Chi-restraints excluded: chain B residue 825 THR Chi-restraints excluded: chain B residue 831 ASN Chi-restraints excluded: chain B residue 912 GLN Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain C residue 392 ILE Chi-restraints excluded: chain C residue 423 ASP Chi-restraints excluded: chain C residue 705 LEU Chi-restraints excluded: chain C residue 825 THR Chi-restraints excluded: chain C residue 831 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 282 optimal weight: 20.0000 chunk 76 optimal weight: 0.9980 chunk 82 optimal weight: 0.4980 chunk 45 optimal weight: 5.9990 chunk 218 optimal weight: 0.3980 chunk 103 optimal weight: 9.9990 chunk 252 optimal weight: 6.9990 chunk 58 optimal weight: 2.9990 chunk 122 optimal weight: 0.0170 chunk 267 optimal weight: 1.9990 chunk 36 optimal weight: 10.0000 overall best weight: 0.7820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 299 HIS A 831 ASN B 299 HIS ** B 498 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 502 GLN B 831 ASN ** B 845 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 853 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.096654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.061970 restraints weight = 61137.741| |-----------------------------------------------------------------------------| r_work (start): 0.2918 rms_B_bonded: 4.06 r_work: 0.2750 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.2750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.2977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 23982 Z= 0.113 Angle : 0.550 9.228 32826 Z= 0.286 Chirality : 0.045 0.214 4026 Planarity : 0.004 0.037 4041 Dihedral : 6.764 52.864 4791 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.20 % Allowed : 8.41 % Favored : 90.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.34 (0.16), residues: 2871 helix: 1.91 (0.21), residues: 663 sheet: 0.38 (0.18), residues: 735 loop : -0.63 (0.17), residues: 1473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 642 TYR 0.024 0.001 TYR A 990 PHE 0.015 0.001 PHE C 769 TRP 0.005 0.001 TRP A 419 HIS 0.004 0.001 HIS B 846 Details of bonding type rmsd covalent geometry : bond 0.00238 (23862) covalent geometry : angle 0.52988 (32505) SS BOND : bond 0.00260 ( 39) SS BOND : angle 0.94551 ( 78) hydrogen bonds : bond 0.04036 ( 946) hydrogen bonds : angle 5.55423 ( 2700) link_ALPHA1-2 : bond 0.01829 ( 3) link_ALPHA1-2 : angle 2.27010 ( 9) link_ALPHA1-3 : bond 0.00768 ( 6) link_ALPHA1-3 : angle 2.77349 ( 18) link_ALPHA1-6 : bond 0.00438 ( 3) link_ALPHA1-6 : angle 1.34781 ( 9) link_BETA1-4 : bond 0.00439 ( 21) link_BETA1-4 : angle 1.66312 ( 63) link_NAG-ASN : bond 0.00175 ( 48) link_NAG-ASN : angle 1.55832 ( 144) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5742 Ramachandran restraints generated. 2871 Oldfield, 0 Emsley, 2871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5742 Ramachandran restraints generated. 2871 Oldfield, 0 Emsley, 2871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 130 time to evaluate : 0.723 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 381 LYS cc_start: 0.9026 (mtpp) cc_final: 0.8649 (mtpp) REVERT: A 802 MET cc_start: 0.9462 (tpp) cc_final: 0.9233 (tpp) REVERT: A 850 GLN cc_start: 0.9425 (mt0) cc_final: 0.9076 (mt0) REVERT: A 890 ASN cc_start: 0.9430 (m-40) cc_final: 0.9094 (m-40) REVERT: A 943 GLU cc_start: 0.9030 (mt-10) cc_final: 0.8677 (mt-10) REVERT: A 997 MET cc_start: 0.8422 (mmt) cc_final: 0.8130 (mmm) REVERT: A 1005 MET cc_start: 0.4201 (mmm) cc_final: 0.3989 (mmm) REVERT: B 177 GLU cc_start: 0.8223 (OUTLIER) cc_final: 0.7912 (pm20) REVERT: B 300 MET cc_start: 0.8644 (ttp) cc_final: 0.8418 (ptm) REVERT: B 423 ASP cc_start: 0.9159 (OUTLIER) cc_final: 0.8856 (p0) REVERT: B 425 ILE cc_start: 0.9232 (mm) cc_final: 0.8827 (mt) REVERT: B 997 MET cc_start: 0.8187 (mpp) cc_final: 0.7969 (mmm) REVERT: B 1005 MET cc_start: 0.3905 (mmm) cc_final: 0.3660 (mmm) REVERT: C 177 GLU cc_start: 0.8249 (OUTLIER) cc_final: 0.7936 (pm20) REVERT: C 265 ASP cc_start: 0.9062 (m-30) cc_final: 0.8775 (m-30) REVERT: C 300 MET cc_start: 0.8274 (ttm) cc_final: 0.7901 (ttm) REVERT: C 423 ASP cc_start: 0.9084 (OUTLIER) cc_final: 0.8696 (p0) REVERT: C 425 ILE cc_start: 0.9219 (mm) cc_final: 0.8910 (mt) REVERT: C 634 GLU cc_start: 0.9339 (pt0) cc_final: 0.9052 (mt-10) REVERT: C 802 MET cc_start: 0.9385 (mmm) cc_final: 0.9022 (tpp) REVERT: C 890 ASN cc_start: 0.9416 (m-40) cc_final: 0.9035 (m-40) REVERT: C 943 GLU cc_start: 0.8938 (mt-10) cc_final: 0.8500 (mm-30) outliers start: 30 outliers final: 18 residues processed: 151 average time/residue: 0.1292 time to fit residues: 32.9437 Evaluate side-chains 143 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 121 time to evaluate : 0.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 317 CYS Chi-restraints excluded: chain A residue 466 THR Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 831 ASN Chi-restraints excluded: chain A residue 912 GLN Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 177 GLU Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 423 ASP Chi-restraints excluded: chain B residue 652 LEU Chi-restraints excluded: chain B residue 805 ILE Chi-restraints excluded: chain B residue 831 ASN Chi-restraints excluded: chain B residue 912 GLN Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 177 GLU Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain C residue 392 ILE Chi-restraints excluded: chain C residue 423 ASP Chi-restraints excluded: chain C residue 705 LEU Chi-restraints excluded: chain C residue 805 ILE Chi-restraints excluded: chain C residue 825 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 176 optimal weight: 2.9990 chunk 108 optimal weight: 0.6980 chunk 29 optimal weight: 6.9990 chunk 34 optimal weight: 5.9990 chunk 23 optimal weight: 0.0070 chunk 74 optimal weight: 0.0870 chunk 36 optimal weight: 3.9990 chunk 33 optimal weight: 0.9990 chunk 153 optimal weight: 0.9990 chunk 109 optimal weight: 2.9990 chunk 210 optimal weight: 6.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 831 ASN ** B 498 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 824 GLN B 831 ASN B 845 ASN C 831 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.097058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.062458 restraints weight = 61103.816| |-----------------------------------------------------------------------------| r_work (start): 0.2932 rms_B_bonded: 4.06 r_work: 0.2762 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.2762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.3170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 23982 Z= 0.103 Angle : 0.530 9.784 32826 Z= 0.277 Chirality : 0.044 0.213 4026 Planarity : 0.004 0.037 4041 Dihedral : 6.388 52.865 4791 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 1.28 % Allowed : 8.81 % Favored : 89.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.40 (0.16), residues: 2871 helix: 1.92 (0.21), residues: 663 sheet: 0.47 (0.18), residues: 729 loop : -0.59 (0.17), residues: 1479 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 685 TYR 0.015 0.001 TYR B 957 PHE 0.016 0.001 PHE C 769 TRP 0.004 0.001 TRP C 588 HIS 0.002 0.001 HIS C 846 Details of bonding type rmsd covalent geometry : bond 0.00210 (23862) covalent geometry : angle 0.51160 (32505) SS BOND : bond 0.00239 ( 39) SS BOND : angle 0.87020 ( 78) hydrogen bonds : bond 0.03881 ( 946) hydrogen bonds : angle 5.46612 ( 2700) link_ALPHA1-2 : bond 0.01764 ( 3) link_ALPHA1-2 : angle 2.29109 ( 9) link_ALPHA1-3 : bond 0.00839 ( 6) link_ALPHA1-3 : angle 2.71282 ( 18) link_ALPHA1-6 : bond 0.00562 ( 3) link_ALPHA1-6 : angle 1.24819 ( 9) link_BETA1-4 : bond 0.00457 ( 21) link_BETA1-4 : angle 1.55524 ( 63) link_NAG-ASN : bond 0.00156 ( 48) link_NAG-ASN : angle 1.48056 ( 144) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5742 Ramachandran restraints generated. 2871 Oldfield, 0 Emsley, 2871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5742 Ramachandran restraints generated. 2871 Oldfield, 0 Emsley, 2871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 143 time to evaluate : 0.805 Fit side-chains revert: symmetry clash REVERT: A 802 MET cc_start: 0.9448 (tpp) cc_final: 0.9247 (tpp) REVERT: A 832 LYS cc_start: 0.9311 (tttp) cc_final: 0.9102 (ttmm) REVERT: A 850 GLN cc_start: 0.9411 (mt0) cc_final: 0.9125 (mt0) REVERT: A 890 ASN cc_start: 0.9428 (m-40) cc_final: 0.9085 (m-40) REVERT: A 943 GLU cc_start: 0.9041 (mt-10) cc_final: 0.8691 (mt-10) REVERT: A 997 MET cc_start: 0.8411 (mmt) cc_final: 0.8116 (mmm) REVERT: A 1005 MET cc_start: 0.4193 (mmm) cc_final: 0.3955 (mmm) REVERT: B 177 GLU cc_start: 0.8211 (OUTLIER) cc_final: 0.7903 (pm20) REVERT: B 300 MET cc_start: 0.8590 (ttp) cc_final: 0.8389 (ptm) REVERT: B 398 MET cc_start: 0.9193 (mtt) cc_final: 0.8972 (mtt) REVERT: B 423 ASP cc_start: 0.9132 (OUTLIER) cc_final: 0.8859 (p0) REVERT: B 425 ILE cc_start: 0.9240 (mm) cc_final: 0.8818 (mt) REVERT: B 644 GLU cc_start: 0.9045 (tp30) cc_final: 0.8791 (tp30) REVERT: B 802 MET cc_start: 0.9500 (tpp) cc_final: 0.9284 (tpp) REVERT: B 943 GLU cc_start: 0.8867 (mt-10) cc_final: 0.8320 (mm-30) REVERT: B 997 MET cc_start: 0.8225 (mpp) cc_final: 0.8012 (mmm) REVERT: B 1005 MET cc_start: 0.3789 (mmm) cc_final: 0.3521 (mmm) REVERT: C 177 GLU cc_start: 0.8241 (OUTLIER) cc_final: 0.7961 (pm20) REVERT: C 265 ASP cc_start: 0.9055 (m-30) cc_final: 0.8766 (m-30) REVERT: C 300 MET cc_start: 0.8289 (ttm) cc_final: 0.7892 (ttm) REVERT: C 423 ASP cc_start: 0.9032 (OUTLIER) cc_final: 0.8719 (p0) REVERT: C 425 ILE cc_start: 0.9215 (mm) cc_final: 0.8897 (mt) REVERT: C 634 GLU cc_start: 0.9307 (pt0) cc_final: 0.9084 (mt-10) REVERT: C 890 ASN cc_start: 0.9411 (m-40) cc_final: 0.9041 (m-40) REVERT: C 943 GLU cc_start: 0.8989 (mt-10) cc_final: 0.8525 (mm-30) outliers start: 32 outliers final: 17 residues processed: 166 average time/residue: 0.1336 time to fit residues: 36.9597 Evaluate side-chains 139 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 118 time to evaluate : 0.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 317 CYS Chi-restraints excluded: chain A residue 466 THR Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 831 ASN Chi-restraints excluded: chain A residue 1029 ILE Chi-restraints excluded: chain B residue 177 GLU Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 423 ASP Chi-restraints excluded: chain B residue 805 ILE Chi-restraints excluded: chain C residue 177 GLU Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain C residue 392 ILE Chi-restraints excluded: chain C residue 423 ASP Chi-restraints excluded: chain C residue 705 LEU Chi-restraints excluded: chain C residue 739 VAL Chi-restraints excluded: chain C residue 805 ILE Chi-restraints excluded: chain C residue 825 THR Chi-restraints excluded: chain C residue 831 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 142 optimal weight: 5.9990 chunk 282 optimal weight: 7.9990 chunk 220 optimal weight: 4.9990 chunk 54 optimal weight: 0.0970 chunk 256 optimal weight: 9.9990 chunk 43 optimal weight: 1.9990 chunk 180 optimal weight: 5.9990 chunk 116 optimal weight: 4.9990 chunk 40 optimal weight: 2.9990 chunk 105 optimal weight: 7.9990 chunk 70 optimal weight: 20.0000 overall best weight: 3.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 831 ASN A 853 GLN ** B 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 498 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 824 GLN B 831 ASN B 845 ASN C 824 GLN C 831 ASN C 839 GLN ** C 956 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.094995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.060157 restraints weight = 61654.248| |-----------------------------------------------------------------------------| r_work (start): 0.2874 rms_B_bonded: 4.04 r_work: 0.2703 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.2703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.3193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 23982 Z= 0.239 Angle : 0.591 7.788 32826 Z= 0.306 Chirality : 0.046 0.213 4026 Planarity : 0.005 0.167 4041 Dihedral : 6.383 53.919 4791 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.52 % Allowed : 8.53 % Favored : 89.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.32 (0.16), residues: 2871 helix: 1.93 (0.21), residues: 663 sheet: 0.36 (0.19), residues: 639 loop : -0.60 (0.16), residues: 1569 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.000 ARG C 685 TYR 0.017 0.001 TYR B 550 PHE 0.050 0.001 PHE B 769 TRP 0.007 0.001 TRP C 360 HIS 0.006 0.002 HIS C 846 Details of bonding type rmsd covalent geometry : bond 0.00539 (23862) covalent geometry : angle 0.57383 (32505) SS BOND : bond 0.00318 ( 39) SS BOND : angle 1.04118 ( 78) hydrogen bonds : bond 0.04144 ( 946) hydrogen bonds : angle 5.56263 ( 2700) link_ALPHA1-2 : bond 0.01386 ( 3) link_ALPHA1-2 : angle 1.92199 ( 9) link_ALPHA1-3 : bond 0.00496 ( 6) link_ALPHA1-3 : angle 2.86386 ( 18) link_ALPHA1-6 : bond 0.00205 ( 3) link_ALPHA1-6 : angle 1.62150 ( 9) link_BETA1-4 : bond 0.00361 ( 21) link_BETA1-4 : angle 1.54461 ( 63) link_NAG-ASN : bond 0.00328 ( 48) link_NAG-ASN : angle 1.50828 ( 144) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5742 Ramachandran restraints generated. 2871 Oldfield, 0 Emsley, 2871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5742 Ramachandran restraints generated. 2871 Oldfield, 0 Emsley, 2871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 118 time to evaluate : 0.827 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 644 GLU cc_start: 0.8917 (tp30) cc_final: 0.8651 (tp30) REVERT: A 850 GLN cc_start: 0.9507 (mt0) cc_final: 0.9222 (mt0) REVERT: A 943 GLU cc_start: 0.9085 (mt-10) cc_final: 0.8771 (mt-10) REVERT: A 997 MET cc_start: 0.8440 (mmt) cc_final: 0.8145 (mmm) REVERT: B 177 GLU cc_start: 0.8338 (OUTLIER) cc_final: 0.8066 (pm20) REVERT: B 300 MET cc_start: 0.8597 (ttp) cc_final: 0.8358 (ptm) REVERT: B 423 ASP cc_start: 0.9096 (OUTLIER) cc_final: 0.8834 (p0) REVERT: B 425 ILE cc_start: 0.9222 (mm) cc_final: 0.8787 (mt) REVERT: B 943 GLU cc_start: 0.8937 (mt-10) cc_final: 0.8454 (mm-30) REVERT: B 997 MET cc_start: 0.8281 (mpp) cc_final: 0.8077 (mmm) REVERT: B 1005 MET cc_start: 0.3934 (mmm) cc_final: 0.3693 (mmm) REVERT: C 177 GLU cc_start: 0.8281 (OUTLIER) cc_final: 0.7971 (pm20) REVERT: C 265 ASP cc_start: 0.9108 (m-30) cc_final: 0.8796 (m-30) REVERT: C 423 ASP cc_start: 0.9031 (OUTLIER) cc_final: 0.8689 (p0) REVERT: C 425 ILE cc_start: 0.9188 (mm) cc_final: 0.8834 (mt) REVERT: C 634 GLU cc_start: 0.9360 (pt0) cc_final: 0.9125 (mt-10) REVERT: C 943 GLU cc_start: 0.9026 (mt-10) cc_final: 0.8592 (mm-30) outliers start: 38 outliers final: 26 residues processed: 146 average time/residue: 0.1274 time to fit residues: 31.9386 Evaluate side-chains 139 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 109 time to evaluate : 0.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 317 CYS Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 466 THR Chi-restraints excluded: chain A residue 645 SER Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 831 ASN Chi-restraints excluded: chain A residue 1029 ILE Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 177 GLU Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 423 ASP Chi-restraints excluded: chain B residue 652 LEU Chi-restraints excluded: chain B residue 805 ILE Chi-restraints excluded: chain B residue 831 ASN Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 177 GLU Chi-restraints excluded: chain C residue 268 SER Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain C residue 392 ILE Chi-restraints excluded: chain C residue 423 ASP Chi-restraints excluded: chain C residue 685 ARG Chi-restraints excluded: chain C residue 705 LEU Chi-restraints excluded: chain C residue 739 VAL Chi-restraints excluded: chain C residue 805 ILE Chi-restraints excluded: chain C residue 825 THR Chi-restraints excluded: chain C residue 831 ASN Chi-restraints excluded: chain C residue 912 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 225 optimal weight: 5.9990 chunk 192 optimal weight: 7.9990 chunk 35 optimal weight: 9.9990 chunk 281 optimal weight: 5.9990 chunk 102 optimal weight: 3.9990 chunk 224 optimal weight: 0.6980 chunk 123 optimal weight: 7.9990 chunk 149 optimal weight: 4.9990 chunk 180 optimal weight: 1.9990 chunk 177 optimal weight: 0.8980 chunk 201 optimal weight: 3.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 824 GLN A 831 ASN B 80 ASN B 824 GLN B 831 ASN ** B 845 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 824 GLN C 831 ASN ** C 956 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.095520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.060446 restraints weight = 61459.766| |-----------------------------------------------------------------------------| r_work (start): 0.2880 rms_B_bonded: 4.07 r_work: 0.2711 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.2711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.3295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 23982 Z= 0.191 Angle : 0.582 11.743 32826 Z= 0.300 Chirality : 0.046 0.208 4026 Planarity : 0.004 0.140 4041 Dihedral : 6.292 54.845 4791 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 1.64 % Allowed : 8.97 % Favored : 89.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.21 (0.16), residues: 2871 helix: 1.87 (0.21), residues: 663 sheet: 0.33 (0.20), residues: 609 loop : -0.67 (0.16), residues: 1599 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C 685 TYR 0.016 0.001 TYR A 550 PHE 0.036 0.001 PHE B 769 TRP 0.005 0.001 TRP C 419 HIS 0.008 0.001 HIS A 345 Details of bonding type rmsd covalent geometry : bond 0.00428 (23862) covalent geometry : angle 0.56550 (32505) SS BOND : bond 0.00284 ( 39) SS BOND : angle 1.01291 ( 78) hydrogen bonds : bond 0.04107 ( 946) hydrogen bonds : angle 5.55847 ( 2700) link_ALPHA1-2 : bond 0.01527 ( 3) link_ALPHA1-2 : angle 2.15987 ( 9) link_ALPHA1-3 : bond 0.00589 ( 6) link_ALPHA1-3 : angle 2.75659 ( 18) link_ALPHA1-6 : bond 0.00338 ( 3) link_ALPHA1-6 : angle 1.48879 ( 9) link_BETA1-4 : bond 0.00376 ( 21) link_BETA1-4 : angle 1.48544 ( 63) link_NAG-ASN : bond 0.00258 ( 48) link_NAG-ASN : angle 1.43387 ( 144) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5742 Ramachandran restraints generated. 2871 Oldfield, 0 Emsley, 2871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5742 Ramachandran restraints generated. 2871 Oldfield, 0 Emsley, 2871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 115 time to evaluate : 0.822 Fit side-chains revert: symmetry clash REVERT: A 644 GLU cc_start: 0.8894 (tp30) cc_final: 0.8632 (tp30) REVERT: A 850 GLN cc_start: 0.9494 (mt0) cc_final: 0.9201 (mt0) REVERT: A 943 GLU cc_start: 0.9077 (mt-10) cc_final: 0.8776 (mt-10) REVERT: A 997 MET cc_start: 0.8373 (mmt) cc_final: 0.8057 (mmm) REVERT: B 177 GLU cc_start: 0.8337 (OUTLIER) cc_final: 0.8102 (pm20) REVERT: B 300 MET cc_start: 0.8634 (ttp) cc_final: 0.8403 (ptm) REVERT: B 423 ASP cc_start: 0.9065 (p0) cc_final: 0.8807 (p0) REVERT: B 425 ILE cc_start: 0.9220 (mm) cc_final: 0.8782 (mt) REVERT: B 779 TYR cc_start: 0.9126 (m-80) cc_final: 0.8811 (m-10) REVERT: B 798 PHE cc_start: 0.9149 (t80) cc_final: 0.8753 (t80) REVERT: B 943 GLU cc_start: 0.8907 (mt-10) cc_final: 0.8430 (mm-30) REVERT: B 997 MET cc_start: 0.8211 (mpp) cc_final: 0.7989 (mmm) REVERT: B 1005 MET cc_start: 0.3795 (mmm) cc_final: 0.3545 (mmm) REVERT: C 177 GLU cc_start: 0.8264 (OUTLIER) cc_final: 0.7978 (pm20) REVERT: C 265 ASP cc_start: 0.9115 (m-30) cc_final: 0.8795 (m-30) REVERT: C 423 ASP cc_start: 0.9016 (OUTLIER) cc_final: 0.8692 (p0) REVERT: C 634 GLU cc_start: 0.9354 (pt0) cc_final: 0.9131 (mt-10) REVERT: C 943 GLU cc_start: 0.9017 (mt-10) cc_final: 0.8607 (mm-30) outliers start: 41 outliers final: 29 residues processed: 145 average time/residue: 0.1290 time to fit residues: 32.2939 Evaluate side-chains 143 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 111 time to evaluate : 0.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 268 SER Chi-restraints excluded: chain A residue 300 MET Chi-restraints excluded: chain A residue 317 CYS Chi-restraints excluded: chain A residue 466 THR Chi-restraints excluded: chain A residue 645 SER Chi-restraints excluded: chain A residue 651 MET Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 1019 VAL Chi-restraints excluded: chain A residue 1029 ILE Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 177 GLU Chi-restraints excluded: chain B residue 268 SER Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 652 LEU Chi-restraints excluded: chain B residue 805 ILE Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 177 GLU Chi-restraints excluded: chain C residue 268 SER Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain C residue 392 ILE Chi-restraints excluded: chain C residue 423 ASP Chi-restraints excluded: chain C residue 685 ARG Chi-restraints excluded: chain C residue 705 LEU Chi-restraints excluded: chain C residue 739 VAL Chi-restraints excluded: chain C residue 805 ILE Chi-restraints excluded: chain C residue 825 THR Chi-restraints excluded: chain C residue 831 ASN Chi-restraints excluded: chain C residue 912 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 123 optimal weight: 10.0000 chunk 200 optimal weight: 5.9990 chunk 169 optimal weight: 7.9990 chunk 63 optimal weight: 0.9980 chunk 255 optimal weight: 1.9990 chunk 122 optimal weight: 0.9990 chunk 59 optimal weight: 0.9990 chunk 88 optimal weight: 5.9990 chunk 85 optimal weight: 0.9990 chunk 2 optimal weight: 5.9990 chunk 37 optimal weight: 0.9990 overall best weight: 0.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 831 ASN ** B 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 498 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 831 ASN B 845 ASN C 824 GLN C 831 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.096986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.062402 restraints weight = 62047.519| |-----------------------------------------------------------------------------| r_work (start): 0.2912 rms_B_bonded: 4.08 r_work: 0.2742 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.2742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.3452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 23982 Z= 0.121 Angle : 0.554 11.273 32826 Z= 0.286 Chirality : 0.045 0.211 4026 Planarity : 0.004 0.111 4041 Dihedral : 6.081 57.590 4791 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 1.32 % Allowed : 9.25 % Favored : 89.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.31 (0.16), residues: 2871 helix: 1.91 (0.21), residues: 666 sheet: 0.43 (0.19), residues: 699 loop : -0.68 (0.16), residues: 1506 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 685 TYR 0.020 0.001 TYR B 296 PHE 0.023 0.001 PHE B 769 TRP 0.004 0.001 TRP C 83 HIS 0.016 0.001 HIS B 297 Details of bonding type rmsd covalent geometry : bond 0.00263 (23862) covalent geometry : angle 0.53775 (32505) SS BOND : bond 0.00230 ( 39) SS BOND : angle 0.90484 ( 78) hydrogen bonds : bond 0.03868 ( 946) hydrogen bonds : angle 5.45950 ( 2700) link_ALPHA1-2 : bond 0.01514 ( 3) link_ALPHA1-2 : angle 2.51467 ( 9) link_ALPHA1-3 : bond 0.00809 ( 6) link_ALPHA1-3 : angle 2.66344 ( 18) link_ALPHA1-6 : bond 0.00574 ( 3) link_ALPHA1-6 : angle 1.33670 ( 9) link_BETA1-4 : bond 0.00446 ( 21) link_BETA1-4 : angle 1.43586 ( 63) link_NAG-ASN : bond 0.00170 ( 48) link_NAG-ASN : angle 1.35513 ( 144) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5742 Ramachandran restraints generated. 2871 Oldfield, 0 Emsley, 2871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5742 Ramachandran restraints generated. 2871 Oldfield, 0 Emsley, 2871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 120 time to evaluate : 0.850 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 644 GLU cc_start: 0.8872 (tp30) cc_final: 0.8611 (tp30) REVERT: A 850 GLN cc_start: 0.9464 (mt0) cc_final: 0.9122 (mt0) REVERT: A 943 GLU cc_start: 0.9062 (mt-10) cc_final: 0.8746 (mt-10) REVERT: A 997 MET cc_start: 0.8361 (mmt) cc_final: 0.8038 (mmm) REVERT: B 177 GLU cc_start: 0.8308 (OUTLIER) cc_final: 0.8073 (pm20) REVERT: B 300 MET cc_start: 0.8569 (ttp) cc_final: 0.8331 (ptm) REVERT: B 425 ILE cc_start: 0.9239 (mm) cc_final: 0.8810 (mt) REVERT: B 779 TYR cc_start: 0.9120 (m-80) cc_final: 0.8799 (m-10) REVERT: B 802 MET cc_start: 0.9391 (mmm) cc_final: 0.9093 (tpp) REVERT: B 943 GLU cc_start: 0.8906 (mt-10) cc_final: 0.8449 (mm-30) REVERT: B 997 MET cc_start: 0.8261 (mpp) cc_final: 0.8045 (mmm) REVERT: B 1005 MET cc_start: 0.3784 (mmm) cc_final: 0.3529 (mmm) REVERT: C 177 GLU cc_start: 0.8302 (OUTLIER) cc_final: 0.8009 (pm20) REVERT: C 265 ASP cc_start: 0.9109 (m-30) cc_final: 0.8779 (m-30) REVERT: C 423 ASP cc_start: 0.9004 (OUTLIER) cc_final: 0.8747 (p0) REVERT: C 802 MET cc_start: 0.9414 (mmm) cc_final: 0.8953 (tpp) REVERT: C 890 ASN cc_start: 0.9441 (m-40) cc_final: 0.9069 (m110) REVERT: C 937 ILE cc_start: 0.8904 (mm) cc_final: 0.8669 (tp) REVERT: C 943 GLU cc_start: 0.9023 (mt-10) cc_final: 0.8613 (mm-30) outliers start: 33 outliers final: 23 residues processed: 144 average time/residue: 0.1249 time to fit residues: 31.0363 Evaluate side-chains 139 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 113 time to evaluate : 0.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 317 CYS Chi-restraints excluded: chain A residue 466 THR Chi-restraints excluded: chain A residue 645 SER Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 990 TYR Chi-restraints excluded: chain A residue 1019 VAL Chi-restraints excluded: chain B residue 177 GLU Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 805 ILE Chi-restraints excluded: chain B residue 831 ASN Chi-restraints excluded: chain C residue 177 GLU Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain C residue 392 ILE Chi-restraints excluded: chain C residue 423 ASP Chi-restraints excluded: chain C residue 685 ARG Chi-restraints excluded: chain C residue 705 LEU Chi-restraints excluded: chain C residue 734 MET Chi-restraints excluded: chain C residue 739 VAL Chi-restraints excluded: chain C residue 805 ILE Chi-restraints excluded: chain C residue 825 THR Chi-restraints excluded: chain C residue 831 ASN Chi-restraints excluded: chain C residue 912 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 193 optimal weight: 3.9990 chunk 36 optimal weight: 9.9990 chunk 111 optimal weight: 3.9990 chunk 69 optimal weight: 10.0000 chunk 58 optimal weight: 0.7980 chunk 282 optimal weight: 3.9990 chunk 255 optimal weight: 5.9990 chunk 16 optimal weight: 2.9990 chunk 256 optimal weight: 0.9980 chunk 102 optimal weight: 6.9990 chunk 275 optimal weight: 6.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 831 ASN ** B 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 498 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 831 ASN ** C 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 831 ASN ** C 956 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 = 0.3608 r_free = 0.3608 target = 0.095622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.060688 restraints weight = 61630.986| |-----------------------------------------------------------------------------| r_work (start): 0.2879 rms_B_bonded: 4.04 r_work: 0.2709 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.2709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.3481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 23982 Z= 0.208 Angle : 0.586 10.549 32826 Z= 0.303 Chirality : 0.046 0.205 4026 Planarity : 0.004 0.101 4041 Dihedral : 6.111 59.061 4791 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.32 % Allowed : 9.42 % Favored : 89.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.25 (0.16), residues: 2871 helix: 1.92 (0.21), residues: 666 sheet: 0.31 (0.19), residues: 615 loop : -0.66 (0.16), residues: 1590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 685 TYR 0.020 0.001 TYR A 296 PHE 0.022 0.001 PHE B 769 TRP 0.005 0.001 TRP A 360 HIS 0.014 0.002 HIS A 297 Details of bonding type rmsd covalent geometry : bond 0.00467 (23862) covalent geometry : angle 0.57040 (32505) SS BOND : bond 0.00283 ( 39) SS BOND : angle 1.00176 ( 78) hydrogen bonds : bond 0.04016 ( 946) hydrogen bonds : angle 5.48846 ( 2700) link_ALPHA1-2 : bond 0.01351 ( 3) link_ALPHA1-2 : angle 2.18678 ( 9) link_ALPHA1-3 : bond 0.00533 ( 6) link_ALPHA1-3 : angle 2.72510 ( 18) link_ALPHA1-6 : bond 0.00337 ( 3) link_ALPHA1-6 : angle 1.55373 ( 9) link_BETA1-4 : bond 0.00393 ( 21) link_BETA1-4 : angle 1.45130 ( 63) link_NAG-ASN : bond 0.00277 ( 48) link_NAG-ASN : angle 1.41293 ( 144) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5742 Ramachandran restraints generated. 2871 Oldfield, 0 Emsley, 2871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5742 Ramachandran restraints generated. 2871 Oldfield, 0 Emsley, 2871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 109 time to evaluate : 0.929 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 644 GLU cc_start: 0.8887 (tp30) cc_final: 0.8629 (tp30) REVERT: A 779 TYR cc_start: 0.9090 (m-80) cc_final: 0.8779 (m-10) REVERT: A 850 GLN cc_start: 0.9530 (mt0) cc_final: 0.9262 (mt0) REVERT: A 943 GLU cc_start: 0.9091 (mt-10) cc_final: 0.8776 (mt-10) REVERT: A 997 MET cc_start: 0.8413 (mmt) cc_final: 0.8098 (mmm) REVERT: B 177 GLU cc_start: 0.8298 (OUTLIER) cc_final: 0.8056 (pm20) REVERT: B 425 ILE cc_start: 0.9157 (mm) cc_final: 0.8723 (mt) REVERT: B 779 TYR cc_start: 0.9145 (m-80) cc_final: 0.8846 (m-10) REVERT: B 802 MET cc_start: 0.9365 (mmm) cc_final: 0.8975 (tpp) REVERT: B 943 GLU cc_start: 0.8919 (mt-10) cc_final: 0.8430 (mm-30) REVERT: B 997 MET cc_start: 0.8181 (mpp) cc_final: 0.7957 (mmm) REVERT: B 1005 MET cc_start: 0.3752 (mmm) cc_final: 0.3496 (mmm) REVERT: C 177 GLU cc_start: 0.8301 (OUTLIER) cc_final: 0.8058 (pm20) REVERT: C 265 ASP cc_start: 0.9147 (m-30) cc_final: 0.8812 (m-30) REVERT: C 423 ASP cc_start: 0.8980 (OUTLIER) cc_final: 0.8679 (p0) REVERT: C 943 GLU cc_start: 0.9027 (mt-10) cc_final: 0.8621 (mm-30) outliers start: 33 outliers final: 27 residues processed: 133 average time/residue: 0.1235 time to fit residues: 28.6355 Evaluate side-chains 139 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 109 time to evaluate : 0.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 268 SER Chi-restraints excluded: chain A residue 317 CYS Chi-restraints excluded: chain A residue 466 THR Chi-restraints excluded: chain A residue 645 SER Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 831 ASN Chi-restraints excluded: chain A residue 990 TYR Chi-restraints excluded: chain A residue 1019 VAL Chi-restraints excluded: chain B residue 177 GLU Chi-restraints excluded: chain B residue 268 SER Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 652 LEU Chi-restraints excluded: chain B residue 805 ILE Chi-restraints excluded: chain C residue 177 GLU Chi-restraints excluded: chain C residue 297 HIS Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain C residue 392 ILE Chi-restraints excluded: chain C residue 423 ASP Chi-restraints excluded: chain C residue 685 ARG Chi-restraints excluded: chain C residue 705 LEU Chi-restraints excluded: chain C residue 734 MET Chi-restraints excluded: chain C residue 739 VAL Chi-restraints excluded: chain C residue 805 ILE Chi-restraints excluded: chain C residue 825 THR Chi-restraints excluded: chain C residue 831 ASN Chi-restraints excluded: chain C residue 912 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 59 optimal weight: 0.0870 chunk 52 optimal weight: 20.0000 chunk 261 optimal weight: 0.4980 chunk 201 optimal weight: 4.9990 chunk 171 optimal weight: 4.9990 chunk 173 optimal weight: 0.9980 chunk 241 optimal weight: 0.9990 chunk 113 optimal weight: 10.0000 chunk 93 optimal weight: 9.9990 chunk 139 optimal weight: 2.9990 chunk 233 optimal weight: 0.9990 overall best weight: 0.7162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 498 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 831 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 956 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.095737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.060753 restraints weight = 61073.240| |-----------------------------------------------------------------------------| r_work (start): 0.2883 rms_B_bonded: 4.03 r_work: 0.2712 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.2712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.3483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.173 23982 Z= 0.209 Angle : 0.738 59.200 32826 Z= 0.418 Chirality : 0.046 0.638 4026 Planarity : 0.005 0.127 4041 Dihedral : 6.114 59.051 4791 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.08 % Allowed : 9.58 % Favored : 89.34 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.16), residues: 2871 helix: 1.91 (0.21), residues: 666 sheet: 0.31 (0.19), residues: 615 loop : -0.66 (0.16), residues: 1590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 685 TYR 0.019 0.001 TYR A 296 PHE 0.020 0.001 PHE B 769 TRP 0.005 0.001 TRP C 419 HIS 0.011 0.002 HIS A 297 Details of bonding type rmsd covalent geometry : bond 0.00446 (23862) covalent geometry : angle 0.72713 (32505) SS BOND : bond 0.00242 ( 39) SS BOND : angle 0.98202 ( 78) hydrogen bonds : bond 0.03995 ( 946) hydrogen bonds : angle 5.49776 ( 2700) link_ALPHA1-2 : bond 0.01424 ( 3) link_ALPHA1-2 : angle 2.20873 ( 9) link_ALPHA1-3 : bond 0.00545 ( 6) link_ALPHA1-3 : angle 2.72712 ( 18) link_ALPHA1-6 : bond 0.00329 ( 3) link_ALPHA1-6 : angle 1.54629 ( 9) link_BETA1-4 : bond 0.00367 ( 21) link_BETA1-4 : angle 1.46350 ( 63) link_NAG-ASN : bond 0.00265 ( 48) link_NAG-ASN : angle 1.41707 ( 144) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5063.98 seconds wall clock time: 87 minutes 48.61 seconds (5268.61 seconds total)