Starting phenix.real_space_refine on Sun Sep 13 13:28:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6u7h_20668/09_2026/6u7h_20668.cif Found real_map, /net/cci-nas-00/data/ceres_data/6u7h_20668/09_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_20668/09_2026/6u7h_20668.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6u7h_20668/09_2026/6u7h_20668.map" model { file = "/net/cci-nas-00/data/ceres_data/6u7h_20668/09_2026/6u7h_20668.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6u7h_20668/09_2026/6u7h_20668.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6u7h_20668/09_2026/6u7h_20668.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6u7h_20668/09_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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/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 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 chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 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 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 chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 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 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 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 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 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 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 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 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 chiralities: 11 Time building chain proxies: 4.28, per 1000 atoms: 0.18 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: 2.00 Conformation dependent library (CDL) restraints added in 859.5 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: 0.75 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: 5.20 Time building geometry restraints manager: 2.61 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 - 17.43: 12373 17.43 - 34.86: 902 34.86 - 52.29: 141 52.29 - 69.72: 24 69.72 - 87.15: 36 Dihedral angle restraints: 13476 sinusoidal: 5064 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 13473 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: 1.450 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: 0.010 Extract box with map and model: 0.360 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 20.710 Find NCS groups from input model: 0.580 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 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 : 13.268 87.151 7977 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/Z covalent geometry : bond 0.01327 / 0.77 (23862) covalent geometry : angle 1.78204 / 1.17 (32505) SS BOND : bond 0.01924 / 1.27 ( 39) SS BOND : angle 1.88897 / 1.32 ( 78) hydrogen bonds : bond 0.16488 / 10.71 ( 946) hydrogen bonds : angle 8.60239 / 5.95 ( 2700) link_ALPHA1-2 : bond 0.02266 / 1.14 ( 3) link_ALPHA1-2 : angle 5.06190 / 2.62 ( 9) link_ALPHA1-3 : bond 0.01494 / 0.78 ( 6) link_ALPHA1-3 : angle 4.70243 / 3.38 ( 18) link_ALPHA1-6 : bond 0.00573 / 0.29 ( 3) link_ALPHA1-6 : angle 5.08452 / 2.61 ( 9) link_BETA1-4 : bond 0.02067 / 1.38 ( 21) link_BETA1-4 : angle 3.75851 / 2.51 ( 63) link_NAG-ASN : bond 0.00725 / 0.44 ( 48) link_NAG-ASN : angle 3.94948 / 2.75 ( 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 : 0.950 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: 0.1618 time to fit residues: 66.0916 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 : 0.958 ------------------------------------------------------------------------------- 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... 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 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 C 200 HIS C 365 ASN C 731 ASN C 778 ASN C 824 GLN C 831 ASN C 850 GLN C 933 HIS Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.096000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.060739 restraints weight = 61511.699| |-----------------------------------------------------------------------------| r_work (start): 0.2884 rms_B_bonded: 4.11 r_work: 0.2713 rms_B_bonded: 4.38 restraints_weight: 0.5000 r_work (final): 0.2713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.1785 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 : 0.700 7.089 32826 Z= 0.377 Chirality : 0.049 0.244 4026 Planarity : 0.004 0.038 4041 Dihedral : 6.934 32.088 3129 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 1.12 % Allowed : 5.21 % Favored : 93.67 % 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: 0.06 (0.15), residues: 2871 helix: 1.12 (0.20), residues: 663 sheet: 0.79 (0.20), residues: 609 loop : -0.72 (0.15), residues: 1599 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 72 TYR 0.023 0.002 TYR A 957 PHE 0.021 0.002 PHE B 379 TRP 0.016 0.002 TRP C 588 HIS 0.003 0.001 HIS C 345 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.16 (23862) covalent geometry : angle 0.67738 / 0.37 (32505) SS BOND : bond 0.00369 / 0.22 ( 39) SS BOND : angle 1.17825 / 0.82 ( 78) hydrogen bonds : bond 0.05633 / 3.63 ( 946) hydrogen bonds : angle 6.41456 / 4.41 ( 2700) link_ALPHA1-2 : bond 0.01608 / 0.81 ( 3) link_ALPHA1-2 : angle 2.61057 / 1.34 ( 9) link_ALPHA1-3 : bond 0.00635 / 0.35 ( 6) link_ALPHA1-3 : angle 2.64559 / 1.85 ( 18) link_ALPHA1-6 : bond 0.00099 / 0.05 ( 3) link_ALPHA1-6 : angle 1.75517 / 0.89 ( 9) link_BETA1-4 : bond 0.00621 / 0.36 ( 21) link_BETA1-4 : angle 1.84454 / 1.25 ( 63) link_NAG-ASN : bond 0.00357 / 0.27 ( 48) link_NAG-ASN : angle 2.07620 / 1.46 ( 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 188 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 160 time to evaluate : 0.878 Fit side-chains REVERT: A 890 ASN cc_start: 0.9436 (m-40) cc_final: 0.9174 (m110) REVERT: A 943 GLU cc_start: 0.8828 (mt-10) cc_final: 0.8362 (mt-10) REVERT: A 997 MET cc_start: 0.8555 (mmt) cc_final: 0.8193 (mmm) REVERT: B 644 GLU cc_start: 0.9040 (mm-30) cc_final: 0.8803 (tp30) REVERT: B 997 MET cc_start: 0.8502 (mpp) cc_final: 0.8059 (mmm) REVERT: C 265 ASP cc_start: 0.8967 (m-30) cc_final: 0.8745 (m-30) REVERT: C 890 ASN cc_start: 0.9451 (m-40) cc_final: 0.9038 (m110) REVERT: C 943 GLU cc_start: 0.8793 (mt-10) cc_final: 0.8561 (mt-10) REVERT: C 997 MET cc_start: 0.8605 (mpp) cc_final: 0.8209 (mmm) outliers start: 28 outliers final: 14 residues processed: 182 average time/residue: 0.1407 time to fit residues: 43.8141 Evaluate side-chains 128 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 114 time to evaluate : 0.921 ------------------------------------------------------------------------------- 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 780 VAL Chi-restraints excluded: chain A residue 831 ASN 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 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: 0.7980 chunk 272 optimal weight: 3.9990 chunk 160 optimal weight: 8.9990 chunk 148 optimal weight: 30.0000 chunk 90 optimal weight: 30.0000 chunk 262 optimal weight: 8.9990 chunk 69 optimal weight: 7.9990 chunk 138 optimal weight: 3.9990 chunk 133 optimal weight: 0.0670 chunk 94 optimal weight: 7.9990 chunk 40 optimal weight: 5.9990 overall best weight: 2.9724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 831 ASN A 956 GLN A1020 ASN ** B 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 831 ASN B 956 GLN B1020 ASN C 831 ASN C1020 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.094508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.059325 restraints weight = 61988.794| |-----------------------------------------------------------------------------| r_work (start): 0.2853 rms_B_bonded: 4.07 r_work: 0.2683 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.2683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.2283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 23982 Z= 0.241 Angle : 0.656 8.291 32826 Z= 0.347 Chirality : 0.047 0.239 4026 Planarity : 0.004 0.039 4041 Dihedral : 6.181 28.253 3129 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 1.32 % Allowed : 6.25 % Favored : 92.43 % 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: 0.18 (0.16), residues: 2871 helix: 1.54 (0.21), residues: 654 sheet: 0.50 (0.19), residues: 675 loop : -0.66 (0.16), residues: 1542 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 685 TYR 0.021 0.002 TYR A 550 PHE 0.017 0.002 PHE B 379 TRP 0.008 0.001 TRP B 963 HIS 0.006 0.002 HIS C 846 Details of bonding type rmsd/Z covalent geometry : bond 0.00542 / 0.24 (23862) covalent geometry : angle 0.63786 / 0.34 (32505) SS BOND : bond 0.00402 / 0.23 ( 39) SS BOND : angle 1.08184 / 0.77 ( 78) hydrogen bonds : bond 0.05043 / 3.25 ( 946) hydrogen bonds : angle 6.07579 / 4.18 ( 2700) link_ALPHA1-2 : bond 0.00884 / 0.44 ( 3) link_ALPHA1-2 : angle 2.15233 / 1.10 ( 9) link_ALPHA1-3 : bond 0.00320 / 0.15 ( 6) link_ALPHA1-3 : angle 2.41056 / 1.64 ( 18) link_ALPHA1-6 : bond 0.00333 / 0.17 ( 3) link_ALPHA1-6 : angle 1.87733 / 0.94 ( 9) link_BETA1-4 : bond 0.00416 / 0.23 ( 21) link_BETA1-4 : angle 1.51651 / 1.04 ( 63) link_NAG-ASN : bond 0.00398 / 0.28 ( 48) link_NAG-ASN : angle 1.81438 / 1.27 ( 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 152 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 119 time to evaluate : 0.819 Fit side-chains REVERT: A 802 MET cc_start: 0.9492 (tpp) cc_final: 0.9154 (tpp) REVERT: A 943 GLU cc_start: 0.8969 (mt-10) cc_final: 0.8457 (mt-10) REVERT: A 990 TYR cc_start: 0.8640 (t80) cc_final: 0.8279 (t80) REVERT: A 997 MET cc_start: 0.8428 (mmt) cc_final: 0.8111 (mmm) REVERT: B 423 ASP cc_start: 0.9308 (OUTLIER) cc_final: 0.9020 (p0) REVERT: B 943 GLU cc_start: 0.8911 (mt-10) cc_final: 0.8611 (mt-10) REVERT: B 997 MET cc_start: 0.8278 (mpp) cc_final: 0.8077 (mmm) REVERT: C 265 ASP cc_start: 0.9062 (m-30) cc_final: 0.8800 (m-30) REVERT: C 300 MET cc_start: 0.8257 (ttm) cc_final: 0.8057 (ttm) REVERT: C 423 ASP cc_start: 0.9157 (p0) cc_final: 0.8753 (p0) REVERT: C 802 MET cc_start: 0.9453 (tpp) cc_final: 0.9186 (tpp) REVERT: C 890 ASN cc_start: 0.9466 (m-40) cc_final: 0.9107 (m110) outliers start: 33 outliers final: 14 residues processed: 148 average time/residue: 0.1415 time to fit residues: 35.7641 Evaluate side-chains 121 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 106 time to evaluate : 0.882 ------------------------------------------------------------------------------- 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 453 ASP Chi-restraints excluded: chain A residue 645 SER 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: 0.6980 chunk 83 optimal weight: 5.9990 chunk 274 optimal weight: 0.6980 chunk 120 optimal weight: 0.0270 chunk 47 optimal weight: 5.9990 chunk 107 optimal weight: 0.6980 chunk 134 optimal weight: 9.9990 chunk 35 optimal weight: 9.9990 chunk 206 optimal weight: 4.9990 chunk 171 optimal weight: 0.8980 chunk 98 optimal weight: 0.6980 overall best weight: 0.5638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 831 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 831 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 956 GLN ** C 831 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.096555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.062043 restraints weight = 61512.119| |-----------------------------------------------------------------------------| r_work (start): 0.2920 rms_B_bonded: 4.04 r_work: 0.2751 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.2751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.2727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 23982 Z= 0.111 Angle : 0.566 11.174 32826 Z= 0.299 Chirality : 0.045 0.219 4026 Planarity : 0.004 0.039 4041 Dihedral : 5.470 21.948 3129 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 1.24 % Allowed : 7.33 % Favored : 91.43 % 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: 1.79 (0.20), residues: 666 sheet: 0.45 (0.19), residues: 681 loop : -0.69 (0.16), residues: 1524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 685 TYR 0.019 0.001 TYR B 957 PHE 0.020 0.001 PHE A 769 TRP 0.007 0.001 TRP C 588 HIS 0.003 0.001 HIS B 299 Details of bonding type rmsd/Z covalent geometry : bond 0.00225 / 0.11 (23862) covalent geometry : angle 0.54901 / 0.30 (32505) SS BOND : bond 0.00483 / 0.24 ( 39) SS BOND : angle 0.91440 / 0.63 ( 78) hydrogen bonds : bond 0.04221 / 2.73 ( 946) hydrogen bonds : angle 5.70188 / 3.94 ( 2700) link_ALPHA1-2 : bond 0.01161 / 0.58 ( 3) link_ALPHA1-2 : angle 2.25059 / 1.15 ( 9) link_ALPHA1-3 : bond 0.00668 / 0.37 ( 6) link_ALPHA1-3 : angle 2.43061 / 1.77 ( 18) link_ALPHA1-6 : bond 0.00025 / 0.01 ( 3) link_ALPHA1-6 : angle 1.55562 / 0.78 ( 9) link_BETA1-4 : bond 0.00472 / 0.29 ( 21) link_BETA1-4 : angle 1.41049 / 0.93 ( 63) link_NAG-ASN : bond 0.00217 / 0.13 ( 48) link_NAG-ASN : angle 1.55964 / 1.09 ( 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 179 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 148 time to evaluate : 0.865 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 635 ASP cc_start: 0.8802 (p0) cc_final: 0.8591 (p0) REVERT: A 644 GLU cc_start: 0.8974 (tp30) cc_final: 0.8730 (tp30) REVERT: A 802 MET cc_start: 0.9453 (tpp) cc_final: 0.9173 (tpp) REVERT: A 890 ASN cc_start: 0.9429 (m-40) cc_final: 0.9157 (m110) REVERT: A 943 GLU cc_start: 0.8953 (mt-10) cc_final: 0.8421 (mt-10) REVERT: A 997 MET cc_start: 0.8464 (mmt) cc_final: 0.8185 (mmm) REVERT: B 423 ASP cc_start: 0.9273 (p0) cc_final: 0.9006 (p0) REVERT: B 425 ILE cc_start: 0.9222 (mm) cc_final: 0.8855 (mt) REVERT: B 634 GLU cc_start: 0.9247 (pt0) cc_final: 0.8968 (pt0) REVERT: B 709 ASP cc_start: 0.8991 (p0) cc_final: 0.8785 (p0) REVERT: B 943 GLU cc_start: 0.8875 (mt-10) cc_final: 0.8590 (mt-10) REVERT: B 997 MET cc_start: 0.8200 (mpp) cc_final: 0.7976 (mmm) REVERT: B 1005 MET cc_start: 0.3837 (mmm) cc_final: 0.3616 (mmm) REVERT: C 265 ASP cc_start: 0.9033 (m-30) cc_final: 0.8771 (m-30) REVERT: C 423 ASP cc_start: 0.9125 (OUTLIER) cc_final: 0.8723 (p0) REVERT: C 425 ILE cc_start: 0.9247 (mm) cc_final: 0.8969 (mt) REVERT: C 644 GLU cc_start: 0.8991 (tp30) cc_final: 0.8642 (tp30) REVERT: C 890 ASN cc_start: 0.9421 (m-40) cc_final: 0.9041 (m-40) REVERT: C 943 GLU cc_start: 0.8825 (mt-10) cc_final: 0.8476 (mm-30) outliers start: 31 outliers final: 15 residues processed: 172 average time/residue: 0.1481 time to fit residues: 42.9314 Evaluate side-chains 135 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 119 time to evaluate : 0.920 ------------------------------------------------------------------------------- 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 645 SER Chi-restraints excluded: chain A residue 705 LEU Chi-restraints excluded: chain A residue 805 ILE 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 805 ILE Chi-restraints excluded: chain B residue 825 THR 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 825 THR 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: 0.8980 chunk 82 optimal weight: 0.5980 chunk 45 optimal weight: 0.0010 chunk 218 optimal weight: 6.9990 chunk 103 optimal weight: 5.9990 chunk 252 optimal weight: 6.9990 chunk 58 optimal weight: 3.9990 chunk 122 optimal weight: 6.9990 chunk 267 optimal weight: 2.9990 chunk 36 optimal weight: 9.9990 overall best weight: 1.6990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 299 HIS A 831 ASN ** B 498 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 831 ASN ** B 845 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 853 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 956 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 831 ASN ** C 853 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 956 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.095539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.060857 restraints weight = 61384.507| |-----------------------------------------------------------------------------| r_work (start): 0.2893 rms_B_bonded: 4.03 r_work: 0.2723 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.2723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.2913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 23982 Z= 0.155 Angle : 0.564 9.390 32826 Z= 0.296 Chirality : 0.045 0.214 4026 Planarity : 0.004 0.038 4041 Dihedral : 5.194 21.598 3126 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 1.40 % Allowed : 8.33 % Favored : 90.26 % 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: 0.28 (0.16), residues: 2871 helix: 1.93 (0.21), residues: 663 sheet: 0.35 (0.19), residues: 690 loop : -0.68 (0.16), residues: 1518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 685 TYR 0.027 0.001 TYR A 990 PHE 0.020 0.001 PHE B 769 TRP 0.005 0.001 TRP B 419 HIS 0.005 0.001 HIS B 846 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.15 (23862) covalent geometry : angle 0.54837 / 0.29 (32505) SS BOND : bond 0.00279 / 0.16 ( 39) SS BOND : angle 1.00582 / 0.67 ( 78) hydrogen bonds : bond 0.04169 / 2.69 ( 946) hydrogen bonds : angle 5.61659 / 3.87 ( 2700) link_ALPHA1-2 : bond 0.00870 / 0.44 ( 3) link_ALPHA1-2 : angle 2.06424 / 1.04 ( 9) link_ALPHA1-3 : bond 0.00351 / 0.17 ( 6) link_ALPHA1-3 : angle 2.30663 / 1.62 ( 18) link_ALPHA1-6 : bond 0.00218 / 0.11 ( 3) link_ALPHA1-6 : angle 1.70206 / 0.85 ( 9) link_BETA1-4 : bond 0.00342 / 0.21 ( 21) link_BETA1-4 : angle 1.33624 / 0.91 ( 63) link_NAG-ASN : bond 0.00238 / 0.17 ( 48) link_NAG-ASN : angle 1.47738 / 1.02 ( 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 154 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 119 time to evaluate : 0.892 Fit side-chains revert: symmetry clash REVERT: A 177 GLU cc_start: 0.8250 (OUTLIER) cc_final: 0.7951 (pm20) REVERT: A 644 GLU cc_start: 0.8943 (tp30) cc_final: 0.8732 (tp30) REVERT: A 943 GLU cc_start: 0.9040 (mt-10) cc_final: 0.8702 (mt-10) REVERT: A 997 MET cc_start: 0.8442 (mmt) cc_final: 0.8155 (mmm) REVERT: B 177 GLU cc_start: 0.8252 (OUTLIER) cc_final: 0.7946 (pm20) REVERT: B 423 ASP cc_start: 0.9199 (OUTLIER) cc_final: 0.8931 (p0) REVERT: B 425 ILE cc_start: 0.9235 (mm) cc_final: 0.8823 (mt) REVERT: B 644 GLU cc_start: 0.9067 (tp30) cc_final: 0.8716 (tp30) REVERT: B 709 ASP cc_start: 0.9003 (p0) cc_final: 0.8782 (p0) REVERT: B 943 GLU cc_start: 0.8940 (mt-10) cc_final: 0.8679 (mt-10) REVERT: B 997 MET cc_start: 0.8175 (mpp) cc_final: 0.7971 (mmm) REVERT: B 1005 MET cc_start: 0.3904 (mmm) cc_final: 0.3648 (mmm) REVERT: C 177 GLU cc_start: 0.8273 (OUTLIER) cc_final: 0.7960 (pm20) REVERT: C 265 ASP cc_start: 0.9075 (m-30) cc_final: 0.8796 (m-30) REVERT: C 300 MET cc_start: 0.8243 (ttm) cc_final: 0.7917 (ttm) REVERT: C 423 ASP cc_start: 0.9112 (OUTLIER) cc_final: 0.8727 (p0) REVERT: C 425 ILE cc_start: 0.9217 (mm) cc_final: 0.8896 (mt) REVERT: C 802 MET cc_start: 0.9394 (mmm) cc_final: 0.9023 (tpp) REVERT: C 890 ASN cc_start: 0.9440 (m-40) cc_final: 0.9079 (m110) REVERT: C 943 GLU cc_start: 0.8913 (mt-10) cc_final: 0.8528 (mm-30) outliers start: 35 outliers final: 20 residues processed: 145 average time/residue: 0.1407 time to fit residues: 35.0399 Evaluate side-chains 137 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 112 time to evaluate : 0.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 177 GLU 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 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 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 831 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 176 optimal weight: 1.9990 chunk 108 optimal weight: 0.9990 chunk 29 optimal weight: 9.9990 chunk 34 optimal weight: 10.0000 chunk 23 optimal weight: 3.9990 chunk 74 optimal weight: 0.0070 chunk 36 optimal weight: 6.9990 chunk 33 optimal weight: 2.9990 chunk 153 optimal weight: 0.9980 chunk 109 optimal weight: 1.9990 chunk 210 optimal weight: 6.9990 overall best weight: 1.2004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 831 ASN B 299 HIS ** B 498 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 831 ASN ** B 845 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 831 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.096101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.061475 restraints weight = 61150.919| |-----------------------------------------------------------------------------| r_work (start): 0.2905 rms_B_bonded: 4.02 r_work: 0.2735 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.2735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.3052 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= 0.126 Angle : 0.540 8.291 32826 Z= 0.285 Chirality : 0.044 0.212 4026 Planarity : 0.004 0.038 4041 Dihedral : 5.021 20.036 3126 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.32 % Allowed : 8.49 % Favored : 90.18 % 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: 0.29 (0.16), residues: 2871 helix: 1.96 (0.21), residues: 663 sheet: 0.39 (0.19), residues: 702 loop : -0.70 (0.16), residues: 1506 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 689 TYR 0.015 0.001 TYR A 990 PHE 0.015 0.001 PHE A 798 TRP 0.004 0.001 TRP B 419 HIS 0.005 0.001 HIS B 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.13 (23862) covalent geometry : angle 0.52518 / 0.28 (32505) SS BOND : bond 0.00252 / 0.14 ( 39) SS BOND : angle 0.94112 / 0.63 ( 78) hydrogen bonds : bond 0.04042 / 2.61 ( 946) hydrogen bonds : angle 5.53120 / 3.81 ( 2700) link_ALPHA1-2 : bond 0.00986 / 0.50 ( 3) link_ALPHA1-2 : angle 2.06717 / 1.05 ( 9) link_ALPHA1-3 : bond 0.00435 / 0.22 ( 6) link_ALPHA1-3 : angle 2.32833 / 1.67 ( 18) link_ALPHA1-6 : bond 0.00113 / 0.06 ( 3) link_ALPHA1-6 : angle 1.61232 / 0.80 ( 9) link_BETA1-4 : bond 0.00376 / 0.23 ( 21) link_BETA1-4 : angle 1.30671 / 0.88 ( 63) link_NAG-ASN : bond 0.00177 / 0.12 ( 48) link_NAG-ASN : angle 1.39673 / 0.97 ( 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 158 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 125 time to evaluate : 0.846 Fit side-chains revert: symmetry clash REVERT: A 850 GLN cc_start: 0.9432 (mt0) cc_final: 0.9154 (mt0) REVERT: A 943 GLU cc_start: 0.9043 (mt-10) cc_final: 0.8699 (mt-10) REVERT: A 997 MET cc_start: 0.8386 (mmt) cc_final: 0.8089 (mmm) REVERT: B 177 GLU cc_start: 0.8265 (OUTLIER) cc_final: 0.7965 (pm20) REVERT: B 423 ASP cc_start: 0.9131 (p0) cc_final: 0.8863 (p0) REVERT: B 425 ILE cc_start: 0.9230 (mm) cc_final: 0.8801 (mt) REVERT: B 709 ASP cc_start: 0.8976 (p0) cc_final: 0.8765 (p0) REVERT: B 943 GLU cc_start: 0.8979 (mt-10) cc_final: 0.8690 (mt-10) REVERT: B 997 MET cc_start: 0.8112 (mpp) cc_final: 0.7881 (mmm) REVERT: B 1005 MET cc_start: 0.3818 (mmm) cc_final: 0.3547 (mmm) REVERT: C 177 GLU cc_start: 0.8274 (OUTLIER) cc_final: 0.7954 (pm20) REVERT: C 265 ASP cc_start: 0.9088 (m-30) cc_final: 0.8800 (m-30) REVERT: C 300 MET cc_start: 0.8255 (ttm) cc_final: 0.7907 (ttm) REVERT: C 423 ASP cc_start: 0.9059 (OUTLIER) cc_final: 0.8666 (p0) REVERT: C 802 MET cc_start: 0.9360 (mmm) cc_final: 0.8971 (tpp) REVERT: C 890 ASN cc_start: 0.9430 (m-40) cc_final: 0.9059 (m110) REVERT: C 943 GLU cc_start: 0.8923 (mt-10) cc_final: 0.8545 (mm-30) outliers start: 33 outliers final: 19 residues processed: 149 average time/residue: 0.1375 time to fit residues: 35.7324 Evaluate side-chains 134 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 112 time to evaluate : 0.833 ------------------------------------------------------------------------------- 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 645 SER Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 805 ILE 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 805 ILE Chi-restraints excluded: chain B residue 825 THR Chi-restraints excluded: chain B residue 912 GLN 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 652 LEU Chi-restraints excluded: chain C residue 705 LEU 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: 3.9990 chunk 282 optimal weight: 0.9980 chunk 220 optimal weight: 9.9990 chunk 54 optimal weight: 0.9980 chunk 256 optimal weight: 7.9990 chunk 43 optimal weight: 5.9990 chunk 180 optimal weight: 5.9990 chunk 116 optimal weight: 0.0970 chunk 40 optimal weight: 0.8980 chunk 105 optimal weight: 7.9990 chunk 70 optimal weight: 6.9990 overall best weight: 1.3980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 831 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 853 GLN ** B 498 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 831 ASN B 845 ASN C 831 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.096203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.061472 restraints weight = 61209.420| |-----------------------------------------------------------------------------| r_work (start): 0.2904 rms_B_bonded: 4.03 r_work: 0.2735 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.2735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 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 : 0.003 0.037 23982 Z= 0.135 Angle : 0.536 7.687 32826 Z= 0.283 Chirality : 0.044 0.210 4026 Planarity : 0.004 0.041 4041 Dihedral : 4.892 23.564 3126 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.16 % Allowed : 8.81 % Favored : 90.02 % 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: 0.37 (0.16), residues: 2871 helix: 1.99 (0.21), residues: 663 sheet: 0.38 (0.19), residues: 732 loop : -0.62 (0.17), residues: 1476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 72 TYR 0.014 0.001 TYR C 957 PHE 0.022 0.001 PHE A 798 TRP 0.004 0.001 TRP A 419 HIS 0.003 0.001 HIS C 846 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 (23862) covalent geometry : angle 0.52136 / 0.28 (32505) SS BOND : bond 0.00251 / 0.14 ( 39) SS BOND : angle 0.93069 / 0.63 ( 78) hydrogen bonds : bond 0.03949 / 2.55 ( 946) hydrogen bonds : angle 5.47994 / 3.78 ( 2700) link_ALPHA1-2 : bond 0.00804 / 0.40 ( 3) link_ALPHA1-2 : angle 1.98494 / 1.00 ( 9) link_ALPHA1-3 : bond 0.00514 / 0.30 ( 6) link_ALPHA1-3 : angle 2.32691 / 1.65 ( 18) link_ALPHA1-6 : bond 0.00102 / 0.05 ( 3) link_ALPHA1-6 : angle 1.61759 / 0.80 ( 9) link_BETA1-4 : bond 0.00372 / 0.23 ( 21) link_BETA1-4 : angle 1.28701 / 0.87 ( 63) link_NAG-ASN : bond 0.00181 / 0.13 ( 48) link_NAG-ASN : angle 1.35499 / 0.94 ( 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: 29 poor density : 127 time to evaluate : 0.896 Fit side-chains revert: symmetry clash REVERT: A 644 GLU cc_start: 0.8882 (tp30) cc_final: 0.8506 (tt0) REVERT: A 850 GLN cc_start: 0.9476 (mt0) cc_final: 0.9173 (mt0) REVERT: A 943 GLU cc_start: 0.9056 (mt-10) cc_final: 0.8734 (mt-10) REVERT: A 997 MET cc_start: 0.8377 (mmt) cc_final: 0.8073 (mmm) REVERT: B 177 GLU cc_start: 0.8296 (OUTLIER) cc_final: 0.7995 (pm20) REVERT: B 300 MET cc_start: 0.8648 (ttp) cc_final: 0.8438 (ptm) REVERT: B 423 ASP cc_start: 0.9083 (p0) cc_final: 0.8826 (p0) REVERT: B 425 ILE cc_start: 0.9263 (mm) cc_final: 0.8835 (mt) REVERT: B 644 GLU cc_start: 0.9013 (tp30) cc_final: 0.8771 (tp30) REVERT: B 709 ASP cc_start: 0.8976 (p0) cc_final: 0.8772 (p0) REVERT: B 943 GLU cc_start: 0.9058 (mt-10) cc_final: 0.8436 (mm-30) REVERT: B 997 MET cc_start: 0.8157 (mpp) cc_final: 0.7942 (mmm) REVERT: B 1005 MET cc_start: 0.3740 (mmm) cc_final: 0.3494 (mmm) REVERT: C 177 GLU cc_start: 0.8266 (OUTLIER) cc_final: 0.7947 (pm20) REVERT: C 265 ASP cc_start: 0.9084 (m-30) cc_final: 0.8773 (m-30) REVERT: C 300 MET cc_start: 0.8246 (ttm) cc_final: 0.7879 (ttm) REVERT: C 423 ASP cc_start: 0.9030 (OUTLIER) cc_final: 0.8642 (p0) REVERT: C 634 GLU cc_start: 0.9320 (pt0) cc_final: 0.8993 (mt-10) REVERT: C 890 ASN cc_start: 0.9434 (m-40) cc_final: 0.9071 (m110) REVERT: C 943 GLU cc_start: 0.8926 (mt-10) cc_final: 0.8540 (mm-30) outliers start: 29 outliers final: 19 residues processed: 149 average time/residue: 0.1322 time to fit residues: 34.2492 Evaluate side-chains 138 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 116 time to evaluate : 0.878 ------------------------------------------------------------------------------- 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 645 SER 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 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 805 ILE Chi-restraints excluded: chain B residue 831 ASN Chi-restraints excluded: chain B residue 912 GLN 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 652 LEU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 225 optimal weight: 5.9990 chunk 192 optimal weight: 8.9990 chunk 35 optimal weight: 9.9990 chunk 281 optimal weight: 40.0000 chunk 102 optimal weight: 5.9990 chunk 224 optimal weight: 0.6980 chunk 123 optimal weight: 9.9990 chunk 149 optimal weight: 2.9990 chunk 180 optimal weight: 0.7980 chunk 177 optimal weight: 0.8980 chunk 201 optimal weight: 7.9990 overall best weight: 2.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 256 ASN ** A 831 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 831 ASN ** B 956 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 831 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.095389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.060564 restraints weight = 61139.480| |-----------------------------------------------------------------------------| r_work (start): 0.2884 rms_B_bonded: 4.01 r_work: 0.2715 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.2715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.3219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 23982 Z= 0.188 Angle : 0.554 7.272 32826 Z= 0.292 Chirality : 0.045 0.208 4026 Planarity : 0.004 0.041 4041 Dihedral : 4.865 23.207 3126 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 1.16 % Allowed : 9.01 % Favored : 89.82 % 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: 0.30 (0.16), residues: 2871 helix: 1.94 (0.21), residues: 666 sheet: 0.40 (0.19), residues: 738 loop : -0.72 (0.16), residues: 1467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 685 TYR 0.026 0.001 TYR A 449 PHE 0.032 0.001 PHE B 798 TRP 0.005 0.001 TRP B 419 HIS 0.005 0.001 HIS A 846 Details of bonding type rmsd/Z covalent geometry : bond 0.00425 / 0.19 (23862) covalent geometry : angle 0.54037 / 0.29 (32505) SS BOND : bond 0.00277 / 0.16 ( 39) SS BOND : angle 0.98938 / 0.67 ( 78) hydrogen bonds : bond 0.04018 / 2.60 ( 946) hydrogen bonds : angle 5.52765 / 3.81 ( 2700) link_ALPHA1-2 : bond 0.00839 / 0.42 ( 3) link_ALPHA1-2 : angle 1.96031 / 0.99 ( 9) link_ALPHA1-3 : bond 0.00307 / 0.15 ( 6) link_ALPHA1-3 : angle 2.31171 / 1.62 ( 18) link_ALPHA1-6 : bond 0.00228 / 0.11 ( 3) link_ALPHA1-6 : angle 1.66302 / 0.82 ( 9) link_BETA1-4 : bond 0.00317 / 0.20 ( 21) link_BETA1-4 : angle 1.26908 / 0.86 ( 63) link_NAG-ASN : bond 0.00244 / 0.17 ( 48) link_NAG-ASN : angle 1.36206 / 0.94 ( 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 149 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 120 time to evaluate : 0.880 Fit side-chains revert: symmetry clash REVERT: A 802 MET cc_start: 0.9470 (mmm) cc_final: 0.9183 (tpp) REVERT: A 850 GLN cc_start: 0.9485 (mt0) cc_final: 0.9244 (mt0) REVERT: A 943 GLU cc_start: 0.9075 (mt-10) cc_final: 0.8769 (mt-10) REVERT: A 997 MET cc_start: 0.8369 (mmt) cc_final: 0.8052 (mmm) REVERT: B 177 GLU cc_start: 0.8333 (OUTLIER) cc_final: 0.8097 (pm20) REVERT: B 300 MET cc_start: 0.8612 (ttp) cc_final: 0.8403 (ptm) REVERT: B 423 ASP cc_start: 0.9045 (p0) cc_final: 0.8800 (p0) REVERT: B 425 ILE cc_start: 0.9235 (mm) cc_final: 0.8801 (mt) REVERT: B 644 GLU cc_start: 0.9026 (tp30) cc_final: 0.8785 (tp30) REVERT: B 709 ASP cc_start: 0.8980 (p0) cc_final: 0.8765 (p0) REVERT: B 943 GLU cc_start: 0.9055 (mt-10) cc_final: 0.8561 (mm-30) REVERT: B 997 MET cc_start: 0.8161 (mpp) cc_final: 0.7944 (mmm) REVERT: B 1005 MET cc_start: 0.3672 (mmm) cc_final: 0.3421 (mmm) REVERT: C 177 GLU cc_start: 0.8247 (OUTLIER) cc_final: 0.7951 (pm20) REVERT: C 265 ASP cc_start: 0.9125 (m-30) cc_final: 0.8809 (m-30) REVERT: C 423 ASP cc_start: 0.9020 (OUTLIER) cc_final: 0.8691 (p0) REVERT: C 634 GLU cc_start: 0.9318 (pt0) cc_final: 0.9002 (mt-10) REVERT: C 943 GLU cc_start: 0.8916 (mt-10) cc_final: 0.8523 (mm-30) outliers start: 29 outliers final: 23 residues processed: 145 average time/residue: 0.1331 time to fit residues: 33.6591 Evaluate side-chains 138 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 112 time to evaluate : 0.690 ------------------------------------------------------------------------------- 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 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 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 B residue 831 ASN Chi-restraints excluded: chain B residue 912 GLN 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 652 LEU Chi-restraints excluded: chain C residue 705 LEU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 123 optimal weight: 10.0000 chunk 200 optimal weight: 6.9990 chunk 169 optimal weight: 7.9990 chunk 63 optimal weight: 1.9990 chunk 255 optimal weight: 0.9980 chunk 122 optimal weight: 0.0670 chunk 59 optimal weight: 0.0770 chunk 88 optimal weight: 0.0970 chunk 85 optimal weight: 5.9990 chunk 2 optimal weight: 5.9990 chunk 37 optimal weight: 6.9990 overall best weight: 0.6476 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 831 ASN ** B 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 498 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 831 ASN C 831 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.096924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.062062 restraints weight = 61057.712| |-----------------------------------------------------------------------------| r_work (start): 0.2921 rms_B_bonded: 4.05 r_work: 0.2754 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.2754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.3402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 23982 Z= 0.107 Angle : 0.535 12.651 32826 Z= 0.281 Chirality : 0.044 0.213 4026 Planarity : 0.004 0.045 4041 Dihedral : 4.782 25.503 3126 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 1.08 % Allowed : 9.21 % Favored : 89.70 % 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: 1.95 (0.21), residues: 666 sheet: 0.48 (0.19), residues: 732 loop : -0.71 (0.17), residues: 1473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 685 TYR 0.014 0.001 TYR A 449 PHE 0.014 0.001 PHE C 229 TRP 0.005 0.001 TRP C 83 HIS 0.003 0.001 HIS B 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00226 / 0.11 (23862) covalent geometry : angle 0.52168 / 0.28 (32505) SS BOND : bond 0.00229 / 0.13 ( 39) SS BOND : angle 0.86451 / 0.58 ( 78) hydrogen bonds : bond 0.03771 / 2.46 ( 946) hydrogen bonds : angle 5.42936 / 3.74 ( 2700) link_ALPHA1-2 : bond 0.01049 / 0.53 ( 3) link_ALPHA1-2 : angle 2.06678 / 1.05 ( 9) link_ALPHA1-3 : bond 0.00570 / 0.30 ( 6) link_ALPHA1-3 : angle 2.33013 / 1.68 ( 18) link_ALPHA1-6 : bond 0.00021 / 0.01 ( 3) link_ALPHA1-6 : angle 1.48721 / 0.73 ( 9) link_BETA1-4 : bond 0.00395 / 0.25 ( 21) link_BETA1-4 : angle 1.26238 / 0.84 ( 63) link_NAG-ASN : bond 0.00159 / 0.10 ( 48) link_NAG-ASN : angle 1.27470 / 0.88 ( 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 155 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 128 time to evaluate : 0.857 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 517 GLU cc_start: 0.8788 (pt0) cc_final: 0.8576 (pm20) REVERT: A 644 GLU cc_start: 0.8837 (tp30) cc_final: 0.8583 (tp30) REVERT: A 802 MET cc_start: 0.9400 (mmm) cc_final: 0.9050 (tpp) REVERT: A 850 GLN cc_start: 0.9438 (mt0) cc_final: 0.9086 (mt0) REVERT: A 943 GLU cc_start: 0.9057 (mt-10) cc_final: 0.8719 (mt-10) REVERT: A 997 MET cc_start: 0.8332 (mmt) cc_final: 0.7998 (mmm) REVERT: B 177 GLU cc_start: 0.8287 (OUTLIER) cc_final: 0.8055 (pm20) REVERT: B 425 ILE cc_start: 0.9263 (mm) cc_final: 0.8837 (mt) REVERT: B 517 GLU cc_start: 0.8805 (pt0) cc_final: 0.8451 (pm20) REVERT: B 644 GLU cc_start: 0.8956 (tp30) cc_final: 0.8737 (tp30) REVERT: B 709 ASP cc_start: 0.8975 (p0) cc_final: 0.8766 (p0) REVERT: B 802 MET cc_start: 0.9389 (mmm) cc_final: 0.9078 (tpp) REVERT: B 943 GLU cc_start: 0.9059 (mt-10) cc_final: 0.8579 (mm-30) REVERT: B 997 MET cc_start: 0.8149 (mpp) cc_final: 0.7922 (mmm) REVERT: B 1005 MET cc_start: 0.3824 (mmm) cc_final: 0.3575 (mmm) REVERT: C 177 GLU cc_start: 0.8234 (OUTLIER) cc_final: 0.7920 (pm20) REVERT: C 265 ASP cc_start: 0.9105 (m-30) cc_final: 0.8786 (m-30) REVERT: C 423 ASP cc_start: 0.8999 (p0) cc_final: 0.8738 (p0) REVERT: C 890 ASN cc_start: 0.9426 (m-40) cc_final: 0.9079 (m-40) REVERT: C 937 ILE cc_start: 0.8968 (mm) cc_final: 0.8745 (tp) REVERT: C 943 GLU cc_start: 0.8947 (mt-10) cc_final: 0.8568 (mm-30) outliers start: 27 outliers final: 22 residues processed: 148 average time/residue: 0.1320 time to fit residues: 34.3368 Evaluate side-chains 147 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 123 time to evaluate : 0.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 297 HIS 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 297 HIS Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 652 LEU Chi-restraints excluded: chain B residue 831 ASN Chi-restraints excluded: chain B residue 912 GLN 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 705 LEU 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: 7.9990 chunk 111 optimal weight: 3.9990 chunk 69 optimal weight: 9.9990 chunk 58 optimal weight: 1.9990 chunk 282 optimal weight: 8.9990 chunk 255 optimal weight: 1.9990 chunk 16 optimal weight: 7.9990 chunk 256 optimal weight: 1.9990 chunk 102 optimal weight: 10.0000 chunk 275 optimal weight: 6.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 498 ASN ** 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 = 0.3634 r_free = 0.3634 target = 0.096650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.061988 restraints weight = 61259.140| |-----------------------------------------------------------------------------| r_work (start): 0.2914 rms_B_bonded: 4.02 r_work: 0.2744 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.2744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.3404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.096 23982 Z= 0.164 Angle : 0.715 59.197 32826 Z= 0.412 Chirality : 0.046 0.459 4026 Planarity : 0.005 0.135 4041 Dihedral : 4.773 25.325 3126 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 0.96 % Allowed : 9.29 % Favored : 89.74 % Cbeta Deviations : 0.07 % 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: 0.33 (0.16), residues: 2871 helix: 1.92 (0.21), residues: 666 sheet: 0.46 (0.19), residues: 735 loop : -0.70 (0.17), residues: 1470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 72 TYR 0.014 0.001 TYR A 449 PHE 0.014 0.001 PHE C 229 TRP 0.006 0.001 TRP C 83 HIS 0.003 0.001 HIS B 846 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.16 (23862) covalent geometry : angle 0.70661 / 0.41 (32505) SS BOND : bond 0.00277 / 0.15 ( 39) SS BOND : angle 0.89948 / 0.61 ( 78) hydrogen bonds : bond 0.03790 / 2.46 ( 946) hydrogen bonds : angle 5.42713 / 3.74 ( 2700) link_ALPHA1-2 : bond 0.00776 / 0.38 ( 3) link_ALPHA1-2 : angle 2.07993 / 1.05 ( 9) link_ALPHA1-3 : bond 0.00514 / 0.27 ( 6) link_ALPHA1-3 : angle 2.34061 / 1.69 ( 18) link_ALPHA1-6 : bond 0.00054 / 0.03 ( 3) link_ALPHA1-6 : angle 1.51058 / 0.75 ( 9) link_BETA1-4 : bond 0.00406 / 0.26 ( 21) link_BETA1-4 : angle 1.26846 / 0.84 ( 63) link_NAG-ASN : bond 0.00168 / 0.11 ( 48) link_NAG-ASN : angle 1.27549 / 0.88 ( 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 147 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 123 time to evaluate : 0.934 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 517 GLU cc_start: 0.8803 (pt0) cc_final: 0.8581 (pm20) REVERT: A 644 GLU cc_start: 0.8839 (tp30) cc_final: 0.8584 (tp30) REVERT: A 802 MET cc_start: 0.9400 (mmm) cc_final: 0.9050 (tpp) REVERT: A 850 GLN cc_start: 0.9458 (mt0) cc_final: 0.9107 (mt0) REVERT: A 943 GLU cc_start: 0.9076 (mt-10) cc_final: 0.8740 (mt-10) REVERT: A 997 MET cc_start: 0.8356 (mmt) cc_final: 0.8026 (mmm) REVERT: B 177 GLU cc_start: 0.8292 (OUTLIER) cc_final: 0.8052 (pm20) REVERT: B 425 ILE cc_start: 0.9266 (mm) cc_final: 0.8843 (mt) REVERT: B 517 GLU cc_start: 0.8819 (pt0) cc_final: 0.8458 (pm20) REVERT: B 644 GLU cc_start: 0.8965 (tp30) cc_final: 0.8745 (tp30) REVERT: B 709 ASP cc_start: 0.8977 (p0) cc_final: 0.8767 (p0) REVERT: B 802 MET cc_start: 0.9388 (mmm) cc_final: 0.9072 (tpp) REVERT: B 943 GLU cc_start: 0.9065 (mt-10) cc_final: 0.8584 (mm-30) REVERT: B 997 MET cc_start: 0.8173 (mpp) cc_final: 0.7950 (mmm) REVERT: B 1005 MET cc_start: 0.3783 (mmm) cc_final: 0.3529 (mmm) REVERT: C 177 GLU cc_start: 0.8244 (OUTLIER) cc_final: 0.7929 (pm20) REVERT: C 265 ASP cc_start: 0.9108 (m-30) cc_final: 0.8790 (m-30) REVERT: C 423 ASP cc_start: 0.8998 (p0) cc_final: 0.8742 (p0) REVERT: C 890 ASN cc_start: 0.9430 (m-40) cc_final: 0.9059 (m110) REVERT: C 937 ILE cc_start: 0.8973 (mm) cc_final: 0.8748 (tp) REVERT: C 943 GLU cc_start: 0.8949 (mt-10) cc_final: 0.8571 (mm-30) outliers start: 24 outliers final: 21 residues processed: 140 average time/residue: 0.1419 time to fit residues: 34.5651 Evaluate side-chains 142 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 119 time to evaluate : 0.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 297 HIS 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 268 SER Chi-restraints excluded: chain B residue 297 HIS Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 652 LEU Chi-restraints excluded: chain B residue 912 GLN 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 652 LEU Chi-restraints excluded: chain C residue 705 LEU Chi-restraints excluded: chain C residue 805 ILE Chi-restraints excluded: chain C residue 825 THR 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: 6.9990 chunk 52 optimal weight: 20.0000 chunk 261 optimal weight: 10.0000 chunk 201 optimal weight: 10.0000 chunk 171 optimal weight: 0.9980 chunk 173 optimal weight: 0.9980 chunk 241 optimal weight: 0.7980 chunk 113 optimal weight: 10.0000 chunk 93 optimal weight: 30.0000 chunk 139 optimal weight: 2.9990 chunk 233 optimal weight: 0.8980 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** ** C 297 HIS ** 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 = 0.3635 r_free = 0.3635 target = 0.096707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.062012 restraints weight = 60737.952| |-----------------------------------------------------------------------------| r_work (start): 0.2916 rms_B_bonded: 4.02 r_work: 0.2747 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.2747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.3410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.096 23982 Z= 0.164 Angle : 0.715 59.197 32826 Z= 0.412 Chirality : 0.046 0.459 4026 Planarity : 0.005 0.135 4041 Dihedral : 4.773 25.325 3126 Min Nonbonded Distance : 1.749 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 0.92 % Allowed : 9.46 % Favored : 89.62 % Cbeta Deviations : 0.07 % 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: 0.33 (0.16), residues: 2871 helix: 1.92 (0.21), residues: 666 sheet: 0.46 (0.19), residues: 735 loop : -0.70 (0.17), residues: 1470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 72 TYR 0.014 0.001 TYR A 449 PHE 0.014 0.001 PHE C 229 TRP 0.006 0.001 TRP C 83 HIS 0.003 0.001 HIS B 846 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.16 (23862) covalent geometry : angle 0.70661 / 0.41 (32505) SS BOND : bond 0.00277 / 0.15 ( 39) SS BOND : angle 0.89948 / 0.61 ( 78) hydrogen bonds : bond 0.03790 / 2.46 ( 946) hydrogen bonds : angle 5.42713 / 3.74 ( 2700) link_ALPHA1-2 : bond 0.00776 / 0.38 ( 3) link_ALPHA1-2 : angle 2.07993 / 1.05 ( 9) link_ALPHA1-3 : bond 0.00514 / 0.27 ( 6) link_ALPHA1-3 : angle 2.34061 / 1.69 ( 18) link_ALPHA1-6 : bond 0.00054 / 0.03 ( 3) link_ALPHA1-6 : angle 1.51058 / 0.75 ( 9) link_BETA1-4 : bond 0.00406 / 0.26 ( 21) link_BETA1-4 : angle 1.26846 / 0.84 ( 63) link_NAG-ASN : bond 0.00168 / 0.11 ( 48) link_NAG-ASN : angle 1.27549 / 0.88 ( 144) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5696.52 seconds wall clock time: 98 minutes 42.01 seconds (5922.01 seconds total)