Starting phenix.real_space_refine (version: 1.19rc7) on Wed Jan 6 22:35:26 2021 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a96_11686/01_2021/7a96_11686.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a96_11686/01_2021/7a96_11686.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a96_11686/01_2021/7a96_11686.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a96_11686/01_2021/7a96_11686.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a96_11686/01_2021/7a96_11686.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a96_11686/01_2021/7a96_11686.pdb" } resolution = 4.8 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 ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.028 Set model interpretation parameters Set stop_for_unknowns flag Set to: True Assert model is a single copy model Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.19rc7-4070/modules/chem_data/mon_lib" Total number of atoms: 29811 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 8337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1065, 8337 Classifications: {'peptide': 1065} Link IDs: {'PTRANS': 52, 'TRANS': 1011, 'PCIS': 1} Chain breaks: 5 Chain: "B" Number of atoms: 8337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1065, 8337 Classifications: {'peptide': 1065} Link IDs: {'PTRANS': 52, 'TRANS': 1011, 'PCIS': 1} Chain breaks: 5 Chain: "C" Number of atoms: 8336 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1065, 8336 Classifications: {'peptide': 1065} Link IDs: {'PTRANS': 53, 'TRANS': 1011} Chain breaks: 5 Chain: "D" Number of atoms: 4801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 588, 4801 Classifications: {'peptide': 588} Link IDs: {'PTRANS': 24, 'TRANS': 562, 'PCIS': 1} Chain breaks: 1 Time building chain proxies: 16.18, per 1000 atoms: 0.54 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 14 through 825 or resid 852 through 1146)) selection = (chain 'B' and (resid 14 through 825 or resid 852 through 1146)) selection = (chain 'C' and (resid 14 through 617 or resid 641 through 1146)) } Number of scatterers: 29811 At special positions: 0 Unit cell: (151.998, 160.622, 246.862, 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 143 16.00 O 5661 8.00 N 4973 7.00 C 19034 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS D 133 " - pdb=" SG CYS D 141 " distance=2.03 Simple disulfide: pdb=" SG CYS D 344 " - pdb=" SG CYS D 361 " distance=2.03 Simple disulfide: pdb=" SG CYS D 530 " - pdb=" SG CYS D 542 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amimo acid : False - 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 Time building additional restraints: 11.09 Conformation dependent library (CDL) restraints added in 4.7 seconds 7486 Ramachandran restraints generated. 3743 Oldfield and 0 Emsley and 3743 emsley8k. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7094 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 54 sheets defined 26.7% alpha, 17.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.83 Creating SS restraints... Processing helix chain 'A' and resid 296 through 304 removed outlier: 3.818A pdb=" N LYS A 300 " --> pdb=" O LEU A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 343 removed outlier: 4.365A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N PHE A 342 " --> pdb=" O PHE A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 removed outlier: 4.036A pdb=" N TYR A 369 " --> pdb=" O TYR A 365 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N ASN A 370 " --> pdb=" O SER A 366 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 365 through 370' Processing helix chain 'A' and resid 385 through 390 removed outlier: 3.552A pdb=" N ASP A 389 " --> pdb=" O LYS A 386 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEU A 390 " --> pdb=" O LEU A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 743 removed outlier: 3.879A pdb=" N TYR A 741 " --> pdb=" O ASP A 737 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ILE A 742 " --> pdb=" O CYS A 738 " (cutoff:3.500A) Processing helix chain 'A' and resid 756 through 782 removed outlier: 3.996A pdb=" N CYS A 760 " --> pdb=" O TYR A 756 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N THR A 761 " --> pdb=" O GLY A 757 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLN A 762 " --> pdb=" O SER A 758 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ALA A 766 " --> pdb=" O GLN A 762 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ALA A 771 " --> pdb=" O LEU A 767 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N GLU A 773 " --> pdb=" O GLY A 769 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N LYS A 776 " --> pdb=" O VAL A 772 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ASN A 777 " --> pdb=" O GLU A 773 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLN A 779 " --> pdb=" O ASP A 775 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.542A pdb=" N LEU A 822 " --> pdb=" O ILE A 818 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N PHE A 823 " --> pdb=" O GLU A 819 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ASN A 824 " --> pdb=" O ASP A 820 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LYS A 825 " --> pdb=" O LEU A 821 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 852 through 856 Processing helix chain 'A' and resid 866 through 884 removed outlier: 3.971A pdb=" N ALA A 871 " --> pdb=" O ASP A 867 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLN A 872 " --> pdb=" O GLU A 868 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N TYR A 873 " --> pdb=" O MET A 869 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N THR A 874 " --> pdb=" O ILE A 870 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 907 removed outlier: 4.219A pdb=" N ALA A 903 " --> pdb=" O ALA A 899 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N TYR A 904 " --> pdb=" O MET A 900 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ARG A 905 " --> pdb=" O GLN A 901 " (cutoff:3.500A) Processing helix chain 'A' and resid 908 through 910 No H-bonds generated for 'chain 'A' and resid 908 through 910' Processing helix chain 'A' and resid 913 through 919 removed outlier: 3.709A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 939 removed outlier: 3.520A pdb=" N ILE A 931 " --> pdb=" O PHE A 927 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLY A 932 " --> pdb=" O ASN A 928 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ILE A 934 " --> pdb=" O ALA A 930 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N SER A 937 " --> pdb=" O LYS A 933 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N SER A 939 " --> pdb=" O GLN A 935 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 968 removed outlier: 4.768A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LEU A 962 " --> pdb=" O ALA A 958 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N VAL A 963 " --> pdb=" O LEU A 959 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LYS A 964 " --> pdb=" O ASN A 960 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N SER A 967 " --> pdb=" O VAL A 963 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.591A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N LEU A 981 " --> pdb=" O LEU A 977 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N SER A 982 " --> pdb=" O ASN A 978 " (cutoff:3.500A) Processing helix chain 'A' and resid 989 through 1032 removed outlier: 3.546A pdb=" N ASP A 994 " --> pdb=" O GLU A 990 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N SER A1003 " --> pdb=" O GLY A 999 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLU A1017 " --> pdb=" O ILE A1013 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N SER A1030 " --> pdb=" O ALA A1026 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 303 removed outlier: 3.706A pdb=" N LYS B 300 " --> pdb=" O LEU B 296 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N CYS B 301 " --> pdb=" O SER B 297 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N LEU B 303 " --> pdb=" O THR B 299 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 342 removed outlier: 4.058A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N PHE B 342 " --> pdb=" O PHE B 338 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 337 through 342' Processing helix chain 'B' and resid 385 through 389 removed outlier: 3.891A pdb=" N ASP B 389 " --> pdb=" O LYS B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 408 removed outlier: 3.796A pdb=" N VAL B 407 " --> pdb=" O GLY B 404 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 404 through 408' Processing helix chain 'B' and resid 737 through 743 removed outlier: 3.815A pdb=" N TYR B 741 " --> pdb=" O ASP B 737 " (cutoff:3.500A) Processing helix chain 'B' and resid 748 through 756 removed outlier: 3.813A pdb=" N LEU B 752 " --> pdb=" O GLU B 748 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LEU B 753 " --> pdb=" O CYS B 749 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N LEU B 754 " --> pdb=" O SER B 750 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N TYR B 756 " --> pdb=" O LEU B 752 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 748 through 756' Processing helix chain 'B' and resid 756 through 782 removed outlier: 4.029A pdb=" N CYS B 760 " --> pdb=" O TYR B 756 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N THR B 761 " --> pdb=" O GLY B 757 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLN B 762 " --> pdb=" O SER B 758 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N GLU B 773 " --> pdb=" O GLY B 769 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LYS B 776 " --> pdb=" O VAL B 772 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLN B 779 " --> pdb=" O ASP B 775 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLU B 780 " --> pdb=" O LYS B 776 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 824 removed outlier: 3.534A pdb=" N PHE B 823 " --> pdb=" O GLU B 819 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ASN B 824 " --> pdb=" O ASP B 820 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 884 removed outlier: 3.722A pdb=" N ALA B 871 " --> pdb=" O ASP B 867 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLN B 872 " --> pdb=" O GLU B 868 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N TYR B 873 " --> pdb=" O MET B 869 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N THR B 883 " --> pdb=" O ALA B 879 " (cutoff:3.500A) Processing helix chain 'B' and resid 887 through 891 removed outlier: 3.687A pdb=" N ALA B 890 " --> pdb=" O THR B 887 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N GLY B 891 " --> pdb=" O PHE B 888 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 887 through 891' Processing helix chain 'B' and resid 897 through 908 removed outlier: 4.029A pdb=" N ALA B 903 " --> pdb=" O ALA B 899 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 919 removed outlier: 3.868A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 939 removed outlier: 3.506A pdb=" N ILE B 923 " --> pdb=" O ASN B 919 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ILE B 931 " --> pdb=" O PHE B 927 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLY B 932 " --> pdb=" O ASN B 928 " (cutoff:3.500A) Processing helix chain 'B' and resid 948 through 965 removed outlier: 4.266A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU B 962 " --> pdb=" O ALA B 958 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N VAL B 963 " --> pdb=" O LEU B 959 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 981 removed outlier: 3.817A pdb=" N LEU B 981 " --> pdb=" O LEU B 977 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1032 removed outlier: 3.548A pdb=" N GLU B 990 " --> pdb=" O PRO B 986 " (cutoff:3.500A) removed outlier: 5.769A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N SER B1003 " --> pdb=" O GLY B 999 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N SER B1030 " --> pdb=" O ALA B1026 " (cutoff:3.500A) Processing helix chain 'B' and resid 1127 through 1129 No H-bonds generated for 'chain 'B' and resid 1127 through 1129' Processing helix chain 'B' and resid 1140 through 1145 removed outlier: 3.838A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU B1145 " --> pdb=" O LEU B1141 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1140 through 1145' Processing helix chain 'C' and resid 294 through 303 removed outlier: 3.540A pdb=" N THR C 299 " --> pdb=" O PRO C 295 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LYS C 300 " --> pdb=" O LEU C 296 " (cutoff:3.500A) Processing helix chain 'C' and resid 337 through 342 removed outlier: 3.902A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 407 removed outlier: 3.775A pdb=" N GLU C 406 " --> pdb=" O ARG C 403 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N VAL C 407 " --> pdb=" O GLY C 404 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 403 through 407' Processing helix chain 'C' and resid 738 through 743 removed outlier: 3.825A pdb=" N ILE C 742 " --> pdb=" O CYS C 738 " (cutoff:3.500A) Processing helix chain 'C' and resid 747 through 755 removed outlier: 4.461A pdb=" N LEU C 752 " --> pdb=" O CYS C 749 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N LEU C 753 " --> pdb=" O SER C 750 " (cutoff:3.500A) Processing helix chain 'C' and resid 756 through 782 removed outlier: 3.815A pdb=" N CYS C 760 " --> pdb=" O TYR C 756 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ARG C 765 " --> pdb=" O THR C 761 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ALA C 766 " --> pdb=" O GLN C 762 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ILE C 770 " --> pdb=" O ALA C 766 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLN C 779 " --> pdb=" O ASP C 775 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 824 removed outlier: 3.810A pdb=" N ASN C 824 " --> pdb=" O ASP C 820 " (cutoff:3.500A) Processing helix chain 'C' and resid 852 through 856 removed outlier: 3.544A pdb=" N PHE C 855 " --> pdb=" O ALA C 852 " (cutoff:3.500A) Processing helix chain 'C' and resid 868 through 882 removed outlier: 3.518A pdb=" N GLN C 872 " --> pdb=" O GLU C 868 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N TYR C 873 " --> pdb=" O MET C 869 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N THR C 874 " --> pdb=" O ILE C 870 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE C 882 " --> pdb=" O LEU C 878 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 907 removed outlier: 3.678A pdb=" N MET C 902 " --> pdb=" O PHE C 898 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ALA C 903 " --> pdb=" O ALA C 899 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ARG C 905 " --> pdb=" O GLN C 901 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N PHE C 906 " --> pdb=" O MET C 902 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ASN C 907 " --> pdb=" O ALA C 903 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 919 removed outlier: 3.948A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 940 removed outlier: 3.595A pdb=" N ILE C 931 " --> pdb=" O PHE C 927 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLY C 932 " --> pdb=" O ASN C 928 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N SER C 940 " --> pdb=" O ASP C 936 " (cutoff:3.500A) Processing helix chain 'C' and resid 946 through 967 removed outlier: 3.543A pdb=" N ASP C 950 " --> pdb=" O GLY C 946 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU C 959 " --> pdb=" O ASN C 955 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL C 963 " --> pdb=" O LEU C 959 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LYS C 964 " --> pdb=" O ASN C 960 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LEU C 966 " --> pdb=" O LEU C 962 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N SER C 967 " --> pdb=" O VAL C 963 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 984 removed outlier: 3.597A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N LEU C 981 " --> pdb=" O LEU C 977 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N SER C 982 " --> pdb=" O ASN C 978 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1032 removed outlier: 5.506A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N SER C1003 " --> pdb=" O GLY C 999 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LYS C1028 " --> pdb=" O LEU C1024 " (cutoff:3.500A) Processing helix chain 'C' and resid 1142 through 1146 removed outlier: 3.681A pdb=" N ASP C1146 " --> pdb=" O PRO C1143 " (cutoff:3.500A) Processing helix chain 'D' and resid 21 through 51 removed outlier: 3.737A pdb=" N LYS D 26 " --> pdb=" O GLU D 22 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N THR D 27 " --> pdb=" O GLU D 23 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N PHE D 28 " --> pdb=" O GLN D 24 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLU D 35 " --> pdb=" O LYS D 31 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N ASP D 38 " --> pdb=" O HIS D 34 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLN D 42 " --> pdb=" O ASP D 38 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N SER D 47 " --> pdb=" O SER D 43 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N TYR D 50 " --> pdb=" O ALA D 46 " (cutoff:3.500A) Processing helix chain 'D' and resid 56 through 80 removed outlier: 4.104A pdb=" N GLN D 60 " --> pdb=" O GLU D 56 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ASN D 61 " --> pdb=" O GLU D 57 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LYS D 68 " --> pdb=" O ASN D 64 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N TRP D 69 " --> pdb=" O ALA D 65 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LYS D 74 " --> pdb=" O SER D 70 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N THR D 78 " --> pdb=" O LYS D 74 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 83 No H-bonds generated for 'chain 'D' and resid 81 through 83' Processing helix chain 'D' and resid 92 through 98 removed outlier: 3.589A pdb=" N GLN D 96 " --> pdb=" O THR D 92 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLN D 98 " --> pdb=" O LYS D 94 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 108 removed outlier: 3.671A pdb=" N VAL D 107 " --> pdb=" O GLY D 104 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N LEU D 108 " --> pdb=" O SER D 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 104 through 108' Processing helix chain 'D' and resid 109 through 129 removed outlier: 3.931A pdb=" N LYS D 114 " --> pdb=" O GLU D 110 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N ARG D 115 " --> pdb=" O ASP D 111 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASN D 117 " --> pdb=" O SER D 113 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N SER D 124 " --> pdb=" O LEU D 120 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N THR D 125 " --> pdb=" O ASN D 121 " (cutoff:3.500A) Processing helix chain 'D' and resid 160 through 170 removed outlier: 3.741A pdb=" N ALA D 164 " --> pdb=" O GLU D 160 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ARG D 169 " --> pdb=" O TRP D 165 " (cutoff:3.500A) Processing helix chain 'D' and resid 171 through 176 removed outlier: 3.505A pdb=" N GLN D 175 " --> pdb=" O GLU D 171 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 193 removed outlier: 3.874A pdb=" N GLU D 182 " --> pdb=" O PRO D 178 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N VAL D 184 " --> pdb=" O TYR D 180 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N VAL D 185 " --> pdb=" O GLU D 181 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLU D 189 " --> pdb=" O VAL D 185 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N MET D 190 " --> pdb=" O LEU D 186 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA D 191 " --> pdb=" O LYS D 187 " (cutoff:3.500A) Processing helix chain 'D' and resid 199 through 205 removed outlier: 3.937A pdb=" N TRP D 203 " --> pdb=" O TYR D 199 " (cutoff:3.500A) Processing helix chain 'D' and resid 206 through 208 No H-bonds generated for 'chain 'D' and resid 206 through 208' Processing helix chain 'D' and resid 218 through 224 removed outlier: 3.698A pdb=" N LEU D 222 " --> pdb=" O SER D 218 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE D 223 " --> pdb=" O ARG D 219 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N GLU D 224 " --> pdb=" O GLY D 220 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 218 through 224' Processing helix chain 'D' and resid 228 through 233 removed outlier: 3.810A pdb=" N GLU D 232 " --> pdb=" O HIS D 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 249 removed outlier: 3.662A pdb=" N HIS D 239 " --> pdb=" O PRO D 235 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N MET D 249 " --> pdb=" O ARG D 245 " (cutoff:3.500A) Processing helix chain 'D' and resid 275 through 280 removed outlier: 3.898A pdb=" N SER D 280 " --> pdb=" O ASN D 277 " (cutoff:3.500A) Processing helix chain 'D' and resid 293 through 300 removed outlier: 3.537A pdb=" N MET D 297 " --> pdb=" O VAL D 293 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N VAL D 298 " --> pdb=" O THR D 294 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ASP D 299 " --> pdb=" O ASP D 295 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N GLN D 300 " --> pdb=" O ALA D 296 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 293 through 300' Processing helix chain 'D' and resid 305 through 313 removed outlier: 3.515A pdb=" N LYS D 309 " --> pdb=" O GLN D 305 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LYS D 313 " --> pdb=" O LYS D 309 " (cutoff:3.500A) Processing helix chain 'D' and resid 313 through 319 removed outlier: 3.952A pdb=" N SER D 317 " --> pdb=" O LYS D 313 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N VAL D 318 " --> pdb=" O PHE D 314 " (cutoff:3.500A) Processing helix chain 'D' and resid 326 through 331 removed outlier: 3.877A pdb=" N SER D 331 " --> pdb=" O PHE D 327 " (cutoff:3.500A) Processing helix chain 'D' and resid 365 through 383 removed outlier: 3.627A pdb=" N LEU D 370 " --> pdb=" O MET D 366 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N HIS D 373 " --> pdb=" O PHE D 369 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N HIS D 374 " --> pdb=" O LEU D 370 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLY D 377 " --> pdb=" O HIS D 373 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N HIS D 378 " --> pdb=" O HIS D 374 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ILE D 379 " --> pdb=" O GLU D 375 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLN D 380 " --> pdb=" O MET D 376 " (cutoff:3.500A) Processing helix chain 'D' and resid 398 through 413 removed outlier: 3.883A pdb=" N GLU D 402 " --> pdb=" O GLU D 398 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLY D 405 " --> pdb=" O HIS D 401 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLU D 406 " --> pdb=" O GLU D 402 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N SER D 411 " --> pdb=" O ILE D 407 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ALA D 412 " --> pdb=" O MET D 408 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ALA D 413 " --> pdb=" O SER D 409 " (cutoff:3.500A) Processing helix chain 'D' and resid 416 through 420 removed outlier: 3.593A pdb=" N SER D 420 " --> pdb=" O HIS D 417 " (cutoff:3.500A) Processing helix chain 'D' and resid 431 through 444 removed outlier: 3.688A pdb=" N GLU D 435 " --> pdb=" O ASP D 431 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ILE D 436 " --> pdb=" O ASN D 432 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N ASN D 437 " --> pdb=" O GLU D 433 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LYS D 441 " --> pdb=" O ASN D 437 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLN D 442 " --> pdb=" O PHE D 438 " (cutoff:3.500A) Processing helix chain 'D' and resid 449 through 466 removed outlier: 3.564A pdb=" N TYR D 454 " --> pdb=" O LEU D 450 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N MET D 462 " --> pdb=" O LYS D 458 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N VAL D 463 " --> pdb=" O TRP D 459 " (cutoff:3.500A) Processing helix chain 'D' and resid 469 through 472 Processing helix chain 'D' and resid 473 through 478 removed outlier: 3.804A pdb=" N TRP D 478 " --> pdb=" O MET D 474 " (cutoff:3.500A) Processing helix chain 'D' and resid 480 through 485 Processing helix chain 'D' and resid 499 through 502 removed outlier: 3.594A pdb=" N SER D 502 " --> pdb=" O ASP D 499 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 499 through 502' Processing helix chain 'D' and resid 503 through 508 Processing helix chain 'D' and resid 513 through 532 removed outlier: 3.838A pdb=" N THR D 517 " --> pdb=" O ILE D 513 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ARG D 518 " --> pdb=" O ARG D 514 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N THR D 519 " --> pdb=" O TYR D 515 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU D 520 " --> pdb=" O TYR D 516 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N PHE D 523 " --> pdb=" O THR D 519 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ALA D 528 " --> pdb=" O GLN D 524 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ALA D 532 " --> pdb=" O ALA D 528 " (cutoff:3.500A) Processing helix chain 'D' and resid 549 through 560 removed outlier: 3.516A pdb=" N LYS D 553 " --> pdb=" O GLU D 549 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ASN D 556 " --> pdb=" O GLN D 552 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N MET D 557 " --> pdb=" O LYS D 553 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU D 558 " --> pdb=" O LEU D 554 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU D 560 " --> pdb=" O ASN D 556 " (cutoff:3.500A) Processing helix chain 'D' and resid 565 through 572 removed outlier: 3.528A pdb=" N ALA D 569 " --> pdb=" O PRO D 565 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ASN D 572 " --> pdb=" O LEU D 568 " (cutoff:3.500A) Processing helix chain 'D' and resid 581 through 586 Processing helix chain 'D' and resid 588 through 596 removed outlier: 3.660A pdb=" N LYS D 596 " --> pdb=" O PHE D 592 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 31 removed outlier: 3.924A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N TRP A 64 " --> pdb=" O ALA A 27 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N THR A 29 " --> pdb=" O VAL A 62 " (cutoff:3.500A) removed outlier: 8.143A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N THR A 63 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N VAL A 267 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLU A 191 " --> pdb=" O LYS A 206 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LYS A 206 " --> pdb=" O GLU A 191 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 27 through 31 removed outlier: 3.924A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N TRP A 64 " --> pdb=" O ALA A 27 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N THR A 29 " --> pdb=" O VAL A 62 " (cutoff:3.500A) removed outlier: 8.143A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N THR A 63 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N VAL A 267 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N LYS A 195 " --> pdb=" O LYS A 202 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LYS A 202 " --> pdb=" O LYS A 195 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N PHE A 201 " --> pdb=" O LEU A 229 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 55 removed outlier: 4.281A pdb=" N HIS A 49 " --> pdb=" O LEU A 277 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LEU A 277 " --> pdb=" O HIS A 49 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N THR A 51 " --> pdb=" O PHE A 275 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N PHE A 275 " --> pdb=" O THR A 51 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ARG A 273 " --> pdb=" O ASP A 53 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N PHE A 55 " --> pdb=" O GLN A 271 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLN A 271 " --> pdb=" O PHE A 55 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VAL A 289 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS A 278 " --> pdb=" O ASP A 287 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 6.956A pdb=" N GLY A 142 " --> pdb=" O SER A 155 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N SER A 155 " --> pdb=" O GLY A 142 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.550A pdb=" N GLN A 239 " --> pdb=" O ILE A 105 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 4.967A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N ASN A 121 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 325 through 328 removed outlier: 3.632A pdb=" N ASN A 542 " --> pdb=" O ILE A 326 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N VAL A 539 " --> pdb=" O GLY A 550 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 376 through 379 removed outlier: 3.805A pdb=" N CYS A 432 " --> pdb=" O LEU A 513 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU A 513 " --> pdb=" O CYS A 432 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 452 through 453 Processing sheet with id=AA9, first strand: chain 'A' and resid 473 through 474 removed outlier: 3.506A pdb=" N TYR A 473 " --> pdb=" O TYR A 489 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N TYR A 489 " --> pdb=" O TYR A 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 564 through 567 removed outlier: 4.001A pdb=" N PHE B 43 " --> pdb=" O PHE A 565 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 575 through 578 removed outlier: 3.797A pdb=" N GLU A 583 " --> pdb=" O ASP A 578 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 595 through 598 Processing sheet with id=AB4, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.570A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.263A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N SER A 673 " --> pdb=" O ILE A 693 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N TYR A 695 " --> pdb=" O CYS A 671 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N CYS A 671 " --> pdb=" O TYR A 695 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ILE A 666 " --> pdb=" O ILE A 670 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 701 through 703 Processing sheet with id=AB6, first strand: chain 'A' and resid 712 through 715 removed outlier: 3.714A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLN A1113 " --> pdb=" O VAL A1104 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 718 through 722 removed outlier: 3.647A pdb=" N VAL A1068 " --> pdb=" O THR A 719 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N SER A 721 " --> pdb=" O THR A1066 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 725 through 728 removed outlier: 3.705A pdb=" N GLU A 725 " --> pdb=" O PHE A1062 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AC1, first strand: chain 'A' and resid 787 through 789 removed outlier: 6.266A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'A' and resid 1120 through 1122 removed outlier: 3.691A pdb=" N ILE A1081 " --> pdb=" O HIS A1088 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 27 through 28 removed outlier: 4.167A pdb=" N THR B 63 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N VAL B 267 " --> pdb=" O THR B 63 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N GLU B 191 " --> pdb=" O LYS B 206 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LYS B 206 " --> pdb=" O GLU B 191 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N TYR B 204 " --> pdb=" O VAL B 193 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LYS B 195 " --> pdb=" O LYS B 202 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 49 through 50 removed outlier: 3.962A pdb=" N HIS B 49 " --> pdb=" O LEU B 277 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LEU B 277 " --> pdb=" O HIS B 49 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 54 through 55 removed outlier: 3.502A pdb=" N PHE B 55 " --> pdb=" O GLN B 271 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.566A pdb=" N GLN B 239 " --> pdb=" O ILE B 105 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 152 through 158 removed outlier: 3.743A pdb=" N MET B 153 " --> pdb=" O TYR B 144 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N GLY B 142 " --> pdb=" O SER B 155 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N PHE B 157 " --> pdb=" O PHE B 140 " (cutoff:3.500A) removed outlier: 7.583A pdb=" N PHE B 140 " --> pdb=" O PHE B 157 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N LEU B 141 " --> pdb=" O LEU B 244 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N ARG B 246 " --> pdb=" O LEU B 141 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N VAL B 143 " --> pdb=" O ARG B 246 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 312 through 317 removed outlier: 6.594A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N VAL B 610 " --> pdb=" O ILE B 651 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N CYS B 649 " --> pdb=" O TYR B 612 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 325 through 327 removed outlier: 3.753A pdb=" N VAL B 539 " --> pdb=" O GLY B 550 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N THR B 553 " --> pdb=" O ASP B 586 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N LEU B 585 " --> pdb=" O VAL B 576 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 356 through 358 removed outlier: 3.760A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N GLU B 516 " --> pdb=" O ASN B 394 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ILE B 434 " --> pdb=" O VAL B 511 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU B 513 " --> pdb=" O CYS B 432 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N CYS B 432 " --> pdb=" O LEU B 513 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 391 through 392 Processing sheet with id=AD3, first strand: chain 'B' and resid 452 through 454 removed outlier: 4.017A pdb=" N TYR B 453 " --> pdb=" O GLN B 493 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 565 through 566 removed outlier: 6.992A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'B' and resid 654 through 660 removed outlier: 6.366A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.993A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 9.211A pdb=" N VAL B 656 " --> pdb=" O THR B 696 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N SER B 673 " --> pdb=" O ILE B 693 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N TYR B 695 " --> pdb=" O CYS B 671 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N CYS B 671 " --> pdb=" O TYR B 695 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 702 through 703 Processing sheet with id=AD7, first strand: chain 'B' and resid 712 through 715 Processing sheet with id=AD8, first strand: chain 'B' and resid 718 through 722 removed outlier: 3.713A pdb=" N SER B 721 " --> pdb=" O THR B1066 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLU B 725 " --> pdb=" O PHE B1062 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 718 through 722 removed outlier: 3.713A pdb=" N SER B 721 " --> pdb=" O THR B1066 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA B1056 " --> pdb=" O GLY B1059 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AE2, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.685A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'B' and resid 1093 through 1097 Processing sheet with id=AE4, first strand: chain 'C' and resid 27 through 29 removed outlier: 3.686A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N THR C 63 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N VAL C 267 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ALA C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLU C 191 " --> pdb=" O LYS C 206 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LYS C 195 " --> pdb=" O LYS C 202 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LYS C 202 " --> pdb=" O LYS C 195 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N GLU C 224 " --> pdb=" O SER C 205 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 48 through 55 removed outlier: 4.407A pdb=" N HIS C 49 " --> pdb=" O LEU C 277 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LEU C 277 " --> pdb=" O HIS C 49 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N THR C 51 " --> pdb=" O PHE C 275 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N PHE C 275 " --> pdb=" O THR C 51 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ASP C 53 " --> pdb=" O ARG C 273 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ARG C 273 " --> pdb=" O ASP C 53 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.532A pdb=" N GLN C 239 " --> pdb=" O ILE C 105 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N VAL C 127 " --> pdb=" O VAL C 120 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 153 through 158 removed outlier: 4.268A pdb=" N MET C 153 " --> pdb=" O TYR C 144 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N GLY C 142 " --> pdb=" O SER C 155 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N PHE C 157 " --> pdb=" O PHE C 140 " (cutoff:3.500A) removed outlier: 8.129A pdb=" N PHE C 140 " --> pdb=" O PHE C 157 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 311 through 312 removed outlier: 3.763A pdb=" N GLY C 311 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N THR C 599 " --> pdb=" O GLY C 311 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N VAL C 610 " --> pdb=" O ILE C 651 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.191A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N SER C 399 " --> pdb=" O ASN C 354 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LYS C 356 " --> pdb=" O ALA C 397 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ALA C 397 " --> pdb=" O LYS C 356 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 5.981A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N TRP C 436 " --> pdb=" O ARG C 509 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N CYS C 432 " --> pdb=" O LEU C 513 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 452 through 453 Processing sheet with id=AF2, first strand: chain 'C' and resid 540 through 543 Processing sheet with id=AF3, first strand: chain 'C' and resid 551 through 553 removed outlier: 3.636A pdb=" N THR C 553 " --> pdb=" O ASP C 586 " (cutoff:3.500A) removed outlier: 5.760A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.048A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.812A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N SER C 673 " --> pdb=" O ILE C 693 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N TYR C 695 " --> pdb=" O CYS C 671 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N CYS C 671 " --> pdb=" O TYR C 695 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 717 through 728 removed outlier: 3.833A pdb=" N ASN C 717 " --> pdb=" O ALA C1070 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N VAL C1068 " --> pdb=" O THR C 719 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N SER C 721 " --> pdb=" O THR C1066 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N THR C 723 " --> pdb=" O HIS C1064 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N HIS C1064 " --> pdb=" O THR C 723 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N GLU C 725 " --> pdb=" O PHE C1062 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N PHE C1062 " --> pdb=" O GLU C 725 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LEU C 727 " --> pdb=" O VAL C1060 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ALA C1056 " --> pdb=" O GLY C1059 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 734 through 736 removed outlier: 3.633A pdb=" N THR C 859 " --> pdb=" O SER C 735 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 1120 through 1121 Processing sheet with id=AF8, first strand: chain 'C' and resid 1094 through 1097 removed outlier: 3.704A pdb=" N GLN C1113 " --> pdb=" O VAL C1104 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'D' and resid 347 through 348 removed outlier: 4.456A pdb=" N THR D 347 " --> pdb=" O LEU D 359 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N LEU D 359 " --> pdb=" O THR D 347 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF9 811 hydrogen bonds defined for protein. 2196 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 13.98 Time building geometry restraints manager: 12.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6067 1.33 - 1.45: 7547 1.45 - 1.57: 16719 1.57 - 1.69: 0 1.69 - 1.81: 194 Bond restraints: 30527 Sorted by residual: bond pdb=" N VAL D 283 " pdb=" CA VAL D 283 " ideal model delta sigma weight residual 1.458 1.494 -0.036 7.70e-03 1.69e+04 2.16e+01 bond pdb=" N VAL B1129 " pdb=" CA VAL B1129 " ideal model delta sigma weight residual 1.457 1.497 -0.040 1.15e-02 7.56e+03 1.21e+01 bond pdb=" N PHE B 329 " pdb=" CA PHE B 329 " ideal model delta sigma weight residual 1.462 1.488 -0.026 7.70e-03 1.69e+04 1.11e+01 bond pdb=" N VAL D 226 " pdb=" CA VAL D 226 " ideal model delta sigma weight residual 1.454 1.493 -0.039 1.19e-02 7.06e+03 1.10e+01 bond pdb=" N LEU D 423 " pdb=" CA LEU D 423 " ideal model delta sigma weight residual 1.453 1.493 -0.040 1.22e-02 6.72e+03 1.05e+01 ... (remaining 30522 not shown) Histogram of bond angle deviations from ideal: 99.83 - 106.66: 901 106.66 - 113.49: 16265 113.49 - 120.33: 11106 120.33 - 127.16: 12940 127.16 - 133.99: 311 Bond angle restraints: 41523 Sorted by residual: angle pdb=" N VAL D 226 " pdb=" CA VAL D 226 " pdb=" C VAL D 226 " ideal model delta sigma weight residual 111.90 102.71 9.19 8.10e-01 1.52e+00 1.29e+02 angle pdb=" N PRO A 330 " pdb=" CA PRO A 330 " pdb=" C PRO A 330 " ideal model delta sigma weight residual 111.41 121.77 -10.36 1.50e+00 4.44e-01 4.77e+01 angle pdb=" CA LEU D 423 " pdb=" C LEU D 423 " pdb=" O LEU D 423 " ideal model delta sigma weight residual 121.89 116.72 5.17 1.17e+00 7.31e-01 1.95e+01 angle pdb=" CA SER B 155 " pdb=" C SER B 155 " pdb=" N GLU B 156 " ideal model delta sigma weight residual 119.46 116.81 2.65 6.10e-01 2.69e+00 1.89e+01 angle pdb=" C PHE B 347 " pdb=" CA PHE B 347 " pdb=" CB PHE B 347 " ideal model delta sigma weight residual 116.53 110.20 6.33 1.47e+00 4.63e-01 1.85e+01 ... (remaining 41518 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.62: 17793 16.62 - 33.25: 364 33.25 - 49.87: 16 49.87 - 66.49: 7 66.49 - 83.12: 1 Dihedral angle restraints: 18181 sinusoidal: 7155 harmonic: 11026 Sorted by residual: dihedral pdb=" CB CYS B 480 " pdb=" SG CYS B 480 " pdb=" SG CYS B 488 " pdb=" CB CYS B 488 " ideal model delta sinusoidal sigma weight residual -86.00 -123.77 37.77 1 1.00e+01 1.00e-02 2.01e+01 dihedral pdb=" N SER D 602 " pdb=" C SER D 602 " pdb=" CA SER D 602 " pdb=" CB SER D 602 " ideal model delta harmonic sigma weight residual 122.80 133.27 -10.47 0 2.50e+00 1.60e-01 1.75e+01 dihedral pdb=" C SER D 602 " pdb=" N SER D 602 " pdb=" CA SER D 602 " pdb=" CB SER D 602 " ideal model delta harmonic sigma weight residual -122.60 -132.99 10.39 0 2.50e+00 1.60e-01 1.73e+01 ... (remaining 18178 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.085: 4233 0.085 - 0.171: 378 0.171 - 0.256: 17 0.256 - 0.341: 3 0.341 - 0.427: 2 Chirality restraints: 4633 Sorted by residual: chirality pdb=" CA SER D 602 " pdb=" N SER D 602 " pdb=" C SER D 602 " pdb=" CB SER D 602 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.55e+00 chirality pdb=" CA VAL D 226 " pdb=" N VAL D 226 " pdb=" C VAL D 226 " pdb=" CB VAL D 226 " both_signs ideal model delta sigma weight residual False 2.44 2.83 -0.39 2.00e-01 2.50e+01 3.84e+00 chirality pdb=" CA PRO A 330 " pdb=" N PRO A 330 " pdb=" C PRO A 330 " pdb=" CB PRO A 330 " both_signs ideal model delta sigma weight residual False 2.72 2.45 0.27 2.00e-01 2.50e+01 1.83e+00 ... (remaining 4630 not shown) Planarity restraints: 5390 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY D 422 " 0.014 2.00e-02 2.50e+03 2.76e-02 7.62e+00 pdb=" C GLY D 422 " -0.048 2.00e-02 2.50e+03 pdb=" O GLY D 422 " 0.018 2.00e-02 2.50e+03 pdb=" N LEU D 423 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 326 " 0.013 2.00e-02 2.50e+03 2.57e-02 6.61e+00 pdb=" C ILE A 326 " -0.044 2.00e-02 2.50e+03 pdb=" O ILE A 326 " 0.017 2.00e-02 2.50e+03 pdb=" N VAL A 327 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN B 334 " -0.012 2.00e-02 2.50e+03 2.37e-02 5.64e+00 pdb=" C ASN B 334 " 0.041 2.00e-02 2.50e+03 pdb=" O ASN B 334 " -0.015 2.00e-02 2.50e+03 pdb=" N LEU B 335 " -0.014 2.00e-02 2.50e+03 ... (remaining 5387 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 4943 2.77 - 3.30: 25821 3.30 - 3.83: 45768 3.83 - 4.37: 53695 4.37 - 4.90: 93781 Nonbonded interactions: 224008 Sorted by model distance: nonbonded pdb=" O ASN B 439 " pdb=" OG SER B 443 " model vdw 2.236 2.440 nonbonded pdb=" OG SER C 98 " pdb=" O LYS C 182 " model vdw 2.293 2.440 nonbonded pdb=" O GLY B 880 " pdb=" OG SER B 884 " model vdw 2.297 2.440 nonbonded pdb=" OG SER C 721 " pdb=" OG1 THR C1066 " model vdw 2.307 2.440 nonbonded pdb=" OG SER B 721 " pdb=" OG1 THR B1066 " model vdw 2.309 2.440 ... (remaining 224003 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Set up NCS constraints 0 29811 True False No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 143 5.16 5 C 19034 2.51 5 N 4973 2.21 5 O 5661 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables 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: 8.710 Set model interpretation parameters: 2.790 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 30.610 Check model and map are aligned: 0.000 Convert atoms to be neutral: 0.150 Process input model: 84.330 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:2.310 Internal consistency checks: 0.000 Total: 129.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.003 0.040 30527 Angle : 0.491 10.355 41523 Chirality : 0.044 0.427 4633 Planarity : 0.003 0.038 5390 Dihedral : 5.854 83.118 10952 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.03 % Allowed : 10.77 % Favored : 89.21 % Rotamer Outliers : 0.82 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 1.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.46 (0.10), residues: 3743 helix: -4.11 (0.08), residues: 814 sheet: -2.13 (0.19), residues: 642 loop : -2.88 (0.10), residues: 2287 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7486 Ramachandran restraints generated. 3743 Oldfield and 0 Emsley and 3743 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7486 Ramachandran restraints generated. 3743 Oldfield and 0 Emsley and 3743 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 3312 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 27 poor density : 336 time to evaluate : 3.665 Fit side-chains outliers start: 27 outliers final: 3 residues processed: 360 average time/residue: 0.4360 time to fit residues: 162.6855 Evaluate side-chains 135 residues out of total 3312 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 3 poor density : 132 time to evaluate : 3.591 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.2762 time to fit residues: 5.6105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 317 optimal weight: 6.9990 chunk 284 optimal weight: 0.9980 chunk 158 optimal weight: 0.9980 chunk 97 optimal weight: 0.0980 chunk 192 optimal weight: 4.9990 chunk 152 optimal weight: 1.9990 chunk 294 optimal weight: 4.9990 chunk 114 optimal weight: 0.8980 chunk 179 optimal weight: 6.9990 chunk 219 optimal weight: 5.9990 chunk 341 optimal weight: 0.0040 overall best weight: 0.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN A 61 ASN A 134 GLN A 207 HIS ** A 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 370 ASN A 394 ASN A 414 GLN A 460 ASN A 540 ASN A 564 GLN A 580 GLN A 675 GLN A 762 GLN ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 779 GLN A 784 GLN A 787 GLN A 872 GLN A 926 GLN A 935 GLN A 957 GLN A 992 GLN A1005 GLN A1036 GLN A1054 GLN A1064 HIS A1083 HIS A1119 ASN A1134 ASN A1142 GLN B 30 ASN B 61 ASN B 87 ASN B 115 GLN B 196 ASN B 207 HIS B 218 GLN B 271 GLN B 321 GLN B 540 ASN B 564 GLN B 641 ASN B 755 GLN B 779 GLN B 787 GLN B 804 GLN B 895 GLN B 920 GLN B 935 GLN B 954 GLN B1005 GLN ** B1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1119 ASN C 17 ASN C 49 HIS C 115 GLN C 125 ASN C 134 GLN C 183 GLN C 239 GLN C 271 GLN C 314 GLN C 321 GLN C 343 ASN C 409 GLN C 493 GLN C 519 HIS C 580 GLN C 607 GLN C 675 GLN C 774 GLN C 784 GLN C 787 GLN C 804 GLN C 872 GLN C 895 GLN C 920 GLN C 935 GLN C 954 GLN C 992 GLN ** C1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1083 HIS C1113 GLN C1134 ASN D 42 GLN D 81 GLN D 96 GLN D 101 GLN D 287 GLN D 290 ASN D 300 GLN D 305 GLN D 340 GLN D 380 GLN D 397 ASN ** D 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 442 GLN D 526 GLN D 531 GLN D 598 GLN D 599 ASN Total number of N/Q/H flips: 97 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.2601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.002 0.040 30527 Angle : 0.490 17.678 41523 Chirality : 0.041 0.185 4633 Planarity : 0.003 0.047 5390 Dihedral : 2.801 26.206 4058 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer Outliers : 0.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.86 (0.12), residues: 3743 helix: -1.38 (0.16), residues: 836 sheet: -1.47 (0.19), residues: 662 loop : -2.32 (0.11), residues: 2245 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7486 Ramachandran restraints generated. 3743 Oldfield and 0 Emsley and 3743 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7486 Ramachandran restraints generated. 3743 Oldfield and 0 Emsley and 3743 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 3312 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 6 poor density : 166 time to evaluate : 3.617 Fit side-chains outliers start: 6 outliers final: 0 residues processed: 172 average time/residue: 0.4093 time to fit residues: 76.0131 Evaluate side-chains 92 residues out of total 3312 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 92 time to evaluate : 3.823 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.2511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 189 optimal weight: 0.2980 chunk 105 optimal weight: 0.0970 chunk 284 optimal weight: 2.9990 chunk 232 optimal weight: 4.9990 chunk 94 optimal weight: 5.9990 chunk 342 optimal weight: 3.9990 chunk 369 optimal weight: 7.9990 chunk 304 optimal weight: 4.9990 chunk 339 optimal weight: 6.9990 chunk 116 optimal weight: 9.9990 chunk 274 optimal weight: 7.9990 overall best weight: 2.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 HIS A 66 HIS A 69 HIS ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 540 ASN ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 710 ASN A 824 ASN A 919 ASN A 953 ASN A 992 GLN A1002 GLN ** B 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 49 HIS B 66 HIS B 125 ASN ** B 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 710 ASN ** B 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 99 ASN C 334 ASN C 437 ASN C 498 GLN ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 895 GLN C 907 ASN C 965 GLN C 969 ASN C1101 HIS C1119 ASN D 34 HIS D 58 ASN ** D 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 290 ASN D 378 HIS ** D 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 397 ASN ** D 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.5180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.005 0.065 30527 Angle : 0.674 13.669 41523 Chirality : 0.042 0.172 4633 Planarity : 0.005 0.047 5390 Dihedral : 4.289 23.473 4058 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 15.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.21 (0.13), residues: 3743 helix: -0.46 (0.16), residues: 918 sheet: -1.16 (0.18), residues: 719 loop : -2.09 (0.12), residues: 2106 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7486 Ramachandran restraints generated. 3743 Oldfield and 0 Emsley and 3743 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7486 Ramachandran restraints generated. 3743 Oldfield and 0 Emsley and 3743 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 3312 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 105 time to evaluate : 3.490 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 105 average time/residue: 0.4312 time to fit residues: 51.3472 Evaluate side-chains 74 residues out of total 3312 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 74 time to evaluate : 4.112 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.0947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 337 optimal weight: 6.9990 chunk 257 optimal weight: 8.9990 chunk 177 optimal weight: 0.9980 chunk 37 optimal weight: 10.0000 chunk 163 optimal weight: 8.9990 chunk 229 optimal weight: 0.5980 chunk 343 optimal weight: 10.0000 chunk 363 optimal weight: 8.9990 chunk 179 optimal weight: 4.9990 chunk 325 optimal weight: 8.9990 chunk 97 optimal weight: 2.9990 overall best weight: 3.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 GLN ** A 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 87 ASN A 146 HIS A 196 ASN ** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 474 GLN A 493 GLN A 540 ASN ** A 607 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 641 ASN A 644 GLN ** A 928 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 17 ASN ** B 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 211 ASN ** B 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 564 GLN ** B 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1054 GLN B1101 HIS ** C 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 183 GLN C 211 ASN ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 895 GLN ** C 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 953 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1135 ASN D 34 HIS D 61 ASN D 63 ASN D 228 HIS ** D 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 508 ASN D 572 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.6792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.006 0.056 30527 Angle : 0.723 15.043 41523 Chirality : 0.043 0.166 4633 Planarity : 0.005 0.053 5390 Dihedral : 4.911 30.304 4058 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 22.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer Outliers : 0.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.08 (0.13), residues: 3743 helix: -0.25 (0.16), residues: 957 sheet: -1.04 (0.19), residues: 701 loop : -2.12 (0.12), residues: 2085 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7486 Ramachandran restraints generated. 3743 Oldfield and 0 Emsley and 3743 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7486 Ramachandran restraints generated. 3743 Oldfield and 0 Emsley and 3743 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 3312 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 2 poor density : 94 time to evaluate : 3.709 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 96 average time/residue: 0.4508 time to fit residues: 49.1291 Evaluate side-chains 71 residues out of total 3312 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 1 poor density : 70 time to evaluate : 3.592 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2768 time to fit residues: 4.9966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 302 optimal weight: 6.9990 chunk 206 optimal weight: 3.9990 chunk 5 optimal weight: 8.9990 chunk 270 optimal weight: 2.9990 chunk 149 optimal weight: 50.0000 chunk 310 optimal weight: 0.9990 chunk 251 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 185 optimal weight: 1.9990 chunk 326 optimal weight: 5.9990 chunk 91 optimal weight: 0.3980 overall best weight: 2.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 GLN ** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 540 ASN A 607 GLN ** B 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1054 GLN C 99 ASN C 544 ASN C 774 GLN C 895 GLN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 953 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 63 ASN D 228 HIS ** D 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 394 ASN D 401 HIS ** D 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 580 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.6967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.004 0.037 30527 Angle : 0.562 11.927 41523 Chirality : 0.041 0.174 4633 Planarity : 0.004 0.051 5390 Dihedral : 4.334 27.296 4058 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 16.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.73 (0.13), residues: 3743 helix: 0.21 (0.17), residues: 960 sheet: -0.97 (0.19), residues: 722 loop : -1.93 (0.13), residues: 2061 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7486 Ramachandran restraints generated. 3743 Oldfield and 0 Emsley and 3743 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7486 Ramachandran restraints generated. 3743 Oldfield and 0 Emsley and 3743 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 3312 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 90 time to evaluate : 4.098 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 90 average time/residue: 0.4332 time to fit residues: 45.1704 Evaluate side-chains 76 residues out of total 3312 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 76 time to evaluate : 3.696 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.7295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 122 optimal weight: 5.9990 chunk 327 optimal weight: 10.0000 chunk 71 optimal weight: 4.9990 chunk 213 optimal weight: 6.9990 chunk 89 optimal weight: 6.9990 chunk 363 optimal weight: 10.0000 chunk 301 optimal weight: 0.9980 chunk 168 optimal weight: 0.9990 chunk 30 optimal weight: 5.9990 chunk 120 optimal weight: 3.9990 chunk 190 optimal weight: 1.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 GLN A 61 ASN A 185 ASN A 207 HIS ** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 540 ASN A 607 GLN ** A1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 99 ASN B 314 GLN B 439 ASN ** B 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1101 HIS C 121 ASN ** C 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 564 GLN C 690 GLN C 895 GLN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 953 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 969 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 63 ASN D 149 ASN D 277 ASN ** D 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.7753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.005 0.044 30527 Angle : 0.630 14.063 41523 Chirality : 0.041 0.193 4633 Planarity : 0.004 0.074 5390 Dihedral : 4.685 27.678 4058 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 20.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.80 (0.13), residues: 3743 helix: 0.16 (0.17), residues: 954 sheet: -1.04 (0.19), residues: 712 loop : -1.96 (0.13), residues: 2077 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7486 Ramachandran restraints generated. 3743 Oldfield and 0 Emsley and 3743 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7486 Ramachandran restraints generated. 3743 Oldfield and 0 Emsley and 3743 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 3312 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 91 time to evaluate : 3.449 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 91 average time/residue: 0.4404 time to fit residues: 46.0535 Evaluate side-chains 71 residues out of total 3312 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 71 time to evaluate : 3.596 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.6087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 350 optimal weight: 9.9990 chunk 41 optimal weight: 8.9990 chunk 207 optimal weight: 5.9990 chunk 265 optimal weight: 0.9990 chunk 205 optimal weight: 0.5980 chunk 306 optimal weight: 1.9990 chunk 203 optimal weight: 0.4980 chunk 362 optimal weight: 9.9990 chunk 226 optimal weight: 1.9990 chunk 220 optimal weight: 10.0000 chunk 167 optimal weight: 0.8980 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 GLN ** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 607 GLN ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 953 ASN ** A1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 125 ASN ** B 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 907 ASN ** C 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 690 GLN C 895 GLN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 949 GLN C 953 ASN C 957 GLN ** C 969 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 63 ASN ** D 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.7548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.002 0.040 30527 Angle : 0.487 12.801 41523 Chirality : 0.041 0.175 4633 Planarity : 0.004 0.064 5390 Dihedral : 4.002 22.253 4058 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 12.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.32 (0.14), residues: 3743 helix: 0.82 (0.17), residues: 965 sheet: -0.88 (0.19), residues: 734 loop : -1.77 (0.13), residues: 2044 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7486 Ramachandran restraints generated. 3743 Oldfield and 0 Emsley and 3743 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7486 Ramachandran restraints generated. 3743 Oldfield and 0 Emsley and 3743 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 3312 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 99 time to evaluate : 3.948 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 99 average time/residue: 0.4634 time to fit residues: 51.8665 Evaluate side-chains 75 residues out of total 3312 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 75 time to evaluate : 3.717 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.9161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 224 optimal weight: 9.9990 chunk 144 optimal weight: 30.0000 chunk 216 optimal weight: 7.9990 chunk 109 optimal weight: 7.9990 chunk 71 optimal weight: 5.9990 chunk 70 optimal weight: 0.0030 chunk 230 optimal weight: 0.8980 chunk 246 optimal weight: 20.0000 chunk 179 optimal weight: 0.0070 chunk 33 optimal weight: 9.9990 chunk 284 optimal weight: 2.9990 overall best weight: 1.9812 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 GLN ** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 607 GLN ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 HIS ** B 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 907 ASN ** B1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 690 GLN C 895 GLN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 969 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.7945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.004 0.041 30527 Angle : 0.561 12.145 41523 Chirality : 0.041 0.177 4633 Planarity : 0.004 0.066 5390 Dihedral : 4.274 24.691 4058 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 17.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.37 (0.13), residues: 3743 helix: 0.74 (0.17), residues: 963 sheet: -0.93 (0.19), residues: 695 loop : -1.75 (0.13), residues: 2085 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7486 Ramachandran restraints generated. 3743 Oldfield and 0 Emsley and 3743 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7486 Ramachandran restraints generated. 3743 Oldfield and 0 Emsley and 3743 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 3312 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 92 time to evaluate : 3.809 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 92 average time/residue: 0.4442 time to fit residues: 46.7320 Evaluate side-chains 73 residues out of total 3312 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 73 time to evaluate : 3.642 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.7976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 329 optimal weight: 7.9990 chunk 347 optimal weight: 6.9990 chunk 316 optimal weight: 2.9990 chunk 337 optimal weight: 10.0000 chunk 203 optimal weight: 0.9990 chunk 147 optimal weight: 9.9990 chunk 265 optimal weight: 5.9990 chunk 103 optimal weight: 1.9990 chunk 305 optimal weight: 2.9990 chunk 319 optimal weight: 10.0000 chunk 336 optimal weight: 10.0000 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 GLN A 148 ASN ** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 540 ASN ** A 607 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 928 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 690 GLN C 895 GLN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 969 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1064 HIS ** C1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 63 ASN ** D 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.8648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.005 0.050 30527 Angle : 0.674 14.568 41523 Chirality : 0.043 0.247 4633 Planarity : 0.005 0.078 5390 Dihedral : 4.968 28.667 4058 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 24.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.55 % Favored : 93.45 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.79 (0.13), residues: 3743 helix: 0.09 (0.16), residues: 957 sheet: -1.11 (0.19), residues: 665 loop : -1.88 (0.13), residues: 2121 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7486 Ramachandran restraints generated. 3743 Oldfield and 0 Emsley and 3743 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7486 Ramachandran restraints generated. 3743 Oldfield and 0 Emsley and 3743 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 3312 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 91 time to evaluate : 4.103 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 91 average time/residue: 0.4556 time to fit residues: 47.7429 Evaluate side-chains 71 residues out of total 3312 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 71 time to evaluate : 3.764 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.1064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 221 optimal weight: 2.9990 chunk 357 optimal weight: 4.9990 chunk 217 optimal weight: 5.9990 chunk 169 optimal weight: 0.8980 chunk 248 optimal weight: 10.0000 chunk 374 optimal weight: 6.9990 chunk 344 optimal weight: 10.0000 chunk 298 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 230 optimal weight: 0.8980 chunk 182 optimal weight: 1.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 GLN ** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 540 ASN A 607 GLN ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 895 GLN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 969 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.8547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.003 0.043 30527 Angle : 0.555 11.631 41523 Chirality : 0.042 0.218 4633 Planarity : 0.004 0.057 5390 Dihedral : 4.495 25.762 4058 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 17.39 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.08 % Favored : 94.87 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.50 (0.13), residues: 3743 helix: 0.53 (0.17), residues: 955 sheet: -1.01 (0.19), residues: 670 loop : -1.78 (0.13), residues: 2118 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7486 Ramachandran restraints generated. 3743 Oldfield and 0 Emsley and 3743 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7486 Ramachandran restraints generated. 3743 Oldfield and 0 Emsley and 3743 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 3312 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 90 time to evaluate : 4.265 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 90 average time/residue: 0.4851 time to fit residues: 50.3848 Evaluate side-chains 72 residues out of total 3312 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 72 time to evaluate : 3.701 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.8909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 236 optimal weight: 10.0000 chunk 317 optimal weight: 2.9990 chunk 91 optimal weight: 5.9990 chunk 275 optimal weight: 4.9990 chunk 44 optimal weight: 0.3980 chunk 82 optimal weight: 1.9990 chunk 298 optimal weight: 3.9990 chunk 125 optimal weight: 0.5980 chunk 306 optimal weight: 3.9990 chunk 37 optimal weight: 9.9990 chunk 55 optimal weight: 10.0000 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 GLN ** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 607 GLN ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 314 GLN ** B 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 134 GLN ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 895 GLN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 969 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Group ADP refinement ******************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.063470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.043282 restraints weight = 289363.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.044515 restraints weight = 165557.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.044862 restraints weight = 103155.705| |-----------------------------------------------------------------------------| GEOMETRY RESTRAINTS LIBRARY: GEOSTD + MONOMER LIBRARY + CDL V1.2 DEVIATIONS FROM IDEAL VALUES. BOND : 0.004 0.041 30527 ANGLE : 0.569 12.058 41523 CHIRALITY : 0.041 0.220 4633 PLANARITY : 0.004 0.055 5390 DIHEDRAL : 4.489 25.239 4058 MIN NONBONDED DISTANCE : 2.089 MOLPROBITY STATISTICS. ALL-ATOM CLASHSCORE : 17.83 RAMACHANDRAN PLOT: OUTLIERS : 0.05 % ALLOWED : 5.85 % FAVORED : 94.10 % ROTAMER OUTLIERS : 0.00 % CBETA DEVIATIONS : 0.00 % PEPTIDE PLANE: CIS-PROLINE : 1.63 % CIS-GENERAL : 0.00 % TWISTED PROLINE : 0.00 % TWISTED GENERAL : 0.00 % RAMA-Z (RAMACHANDRAN PLOT Z-SCORE): INTERPRETATION: BAD |RAMA-Z| > 3; SUSPICIOUS 2 < |RAMA-Z| < 3; GOOD |RAMA-Z| < 2. SCORES FOR WHOLE/HELIX/SHEET/LOOP ARE SCALED INDEPENDENTLY; THEREFORE, THE VALUES ARE NOT RELATED IN A SIMPLE MANNER. WHOLE: -1.44 (0.13), RESIDUES: 3743 HELIX: 0.66 (0.17), RESIDUES: 948 SHEET: -1.05 (0.19), RESIDUES: 676 LOOP : -1.73 (0.13), RESIDUES: 2119 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.8724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.004 0.041 30527 Angle : 0.569 12.058 41523 Chirality : 0.041 0.220 4633 Planarity : 0.004 0.055 5390 Dihedral : 4.489 25.239 4058 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 17.83 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.85 % Favored : 94.10 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.13), residues: 3743 helix: 0.66 (0.17), residues: 948 sheet: -1.05 (0.19), residues: 676 loop : -1.73 (0.13), residues: 2119 =============================================================================== Job complete usr+sys time: 4617.56 seconds wall clock time: 87 minutes 43.85 seconds (5263.85 seconds total)