Starting phenix.real_space_refine on Fri Mar 6 10:03:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7a96_11686/03_2026/7a96_11686.cif Found real_map, /net/cci-nas-00/data/ceres_data/7a96_11686/03_2026/7a96_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/cci-nas-00/data/ceres_data/7a96_11686/03_2026/7a96_11686.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7a96_11686/03_2026/7a96_11686.map" model { file = "/net/cci-nas-00/data/ceres_data/7a96_11686/03_2026/7a96_11686.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7a96_11686/03_2026/7a96_11686.cif" } 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 Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.028 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 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. Process input model Symmetric amino acids flipped. Time to flip 178 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: {'PCIS': 1, 'PTRANS': 52, 'TRANS': 1011} 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: {'PCIS': 1, 'PTRANS': 52, 'TRANS': 1011} 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: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 562} Chain breaks: 1 Time building chain proxies: 6.33, per 1000 atoms: 0.21 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.25 Conformation dependent library (CDL) restraints added in 1.3 seconds 7486 Ramachandran restraints generated. 3743 Oldfield, 0 Emsley, 3743 emsley8k and 0 Phi/Psi/2. 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: 1.15 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: 7.03 Time building geometry restraints manager: 3.08 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: 0.00 - 2.07: 40946 2.07 - 4.14: 528 4.14 - 6.21: 45 6.21 - 8.28: 2 8.28 - 10.36: 2 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 3.040 nonbonded pdb=" OG SER C 98 " pdb=" O LYS C 182 " model vdw 2.293 3.040 nonbonded pdb=" O GLY B 880 " pdb=" OG SER B 884 " model vdw 2.297 3.040 nonbonded pdb=" OG SER C 721 " pdb=" OG1 THR C1066 " model vdw 2.307 3.040 nonbonded pdb=" OG SER B 721 " pdb=" OG1 THR B1066 " model vdw 2.309 3.040 ... (remaining 224003 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 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)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.500 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 27.720 Find NCS groups from input model: 0.550 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 30572 Z= 0.208 Angle : 0.492 10.355 41613 Z= 0.323 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 : 3.91 Ramachandran Plot: Outliers : 0.03 % Allowed : 10.77 % Favored : 89.21 % Rotamer: Outliers : 0.82 % Allowed : 3.59 % Favored : 95.59 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 1.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -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 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 646 TYR 0.009 0.000 TYR A1138 PHE 0.005 0.000 PHE A 329 TRP 0.002 0.000 TRP D 478 HIS 0.003 0.000 HIS C1083 Details of bonding type rmsd covalent geometry : bond 0.00285 (30527) covalent geometry : angle 0.49207 (41523) SS BOND : bond 0.00107 ( 45) SS BOND : angle 0.39616 ( 90) hydrogen bonds : bond 0.33986 ( 793) hydrogen bonds : angle 9.60664 ( 2196) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7486 Ramachandran restraints generated. 3743 Oldfield, 0 Emsley, 3743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7486 Ramachandran restraints generated. 3743 Oldfield, 0 Emsley, 3743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 3312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 336 time to evaluate : 1.121 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 212 LEU cc_start: 0.6780 (OUTLIER) cc_final: 0.6537 (pt) REVERT: A 276 LEU cc_start: 0.9449 (tp) cc_final: 0.9151 (tp) REVERT: A 595 VAL cc_start: 0.9116 (t) cc_final: 0.8870 (t) REVERT: A 740 MET cc_start: 0.9505 (tpt) cc_final: 0.8909 (ttt) REVERT: A 784 GLN cc_start: 0.7681 (mm-40) cc_final: 0.7414 (mp10) REVERT: A 888 PHE cc_start: 0.9149 (p90) cc_final: 0.8748 (p90) REVERT: A 955 ASN cc_start: 0.9169 (m-40) cc_final: 0.8914 (m110) REVERT: A 984 LEU cc_start: 0.9060 (mt) cc_final: 0.8653 (tp) REVERT: A 994 ASP cc_start: 0.9255 (t70) cc_final: 0.8992 (p0) REVERT: A 1018 ILE cc_start: 0.9608 (mm) cc_final: 0.9295 (tp) REVERT: A 1081 ILE cc_start: 0.9114 (mt) cc_final: 0.8908 (tp) REVERT: B 297 SER cc_start: 0.9267 (m) cc_final: 0.8932 (p) REVERT: B 650 LEU cc_start: 0.9608 (tp) cc_final: 0.9276 (pt) REVERT: B 740 MET cc_start: 0.9051 (tpt) cc_final: 0.8548 (ttm) REVERT: B 742 ILE cc_start: 0.9833 (mt) cc_final: 0.9581 (tp) REVERT: B 752 LEU cc_start: 0.8996 (mt) cc_final: 0.8619 (pt) REVERT: B 759 PHE cc_start: 0.9131 (m-80) cc_final: 0.8906 (m-80) REVERT: B 780 GLU cc_start: 0.9374 (mt-10) cc_final: 0.9067 (mm-30) REVERT: B 858 LEU cc_start: 0.9230 (mt) cc_final: 0.8801 (tp) REVERT: B 878 LEU cc_start: 0.9582 (mt) cc_final: 0.9235 (mt) REVERT: B 882 ILE cc_start: 0.9478 (pt) cc_final: 0.9213 (tp) REVERT: B 965 GLN cc_start: 0.9386 (mt0) cc_final: 0.8801 (pt0) REVERT: C 88 ASP cc_start: 0.8640 (m-30) cc_final: 0.8170 (p0) REVERT: C 153 MET cc_start: 0.7340 (ppp) cc_final: 0.6972 (ppp) REVERT: C 417 LYS cc_start: 0.9564 (pttp) cc_final: 0.9332 (tmmt) REVERT: C 731 MET cc_start: 0.9083 (ptm) cc_final: 0.8541 (ptm) REVERT: C 740 MET cc_start: 0.9037 (tpt) cc_final: 0.8694 (ttm) REVERT: C 773 GLU cc_start: 0.9484 (tt0) cc_final: 0.9205 (tm-30) REVERT: C 902 MET cc_start: 0.9394 (tpp) cc_final: 0.8799 (tpp) REVERT: C 1018 ILE cc_start: 0.9690 (mm) cc_final: 0.9181 (tp) REVERT: C 1021 SER cc_start: 0.9293 (m) cc_final: 0.8793 (p) REVERT: C 1029 MET cc_start: 0.9155 (tpt) cc_final: 0.8866 (tpp) REVERT: C 1040 VAL cc_start: 0.8699 (t) cc_final: 0.8435 (t) REVERT: C 1081 ILE cc_start: 0.9577 (mt) cc_final: 0.9280 (tp) REVERT: D 213 ASP cc_start: 0.9188 (OUTLIER) cc_final: 0.8950 (p0) REVERT: D 366 MET cc_start: 0.9482 (ttt) cc_final: 0.9276 (ttt) REVERT: D 516 TYR cc_start: 0.8818 (t80) cc_final: 0.8167 (t80) outliers start: 27 outliers final: 6 residues processed: 360 average time/residue: 0.1919 time to fit residues: 111.9795 Evaluate side-chains 168 residues out of total 3312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 160 time to evaluate : 1.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 7.9990 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 6.9990 chunk 155 optimal weight: 30.0000 chunk 244 optimal weight: 0.5980 chunk 183 optimal weight: 6.9990 chunk 298 optimal weight: 6.9990 overall best weight: 3.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 HIS A 52 GLN A 61 ASN A 66 HIS A 69 HIS A 134 GLN A 146 HIS ** A 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 370 ASN A 394 ASN A 414 GLN A 422 ASN A 460 ASN A 493 GLN A 498 GLN A 540 ASN A 564 GLN A 580 GLN ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 675 GLN A 710 ASN A 762 GLN A 779 GLN A 787 GLN A 872 GLN A 926 GLN A 953 ASN A 957 GLN A 992 GLN A1002 GLN A1011 GLN A1054 GLN A1064 HIS A1119 ASN A1134 ASN A1142 GLN B 30 ASN B 49 HIS B 61 ASN B 66 HIS B 87 ASN B 99 ASN B 115 GLN B 183 GLN B 207 HIS B 218 GLN ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 321 GLN B 564 GLN B 641 ASN B 655 HIS B 755 GLN B 787 GLN B 804 GLN B 895 GLN B 920 GLN B 935 GLN B 954 GLN B 965 GLN B1005 GLN B1048 HIS ** B1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 17 ASN C 49 HIS ** C 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 99 ASN 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 414 GLN C 450 ASN C 493 GLN C 501 ASN C 519 HIS C 564 GLN C 580 GLN C 607 GLN C 675 GLN ** C 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 784 GLN C 787 GLN C 804 GLN C 872 GLN C 901 GLN C 920 GLN C 954 GLN C 992 GLN ** C1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1113 GLN C1134 ASN C1135 ASN D 42 GLN D 58 ASN D 81 GLN D 96 GLN D 101 GLN D 287 GLN D 300 GLN D 305 GLN D 340 GLN D 373 HIS D 380 GLN D 394 ASN D 397 ASN ** D 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 109 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.052201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.038542 restraints weight = 336504.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.039237 restraints weight = 193876.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.039597 restraints weight = 110171.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.039631 restraints weight = 94324.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.039738 restraints weight = 85413.154| |-----------------------------------------------------------------------------| r_work (final): 0.2763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.3425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 1.206 30572 Z= 0.478 Angle : 0.832 22.549 41613 Z= 0.430 Chirality : 0.045 0.247 4633 Planarity : 0.006 0.062 5390 Dihedral : 3.868 40.251 4058 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 0.12 % Allowed : 2.42 % Favored : 97.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.61 (0.12), residues: 3743 helix: -0.91 (0.16), residues: 879 sheet: -1.53 (0.18), residues: 703 loop : -2.23 (0.12), residues: 2161 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.028 0.001 ARG C1019 TYR 0.035 0.003 TYR A 369 PHE 0.029 0.003 PHE B 643 TRP 0.017 0.002 TRP C 104 HIS 0.013 0.002 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.01170 (30527) covalent geometry : angle 0.83163 (41523) SS BOND : bond 0.00392 ( 45) SS BOND : angle 1.13245 ( 90) hydrogen bonds : bond 0.05691 ( 793) hydrogen bonds : angle 6.30338 ( 2196) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7486 Ramachandran restraints generated. 3743 Oldfield, 0 Emsley, 3743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7486 Ramachandran restraints generated. 3743 Oldfield, 0 Emsley, 3743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 3312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 140 time to evaluate : 0.904 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 449 TYR cc_start: 0.9155 (m-10) cc_final: 0.8926 (m-10) REVERT: A 611 LEU cc_start: 0.9329 (tp) cc_final: 0.9040 (tp) REVERT: A 697 MET cc_start: 0.8408 (ppp) cc_final: 0.8095 (ppp) REVERT: A 731 MET cc_start: 0.9347 (pmm) cc_final: 0.9005 (pmm) REVERT: A 740 MET cc_start: 0.9483 (tpt) cc_final: 0.9006 (ttt) REVERT: A 759 PHE cc_start: 0.9126 (m-80) cc_final: 0.8706 (m-80) REVERT: A 762 GLN cc_start: 0.9683 (mt0) cc_final: 0.9011 (mp10) REVERT: A 909 ILE cc_start: 0.9611 (pt) cc_final: 0.9358 (mm) REVERT: A 984 LEU cc_start: 0.9155 (mt) cc_final: 0.8803 (tp) REVERT: A 994 ASP cc_start: 0.9281 (t70) cc_final: 0.8867 (p0) REVERT: B 40 ASP cc_start: 0.8749 (t0) cc_final: 0.8483 (t70) REVERT: B 55 PHE cc_start: 0.9054 (m-10) cc_final: 0.8554 (m-10) REVERT: B 595 VAL cc_start: 0.9421 (t) cc_final: 0.9189 (t) REVERT: B 740 MET cc_start: 0.9308 (tpt) cc_final: 0.8862 (ttt) REVERT: B 780 GLU cc_start: 0.9363 (mt-10) cc_final: 0.9114 (mt-10) REVERT: B 858 LEU cc_start: 0.9533 (mt) cc_final: 0.9128 (tp) REVERT: B 878 LEU cc_start: 0.9717 (mt) cc_final: 0.9506 (mt) REVERT: C 153 MET cc_start: 0.7850 (ppp) cc_final: 0.7526 (ppp) REVERT: C 297 SER cc_start: 0.9350 (m) cc_final: 0.9030 (p) REVERT: C 731 MET cc_start: 0.9476 (ptm) cc_final: 0.9073 (ptm) REVERT: C 740 MET cc_start: 0.9403 (tpt) cc_final: 0.8923 (ttt) REVERT: C 902 MET cc_start: 0.9805 (tpp) cc_final: 0.9556 (tpp) REVERT: C 1029 MET cc_start: 0.9576 (tpt) cc_final: 0.9320 (tpp) REVERT: D 516 TYR cc_start: 0.8908 (t80) cc_final: 0.8173 (t80) outliers start: 4 outliers final: 0 residues processed: 143 average time/residue: 0.1734 time to fit residues: 41.8907 Evaluate side-chains 96 residues out of total 3312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 96 time to evaluate : 1.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 360 optimal weight: 10.0000 chunk 148 optimal weight: 0.5980 chunk 371 optimal weight: 0.9990 chunk 241 optimal weight: 0.9990 chunk 361 optimal weight: 5.9990 chunk 81 optimal weight: 6.9990 chunk 374 optimal weight: 9.9990 chunk 211 optimal weight: 1.9990 chunk 89 optimal weight: 0.6980 chunk 106 optimal weight: 9.9990 chunk 213 optimal weight: 0.8980 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 498 GLN A 919 ASN A1011 GLN A1036 GLN B 183 GLN B 245 HIS ** B 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 540 ASN B 895 GLN B1101 HIS ** C 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 965 GLN ** C1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 401 HIS ** D 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.054107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.038699 restraints weight = 327903.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.039711 restraints weight = 163688.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.040408 restraints weight = 99493.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.040825 restraints weight = 70143.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.041115 restraints weight = 56344.622| |-----------------------------------------------------------------------------| r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.3500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 30572 Z= 0.109 Angle : 0.499 16.304 41613 Z= 0.250 Chirality : 0.041 0.233 4633 Planarity : 0.003 0.045 5390 Dihedral : 3.131 29.019 4058 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 0.09 % Allowed : 1.30 % Favored : 98.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.95 (0.13), residues: 3743 helix: 0.16 (0.18), residues: 859 sheet: -1.20 (0.18), residues: 701 loop : -2.01 (0.12), residues: 2183 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 514 TYR 0.030 0.001 TYR D 279 PHE 0.016 0.001 PHE C 643 TRP 0.010 0.001 TRP A 152 HIS 0.006 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00221 (30527) covalent geometry : angle 0.49823 (41523) SS BOND : bond 0.00117 ( 45) SS BOND : angle 0.87229 ( 90) hydrogen bonds : bond 0.04759 ( 793) hydrogen bonds : angle 5.26525 ( 2196) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7486 Ramachandran restraints generated. 3743 Oldfield, 0 Emsley, 3743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7486 Ramachandran restraints generated. 3743 Oldfield, 0 Emsley, 3743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 3312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 123 time to evaluate : 1.167 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.3187 (ptt) cc_final: 0.2260 (ptt) REVERT: A 449 TYR cc_start: 0.9126 (m-10) cc_final: 0.8785 (m-80) REVERT: A 731 MET cc_start: 0.9356 (pmm) cc_final: 0.9011 (pmm) REVERT: A 759 PHE cc_start: 0.9119 (m-80) cc_final: 0.8505 (m-80) REVERT: A 762 GLN cc_start: 0.9668 (mt0) cc_final: 0.8953 (mp10) REVERT: A 775 ASP cc_start: 0.9244 (m-30) cc_final: 0.9034 (m-30) REVERT: A 909 ILE cc_start: 0.9596 (pt) cc_final: 0.9376 (mm) REVERT: A 984 LEU cc_start: 0.9035 (mt) cc_final: 0.8627 (tp) REVERT: A 994 ASP cc_start: 0.9234 (t70) cc_final: 0.8778 (p0) REVERT: A 1036 GLN cc_start: 0.8616 (OUTLIER) cc_final: 0.8371 (mm-40) REVERT: B 40 ASP cc_start: 0.8869 (t0) cc_final: 0.8619 (t70) REVERT: B 55 PHE cc_start: 0.8950 (m-10) cc_final: 0.8387 (m-10) REVERT: B 740 MET cc_start: 0.9217 (tpt) cc_final: 0.8693 (ttm) REVERT: B 780 GLU cc_start: 0.9282 (mt-10) cc_final: 0.9012 (mt-10) REVERT: B 858 LEU cc_start: 0.9541 (mt) cc_final: 0.9093 (tp) REVERT: C 153 MET cc_start: 0.7578 (ppp) cc_final: 0.7195 (ppp) REVERT: C 297 SER cc_start: 0.9240 (m) cc_final: 0.8922 (p) REVERT: C 731 MET cc_start: 0.9585 (ptm) cc_final: 0.8945 (ptm) REVERT: C 740 MET cc_start: 0.9375 (tpt) cc_final: 0.8857 (ttt) REVERT: C 902 MET cc_start: 0.9744 (tpp) cc_final: 0.9482 (tpp) REVERT: C 1021 SER cc_start: 0.9649 (m) cc_final: 0.9448 (p) REVERT: D 474 MET cc_start: 0.8739 (tmm) cc_final: 0.8451 (tmm) REVERT: D 480 MET cc_start: 0.9695 (mmp) cc_final: 0.9379 (mpp) REVERT: D 516 TYR cc_start: 0.8867 (t80) cc_final: 0.8109 (t80) REVERT: D 557 MET cc_start: 0.8447 (ppp) cc_final: 0.8194 (ppp) outliers start: 3 outliers final: 0 residues processed: 126 average time/residue: 0.1758 time to fit residues: 38.1328 Evaluate side-chains 93 residues out of total 3312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 92 time to evaluate : 1.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 68 optimal weight: 0.9990 chunk 91 optimal weight: 5.9990 chunk 157 optimal weight: 6.9990 chunk 275 optimal weight: 1.9990 chunk 182 optimal weight: 2.9990 chunk 213 optimal weight: 2.9990 chunk 274 optimal weight: 0.9990 chunk 254 optimal weight: 10.0000 chunk 61 optimal weight: 5.9990 chunk 314 optimal weight: 1.9990 chunk 355 optimal weight: 9.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A 354 ASN A 580 GLN A 824 ASN A 895 GLN A1036 GLN ** B 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 779 GLN B 895 GLN B1054 GLN ** C 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 334 ASN C 437 ASN C 450 ASN C 907 ASN C 935 GLN ** C1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 373 HIS ** D 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.046851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.2635 r_free = 0.2635 target = 0.028241 restraints weight = 299217.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2683 r_free = 0.2683 target = 0.029334 restraints weight = 170033.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.2715 r_free = 0.2715 target = 0.030122 restraints weight = 114331.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.2737 r_free = 0.2737 target = 0.030621 restraints weight = 86097.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2749 r_free = 0.2749 target = 0.030902 restraints weight = 70580.178| |-----------------------------------------------------------------------------| r_work (final): 0.2695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.4328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 30572 Z= 0.178 Angle : 0.561 15.807 41613 Z= 0.286 Chirality : 0.041 0.237 4633 Planarity : 0.004 0.044 5390 Dihedral : 3.395 21.399 4058 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 0.06 % Allowed : 2.29 % Favored : 97.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.67 (0.13), residues: 3743 helix: 0.39 (0.17), residues: 905 sheet: -1.01 (0.19), residues: 685 loop : -1.88 (0.13), residues: 2153 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 905 TYR 0.014 0.001 TYR D 521 PHE 0.018 0.001 PHE B 759 TRP 0.024 0.001 TRP D 271 HIS 0.008 0.001 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00363 (30527) covalent geometry : angle 0.56081 (41523) SS BOND : bond 0.00223 ( 45) SS BOND : angle 0.74280 ( 90) hydrogen bonds : bond 0.03956 ( 793) hydrogen bonds : angle 4.96509 ( 2196) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7486 Ramachandran restraints generated. 3743 Oldfield, 0 Emsley, 3743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7486 Ramachandran restraints generated. 3743 Oldfield, 0 Emsley, 3743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 3312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 103 time to evaluate : 1.200 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.3738 (ptt) cc_final: 0.2683 (ptt) REVERT: A 449 TYR cc_start: 0.9181 (m-10) cc_final: 0.8956 (m-10) REVERT: A 611 LEU cc_start: 0.9456 (tp) cc_final: 0.9202 (tp) REVERT: A 731 MET cc_start: 0.9365 (pmm) cc_final: 0.9065 (pmm) REVERT: A 740 MET cc_start: 0.9460 (tpt) cc_final: 0.9155 (tpp) REVERT: A 775 ASP cc_start: 0.9358 (m-30) cc_final: 0.9131 (m-30) REVERT: A 994 ASP cc_start: 0.9265 (t70) cc_final: 0.8795 (p0) REVERT: B 55 PHE cc_start: 0.8926 (m-10) cc_final: 0.8556 (m-10) REVERT: B 740 MET cc_start: 0.9228 (tpt) cc_final: 0.8725 (ttt) REVERT: C 153 MET cc_start: 0.7827 (ppp) cc_final: 0.7434 (ppp) REVERT: C 297 SER cc_start: 0.9353 (m) cc_final: 0.9013 (p) REVERT: C 731 MET cc_start: 0.9674 (ptm) cc_final: 0.8986 (ptm) REVERT: C 902 MET cc_start: 0.9796 (tpp) cc_final: 0.9495 (tpp) REVERT: C 1050 MET cc_start: 0.9054 (pmm) cc_final: 0.8788 (pmm) REVERT: D 462 MET cc_start: 0.8685 (ppp) cc_final: 0.8392 (ppp) REVERT: D 480 MET cc_start: 0.9660 (mmp) cc_final: 0.9357 (mpp) REVERT: D 516 TYR cc_start: 0.9012 (t80) cc_final: 0.8277 (t80) REVERT: D 557 MET cc_start: 0.8741 (ppp) cc_final: 0.8462 (ppp) outliers start: 2 outliers final: 0 residues processed: 105 average time/residue: 0.1866 time to fit residues: 33.5771 Evaluate side-chains 86 residues out of total 3312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 86 time to evaluate : 1.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 291 optimal weight: 3.9990 chunk 287 optimal weight: 3.9990 chunk 209 optimal weight: 0.2980 chunk 279 optimal weight: 0.4980 chunk 104 optimal weight: 2.9990 chunk 138 optimal weight: 0.2980 chunk 85 optimal weight: 3.9990 chunk 105 optimal weight: 8.9990 chunk 290 optimal weight: 6.9990 chunk 58 optimal weight: 0.9980 chunk 132 optimal weight: 7.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 564 GLN A 644 GLN B 196 ASN B 271 GLN B 895 GLN ** C 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 751 ASN ** C1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 380 GLN D 437 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.052229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.038677 restraints weight = 330817.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.039411 restraints weight = 180759.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.039822 restraints weight = 101149.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.039936 restraints weight = 77202.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.039977 restraints weight = 73656.234| |-----------------------------------------------------------------------------| r_work (final): 0.2754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.4455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 30572 Z= 0.107 Angle : 0.475 13.244 41613 Z= 0.239 Chirality : 0.041 0.220 4633 Planarity : 0.003 0.045 5390 Dihedral : 3.173 23.036 4058 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 0.03 % Allowed : 1.03 % Favored : 98.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.43 (0.13), residues: 3743 helix: 0.68 (0.18), residues: 914 sheet: -0.85 (0.19), residues: 705 loop : -1.78 (0.13), residues: 2124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B1000 TYR 0.009 0.001 TYR B 265 PHE 0.009 0.001 PHE B 377 TRP 0.017 0.001 TRP D 271 HIS 0.005 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00223 (30527) covalent geometry : angle 0.47387 (41523) SS BOND : bond 0.00140 ( 45) SS BOND : angle 0.79070 ( 90) hydrogen bonds : bond 0.03625 ( 793) hydrogen bonds : angle 4.61727 ( 2196) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7486 Ramachandran restraints generated. 3743 Oldfield, 0 Emsley, 3743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7486 Ramachandran restraints generated. 3743 Oldfield, 0 Emsley, 3743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 3312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 109 time to evaluate : 1.050 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.4105 (ptt) cc_final: 0.2763 (ptt) REVERT: A 449 TYR cc_start: 0.9192 (m-10) cc_final: 0.8978 (m-10) REVERT: A 731 MET cc_start: 0.9370 (pmm) cc_final: 0.9050 (pmm) REVERT: A 740 MET cc_start: 0.9448 (tpt) cc_final: 0.9194 (tpp) REVERT: A 742 ILE cc_start: 0.8959 (mt) cc_final: 0.8612 (tp) REVERT: A 994 ASP cc_start: 0.9186 (t70) cc_final: 0.8695 (p0) REVERT: A 1050 MET cc_start: 0.9134 (mtp) cc_final: 0.8609 (mmm) REVERT: B 55 PHE cc_start: 0.8656 (m-10) cc_final: 0.8059 (m-10) REVERT: B 740 MET cc_start: 0.9167 (tpt) cc_final: 0.8658 (ttt) REVERT: C 153 MET cc_start: 0.7810 (ppp) cc_final: 0.7430 (ppp) REVERT: C 297 SER cc_start: 0.9219 (m) cc_final: 0.8855 (p) REVERT: C 731 MET cc_start: 0.9664 (ptm) cc_final: 0.9016 (ptm) REVERT: C 902 MET cc_start: 0.9842 (tpp) cc_final: 0.9477 (tpp) REVERT: C 936 ASP cc_start: 0.9406 (m-30) cc_final: 0.9057 (p0) REVERT: C 1050 MET cc_start: 0.9098 (pmm) cc_final: 0.8773 (pmm) REVERT: D 270 MET cc_start: 0.4368 (ppp) cc_final: 0.3840 (ppp) REVERT: D 462 MET cc_start: 0.8565 (ppp) cc_final: 0.8208 (ppp) REVERT: D 480 MET cc_start: 0.9741 (mmp) cc_final: 0.9411 (mpp) REVERT: D 516 TYR cc_start: 0.8961 (t80) cc_final: 0.8226 (t80) REVERT: D 557 MET cc_start: 0.8738 (ppp) cc_final: 0.8451 (ppp) outliers start: 1 outliers final: 0 residues processed: 110 average time/residue: 0.1830 time to fit residues: 34.5770 Evaluate side-chains 86 residues out of total 3312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 86 time to evaluate : 1.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 152 optimal weight: 0.9980 chunk 238 optimal weight: 8.9990 chunk 255 optimal weight: 0.8980 chunk 92 optimal weight: 3.9990 chunk 205 optimal weight: 3.9990 chunk 190 optimal weight: 3.9990 chunk 219 optimal weight: 9.9990 chunk 191 optimal weight: 1.9990 chunk 321 optimal weight: 0.0570 chunk 145 optimal weight: 7.9990 chunk 160 optimal weight: 0.9990 overall best weight: 0.9902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 928 ASN A 953 ASN B 271 GLN B 895 GLN ** C 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 211 ASN ** C 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 34 HIS D 63 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.047049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.2636 r_free = 0.2636 target = 0.028370 restraints weight = 294476.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2685 r_free = 0.2685 target = 0.029467 restraints weight = 166969.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.2719 r_free = 0.2719 target = 0.030250 restraints weight = 111886.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2739 r_free = 0.2739 target = 0.030714 restraints weight = 84187.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2754 r_free = 0.2754 target = 0.031059 restraints weight = 69408.149| |-----------------------------------------------------------------------------| r_work (final): 0.2697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.4717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 30572 Z= 0.105 Angle : 0.461 12.324 41613 Z= 0.231 Chirality : 0.040 0.263 4633 Planarity : 0.003 0.045 5390 Dihedral : 3.063 18.507 4058 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 0.06 % Allowed : 0.85 % Favored : 99.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.21 (0.14), residues: 3743 helix: 0.96 (0.18), residues: 922 sheet: -0.74 (0.19), residues: 714 loop : -1.70 (0.13), residues: 2107 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1107 TYR 0.009 0.001 TYR A 91 PHE 0.011 0.001 PHE A 329 TRP 0.013 0.001 TRP A 886 HIS 0.005 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00218 (30527) covalent geometry : angle 0.46025 (41523) SS BOND : bond 0.00123 ( 45) SS BOND : angle 0.65618 ( 90) hydrogen bonds : bond 0.03306 ( 793) hydrogen bonds : angle 4.35302 ( 2196) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7486 Ramachandran restraints generated. 3743 Oldfield, 0 Emsley, 3743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7486 Ramachandran restraints generated. 3743 Oldfield, 0 Emsley, 3743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 3312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 104 time to evaluate : 1.120 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.3765 (ptt) cc_final: 0.2420 (ptt) REVERT: A 731 MET cc_start: 0.9382 (pmm) cc_final: 0.9010 (pmm) REVERT: A 740 MET cc_start: 0.9457 (tpt) cc_final: 0.9203 (tpp) REVERT: A 742 ILE cc_start: 0.8948 (mt) cc_final: 0.8588 (tp) REVERT: A 762 GLN cc_start: 0.9654 (mt0) cc_final: 0.9426 (mt0) REVERT: A 994 ASP cc_start: 0.9261 (t70) cc_final: 0.8784 (p0) REVERT: A 1050 MET cc_start: 0.9140 (mtp) cc_final: 0.8743 (mmm) REVERT: B 55 PHE cc_start: 0.8564 (m-10) cc_final: 0.8303 (m-10) REVERT: B 297 SER cc_start: 0.9238 (m) cc_final: 0.9018 (p) REVERT: B 543 PHE cc_start: 0.9412 (m-80) cc_final: 0.9189 (m-80) REVERT: B 740 MET cc_start: 0.9189 (tpt) cc_final: 0.8667 (ttt) REVERT: C 153 MET cc_start: 0.7825 (ppp) cc_final: 0.7437 (ppp) REVERT: C 297 SER cc_start: 0.9214 (m) cc_final: 0.8868 (p) REVERT: C 731 MET cc_start: 0.9692 (ptm) cc_final: 0.9009 (ptm) REVERT: C 902 MET cc_start: 0.9837 (tpp) cc_final: 0.9480 (tpp) REVERT: C 936 ASP cc_start: 0.9464 (m-30) cc_final: 0.9153 (p0) REVERT: C 1050 MET cc_start: 0.9176 (pmm) cc_final: 0.8513 (pmm) REVERT: D 270 MET cc_start: 0.4510 (ppp) cc_final: 0.4007 (ppp) REVERT: D 360 MET cc_start: 0.8094 (mmm) cc_final: 0.7820 (mmm) REVERT: D 462 MET cc_start: 0.8614 (ppp) cc_final: 0.8281 (ppp) REVERT: D 480 MET cc_start: 0.9649 (mmp) cc_final: 0.9357 (mpp) REVERT: D 516 TYR cc_start: 0.8981 (t80) cc_final: 0.8188 (t80) REVERT: D 557 MET cc_start: 0.8770 (ppp) cc_final: 0.8491 (ppp) outliers start: 2 outliers final: 1 residues processed: 106 average time/residue: 0.1793 time to fit residues: 32.7668 Evaluate side-chains 85 residues out of total 3312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 84 time to evaluate : 1.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 188 optimal weight: 0.9990 chunk 242 optimal weight: 0.9980 chunk 73 optimal weight: 0.0270 chunk 190 optimal weight: 0.2980 chunk 69 optimal weight: 0.0170 chunk 175 optimal weight: 0.0970 chunk 124 optimal weight: 7.9990 chunk 169 optimal weight: 0.9990 chunk 25 optimal weight: 8.9990 chunk 99 optimal weight: 0.0040 chunk 181 optimal weight: 1.9990 overall best weight: 0.0886 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 354 ASN A 493 GLN A 928 ASN ** A1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1119 ASN B 271 GLN B 895 GLN ** C 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 450 ASN ** C1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 34 HIS D 63 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.053464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.039831 restraints weight = 325780.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.040855 restraints weight = 168483.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.041698 restraints weight = 86433.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.041527 restraints weight = 72985.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.041593 restraints weight = 62837.303| |-----------------------------------------------------------------------------| r_work (final): 0.2792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.4651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 30572 Z= 0.076 Angle : 0.449 11.185 41613 Z= 0.222 Chirality : 0.041 0.200 4633 Planarity : 0.003 0.047 5390 Dihedral : 2.856 16.802 4058 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 0.03 % Allowed : 0.63 % Favored : 99.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.13 (0.14), residues: 3743 helix: 0.98 (0.18), residues: 920 sheet: -0.61 (0.19), residues: 725 loop : -1.66 (0.13), residues: 2098 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 319 TYR 0.010 0.001 TYR A 91 PHE 0.012 0.001 PHE C 318 TRP 0.014 0.001 TRP D 271 HIS 0.010 0.001 HIS D 34 Details of bonding type rmsd covalent geometry : bond 0.00157 (30527) covalent geometry : angle 0.44897 (41523) SS BOND : bond 0.00169 ( 45) SS BOND : angle 0.55952 ( 90) hydrogen bonds : bond 0.03213 ( 793) hydrogen bonds : angle 4.11906 ( 2196) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7486 Ramachandran restraints generated. 3743 Oldfield, 0 Emsley, 3743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7486 Ramachandran restraints generated. 3743 Oldfield, 0 Emsley, 3743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 3312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 108 time to evaluate : 1.223 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.4319 (ptt) cc_final: 0.3340 (ptt) REVERT: A 731 MET cc_start: 0.9374 (pmm) cc_final: 0.8984 (pmm) REVERT: A 742 ILE cc_start: 0.8850 (mt) cc_final: 0.8512 (tp) REVERT: A 762 GLN cc_start: 0.9617 (mt0) cc_final: 0.9383 (mt0) REVERT: A 994 ASP cc_start: 0.9169 (t70) cc_final: 0.8722 (p0) REVERT: A 1050 MET cc_start: 0.9185 (mtp) cc_final: 0.8849 (mmm) REVERT: B 55 PHE cc_start: 0.8459 (m-10) cc_final: 0.8066 (m-10) REVERT: B 297 SER cc_start: 0.9135 (m) cc_final: 0.8916 (p) REVERT: B 543 PHE cc_start: 0.9393 (m-80) cc_final: 0.9167 (m-80) REVERT: B 740 MET cc_start: 0.9147 (tpt) cc_final: 0.8649 (ttt) REVERT: B 780 GLU cc_start: 0.9293 (mt-10) cc_final: 0.9025 (mt-10) REVERT: B 895 GLN cc_start: 0.8797 (OUTLIER) cc_final: 0.8202 (pp30) REVERT: C 153 MET cc_start: 0.7823 (ppp) cc_final: 0.7487 (ppp) REVERT: C 297 SER cc_start: 0.9112 (m) cc_final: 0.8743 (p) REVERT: C 731 MET cc_start: 0.9649 (ptm) cc_final: 0.9012 (ptm) REVERT: C 902 MET cc_start: 0.9824 (tpp) cc_final: 0.9354 (tpp) REVERT: C 936 ASP cc_start: 0.9372 (m-30) cc_final: 0.9090 (p0) REVERT: C 1050 MET cc_start: 0.9132 (pmm) cc_final: 0.8805 (pmm) REVERT: D 270 MET cc_start: 0.4505 (ppp) cc_final: 0.3996 (ppp) REVERT: D 462 MET cc_start: 0.8569 (ppp) cc_final: 0.8201 (ppp) REVERT: D 480 MET cc_start: 0.9724 (mmp) cc_final: 0.9420 (mpp) REVERT: D 516 TYR cc_start: 0.8954 (t80) cc_final: 0.8238 (t80) REVERT: D 557 MET cc_start: 0.8733 (ppp) cc_final: 0.8442 (ppp) outliers start: 1 outliers final: 0 residues processed: 109 average time/residue: 0.1740 time to fit residues: 33.2244 Evaluate side-chains 88 residues out of total 3312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 87 time to evaluate : 1.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 167 optimal weight: 9.9990 chunk 216 optimal weight: 5.9990 chunk 256 optimal weight: 20.0000 chunk 333 optimal weight: 0.9980 chunk 281 optimal weight: 1.9990 chunk 6 optimal weight: 0.6980 chunk 42 optimal weight: 10.0000 chunk 241 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 108 optimal weight: 0.0170 chunk 299 optimal weight: 0.0170 overall best weight: 0.5256 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 271 GLN B 895 GLN ** C 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.052827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.039452 restraints weight = 330570.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.040052 restraints weight = 183165.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.040383 restraints weight = 102955.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.040536 restraints weight = 86416.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.040642 restraints weight = 78322.788| |-----------------------------------------------------------------------------| r_work (final): 0.2772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.4736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 30572 Z= 0.076 Angle : 0.438 11.569 41613 Z= 0.217 Chirality : 0.040 0.202 4633 Planarity : 0.003 0.044 5390 Dihedral : 2.802 17.573 4058 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 0.03 % Allowed : 0.09 % Favored : 99.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.01 (0.14), residues: 3743 helix: 1.13 (0.18), residues: 918 sheet: -0.54 (0.19), residues: 714 loop : -1.60 (0.13), residues: 2111 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 319 TYR 0.009 0.001 TYR A 91 PHE 0.010 0.001 PHE A 329 TRP 0.011 0.001 TRP D 271 HIS 0.003 0.000 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00161 (30527) covalent geometry : angle 0.43671 (41523) SS BOND : bond 0.00091 ( 45) SS BOND : angle 0.73180 ( 90) hydrogen bonds : bond 0.03062 ( 793) hydrogen bonds : angle 4.06240 ( 2196) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7486 Ramachandran restraints generated. 3743 Oldfield, 0 Emsley, 3743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7486 Ramachandran restraints generated. 3743 Oldfield, 0 Emsley, 3743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 3312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 104 time to evaluate : 1.202 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.3887 (ptt) cc_final: 0.2804 (ptt) REVERT: A 731 MET cc_start: 0.9339 (pmm) cc_final: 0.8961 (pmm) REVERT: A 742 ILE cc_start: 0.8887 (mt) cc_final: 0.8545 (tp) REVERT: A 762 GLN cc_start: 0.9625 (mt0) cc_final: 0.9399 (mt0) REVERT: A 994 ASP cc_start: 0.9216 (t70) cc_final: 0.8727 (p0) REVERT: A 1050 MET cc_start: 0.9250 (mtp) cc_final: 0.8770 (mmm) REVERT: B 55 PHE cc_start: 0.8513 (m-10) cc_final: 0.8069 (m-10) REVERT: B 177 MET cc_start: -0.0033 (ptt) cc_final: -0.3573 (mtt) REVERT: B 297 SER cc_start: 0.9219 (m) cc_final: 0.9014 (p) REVERT: B 543 PHE cc_start: 0.9433 (m-80) cc_final: 0.9202 (m-80) REVERT: B 740 MET cc_start: 0.9172 (tpt) cc_final: 0.8670 (ttt) REVERT: B 780 GLU cc_start: 0.9240 (mt-10) cc_final: 0.9029 (mt-10) REVERT: C 153 MET cc_start: 0.7833 (ppp) cc_final: 0.7486 (ppp) REVERT: C 297 SER cc_start: 0.9176 (m) cc_final: 0.8821 (p) REVERT: C 731 MET cc_start: 0.9666 (ptm) cc_final: 0.9060 (ptm) REVERT: C 902 MET cc_start: 0.9827 (tpp) cc_final: 0.9395 (tpp) REVERT: C 936 ASP cc_start: 0.9367 (m-30) cc_final: 0.9106 (p0) REVERT: C 1050 MET cc_start: 0.9145 (pmm) cc_final: 0.8842 (pmm) REVERT: D 270 MET cc_start: 0.4795 (ppp) cc_final: 0.4296 (ppp) REVERT: D 462 MET cc_start: 0.8530 (ppp) cc_final: 0.8145 (ppp) REVERT: D 516 TYR cc_start: 0.8961 (t80) cc_final: 0.8249 (t80) REVERT: D 557 MET cc_start: 0.8802 (ppp) cc_final: 0.8529 (ppp) outliers start: 1 outliers final: 0 residues processed: 105 average time/residue: 0.1767 time to fit residues: 32.3234 Evaluate side-chains 85 residues out of total 3312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 85 time to evaluate : 1.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 144 optimal weight: 30.0000 chunk 76 optimal weight: 4.9990 chunk 298 optimal weight: 4.9990 chunk 24 optimal weight: 10.0000 chunk 120 optimal weight: 0.7980 chunk 270 optimal weight: 3.9990 chunk 157 optimal weight: 2.9990 chunk 233 optimal weight: 6.9990 chunk 26 optimal weight: 2.9990 chunk 223 optimal weight: 0.9980 chunk 118 optimal weight: 0.9980 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 GLN A 493 GLN A 607 GLN ** B 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 895 GLN ** C 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 450 ASN ** C1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1054 GLN ** C1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 580 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.046037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.2598 r_free = 0.2598 target = 0.027576 restraints weight = 301472.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2645 r_free = 0.2645 target = 0.028597 restraints weight = 170855.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2677 r_free = 0.2677 target = 0.029317 restraints weight = 115187.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.2699 r_free = 0.2699 target = 0.029832 restraints weight = 87557.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2713 r_free = 0.2713 target = 0.030143 restraints weight = 71635.520| |-----------------------------------------------------------------------------| r_work (final): 0.2657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.5289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 30572 Z= 0.164 Angle : 0.523 12.694 41613 Z= 0.267 Chirality : 0.040 0.199 4633 Planarity : 0.003 0.043 5390 Dihedral : 3.209 16.726 4058 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.77 % Favored : 96.21 % Rotamer: Outliers : 0.03 % Allowed : 0.33 % Favored : 99.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.01 (0.14), residues: 3743 helix: 1.10 (0.18), residues: 930 sheet: -0.61 (0.19), residues: 735 loop : -1.57 (0.13), residues: 2078 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1107 TYR 0.013 0.001 TYR C1067 PHE 0.017 0.001 PHE A 377 TRP 0.015 0.001 TRP B 886 HIS 0.006 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00337 (30527) covalent geometry : angle 0.52207 (41523) SS BOND : bond 0.00163 ( 45) SS BOND : angle 0.82424 ( 90) hydrogen bonds : bond 0.03272 ( 793) hydrogen bonds : angle 4.33381 ( 2196) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7486 Ramachandran restraints generated. 3743 Oldfield, 0 Emsley, 3743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7486 Ramachandran restraints generated. 3743 Oldfield, 0 Emsley, 3743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 3312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 94 time to evaluate : 1.225 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.3962 (ptt) cc_final: 0.2610 (ptt) REVERT: A 611 LEU cc_start: 0.9573 (tp) cc_final: 0.9359 (tp) REVERT: A 697 MET cc_start: 0.8725 (ppp) cc_final: 0.8414 (ppp) REVERT: A 731 MET cc_start: 0.9345 (pmm) cc_final: 0.9108 (pmm) REVERT: A 742 ILE cc_start: 0.8981 (mt) cc_final: 0.8644 (tp) REVERT: B 55 PHE cc_start: 0.8628 (m-10) cc_final: 0.8143 (m-10) REVERT: B 543 PHE cc_start: 0.9434 (m-80) cc_final: 0.9192 (m-80) REVERT: B 740 MET cc_start: 0.9200 (tpt) cc_final: 0.8669 (ttt) REVERT: C 153 MET cc_start: 0.7981 (ppp) cc_final: 0.7616 (ppp) REVERT: C 297 SER cc_start: 0.9306 (m) cc_final: 0.8947 (p) REVERT: C 731 MET cc_start: 0.9699 (ptm) cc_final: 0.8979 (ptm) REVERT: C 902 MET cc_start: 0.9807 (tpp) cc_final: 0.9379 (tpp) REVERT: D 62 MET cc_start: 0.8353 (mtm) cc_final: 0.8017 (mpp) REVERT: D 270 MET cc_start: 0.4991 (ppp) cc_final: 0.4355 (ppp) REVERT: D 462 MET cc_start: 0.8587 (ppp) cc_final: 0.8227 (ppp) REVERT: D 516 TYR cc_start: 0.9060 (t80) cc_final: 0.8430 (t80) REVERT: D 557 MET cc_start: 0.8882 (ppp) cc_final: 0.8605 (ppp) outliers start: 1 outliers final: 0 residues processed: 95 average time/residue: 0.1693 time to fit residues: 28.2952 Evaluate side-chains 83 residues out of total 3312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 83 time to evaluate : 1.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 282 optimal weight: 0.7980 chunk 31 optimal weight: 0.3980 chunk 73 optimal weight: 0.0020 chunk 343 optimal weight: 8.9990 chunk 25 optimal weight: 1.9990 chunk 197 optimal weight: 5.9990 chunk 291 optimal weight: 3.9990 chunk 100 optimal weight: 0.6980 chunk 51 optimal weight: 3.9990 chunk 296 optimal weight: 0.6980 chunk 231 optimal weight: 6.9990 overall best weight: 0.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 271 GLN B 895 GLN ** C 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.051960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.037967 restraints weight = 330623.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.038874 restraints weight = 172149.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.039410 restraints weight = 103164.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.039637 restraints weight = 65702.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.039788 restraints weight = 59730.387| |-----------------------------------------------------------------------------| r_work (final): 0.2747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.5238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 30572 Z= 0.078 Angle : 0.449 10.806 41613 Z= 0.222 Chirality : 0.041 0.183 4633 Planarity : 0.003 0.097 5390 Dihedral : 3.018 18.244 4058 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.91 % Favored : 97.06 % Rotamer: Outliers : 0.03 % Allowed : 0.15 % Favored : 99.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.85 (0.14), residues: 3743 helix: 1.32 (0.18), residues: 922 sheet: -0.53 (0.19), residues: 721 loop : -1.49 (0.13), residues: 2100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 319 TYR 0.010 0.001 TYR B 674 PHE 0.012 0.001 PHE A 329 TRP 0.013 0.001 TRP A 886 HIS 0.005 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00162 (30527) covalent geometry : angle 0.44835 (41523) SS BOND : bond 0.00107 ( 45) SS BOND : angle 0.67518 ( 90) hydrogen bonds : bond 0.03060 ( 793) hydrogen bonds : angle 4.06135 ( 2196) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7486 Ramachandran restraints generated. 3743 Oldfield, 0 Emsley, 3743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7486 Ramachandran restraints generated. 3743 Oldfield, 0 Emsley, 3743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 3312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 96 time to evaluate : 1.172 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.4243 (ptt) cc_final: 0.3092 (ptt) REVERT: A 731 MET cc_start: 0.9402 (pmm) cc_final: 0.9161 (pmm) REVERT: A 742 ILE cc_start: 0.8887 (mt) cc_final: 0.8571 (tp) REVERT: A 762 GLN cc_start: 0.9575 (mt0) cc_final: 0.9317 (mt0) REVERT: A 1050 MET cc_start: 0.9305 (mtp) cc_final: 0.8795 (mmm) REVERT: B 55 PHE cc_start: 0.8518 (m-10) cc_final: 0.8071 (m-10) REVERT: B 297 SER cc_start: 0.9235 (m) cc_final: 0.9018 (p) REVERT: B 740 MET cc_start: 0.9122 (tpt) cc_final: 0.8595 (ttt) REVERT: B 869 MET cc_start: 0.9572 (ptm) cc_final: 0.9341 (ppp) REVERT: B 1010 GLN cc_start: 0.9489 (mt0) cc_final: 0.9115 (pp30) REVERT: C 153 MET cc_start: 0.7908 (ppp) cc_final: 0.7532 (ppp) REVERT: C 297 SER cc_start: 0.9174 (m) cc_final: 0.8803 (p) REVERT: C 731 MET cc_start: 0.9687 (ptm) cc_final: 0.9028 (ptm) REVERT: C 902 MET cc_start: 0.9847 (tpp) cc_final: 0.9384 (tpp) REVERT: D 62 MET cc_start: 0.8269 (mtm) cc_final: 0.8007 (mpp) REVERT: D 270 MET cc_start: 0.4975 (ppp) cc_final: 0.4331 (ppp) REVERT: D 462 MET cc_start: 0.8562 (ppp) cc_final: 0.8184 (ppp) REVERT: D 516 TYR cc_start: 0.9035 (t80) cc_final: 0.8390 (t80) REVERT: D 557 MET cc_start: 0.8829 (ppp) cc_final: 0.8541 (ppp) outliers start: 1 outliers final: 1 residues processed: 97 average time/residue: 0.1686 time to fit residues: 28.6635 Evaluate side-chains 83 residues out of total 3312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 82 time to evaluate : 1.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 168 optimal weight: 0.9990 chunk 301 optimal weight: 1.9990 chunk 273 optimal weight: 5.9990 chunk 73 optimal weight: 0.6980 chunk 161 optimal weight: 6.9990 chunk 275 optimal weight: 0.0970 chunk 84 optimal weight: 5.9990 chunk 174 optimal weight: 0.9980 chunk 367 optimal weight: 9.9990 chunk 91 optimal weight: 0.9980 chunk 170 optimal weight: 3.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 GLN ** A1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 271 GLN B 895 GLN B 907 ASN ** C 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 450 ASN ** C1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.051672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.037658 restraints weight = 332143.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.038597 restraints weight = 171026.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.039088 restraints weight = 104767.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.039351 restraints weight = 66257.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.039500 restraints weight = 59170.434| |-----------------------------------------------------------------------------| r_work (final): 0.2747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.5337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 30572 Z= 0.087 Angle : 0.445 11.070 41613 Z= 0.222 Chirality : 0.040 0.178 4633 Planarity : 0.003 0.088 5390 Dihedral : 2.971 15.872 4058 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.10 % Favored : 96.87 % Rotamer: Outliers : 0.03 % Allowed : 0.18 % Favored : 99.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.80 (0.14), residues: 3743 helix: 1.33 (0.18), residues: 932 sheet: -0.48 (0.19), residues: 724 loop : -1.46 (0.13), residues: 2087 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 319 TYR 0.009 0.001 TYR A 91 PHE 0.011 0.001 PHE A 329 TRP 0.011 0.001 TRP A 886 HIS 0.004 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00183 (30527) covalent geometry : angle 0.44430 (41523) SS BOND : bond 0.00117 ( 45) SS BOND : angle 0.69230 ( 90) hydrogen bonds : bond 0.02955 ( 793) hydrogen bonds : angle 4.03987 ( 2196) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5013.81 seconds wall clock time: 87 minutes 52.79 seconds (5272.79 seconds total)