Starting phenix.real_space_refine on Fri Mar 6 08:00:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wjy_32552/03_2026/7wjy_32552.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wjy_32552/03_2026/7wjy_32552.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.24 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7wjy_32552/03_2026/7wjy_32552.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wjy_32552/03_2026/7wjy_32552.map" model { file = "/net/cci-nas-00/data/ceres_data/7wjy_32552/03_2026/7wjy_32552.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wjy_32552/03_2026/7wjy_32552.cif" } resolution = 3.24 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.024 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 125 5.16 5 C 18774 2.51 5 N 4886 2.21 5 O 5644 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 38 residue(s): 0.02s 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: 29429 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 8014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1030, 8014 Classifications: {'peptide': 1030} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 58, 'TRANS': 971} Chain breaks: 7 Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 6, 'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 41 Chain: "B" Number of atoms: 971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 971 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 2, 'TRANS': 122} Chain: "C" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 805 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 7, 'TRANS': 99} Chain: "D" Number of atoms: 7978 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1025, 7978 Classifications: {'peptide': 1025} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 56, 'TRANS': 968} Chain breaks: 7 Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 6, 'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 41 Chain: "E" Number of atoms: 1698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1698 Classifications: {'peptide': 226} Link IDs: {'PTRANS': 11, 'TRANS': 214} Chain: "F" Number of atoms: 1577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1577 Classifications: {'peptide': 210} Link IDs: {'PTRANS': 16, 'TRANS': 193} Chain: "G" Number of atoms: 8050 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1033, 8050 Classifications: {'peptide': 1033} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 58, 'TRANS': 974} Chain breaks: 7 Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 6, 'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 41 Chain: "A" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "D" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "G" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Time building chain proxies: 5.79, per 1000 atoms: 0.20 Number of scatterers: 29429 At special positions: 0 Unit cell: (152.152, 147.896, 223.44, 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 125 16.00 O 5644 8.00 N 4886 7.00 C 18774 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 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 22 " - pdb=" SG CYS B 96 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 87 " distance=2.03 Simple disulfide: pdb=" SG CYS D 131 " - pdb=" SG CYS D 166 " distance=2.03 Simple disulfide: pdb=" SG CYS D 291 " - pdb=" SG CYS D 301 " distance=2.03 Simple disulfide: pdb=" SG CYS D 336 " - pdb=" SG CYS D 361 " distance=2.03 Simple disulfide: pdb=" SG CYS D 379 " - pdb=" SG CYS D 432 " distance=2.03 Simple disulfide: pdb=" SG CYS D 391 " - pdb=" SG CYS D 525 " distance=2.08 Simple disulfide: pdb=" SG CYS D 480 " - pdb=" SG CYS D 488 " distance=2.03 Simple disulfide: pdb=" SG CYS D 538 " - pdb=" SG CYS D 590 " distance=2.03 Simple disulfide: pdb=" SG CYS D 617 " - pdb=" SG CYS D 649 " distance=2.03 Simple disulfide: pdb=" SG CYS D 662 " - pdb=" SG CYS D 671 " distance=2.03 Simple disulfide: pdb=" SG CYS D 738 " - pdb=" SG CYS D 760 " distance=2.03 Simple disulfide: pdb=" SG CYS D 743 " - pdb=" SG CYS D 749 " distance=2.03 Simple disulfide: pdb=" SG CYS D1032 " - pdb=" SG CYS D1043 " distance=2.03 Simple disulfide: pdb=" SG CYS D1082 " - pdb=" SG CYS D1126 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 153 " - pdb=" SG CYS E 209 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 87 " distance=2.03 Simple disulfide: pdb=" SG CYS F 136 " - pdb=" SG CYS F 195 " distance=2.04 Simple disulfide: pdb=" SG CYS G 131 " - pdb=" SG CYS G 166 " distance=2.03 Simple disulfide: pdb=" SG CYS G 291 " - pdb=" SG CYS G 301 " distance=2.03 Simple disulfide: pdb=" SG CYS G 336 " - pdb=" SG CYS G 361 " distance=2.03 Simple disulfide: pdb=" SG CYS G 379 " - pdb=" SG CYS G 432 " distance=2.03 Simple disulfide: pdb=" SG CYS G 391 " - pdb=" SG CYS G 525 " distance=2.04 Simple disulfide: pdb=" SG CYS G 480 " - pdb=" SG CYS G 488 " distance=2.03 Simple disulfide: pdb=" SG CYS G 538 " - pdb=" SG CYS G 590 " distance=2.03 Simple disulfide: pdb=" SG CYS G 617 " - pdb=" SG CYS G 649 " distance=2.03 Simple disulfide: pdb=" SG CYS G 662 " - pdb=" SG CYS G 671 " distance=2.03 Simple disulfide: pdb=" SG CYS G 738 " - pdb=" SG CYS G 760 " distance=2.03 Simple disulfide: pdb=" SG CYS G 743 " - pdb=" SG CYS G 749 " distance=2.03 Simple disulfide: pdb=" SG CYS G1032 " - pdb=" SG CYS G1043 " distance=2.03 Simple disulfide: pdb=" SG CYS G1082 " - pdb=" SG CYS G1126 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A1301 " - " ASN A 282 " " NAG A1302 " - " ASN A 331 " " NAG A1303 " - " ASN A 709 " " NAG A1304 " - " ASN A 717 " " NAG A1305 " - " ASN A 801 " " NAG A1306 " - " ASN A1098 " " NAG A1307 " - " ASN A1134 " " NAG D1301 " - " ASN D 234 " " NAG D1302 " - " ASN D 282 " " NAG D1303 " - " ASN D 331 " " NAG D1304 " - " ASN D 616 " " NAG D1305 " - " ASN D 709 " " NAG D1306 " - " ASN D 717 " " NAG D1307 " - " ASN D 801 " " NAG D1308 " - " ASN D1098 " " NAG D1309 " - " ASN D1134 " " NAG G1301 " - " ASN G 282 " " NAG G1302 " - " ASN G 331 " " NAG G1303 " - " ASN G 616 " " NAG G1304 " - " ASN G 709 " " NAG G1305 " - " ASN G 717 " " NAG G1306 " - " ASN G 801 " " NAG G1307 " - " ASN G1098 " " NAG G1308 " - " ASN G1134 " Time building additional restraints: 2.56 Conformation dependent library (CDL) restraints added in 1.1 seconds 7400 Ramachandran restraints generated. 3700 Oldfield, 0 Emsley, 3700 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7016 Finding SS restraints... Secondary structure from input PDB file: 62 helices and 62 sheets defined 18.1% alpha, 18.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.89 Creating SS restraints... Processing helix chain 'A' and resid 294 through 303 removed outlier: 3.901A pdb=" N GLU A 298 " --> pdb=" O ASP A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 370 removed outlier: 4.073A pdb=" N TYR A 369 " --> pdb=" O SER A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 390 removed outlier: 3.773A pdb=" N ASP A 389 " --> pdb=" O LYS A 386 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N LEU A 390 " --> pdb=" O LEU A 387 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 386 through 390' Processing helix chain 'A' and resid 502 through 506 removed outlier: 3.526A pdb=" N HIS A 505 " --> pdb=" O GLY A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 742 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.668A pdb=" N ASN A 751 " --> pdb=" O THR A 747 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LEU A 754 " --> pdb=" O SER A 750 " (cutoff:3.500A) Processing helix chain 'A' and resid 757 through 781 removed outlier: 4.329A pdb=" N THR A 761 " --> pdb=" O GLY A 757 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU A 763 " --> pdb=" O PHE A 759 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL A 781 " --> pdb=" O ASN A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 824 Processing helix chain 'A' and resid 848 through 853 Processing helix chain 'A' and resid 866 through 882 removed outlier: 3.598A pdb=" N ALA A 879 " --> pdb=" O SER A 875 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLY A 880 " --> pdb=" O ALA A 876 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ILE A 882 " --> pdb=" O LEU A 878 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 907 removed outlier: 3.794A pdb=" N ALA A 903 " --> pdb=" O PRO A 899 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 919 Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.883A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 946 through 965 removed outlier: 4.211A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 977 through 982 removed outlier: 3.501A pdb=" N PHE A 981 " --> pdb=" O LEU A 977 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N SER A 982 " --> pdb=" O ASN A 978 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 977 through 982' Processing helix chain 'A' and resid 985 through 990 removed outlier: 3.901A pdb=" N GLU A 990 " --> pdb=" O PRO A 986 " (cutoff:3.500A) Processing helix chain 'A' and resid 992 through 1032 removed outlier: 3.815A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) removed outlier: 4.979A pdb=" N THR A 998 " --> pdb=" O ASP A 994 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ALA A1020 " --> pdb=" O ALA A1016 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1147 removed outlier: 4.063A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ASP A1146 " --> pdb=" O GLN A1142 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N SER A1147 " --> pdb=" O PRO A1143 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 91 removed outlier: 4.184A pdb=" N THR B 91 " --> pdb=" O ALA B 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 78 through 82 removed outlier: 3.681A pdb=" N GLU C 82 " --> pdb=" O ALA C 79 " (cutoff:3.500A) Processing helix chain 'D' and resid 294 through 302 Processing helix chain 'D' and resid 338 through 343 Processing helix chain 'D' and resid 366 through 370 removed outlier: 3.863A pdb=" N TYR D 369 " --> pdb=" O SER D 366 " (cutoff:3.500A) Processing helix chain 'D' and resid 386 through 390 removed outlier: 3.543A pdb=" N ASP D 389 " --> pdb=" O LYS D 386 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N LEU D 390 " --> pdb=" O LEU D 387 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 386 through 390' Processing helix chain 'D' and resid 502 through 506 removed outlier: 3.542A pdb=" N HIS D 505 " --> pdb=" O GLY D 502 " (cutoff:3.500A) Processing helix chain 'D' and resid 737 through 742 Processing helix chain 'D' and resid 747 through 755 removed outlier: 3.703A pdb=" N ASN D 751 " --> pdb=" O THR D 747 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLN D 755 " --> pdb=" O ASN D 751 " (cutoff:3.500A) Processing helix chain 'D' and resid 761 through 782 removed outlier: 4.195A pdb=" N THR D 778 " --> pdb=" O GLN D 774 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLN D 779 " --> pdb=" O ASP D 775 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N PHE D 782 " --> pdb=" O THR D 778 " (cutoff:3.500A) Processing helix chain 'D' and resid 817 through 826 removed outlier: 4.377A pdb=" N LEU D 821 " --> pdb=" O PRO D 817 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N LEU D 822 " --> pdb=" O ILE D 818 " (cutoff:3.500A) removed outlier: 5.234A pdb=" N PHE D 823 " --> pdb=" O GLU D 819 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ASN D 824 " --> pdb=" O ASP D 820 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N VAL D 826 " --> pdb=" O LEU D 822 " (cutoff:3.500A) Processing helix chain 'D' and resid 848 through 853 Processing helix chain 'D' and resid 854 through 857 Processing helix chain 'D' and resid 866 through 877 removed outlier: 3.586A pdb=" N LEU D 877 " --> pdb=" O TYR D 873 " (cutoff:3.500A) Processing helix chain 'D' and resid 886 through 891 removed outlier: 4.187A pdb=" N ALA D 890 " --> pdb=" O TRP D 886 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N GLY D 891 " --> pdb=" O THR D 887 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 886 through 891' Processing helix chain 'D' and resid 897 through 906 removed outlier: 3.801A pdb=" N ALA D 903 " --> pdb=" O PRO D 899 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N TYR D 904 " --> pdb=" O MET D 900 " (cutoff:3.500A) Processing helix chain 'D' and resid 919 through 941 removed outlier: 3.937A pdb=" N LYS D 933 " --> pdb=" O SER D 929 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ILE D 934 " --> pdb=" O ALA D 930 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLN D 935 " --> pdb=" O ILE D 931 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ASP D 936 " --> pdb=" O GLY D 932 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N SER D 939 " --> pdb=" O GLN D 935 " (cutoff:3.500A) Processing helix chain 'D' and resid 946 through 964 removed outlier: 3.925A pdb=" N VAL D 951 " --> pdb=" O LYS D 947 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N VAL D 952 " --> pdb=" O LEU D 948 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ASN D 960 " --> pdb=" O ALA D 956 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N VAL D 963 " --> pdb=" O LEU D 959 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LYS D 964 " --> pdb=" O ASN D 960 " (cutoff:3.500A) Processing helix chain 'D' and resid 976 through 981 removed outlier: 3.637A pdb=" N ILE D 980 " --> pdb=" O VAL D 976 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N PHE D 981 " --> pdb=" O LEU D 977 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 976 through 981' Processing helix chain 'D' and resid 988 through 994 removed outlier: 3.700A pdb=" N ASP D 994 " --> pdb=" O GLU D 990 " (cutoff:3.500A) Processing helix chain 'D' and resid 997 through 1028 removed outlier: 3.546A pdb=" N ALA D1020 " --> pdb=" O ALA D1016 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 91 removed outlier: 4.199A pdb=" N THR E 91 " --> pdb=" O ALA E 88 " (cutoff:3.500A) Processing helix chain 'F' and resid 78 through 82 removed outlier: 3.526A pdb=" N GLU F 82 " --> pdb=" O ALA F 79 " (cutoff:3.500A) Processing helix chain 'G' and resid 294 through 303 Processing helix chain 'G' and resid 337 through 342 removed outlier: 3.713A pdb=" N VAL G 341 " --> pdb=" O PRO G 337 " (cutoff:3.500A) Processing helix chain 'G' and resid 364 through 368 removed outlier: 3.898A pdb=" N VAL G 367 " --> pdb=" O ASP G 364 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU G 368 " --> pdb=" O TYR G 365 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 364 through 368' Processing helix chain 'G' and resid 403 through 408 removed outlier: 4.225A pdb=" N GLU G 406 " --> pdb=" O ARG G 403 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N VAL G 407 " --> pdb=" O GLY G 404 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ARG G 408 " --> pdb=" O ASP G 405 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 403 through 408' Processing helix chain 'G' and resid 417 through 422 removed outlier: 4.024A pdb=" N TYR G 421 " --> pdb=" O ASN G 417 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ASN G 422 " --> pdb=" O ILE G 418 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 417 through 422' Processing helix chain 'G' and resid 445 through 450 removed outlier: 4.641A pdb=" N TYR G 449 " --> pdb=" O SER G 446 " (cutoff:3.500A) Processing helix chain 'G' and resid 502 through 506 Processing helix chain 'G' and resid 746 through 755 removed outlier: 3.532A pdb=" N LEU G 752 " --> pdb=" O GLU G 748 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LEU G 754 " --> pdb=" O SER G 750 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N GLN G 755 " --> pdb=" O ASN G 751 " (cutoff:3.500A) Processing helix chain 'G' and resid 761 through 781 removed outlier: 3.546A pdb=" N VAL G 781 " --> pdb=" O ASN G 777 " (cutoff:3.500A) Processing helix chain 'G' and resid 816 through 826 removed outlier: 3.516A pdb=" N ASN G 824 " --> pdb=" O ASP G 820 " (cutoff:3.500A) Processing helix chain 'G' and resid 848 through 855 Processing helix chain 'G' and resid 866 through 884 removed outlier: 3.645A pdb=" N LEU G 877 " --> pdb=" O TYR G 873 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LEU G 878 " --> pdb=" O THR G 874 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ILE G 882 " --> pdb=" O LEU G 878 " (cutoff:3.500A) Processing helix chain 'G' and resid 886 through 891 removed outlier: 4.299A pdb=" N ALA G 890 " --> pdb=" O TRP G 886 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLY G 891 " --> pdb=" O THR G 887 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 886 through 891' Processing helix chain 'G' and resid 897 through 906 removed outlier: 3.635A pdb=" N TYR G 904 " --> pdb=" O MET G 900 " (cutoff:3.500A) Processing helix chain 'G' and resid 912 through 916 removed outlier: 3.925A pdb=" N VAL G 915 " --> pdb=" O THR G 912 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU G 916 " --> pdb=" O GLN G 913 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 912 through 916' Processing helix chain 'G' and resid 919 through 941 removed outlier: 3.554A pdb=" N SER G 929 " --> pdb=" O ASN G 925 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N GLY G 932 " --> pdb=" O ASN G 928 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N LYS G 933 " --> pdb=" O SER G 929 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N GLN G 935 " --> pdb=" O ILE G 931 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ASP G 936 " --> pdb=" O GLY G 932 " (cutoff:3.500A) Processing helix chain 'G' and resid 945 through 962 removed outlier: 4.313A pdb=" N VAL G 951 " --> pdb=" O LYS G 947 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N VAL G 952 " --> pdb=" O LEU G 948 " (cutoff:3.500A) Processing helix chain 'G' and resid 963 through 968 removed outlier: 3.717A pdb=" N SER G 968 " --> pdb=" O GLN G 965 " (cutoff:3.500A) Processing helix chain 'G' and resid 976 through 983 Processing helix chain 'G' and resid 985 through 1029 removed outlier: 3.959A pdb=" N VAL G 991 " --> pdb=" O PRO G 987 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ASP G 994 " --> pdb=" O GLU G 990 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N LEU G 996 " --> pdb=" O GLN G 992 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N THR G 998 " --> pdb=" O ASP G 994 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLY G 999 " --> pdb=" O ARG G 995 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU G1001 " --> pdb=" O ILE G 997 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N SER G1003 " --> pdb=" O GLY G 999 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLU G1017 " --> pdb=" O ILE G1013 " (cutoff:3.500A) Processing helix chain 'G' and resid 1143 through 1147 removed outlier: 4.206A pdb=" N SER G1147 " --> pdb=" O GLU G1144 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 31 Processing sheet with id=AA2, first strand: chain 'A' and resid 50 through 55 removed outlier: 3.587A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 removed outlier: 4.434A pdb=" N GLY A 107 " --> pdb=" O ARG A 237 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU A 118 " --> pdb=" O LYS A 129 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LYS A 129 " --> pdb=" O LEU A 118 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 224 through 227 removed outlier: 7.065A pdb=" N ILE A 201 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 314 removed outlier: 3.515A pdb=" N THR A 599 " --> pdb=" O GLY A 311 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 355 through 357 removed outlier: 3.548A pdb=" N ALA A 397 " --> pdb=" O LYS A 356 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 379 through 380 Processing sheet with id=AA8, first strand: chain 'A' and resid 539 through 543 Processing sheet with id=AA9, first strand: chain 'A' and resid 565 through 567 removed outlier: 3.913A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 660 removed outlier: 3.571A pdb=" N GLU A 654 " --> pdb=" O ILE A 692 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N THR A 696 " --> pdb=" O VAL A 656 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N ASN A 658 " --> pdb=" O THR A 696 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N SER A 691 " --> pdb=" O GLN A 675 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N GLN A 675 " --> pdb=" O SER A 691 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 712 through 722 removed outlier: 6.826A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N MET A1050 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.924A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 725 through 727 removed outlier: 3.668A pdb=" N ALA A1056 " --> pdb=" O GLY A1059 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 787 through 789 Processing sheet with id=AB5, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.839A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AB7, first strand: chain 'B' and resid 5 through 7 Processing sheet with id=AB8, first strand: chain 'B' and resid 11 through 12 removed outlier: 3.782A pdb=" N THR B 120 " --> pdb=" O TYR B 94 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N TYR B 94 " --> pdb=" O THR B 120 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N VAL B 122 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ALA B 92 " --> pdb=" O VAL B 122 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N ARG B 38 " --> pdb=" O TRP B 47 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N TRP B 47 " --> pdb=" O ARG B 38 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 11 through 12 removed outlier: 3.665A pdb=" N VAL C 12 " --> pdb=" O THR C 106 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'C' and resid 20 through 23 removed outlier: 3.868A pdb=" N ILE C 20 " --> pdb=" O LEU C 72 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 44 through 45 Processing sheet with id=AC3, first strand: chain 'D' and resid 27 through 31 removed outlier: 3.826A pdb=" N SER D 60 " --> pdb=" O SER D 31 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 47 through 55 removed outlier: 4.088A pdb=" N ASP D 287 " --> pdb=" O LYS D 278 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 84 through 85 removed outlier: 4.075A pdb=" N GLY D 107 " --> pdb=" O ARG D 237 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 89 through 96 removed outlier: 4.124A pdb=" N PHE D 92 " --> pdb=" O PHE D 190 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLU D 189 " --> pdb=" O LYS D 204 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VAL D 191 " --> pdb=" O TYR D 202 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N ILE D 201 " --> pdb=" O LEU D 226 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU D 226 " --> pdb=" O ILE D 201 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 128 through 129 Processing sheet with id=AC8, first strand: chain 'D' and resid 311 through 316 removed outlier: 7.300A pdb=" N VAL D 595 " --> pdb=" O THR D 315 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLY D 594 " --> pdb=" O GLN D 613 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 354 through 357 removed outlier: 4.127A pdb=" N ASN D 354 " --> pdb=" O SER D 399 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N SER D 399 " --> pdb=" O ASN D 354 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ALA D 397 " --> pdb=" O LYS D 356 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 379 through 380 Processing sheet with id=AD2, first strand: chain 'D' and resid 538 through 543 removed outlier: 3.846A pdb=" N PHE D 543 " --> pdb=" O LEU D 546 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 654 through 655 removed outlier: 6.449A pdb=" N GLU D 654 " --> pdb=" O ALA D 694 " (cutoff:3.500A) removed outlier: 8.652A pdb=" N THR D 696 " --> pdb=" O GLU D 654 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N SER D 691 " --> pdb=" O GLN D 675 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N GLN D 675 " --> pdb=" O SER D 691 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 712 through 728 removed outlier: 6.693A pdb=" N ALA D 713 " --> pdb=" O ASN D1074 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N ASN D1074 " --> pdb=" O ALA D 713 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N GLU D1072 " --> pdb=" O PRO D 715 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL D1068 " --> pdb=" O THR D 719 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N GLY D1059 " --> pdb=" O SER D1055 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N SER D1055 " --> pdb=" O GLY D1059 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N VAL D1061 " --> pdb=" O PRO D1053 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N LEU D1063 " --> pdb=" O SER D1051 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N SER D1051 " --> pdb=" O LEU D1063 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N VAL D1065 " --> pdb=" O LEU D1049 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 734 through 735 Processing sheet with id=AD6, first strand: chain 'D' and resid 1120 through 1121 Processing sheet with id=AD7, first strand: chain 'D' and resid 1094 through 1097 Processing sheet with id=AD8, first strand: chain 'E' and resid 5 through 7 Processing sheet with id=AD9, first strand: chain 'E' and resid 11 through 12 removed outlier: 3.757A pdb=" N THR E 120 " --> pdb=" O TYR E 94 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N TYR E 94 " --> pdb=" O THR E 120 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N VAL E 122 " --> pdb=" O ALA E 92 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ALA E 92 " --> pdb=" O VAL E 122 " (cutoff:3.500A) removed outlier: 5.836A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'E' and resid 155 through 156 removed outlier: 4.230A pdb=" N SER E 192 " --> pdb=" O PHE E 179 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'E' and resid 164 through 166 removed outlier: 3.969A pdb=" N THR E 164 " --> pdb=" O ASN E 212 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'F' and resid 11 through 12 removed outlier: 3.575A pdb=" N VAL F 12 " --> pdb=" O THR F 106 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE3 Processing sheet with id=AE4, first strand: chain 'F' and resid 20 through 23 removed outlier: 3.876A pdb=" N ILE F 20 " --> pdb=" O LEU F 72 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'F' and resid 43 through 45 Processing sheet with id=AE6, first strand: chain 'F' and resid 117 through 120 removed outlier: 3.895A pdb=" N PHE F 120 " --> pdb=" O VAL F 135 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N VAL F 135 " --> pdb=" O PHE F 120 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'F' and resid 150 through 151 removed outlier: 4.179A pdb=" N LYS F 151 " --> pdb=" O SER F 194 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N SER F 194 " --> pdb=" O LYS F 151 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'F' and resid 168 through 169 removed outlier: 3.574A pdb=" N ALA F 175 " --> pdb=" O LYS F 168 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'G' and resid 28 through 30 Processing sheet with id=AF1, first strand: chain 'G' and resid 36 through 37 removed outlier: 7.454A pdb=" N VAL G 36 " --> pdb=" O LEU G 223 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF1 Processing sheet with id=AF2, first strand: chain 'G' and resid 48 through 49 removed outlier: 3.577A pdb=" N VAL G 289 " --> pdb=" O LEU G 276 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N ASP G 287 " --> pdb=" O LYS G 278 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'G' and resid 54 through 55 removed outlier: 3.642A pdb=" N PHE G 55 " --> pdb=" O GLN G 271 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'G' and resid 66 through 67 Processing sheet with id=AF5, first strand: chain 'G' and resid 89 through 92 removed outlier: 4.007A pdb=" N GLU G 96 " --> pdb=" O ASN G 186 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'G' and resid 89 through 92 Processing sheet with id=AF7, first strand: chain 'G' and resid 101 through 107 removed outlier: 4.114A pdb=" N GLY G 103 " --> pdb=" O LEU G 241 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLY G 107 " --> pdb=" O ARG G 237 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'G' and resid 121 through 122 removed outlier: 3.531A pdb=" N ASN G 125 " --> pdb=" O ASN G 122 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'G' and resid 311 through 314 Processing sheet with id=AG1, first strand: chain 'G' and resid 354 through 358 removed outlier: 4.120A pdb=" N ASN G 354 " --> pdb=" O SER G 399 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N SER G 399 " --> pdb=" O ASN G 354 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N VAL G 395 " --> pdb=" O ILE G 358 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL G 512 " --> pdb=" O ASP G 398 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'G' and resid 375 through 376 removed outlier: 3.510A pdb=" N ALA G 435 " --> pdb=" O THR G 376 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'G' and resid 391 through 392 removed outlier: 3.938A pdb=" N PHE G 392 " --> pdb=" O VAL G 524 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'G' and resid 538 through 543 removed outlier: 3.601A pdb=" N VAL G 539 " --> pdb=" O GLY G 550 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLY G 550 " --> pdb=" O VAL G 539 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLY G 548 " --> pdb=" O PHE G 541 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N THR G 553 " --> pdb=" O ASP G 586 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'G' and resid 654 through 655 removed outlier: 6.024A pdb=" N GLU G 654 " --> pdb=" O ALA G 694 " (cutoff:3.500A) removed outlier: 8.226A pdb=" N THR G 696 " --> pdb=" O GLU G 654 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N GLN G 675 " --> pdb=" O SER G 691 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'G' and resid 715 through 728 removed outlier: 6.296A pdb=" N GLU G1072 " --> pdb=" O PRO G 715 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N GLY G1059 " --> pdb=" O SER G1055 " (cutoff:3.500A) removed outlier: 5.833A pdb=" N SER G1055 " --> pdb=" O GLY G1059 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N VAL G1061 " --> pdb=" O PRO G1053 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N LEU G1063 " --> pdb=" O SER G1051 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N SER G1051 " --> pdb=" O LEU G1063 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N VAL G1065 " --> pdb=" O LEU G1049 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'G' and resid 1120 through 1125 removed outlier: 4.674A pdb=" N ALA G1087 " --> pdb=" O SER G1123 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'G' and resid 1094 through 1097 748 hydrogen bonds defined for protein. 1980 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.91 Time building geometry restraints manager: 3.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 9289 1.34 - 1.46: 7412 1.46 - 1.59: 13269 1.59 - 1.72: 0 1.72 - 1.84: 154 Bond restraints: 30124 Sorted by residual: bond pdb=" CA ARG G 319 " pdb=" C ARG G 319 " ideal model delta sigma weight residual 1.522 1.469 0.053 1.08e-02 8.57e+03 2.40e+01 bond pdb=" CA PHE G 318 " pdb=" C PHE G 318 " ideal model delta sigma weight residual 1.524 1.466 0.058 1.30e-02 5.92e+03 1.99e+01 bond pdb=" CA CYS D 525 " pdb=" CB CYS D 525 " ideal model delta sigma weight residual 1.524 1.584 -0.060 1.62e-02 3.81e+03 1.39e+01 bond pdb=" CA ASP D 985 " pdb=" C ASP D 985 " ideal model delta sigma weight residual 1.524 1.480 0.043 1.26e-02 6.30e+03 1.18e+01 bond pdb=" N ARG G 319 " pdb=" CA ARG G 319 " ideal model delta sigma weight residual 1.461 1.420 0.041 1.19e-02 7.06e+03 1.18e+01 ... (remaining 30119 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.66: 40575 2.66 - 5.32: 424 5.32 - 7.98: 22 7.98 - 10.63: 5 10.63 - 13.29: 3 Bond angle restraints: 41029 Sorted by residual: angle pdb=" N PRO D 986 " pdb=" CA PRO D 986 " pdb=" C PRO D 986 " ideal model delta sigma weight residual 110.70 123.99 -13.29 1.22e+00 6.72e-01 1.19e+02 angle pdb=" N GLN G 134 " pdb=" CA GLN G 134 " pdb=" C GLN G 134 " ideal model delta sigma weight residual 113.19 101.76 11.43 1.58e+00 4.01e-01 5.23e+01 angle pdb=" N VAL A 991 " pdb=" CA VAL A 991 " pdb=" C VAL A 991 " ideal model delta sigma weight residual 113.71 106.99 6.72 9.50e-01 1.11e+00 5.00e+01 angle pdb=" C ASP D 985 " pdb=" N PRO D 986 " pdb=" CA PRO D 986 " ideal model delta sigma weight residual 120.38 113.36 7.02 1.03e+00 9.43e-01 4.64e+01 angle pdb=" N GLU D 988 " pdb=" CA GLU D 988 " pdb=" C GLU D 988 " ideal model delta sigma weight residual 113.50 105.88 7.62 1.23e+00 6.61e-01 3.84e+01 ... (remaining 41024 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 17295 17.94 - 35.88: 776 35.88 - 53.81: 142 53.81 - 71.75: 26 71.75 - 89.69: 12 Dihedral angle restraints: 18251 sinusoidal: 7336 harmonic: 10915 Sorted by residual: dihedral pdb=" CB CYS D 391 " pdb=" SG CYS D 391 " pdb=" SG CYS D 525 " pdb=" CB CYS D 525 " ideal model delta sinusoidal sigma weight residual -86.00 -40.70 -45.30 1 1.00e+01 1.00e-02 2.85e+01 dihedral pdb=" CA ASN D 99 " pdb=" C ASN D 99 " pdb=" N ILE D 100 " pdb=" CA ILE D 100 " ideal model delta harmonic sigma weight residual 180.00 -157.99 -22.01 0 5.00e+00 4.00e-02 1.94e+01 dihedral pdb=" CA ARG F 191 " pdb=" C ARG F 191 " pdb=" N SER F 192 " pdb=" CA SER F 192 " ideal model delta harmonic sigma weight residual 180.00 160.91 19.09 0 5.00e+00 4.00e-02 1.46e+01 ... (remaining 18248 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.154: 4692 0.154 - 0.308: 16 0.308 - 0.463: 1 0.463 - 0.617: 2 0.617 - 0.771: 1 Chirality restraints: 4712 Sorted by residual: chirality pdb=" C1 NAG G1301 " pdb=" ND2 ASN G 282 " pdb=" C2 NAG G1301 " pdb=" O5 NAG G1301 " both_signs ideal model delta sigma weight residual False -2.40 -1.63 -0.77 2.00e-01 2.50e+01 1.49e+01 chirality pdb=" C1 NAG A1301 " pdb=" ND2 ASN A 282 " pdb=" C2 NAG A1301 " pdb=" O5 NAG A1301 " both_signs ideal model delta sigma weight residual False -2.40 -1.85 -0.55 2.00e-01 2.50e+01 7.69e+00 chirality pdb=" CA PRO D 986 " pdb=" N PRO D 986 " pdb=" C PRO D 986 " pdb=" CB PRO D 986 " both_signs ideal model delta sigma weight residual False 2.72 2.24 0.47 2.00e-01 2.50e+01 5.62e+00 ... (remaining 4709 not shown) Planarity restraints: 5309 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1301 " -0.354 2.00e-02 2.50e+03 3.03e-01 1.15e+03 pdb=" C7 NAG A1301 " 0.087 2.00e-02 2.50e+03 pdb=" C8 NAG A1301 " -0.146 2.00e-02 2.50e+03 pdb=" N2 NAG A1301 " 0.539 2.00e-02 2.50e+03 pdb=" O7 NAG A1301 " -0.126 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG D1302 " 0.305 2.00e-02 2.50e+03 2.58e-01 8.31e+02 pdb=" C7 NAG D1302 " -0.078 2.00e-02 2.50e+03 pdb=" C8 NAG D1302 " 0.185 2.00e-02 2.50e+03 pdb=" N2 NAG D1302 " -0.445 2.00e-02 2.50e+03 pdb=" O7 NAG D1302 " 0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG D1305 " 0.304 2.00e-02 2.50e+03 2.56e-01 8.16e+02 pdb=" C7 NAG D1305 " -0.082 2.00e-02 2.50e+03 pdb=" C8 NAG D1305 " 0.191 2.00e-02 2.50e+03 pdb=" N2 NAG D1305 " -0.436 2.00e-02 2.50e+03 pdb=" O7 NAG D1305 " 0.023 2.00e-02 2.50e+03 ... (remaining 5306 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 3133 2.75 - 3.29: 28938 3.29 - 3.83: 48557 3.83 - 4.36: 56436 4.36 - 4.90: 96591 Nonbonded interactions: 233655 Sorted by model distance: nonbonded pdb=" OG1 THR A 470 " pdb=" OE1 GLN B 82 " model vdw 2.216 3.040 nonbonded pdb=" OG1 THR D 470 " pdb=" OE1 GLN E 82 " model vdw 2.220 3.040 nonbonded pdb=" OE1 GLN G 52 " pdb=" OG1 THR G 274 " model vdw 2.235 3.040 nonbonded pdb=" O GLY A 880 " pdb=" OG SER A 884 " model vdw 2.239 3.040 nonbonded pdb=" OG SER C 31 " pdb=" OD1 ASP C 49 " model vdw 2.240 3.040 ... (remaining 233650 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 26 through 243 or resid 262 through 1307)) selection = (chain 'D' and resid 26 through 1307) selection = (chain 'G' and (resid 26 through 68 or resid 80 through 243 or resid 262 through \ 1307)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.930 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.440 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 24.930 Find NCS groups from input model: 0.570 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:1.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6816 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 0.060 30193 Z= 0.212 Angle : 0.709 13.292 41191 Z= 0.441 Chirality : 0.046 0.771 4712 Planarity : 0.011 0.303 5285 Dihedral : 10.315 89.691 11100 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.22 % Allowed : 8.14 % Favored : 91.65 % Rotamer: Outliers : 6.82 % Allowed : 8.65 % Favored : 84.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.98 (0.11), residues: 3700 helix: -3.29 (0.13), residues: 619 sheet: -2.55 (0.16), residues: 894 loop : -3.83 (0.10), residues: 2187 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 357 TYR 0.007 0.001 TYR G 202 PHE 0.023 0.001 PHE G 318 TRP 0.007 0.001 TRP A 64 HIS 0.002 0.000 HIS E 213 Details of bonding type rmsd covalent geometry : bond 0.00334 (30124) covalent geometry : angle 0.70076 (41029) SS BOND : bond 0.00697 ( 45) SS BOND : angle 0.78592 ( 90) hydrogen bonds : bond 0.26321 ( 744) hydrogen bonds : angle 8.98290 ( 1980) link_NAG-ASN : bond 0.00347 ( 24) link_NAG-ASN : angle 2.59304 ( 72) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7400 Ramachandran restraints generated. 3700 Oldfield, 0 Emsley, 3700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7400 Ramachandran restraints generated. 3700 Oldfield, 0 Emsley, 3700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 930 residues out of total 3264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 219 poor density : 711 time to evaluate : 0.983 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: A 90 VAL cc_start: 0.8370 (m) cc_final: 0.8005 (p) REVERT: A 105 ILE cc_start: 0.8071 (mt) cc_final: 0.7752 (mp) REVERT: A 132 GLU cc_start: 0.7303 (mp0) cc_final: 0.7064 (mp0) REVERT: A 168 PHE cc_start: 0.7492 (OUTLIER) cc_final: 0.6851 (m-80) REVERT: A 188 ARG cc_start: 0.7111 (ptp90) cc_final: 0.6870 (ptp90) REVERT: A 200 LYS cc_start: 0.7587 (mttm) cc_final: 0.7342 (mttm) REVERT: A 269 TYR cc_start: 0.7917 (m-80) cc_final: 0.7638 (m-80) REVERT: A 316 SER cc_start: 0.7898 (t) cc_final: 0.7514 (p) REVERT: A 325 SER cc_start: 0.8032 (OUTLIER) cc_final: 0.7668 (m) REVERT: A 532 ASN cc_start: 0.7162 (t0) cc_final: 0.6789 (t0) REVERT: A 537 LYS cc_start: 0.7845 (OUTLIER) cc_final: 0.7631 (ttpp) REVERT: A 603 ASN cc_start: 0.7570 (t0) cc_final: 0.7369 (t0) REVERT: A 675 GLN cc_start: 0.6425 (mm-40) cc_final: 0.6162 (mm-40) REVERT: A 733 LYS cc_start: 0.8129 (mtmt) cc_final: 0.7810 (mtmt) REVERT: A 736 VAL cc_start: 0.8569 (m) cc_final: 0.8246 (t) REVERT: A 737 ASP cc_start: 0.6628 (t0) cc_final: 0.6417 (t70) REVERT: A 776 LYS cc_start: 0.7826 (ttpt) cc_final: 0.7479 (ttpt) REVERT: A 823 PHE cc_start: 0.7324 (m-80) cc_final: 0.7076 (m-80) REVERT: A 849 LEU cc_start: 0.8076 (tp) cc_final: 0.7873 (tp) REVERT: A 878 LEU cc_start: 0.8687 (OUTLIER) cc_final: 0.8324 (tp) REVERT: A 922 LEU cc_start: 0.8227 (tp) cc_final: 0.7982 (tt) REVERT: A 934 ILE cc_start: 0.7910 (mt) cc_final: 0.7695 (mm) REVERT: A 947 LYS cc_start: 0.7744 (OUTLIER) cc_final: 0.7496 (mtmm) REVERT: A 949 GLN cc_start: 0.6988 (mm110) cc_final: 0.6761 (mm-40) REVERT: A 969 LYS cc_start: 0.7931 (OUTLIER) cc_final: 0.7465 (pptt) REVERT: A 979 ASP cc_start: 0.6392 (m-30) cc_final: 0.6174 (t0) REVERT: A 1017 GLU cc_start: 0.6955 (tm-30) cc_final: 0.6654 (tm-30) REVERT: A 1028 LYS cc_start: 0.8361 (mttm) cc_final: 0.8053 (mttm) REVERT: A 1144 GLU cc_start: 0.6853 (tp30) cc_final: 0.6292 (tp30) REVERT: D 54 LEU cc_start: 0.7606 (mm) cc_final: 0.7054 (mt) REVERT: D 61 ASN cc_start: 0.7084 (m-40) cc_final: 0.6881 (p0) REVERT: D 105 ILE cc_start: 0.7878 (mt) cc_final: 0.7554 (mt) REVERT: D 126 VAL cc_start: 0.6926 (t) cc_final: 0.6702 (m) REVERT: D 188 ARG cc_start: 0.7247 (mtt-85) cc_final: 0.6875 (mtt-85) REVERT: D 189 GLU cc_start: 0.6803 (mm-30) cc_final: 0.6522 (mm-30) REVERT: D 206 THR cc_start: 0.8291 (t) cc_final: 0.7921 (t) REVERT: D 239 GLN cc_start: 0.6596 (tp40) cc_final: 0.6394 (tm-30) REVERT: D 307 THR cc_start: 0.8387 (m) cc_final: 0.8177 (p) REVERT: D 346 ARG cc_start: 0.7393 (mtt-85) cc_final: 0.6836 (mtt-85) REVERT: D 365 TYR cc_start: 0.6760 (m-80) cc_final: 0.6515 (m-80) REVERT: D 380 TYR cc_start: 0.6074 (m-80) cc_final: 0.5830 (m-80) REVERT: D 393 THR cc_start: 0.7998 (OUTLIER) cc_final: 0.7744 (p) REVERT: D 513 LEU cc_start: 0.7157 (mt) cc_final: 0.6938 (mt) REVERT: D 523 THR cc_start: 0.5854 (OUTLIER) cc_final: 0.5626 (p) REVERT: D 551 VAL cc_start: 0.8119 (t) cc_final: 0.7800 (m) REVERT: D 692 ILE cc_start: 0.8184 (mm) cc_final: 0.7684 (mt) REVERT: D 705 VAL cc_start: 0.8426 (t) cc_final: 0.8185 (p) REVERT: D 755 GLN cc_start: 0.7478 (mm-40) cc_final: 0.7156 (mm-40) REVERT: D 854 LYS cc_start: 0.8379 (ttmm) cc_final: 0.8032 (ttpp) REVERT: D 878 LEU cc_start: 0.8587 (OUTLIER) cc_final: 0.8364 (tt) REVERT: D 886 TRP cc_start: 0.8416 (p90) cc_final: 0.8003 (p90) REVERT: D 921 LYS cc_start: 0.7859 (tptp) cc_final: 0.7658 (tptp) REVERT: D 945 LEU cc_start: 0.7899 (mm) cc_final: 0.7601 (mp) REVERT: D 969 LYS cc_start: 0.8178 (OUTLIER) cc_final: 0.7975 (pttt) REVERT: D 1017 GLU cc_start: 0.6994 (tm-30) cc_final: 0.6701 (tm-30) REVERT: D 1029 MET cc_start: 0.7706 (ttm) cc_final: 0.7453 (ttm) REVERT: D 1066 THR cc_start: 0.7814 (p) cc_final: 0.7560 (p) REVERT: D 1086 LYS cc_start: 0.7955 (OUTLIER) cc_final: 0.7611 (pttm) REVERT: D 1118 ASP cc_start: 0.6538 (t0) cc_final: 0.6220 (t0) REVERT: D 1139 ASP cc_start: 0.7438 (p0) cc_final: 0.7230 (p0) REVERT: E 156 LYS cc_start: -0.1056 (OUTLIER) cc_final: -0.2090 (ttmp) REVERT: F 200 GLU cc_start: 0.0797 (OUTLIER) cc_final: 0.0147 (pm20) REVERT: G 28 TYR cc_start: 0.7786 (m-80) cc_final: 0.7520 (m-10) REVERT: G 53 ASP cc_start: 0.6028 (t0) cc_final: 0.5623 (t0) REVERT: G 99 ASN cc_start: 0.7689 (m-40) cc_final: 0.7429 (m-40) REVERT: G 129 LYS cc_start: 0.7567 (ttmm) cc_final: 0.7138 (mtmt) REVERT: G 136 CYS cc_start: 0.3102 (OUTLIER) cc_final: 0.2775 (p) REVERT: G 186 ASN cc_start: 0.7233 (p0) cc_final: 0.6558 (p0) REVERT: G 187 LEU cc_start: 0.7600 (tp) cc_final: 0.7210 (tp) REVERT: G 189 GLU cc_start: 0.7114 (OUTLIER) cc_final: 0.6066 (mm-30) REVERT: G 269 TYR cc_start: 0.7588 (m-80) cc_final: 0.7240 (m-80) REVERT: G 327 VAL cc_start: 0.8409 (t) cc_final: 0.8110 (p) REVERT: G 364 ASP cc_start: 0.7313 (t70) cc_final: 0.6962 (t70) REVERT: G 422 ASN cc_start: 0.7398 (m-40) cc_final: 0.6672 (m-40) REVERT: G 444 LYS cc_start: 0.6712 (OUTLIER) cc_final: 0.6441 (tppt) REVERT: G 453 TYR cc_start: 0.5322 (t80) cc_final: 0.4869 (t80) REVERT: G 493 ARG cc_start: 0.6581 (OUTLIER) cc_final: 0.6034 (mmp-170) REVERT: G 546 LEU cc_start: 0.7812 (OUTLIER) cc_final: 0.7540 (tt) REVERT: G 574 ASP cc_start: 0.7000 (t0) cc_final: 0.6769 (t0) REVERT: G 576 VAL cc_start: 0.8700 (p) cc_final: 0.8388 (t) REVERT: G 663 ASP cc_start: 0.6948 (t70) cc_final: 0.6554 (t70) REVERT: G 673 SER cc_start: 0.8668 (p) cc_final: 0.8290 (m) REVERT: G 711 SER cc_start: 0.8114 (m) cc_final: 0.7878 (p) REVERT: G 718 PHE cc_start: 0.7541 (p90) cc_final: 0.6991 (p90) REVERT: G 725 GLU cc_start: 0.6915 (tt0) cc_final: 0.6411 (tt0) REVERT: G 727 LEU cc_start: 0.7835 (mt) cc_final: 0.7563 (mt) REVERT: G 764 LYS cc_start: 0.8296 (tttt) cc_final: 0.8076 (ttmm) REVERT: G 776 LYS cc_start: 0.7500 (ttpt) cc_final: 0.7170 (ttpt) REVERT: G 790 LYS cc_start: 0.7557 (mtmm) cc_final: 0.7295 (mtmm) REVERT: G 821 LEU cc_start: 0.7902 (tt) cc_final: 0.7496 (mp) REVERT: G 855 PHE cc_start: 0.8121 (m-10) cc_final: 0.7824 (m-10) REVERT: G 921 LYS cc_start: 0.8026 (mmmt) cc_final: 0.7732 (mmmm) REVERT: G 976 VAL cc_start: 0.8549 (t) cc_final: 0.8268 (m) REVERT: G 993 ILE cc_start: 0.8702 (tp) cc_final: 0.8492 (mm) REVERT: G 1028 LYS cc_start: 0.7637 (mttm) cc_final: 0.7409 (mttt) REVERT: G 1111 GLU cc_start: 0.7094 (tt0) cc_final: 0.6785 (tt0) REVERT: G 1118 ASP cc_start: 0.6666 (t70) cc_final: 0.6429 (t70) REVERT: G 1125 ASN cc_start: 0.7379 (p0) cc_final: 0.7117 (p0) REVERT: G 1136 THR cc_start: 0.8114 (OUTLIER) cc_final: 0.7767 (p) outliers start: 219 outliers final: 92 residues processed: 881 average time/residue: 0.1943 time to fit residues: 266.8684 Evaluate side-chains 662 residues out of total 3264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 551 time to evaluate : 1.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 GLN Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 158 ARG Chi-restraints excluded: chain A residue 168 PHE Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 370 ASN Chi-restraints excluded: chain A residue 386 LYS Chi-restraints excluded: chain A residue 400 PHE Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 403 ARG Chi-restraints excluded: chain A residue 440 LYS Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 537 LYS Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 947 LYS Chi-restraints excluded: chain A residue 969 LYS Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain C residue 30 LYS Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 104 LYS Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 68 ILE Chi-restraints excluded: chain D residue 96 GLU Chi-restraints excluded: chain D residue 113 LYS Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 122 ASN Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 132 GLU Chi-restraints excluded: chain D residue 198 TYR Chi-restraints excluded: chain D residue 231 ILE Chi-restraints excluded: chain D residue 362 VAL Chi-restraints excluded: chain D residue 370 ASN Chi-restraints excluded: chain D residue 386 LYS Chi-restraints excluded: chain D residue 393 THR Chi-restraints excluded: chain D residue 400 PHE Chi-restraints excluded: chain D residue 402 ILE Chi-restraints excluded: chain D residue 440 LYS Chi-restraints excluded: chain D residue 458 LYS Chi-restraints excluded: chain D residue 523 THR Chi-restraints excluded: chain D residue 528 LYS Chi-restraints excluded: chain D residue 538 CYS Chi-restraints excluded: chain D residue 588 THR Chi-restraints excluded: chain D residue 590 CYS Chi-restraints excluded: chain D residue 873 TYR Chi-restraints excluded: chain D residue 878 LEU Chi-restraints excluded: chain D residue 969 LYS Chi-restraints excluded: chain D residue 988 GLU Chi-restraints excluded: chain D residue 1041 ASP Chi-restraints excluded: chain D residue 1086 LYS Chi-restraints excluded: chain D residue 1104 VAL Chi-restraints excluded: chain E residue 1 GLU Chi-restraints excluded: chain E residue 52 THR Chi-restraints excluded: chain E residue 156 LYS Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain E residue 205 GLN Chi-restraints excluded: chain F residue 30 LYS Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain F residue 74 ILE Chi-restraints excluded: chain F residue 104 LYS Chi-restraints excluded: chain F residue 128 GLN Chi-restraints excluded: chain F residue 158 LYS Chi-restraints excluded: chain F residue 161 VAL Chi-restraints excluded: chain F residue 197 VAL Chi-restraints excluded: chain F residue 200 GLU Chi-restraints excluded: chain G residue 68 ILE Chi-restraints excluded: chain G residue 127 VAL Chi-restraints excluded: chain G residue 131 CYS Chi-restraints excluded: chain G residue 136 CYS Chi-restraints excluded: chain G residue 189 GLU Chi-restraints excluded: chain G residue 194 ASN Chi-restraints excluded: chain G residue 229 LEU Chi-restraints excluded: chain G residue 351 TYR Chi-restraints excluded: chain G residue 361 CYS Chi-restraints excluded: chain G residue 403 ARG Chi-restraints excluded: chain G residue 408 ARG Chi-restraints excluded: chain G residue 414 GLN Chi-restraints excluded: chain G residue 440 LYS Chi-restraints excluded: chain G residue 444 LYS Chi-restraints excluded: chain G residue 458 LYS Chi-restraints excluded: chain G residue 462 LYS Chi-restraints excluded: chain G residue 468 ILE Chi-restraints excluded: chain G residue 478 LYS Chi-restraints excluded: chain G residue 493 ARG Chi-restraints excluded: chain G residue 511 VAL Chi-restraints excluded: chain G residue 517 LEU Chi-restraints excluded: chain G residue 528 LYS Chi-restraints excluded: chain G residue 546 LEU Chi-restraints excluded: chain G residue 825 LYS Chi-restraints excluded: chain G residue 1041 ASP Chi-restraints excluded: chain G residue 1086 LYS Chi-restraints excluded: chain G residue 1116 THR Chi-restraints excluded: chain G residue 1136 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 197 optimal weight: 4.9990 chunk 215 optimal weight: 0.7980 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 10.0000 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 10.0000 chunk 244 optimal weight: 40.0000 chunk 183 optimal weight: 2.9990 chunk 298 optimal weight: 7.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 GLN ** A 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 388 ASN A 414 GLN A 448 ASN A 762 GLN A 774 GLN A 784 GLN A 901 GLN A 955 ASN A1010 GLN A1011 GLN A1048 HIS B 39 GLN ** B 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 118 GLN C 6 GLN C 33 HIS C 37 GLN C 65 ASN C 88 GLN ** D 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 173 GLN D 186 ASN D 194 ASN D 218 GLN D 271 GLN D 317 ASN D 321 GLN D 388 ASN D 414 GLN D 450 ASN D 540 ASN D 564 GLN D 580 GLN D 762 GLN ** D 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 853 GLN D 895 GLN D 901 GLN D 914 ASN D 949 GLN ** D 960 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 978 ASN D1005 GLN D1011 GLN D1048 HIS D1119 ASN D1125 ASN E 39 GLN E 54 ASN E 118 GLN E 205 GLN F 6 GLN F 33 HIS F 37 GLN F 88 GLN F 110 GLN F 128 GLN F 196 GLN G 165 ASN G 173 GLN G 239 GLN G 370 ASN G 409 GLN G 414 GLN G 481 ASN ** G 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 540 ASN G 542 ASN G 563 GLN G 641 ASN G 690 GLN G 784 GLN G 853 GLN G 901 GLN ** G 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 960 ASN G 965 GLN G1010 GLN ** G1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G1048 HIS Total number of N/Q/H flips: 74 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.196299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.141553 restraints weight = 42646.527| |-----------------------------------------------------------------------------| r_work (start): 0.3562 rms_B_bonded: 2.56 r_work: 0.3424 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3258 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7495 moved from start: 0.2838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.128 30193 Z= 0.391 Angle : 0.749 9.698 41191 Z= 0.389 Chirality : 0.052 0.323 4712 Planarity : 0.006 0.089 5285 Dihedral : 8.242 78.914 4800 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.05 % Allowed : 10.14 % Favored : 89.81 % Rotamer: Outliers : 6.69 % Allowed : 13.01 % Favored : 80.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.48 % 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: -3.98 (0.12), residues: 3700 helix: -1.73 (0.18), residues: 659 sheet: -2.21 (0.16), residues: 874 loop : -3.28 (0.11), residues: 2167 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG G1107 TYR 0.041 0.002 TYR D1067 PHE 0.033 0.003 PHE A 906 TRP 0.019 0.001 TRP E 53 HIS 0.008 0.002 HIS G1088 Details of bonding type rmsd covalent geometry : bond 0.00902 (30124) covalent geometry : angle 0.73474 (41029) SS BOND : bond 0.00504 ( 45) SS BOND : angle 2.11859 ( 90) hydrogen bonds : bond 0.05297 ( 744) hydrogen bonds : angle 5.70913 ( 1980) link_NAG-ASN : bond 0.00333 ( 24) link_NAG-ASN : angle 2.70160 ( 72) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7400 Ramachandran restraints generated. 3700 Oldfield, 0 Emsley, 3700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7400 Ramachandran restraints generated. 3700 Oldfield, 0 Emsley, 3700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 775 residues out of total 3264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 215 poor density : 560 time to evaluate : 1.109 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 62 VAL cc_start: 0.8724 (t) cc_final: 0.8365 (m) REVERT: A 65 PHE cc_start: 0.8554 (m-80) cc_final: 0.8280 (m-10) REVERT: A 132 GLU cc_start: 0.7759 (mt-10) cc_final: 0.7475 (mp0) REVERT: A 133 PHE cc_start: 0.8407 (m-80) cc_final: 0.8132 (m-80) REVERT: A 186 ASN cc_start: 0.8257 (m-40) cc_final: 0.8046 (m-40) REVERT: A 188 ARG cc_start: 0.8459 (ptp90) cc_final: 0.8159 (mtt-85) REVERT: A 220 PHE cc_start: 0.8203 (t80) cc_final: 0.7933 (t80) REVERT: A 231 ILE cc_start: 0.8692 (OUTLIER) cc_final: 0.8419 (tt) REVERT: A 281 GLU cc_start: 0.7489 (OUTLIER) cc_final: 0.7184 (pp20) REVERT: A 307 THR cc_start: 0.8464 (m) cc_final: 0.8169 (t) REVERT: A 316 SER cc_start: 0.8465 (t) cc_final: 0.8242 (p) REVERT: A 324 GLU cc_start: 0.7173 (OUTLIER) cc_final: 0.6941 (tm-30) REVERT: A 532 ASN cc_start: 0.8252 (t0) cc_final: 0.7694 (t0) REVERT: A 537 LYS cc_start: 0.8522 (OUTLIER) cc_final: 0.8306 (ttpp) REVERT: A 578 ASP cc_start: 0.7218 (t0) cc_final: 0.6905 (t70) REVERT: A 603 ASN cc_start: 0.8359 (t0) cc_final: 0.8078 (t0) REVERT: A 675 GLN cc_start: 0.7268 (mm-40) cc_final: 0.6964 (mm-40) REVERT: A 702 GLU cc_start: 0.7454 (tp30) cc_final: 0.7205 (tp30) REVERT: A 726 ILE cc_start: 0.8737 (OUTLIER) cc_final: 0.8534 (mp) REVERT: A 737 ASP cc_start: 0.7481 (t0) cc_final: 0.7145 (t0) REVERT: A 739 THR cc_start: 0.8634 (p) cc_final: 0.8366 (m) REVERT: A 740 MET cc_start: 0.8526 (ttt) cc_final: 0.8174 (tpp) REVERT: A 776 LYS cc_start: 0.8343 (ttpt) cc_final: 0.8010 (ttpt) REVERT: A 795 LYS cc_start: 0.8177 (mptm) cc_final: 0.7893 (mptm) REVERT: A 804 GLN cc_start: 0.8452 (mm-40) cc_final: 0.8028 (mm-40) REVERT: A 934 ILE cc_start: 0.8136 (mt) cc_final: 0.7929 (mm) REVERT: A 949 GLN cc_start: 0.8433 (mm110) cc_final: 0.8173 (mm-40) REVERT: A 950 ASP cc_start: 0.7874 (t70) cc_final: 0.7417 (t0) REVERT: A 954 HIS cc_start: 0.8245 (m-70) cc_final: 0.7978 (m-70) REVERT: A 969 LYS cc_start: 0.8462 (OUTLIER) cc_final: 0.7730 (pptt) REVERT: A 979 ASP cc_start: 0.6929 (m-30) cc_final: 0.6686 (t0) REVERT: A 1017 GLU cc_start: 0.8017 (tm-30) cc_final: 0.7703 (tm-30) REVERT: A 1144 GLU cc_start: 0.8091 (tp30) cc_final: 0.7629 (tp30) REVERT: D 61 ASN cc_start: 0.7882 (m-40) cc_final: 0.7671 (p0) REVERT: D 83 VAL cc_start: 0.8191 (OUTLIER) cc_final: 0.7807 (p) REVERT: D 102 ARG cc_start: 0.7531 (ptt-90) cc_final: 0.7289 (ppt170) REVERT: D 105 ILE cc_start: 0.8385 (OUTLIER) cc_final: 0.8065 (mt) REVERT: D 126 VAL cc_start: 0.7673 (t) cc_final: 0.7422 (m) REVERT: D 141 LEU cc_start: 0.4512 (OUTLIER) cc_final: 0.4052 (mt) REVERT: D 188 ARG cc_start: 0.8259 (mtt-85) cc_final: 0.8027 (mtt-85) REVERT: D 194 ASN cc_start: 0.7356 (OUTLIER) cc_final: 0.7116 (m110) REVERT: D 206 THR cc_start: 0.8495 (OUTLIER) cc_final: 0.8245 (t) REVERT: D 269 TYR cc_start: 0.7758 (m-10) cc_final: 0.7515 (m-10) REVERT: D 284 THR cc_start: 0.7910 (t) cc_final: 0.7675 (p) REVERT: D 319 ARG cc_start: 0.7998 (ttm170) cc_final: 0.7749 (ttm-80) REVERT: D 338 PHE cc_start: 0.7760 (m-80) cc_final: 0.7468 (m-80) REVERT: D 346 ARG cc_start: 0.8073 (mtt-85) cc_final: 0.7820 (mtt-85) REVERT: D 543 PHE cc_start: 0.8400 (m-10) cc_final: 0.8183 (m-10) REVERT: D 559 PHE cc_start: 0.8223 (m-80) cc_final: 0.7992 (m-80) REVERT: D 599 THR cc_start: 0.8429 (m) cc_final: 0.8174 (p) REVERT: D 692 ILE cc_start: 0.8409 (mm) cc_final: 0.8007 (mt) REVERT: D 703 ASN cc_start: 0.8251 (t0) cc_final: 0.8027 (t0) REVERT: D 705 VAL cc_start: 0.8806 (t) cc_final: 0.8433 (p) REVERT: D 737 ASP cc_start: 0.7553 (t70) cc_final: 0.7252 (t0) REVERT: D 808 ASP cc_start: 0.7633 (t0) cc_final: 0.6856 (p0) REVERT: D 816 SER cc_start: 0.8449 (p) cc_final: 0.8154 (t) REVERT: D 921 LYS cc_start: 0.8415 (tptp) cc_final: 0.8147 (tptp) REVERT: D 960 ASN cc_start: 0.8641 (m110) cc_final: 0.8424 (m-40) REVERT: D 969 LYS cc_start: 0.8801 (OUTLIER) cc_final: 0.8578 (pttt) REVERT: D 988 GLU cc_start: 0.7501 (OUTLIER) cc_final: 0.6822 (tm-30) REVERT: D 1005 GLN cc_start: 0.8223 (tt0) cc_final: 0.7996 (tt0) REVERT: D 1019 ARG cc_start: 0.8126 (ttp80) cc_final: 0.7897 (ttp-110) REVERT: D 1050 MET cc_start: 0.8370 (mtm) cc_final: 0.8166 (mtp) REVERT: D 1081 ILE cc_start: 0.8550 (pt) cc_final: 0.8286 (mt) REVERT: D 1084 ASP cc_start: 0.8304 (OUTLIER) cc_final: 0.8102 (m-30) REVERT: D 1086 LYS cc_start: 0.8408 (OUTLIER) cc_final: 0.8142 (pttt) REVERT: D 1118 ASP cc_start: 0.7930 (t0) cc_final: 0.7436 (t0) REVERT: D 1133 VAL cc_start: 0.8461 (m) cc_final: 0.8198 (t) REVERT: D 1139 ASP cc_start: 0.8020 (p0) cc_final: 0.7507 (p0) REVERT: F 200 GLU cc_start: 0.0196 (OUTLIER) cc_final: -0.0406 (pm20) REVERT: G 28 TYR cc_start: 0.8362 (m-80) cc_final: 0.8001 (m-80) REVERT: G 51 THR cc_start: 0.8769 (OUTLIER) cc_final: 0.8531 (p) REVERT: G 96 GLU cc_start: 0.7456 (pm20) cc_final: 0.6556 (pm20) REVERT: G 117 LEU cc_start: 0.7432 (OUTLIER) cc_final: 0.7133 (mt) REVERT: G 129 LYS cc_start: 0.8280 (ttmm) cc_final: 0.8032 (ptmm) REVERT: G 186 ASN cc_start: 0.7645 (p0) cc_final: 0.7127 (p0) REVERT: G 204 LYS cc_start: 0.8350 (OUTLIER) cc_final: 0.8064 (ttmt) REVERT: G 293 LEU cc_start: 0.8866 (tp) cc_final: 0.8645 (tp) REVERT: G 364 ASP cc_start: 0.7841 (t70) cc_final: 0.7637 (t0) REVERT: G 444 LYS cc_start: 0.6906 (OUTLIER) cc_final: 0.6666 (tppt) REVERT: G 478 LYS cc_start: 0.3309 (OUTLIER) cc_final: 0.3075 (tmmt) REVERT: G 493 ARG cc_start: 0.7010 (OUTLIER) cc_final: 0.6465 (mmp-170) REVERT: G 546 LEU cc_start: 0.8221 (tm) cc_final: 0.8017 (tt) REVERT: G 574 ASP cc_start: 0.7723 (t0) cc_final: 0.7519 (t0) REVERT: G 663 ASP cc_start: 0.7666 (t70) cc_final: 0.7352 (t70) REVERT: G 730 SER cc_start: 0.8718 (t) cc_final: 0.8412 (p) REVERT: G 776 LYS cc_start: 0.8318 (ttpt) cc_final: 0.8116 (ttpt) REVERT: G 790 LYS cc_start: 0.7948 (mtmm) cc_final: 0.7704 (mtmm) REVERT: G 821 LEU cc_start: 0.8322 (tt) cc_final: 0.7770 (mp) REVERT: G 825 LYS cc_start: 0.8122 (OUTLIER) cc_final: 0.7857 (mmmm) REVERT: G 851 CYS cc_start: 0.8503 (t) cc_final: 0.8145 (t) REVERT: G 855 PHE cc_start: 0.8405 (m-10) cc_final: 0.8184 (m-80) REVERT: G 869 MET cc_start: 0.8695 (mtm) cc_final: 0.8420 (mtt) REVERT: G 882 ILE cc_start: 0.8646 (pt) cc_final: 0.8289 (mt) REVERT: G 884 SER cc_start: 0.8271 (t) cc_final: 0.7947 (p) REVERT: G 921 LYS cc_start: 0.8137 (mmmt) cc_final: 0.7860 (mmmt) REVERT: G 964 LYS cc_start: 0.8429 (ttpp) cc_final: 0.8066 (ttpp) REVERT: G 970 PHE cc_start: 0.8161 (m-80) cc_final: 0.7823 (m-80) REVERT: G 1017 GLU cc_start: 0.7785 (tm-30) cc_final: 0.7400 (tm-30) REVERT: G 1072 GLU cc_start: 0.8348 (pm20) cc_final: 0.8023 (pm20) REVERT: G 1125 ASN cc_start: 0.8335 (p0) cc_final: 0.8052 (p0) outliers start: 215 outliers final: 129 residues processed: 721 average time/residue: 0.1964 time to fit residues: 221.2885 Evaluate side-chains 655 residues out of total 3264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 152 poor density : 503 time to evaluate : 1.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 125 ASN Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 158 ARG Chi-restraints excluded: chain A residue 168 PHE Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 370 ASN Chi-restraints excluded: chain A residue 386 LYS Chi-restraints excluded: chain A residue 400 PHE Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 403 ARG Chi-restraints excluded: chain A residue 440 LYS Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 537 LYS Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 726 ILE Chi-restraints excluded: chain A residue 848 ASP Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 969 LYS Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain A residue 998 THR Chi-restraints excluded: chain A residue 1014 ARG Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain A residue 1073 LYS Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain C residue 30 LYS Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 104 LYS Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 68 ILE Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain D residue 113 LYS Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 122 ASN Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 132 GLU Chi-restraints excluded: chain D residue 135 PHE Chi-restraints excluded: chain D residue 141 LEU Chi-restraints excluded: chain D residue 194 ASN Chi-restraints excluded: chain D residue 198 TYR Chi-restraints excluded: chain D residue 206 THR Chi-restraints excluded: chain D residue 231 ILE Chi-restraints excluded: chain D residue 335 LEU Chi-restraints excluded: chain D residue 362 VAL Chi-restraints excluded: chain D residue 370 ASN Chi-restraints excluded: chain D residue 386 LYS Chi-restraints excluded: chain D residue 400 PHE Chi-restraints excluded: chain D residue 402 ILE Chi-restraints excluded: chain D residue 440 LYS Chi-restraints excluded: chain D residue 458 LYS Chi-restraints excluded: chain D residue 523 THR Chi-restraints excluded: chain D residue 528 LYS Chi-restraints excluded: chain D residue 553 THR Chi-restraints excluded: chain D residue 556 ASN Chi-restraints excluded: chain D residue 588 THR Chi-restraints excluded: chain D residue 697 MET Chi-restraints excluded: chain D residue 803 SER Chi-restraints excluded: chain D residue 811 LYS Chi-restraints excluded: chain D residue 851 CYS Chi-restraints excluded: chain D residue 859 THR Chi-restraints excluded: chain D residue 878 LEU Chi-restraints excluded: chain D residue 934 ILE Chi-restraints excluded: chain D residue 969 LYS Chi-restraints excluded: chain D residue 988 GLU Chi-restraints excluded: chain D residue 1041 ASP Chi-restraints excluded: chain D residue 1077 THR Chi-restraints excluded: chain D residue 1084 ASP Chi-restraints excluded: chain D residue 1086 LYS Chi-restraints excluded: chain D residue 1100 THR Chi-restraints excluded: chain D residue 1104 VAL Chi-restraints excluded: chain D residue 1129 VAL Chi-restraints excluded: chain E residue 1 GLU Chi-restraints excluded: chain E residue 52 THR Chi-restraints excluded: chain E residue 156 LYS Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain F residue 30 LYS Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain F residue 74 ILE Chi-restraints excluded: chain F residue 104 LYS Chi-restraints excluded: chain F residue 158 LYS Chi-restraints excluded: chain F residue 161 VAL Chi-restraints excluded: chain F residue 197 VAL Chi-restraints excluded: chain F residue 200 GLU Chi-restraints excluded: chain G residue 47 VAL Chi-restraints excluded: chain G residue 51 THR Chi-restraints excluded: chain G residue 68 ILE Chi-restraints excluded: chain G residue 100 ILE Chi-restraints excluded: chain G residue 102 ARG Chi-restraints excluded: chain G residue 117 LEU Chi-restraints excluded: chain G residue 128 ILE Chi-restraints excluded: chain G residue 131 CYS Chi-restraints excluded: chain G residue 204 LYS Chi-restraints excluded: chain G residue 227 VAL Chi-restraints excluded: chain G residue 229 LEU Chi-restraints excluded: chain G residue 231 ILE Chi-restraints excluded: chain G residue 400 PHE Chi-restraints excluded: chain G residue 402 ILE Chi-restraints excluded: chain G residue 403 ARG Chi-restraints excluded: chain G residue 408 ARG Chi-restraints excluded: chain G residue 432 CYS Chi-restraints excluded: chain G residue 440 LYS Chi-restraints excluded: chain G residue 444 LYS Chi-restraints excluded: chain G residue 452 LEU Chi-restraints excluded: chain G residue 458 LYS Chi-restraints excluded: chain G residue 462 LYS Chi-restraints excluded: chain G residue 478 LYS Chi-restraints excluded: chain G residue 493 ARG Chi-restraints excluded: chain G residue 528 LYS Chi-restraints excluded: chain G residue 588 THR Chi-restraints excluded: chain G residue 660 TYR Chi-restraints excluded: chain G residue 708 SER Chi-restraints excluded: chain G residue 746 SER Chi-restraints excluded: chain G residue 752 LEU Chi-restraints excluded: chain G residue 791 THR Chi-restraints excluded: chain G residue 825 LYS Chi-restraints excluded: chain G residue 900 MET Chi-restraints excluded: chain G residue 947 LYS Chi-restraints excluded: chain G residue 960 ASN Chi-restraints excluded: chain G residue 977 LEU Chi-restraints excluded: chain G residue 991 VAL Chi-restraints excluded: chain G residue 992 GLN Chi-restraints excluded: chain G residue 1041 ASP Chi-restraints excluded: chain G residue 1086 LYS Chi-restraints excluded: chain G residue 1104 VAL Chi-restraints excluded: chain G residue 1116 THR Chi-restraints excluded: chain G residue 1141 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 322 optimal weight: 1.9990 chunk 155 optimal weight: 8.9990 chunk 162 optimal weight: 9.9990 chunk 260 optimal weight: 50.0000 chunk 201 optimal weight: 0.7980 chunk 43 optimal weight: 3.9990 chunk 168 optimal weight: 0.9980 chunk 309 optimal weight: 10.0000 chunk 360 optimal weight: 0.9990 chunk 196 optimal weight: 0.6980 chunk 119 optimal weight: 3.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 448 ASN A 949 GLN A 957 GLN A1002 GLN ** B 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 87 ASN ** D 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 774 GLN D 901 GLN ** D 960 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 186 ASN ** G 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 542 ASN G 641 ASN ** G 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 960 ASN G1011 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4329 r_free = 0.4329 target = 0.197642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.143540 restraints weight = 42790.961| |-----------------------------------------------------------------------------| r_work (start): 0.3597 rms_B_bonded: 2.61 r_work: 0.3454 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3283 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7506 moved from start: 0.3113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 30193 Z= 0.192 Angle : 0.613 12.578 41191 Z= 0.316 Chirality : 0.046 0.273 4712 Planarity : 0.005 0.098 5285 Dihedral : 7.436 79.413 4753 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.03 % Allowed : 9.24 % Favored : 90.73 % Rotamer: Outliers : 6.01 % Allowed : 15.56 % Favored : 78.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.48 % Twisted General : 0.09 % 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: -3.49 (0.12), residues: 3700 helix: -1.02 (0.20), residues: 661 sheet: -1.78 (0.16), residues: 883 loop : -3.13 (0.12), residues: 2156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 319 TYR 0.027 0.001 TYR D1067 PHE 0.027 0.002 PHE D 541 TRP 0.014 0.001 TRP G 64 HIS 0.005 0.001 HIS G1088 Details of bonding type rmsd covalent geometry : bond 0.00450 (30124) covalent geometry : angle 0.59745 (41029) SS BOND : bond 0.00285 ( 45) SS BOND : angle 1.73893 ( 90) hydrogen bonds : bond 0.04094 ( 744) hydrogen bonds : angle 5.21703 ( 1980) link_NAG-ASN : bond 0.00278 ( 24) link_NAG-ASN : angle 2.79971 ( 72) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7400 Ramachandran restraints generated. 3700 Oldfield, 0 Emsley, 3700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7400 Ramachandran restraints generated. 3700 Oldfield, 0 Emsley, 3700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 717 residues out of total 3264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 193 poor density : 524 time to evaluate : 0.981 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: A 62 VAL cc_start: 0.8753 (t) cc_final: 0.8456 (m) REVERT: A 132 GLU cc_start: 0.7686 (mt-10) cc_final: 0.7422 (mp0) REVERT: A 133 PHE cc_start: 0.8568 (m-80) cc_final: 0.8272 (m-80) REVERT: A 168 PHE cc_start: 0.8455 (OUTLIER) cc_final: 0.7666 (m-80) REVERT: A 188 ARG cc_start: 0.8470 (ptp90) cc_final: 0.8163 (mtt-85) REVERT: A 216 LEU cc_start: 0.8522 (OUTLIER) cc_final: 0.8291 (mt) REVERT: A 231 ILE cc_start: 0.8676 (OUTLIER) cc_final: 0.8455 (tt) REVERT: A 281 GLU cc_start: 0.7408 (OUTLIER) cc_final: 0.7130 (pp20) REVERT: A 307 THR cc_start: 0.8455 (m) cc_final: 0.8243 (t) REVERT: A 316 SER cc_start: 0.8429 (t) cc_final: 0.8162 (p) REVERT: A 324 GLU cc_start: 0.7059 (tt0) cc_final: 0.6848 (tm-30) REVERT: A 325 SER cc_start: 0.8408 (m) cc_final: 0.7618 (m) REVERT: A 517 LEU cc_start: 0.3171 (OUTLIER) cc_final: 0.2769 (tm) REVERT: A 532 ASN cc_start: 0.8275 (t0) cc_final: 0.8050 (t0) REVERT: A 537 LYS cc_start: 0.8492 (OUTLIER) cc_final: 0.8275 (ttpp) REVERT: A 578 ASP cc_start: 0.7054 (t0) cc_final: 0.6778 (t70) REVERT: A 603 ASN cc_start: 0.8417 (t0) cc_final: 0.8169 (t0) REVERT: A 675 GLN cc_start: 0.7203 (mm-40) cc_final: 0.6892 (mm-40) REVERT: A 702 GLU cc_start: 0.7446 (tp30) cc_final: 0.6598 (tp30) REVERT: A 726 ILE cc_start: 0.8734 (OUTLIER) cc_final: 0.8515 (mp) REVERT: A 776 LYS cc_start: 0.8442 (ttpt) cc_final: 0.8095 (ttpt) REVERT: A 804 GLN cc_start: 0.8477 (mm-40) cc_final: 0.8068 (mm-40) REVERT: A 868 GLU cc_start: 0.7849 (tp30) cc_final: 0.7519 (tp30) REVERT: A 934 ILE cc_start: 0.8242 (mt) cc_final: 0.8023 (mm) REVERT: A 947 LYS cc_start: 0.8486 (mtpt) cc_final: 0.8258 (mtpp) REVERT: A 949 GLN cc_start: 0.8505 (mm-40) cc_final: 0.8208 (mm-40) REVERT: A 969 LYS cc_start: 0.8469 (OUTLIER) cc_final: 0.7749 (pptt) REVERT: A 1017 GLU cc_start: 0.8078 (tm-30) cc_final: 0.7735 (tm-30) REVERT: A 1073 LYS cc_start: 0.8390 (mtmt) cc_final: 0.8042 (mtmm) REVERT: D 61 ASN cc_start: 0.8017 (m-40) cc_final: 0.7721 (p0) REVERT: D 96 GLU cc_start: 0.6370 (tt0) cc_final: 0.5982 (tt0) REVERT: D 105 ILE cc_start: 0.8357 (OUTLIER) cc_final: 0.8043 (mt) REVERT: D 169 GLU cc_start: 0.8318 (tm-30) cc_final: 0.7901 (tm-30) REVERT: D 188 ARG cc_start: 0.8375 (mtt-85) cc_final: 0.8092 (mtt-85) REVERT: D 189 GLU cc_start: 0.7937 (mp0) cc_final: 0.7490 (mp0) REVERT: D 206 THR cc_start: 0.8529 (OUTLIER) cc_final: 0.8273 (t) REVERT: D 239 GLN cc_start: 0.7759 (tm-30) cc_final: 0.7421 (tm-30) REVERT: D 269 TYR cc_start: 0.7813 (m-10) cc_final: 0.7466 (m-10) REVERT: D 284 THR cc_start: 0.7939 (t) cc_final: 0.7736 (p) REVERT: D 319 ARG cc_start: 0.8090 (ttm170) cc_final: 0.7772 (ttm-80) REVERT: D 346 ARG cc_start: 0.8058 (mtt-85) cc_final: 0.7770 (mtt-85) REVERT: D 549 THR cc_start: 0.8557 (OUTLIER) cc_final: 0.8341 (m) REVERT: D 559 PHE cc_start: 0.8079 (m-80) cc_final: 0.7855 (m-80) REVERT: D 599 THR cc_start: 0.8361 (m) cc_final: 0.8113 (p) REVERT: D 692 ILE cc_start: 0.8376 (mm) cc_final: 0.8038 (mt) REVERT: D 705 VAL cc_start: 0.8731 (t) cc_final: 0.8439 (p) REVERT: D 737 ASP cc_start: 0.7505 (t70) cc_final: 0.7246 (t0) REVERT: D 790 LYS cc_start: 0.8246 (mtpp) cc_final: 0.8024 (mtpp) REVERT: D 808 ASP cc_start: 0.7598 (t0) cc_final: 0.6958 (p0) REVERT: D 811 LYS cc_start: 0.7597 (OUTLIER) cc_final: 0.6781 (ptpt) REVERT: D 816 SER cc_start: 0.8452 (p) cc_final: 0.8171 (t) REVERT: D 854 LYS cc_start: 0.8862 (ttmm) cc_final: 0.8587 (ttpp) REVERT: D 921 LYS cc_start: 0.8437 (tptp) cc_final: 0.8192 (tptp) REVERT: D 933 LYS cc_start: 0.8524 (mtpt) cc_final: 0.8320 (mtpt) REVERT: D 960 ASN cc_start: 0.8562 (m110) cc_final: 0.8361 (m-40) REVERT: D 969 LYS cc_start: 0.8665 (OUTLIER) cc_final: 0.8454 (pttt) REVERT: D 988 GLU cc_start: 0.7471 (OUTLIER) cc_final: 0.6750 (tm-30) REVERT: D 1005 GLN cc_start: 0.8231 (tt0) cc_final: 0.7997 (tt0) REVERT: D 1029 MET cc_start: 0.8301 (ttm) cc_final: 0.8059 (ttm) REVERT: D 1050 MET cc_start: 0.8390 (mtm) cc_final: 0.8123 (mtp) REVERT: D 1072 GLU cc_start: 0.8276 (pm20) cc_final: 0.7994 (pm20) REVERT: D 1086 LYS cc_start: 0.8509 (OUTLIER) cc_final: 0.8242 (pttt) REVERT: D 1118 ASP cc_start: 0.7966 (t0) cc_final: 0.7398 (t0) REVERT: D 1139 ASP cc_start: 0.7968 (p0) cc_final: 0.7482 (p0) REVERT: D 1141 LEU cc_start: 0.8539 (OUTLIER) cc_final: 0.8209 (mp) REVERT: F 200 GLU cc_start: 0.0452 (OUTLIER) cc_final: -0.0170 (pm20) REVERT: G 117 LEU cc_start: 0.7498 (OUTLIER) cc_final: 0.7272 (mt) REVERT: G 184 PHE cc_start: 0.8016 (m-80) cc_final: 0.7778 (m-10) REVERT: G 186 ASN cc_start: 0.7640 (p0) cc_final: 0.7121 (p0) REVERT: G 239 GLN cc_start: 0.7732 (tp-100) cc_final: 0.7501 (tp-100) REVERT: G 286 THR cc_start: 0.7914 (m) cc_final: 0.7659 (t) REVERT: G 293 LEU cc_start: 0.8887 (tp) cc_final: 0.8646 (tp) REVERT: G 357 ARG cc_start: 0.7779 (tpt-90) cc_final: 0.7505 (tpt170) REVERT: G 364 ASP cc_start: 0.7823 (t70) cc_final: 0.7565 (t70) REVERT: G 444 LYS cc_start: 0.6908 (OUTLIER) cc_final: 0.6696 (tppt) REVERT: G 478 LYS cc_start: 0.3417 (OUTLIER) cc_final: 0.3159 (tmmt) REVERT: G 493 ARG cc_start: 0.7023 (OUTLIER) cc_final: 0.6586 (mmp-170) REVERT: G 528 LYS cc_start: 0.7300 (OUTLIER) cc_final: 0.6966 (mmmt) REVERT: G 546 LEU cc_start: 0.8228 (tm) cc_final: 0.8016 (tt) REVERT: G 663 ASP cc_start: 0.7592 (t70) cc_final: 0.7240 (t70) REVERT: G 730 SER cc_start: 0.8679 (t) cc_final: 0.8393 (p) REVERT: G 765 ARG cc_start: 0.8313 (ttp-170) cc_final: 0.8102 (mtm-85) REVERT: G 773 GLU cc_start: 0.7830 (tp30) cc_final: 0.7593 (tp30) REVERT: G 775 ASP cc_start: 0.8001 (m-30) cc_final: 0.7712 (m-30) REVERT: G 776 LYS cc_start: 0.8368 (ttpt) cc_final: 0.8108 (ttpt) REVERT: G 790 LYS cc_start: 0.7994 (mtmm) cc_final: 0.7750 (mtmm) REVERT: G 803 SER cc_start: 0.8518 (m) cc_final: 0.8209 (p) REVERT: G 819 GLU cc_start: 0.7839 (mt-10) cc_final: 0.7502 (mt-10) REVERT: G 821 LEU cc_start: 0.8432 (tt) cc_final: 0.7890 (mt) REVERT: G 851 CYS cc_start: 0.8563 (t) cc_final: 0.8119 (t) REVERT: G 869 MET cc_start: 0.8762 (mtm) cc_final: 0.8518 (mtt) REVERT: G 900 MET cc_start: 0.8278 (OUTLIER) cc_final: 0.7951 (mmm) REVERT: G 964 LYS cc_start: 0.8462 (ttpp) cc_final: 0.8121 (ttpp) REVERT: G 970 PHE cc_start: 0.8185 (m-80) cc_final: 0.7691 (m-80) REVERT: G 980 ILE cc_start: 0.8373 (mt) cc_final: 0.8109 (tt) REVERT: G 1017 GLU cc_start: 0.7769 (tm-30) cc_final: 0.7382 (tm-30) REVERT: G 1019 ARG cc_start: 0.8025 (ttp-110) cc_final: 0.7807 (ttp80) REVERT: G 1107 ARG cc_start: 0.7623 (mtt180) cc_final: 0.7354 (mtt-85) REVERT: G 1125 ASN cc_start: 0.8312 (p0) cc_final: 0.8071 (p0) outliers start: 193 outliers final: 128 residues processed: 666 average time/residue: 0.1959 time to fit residues: 203.0881 Evaluate side-chains 650 residues out of total 3264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 151 poor density : 499 time to evaluate : 1.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 158 ARG Chi-restraints excluded: chain A residue 168 PHE Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 370 ASN Chi-restraints excluded: chain A residue 386 LYS Chi-restraints excluded: chain A residue 400 PHE Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 403 ARG Chi-restraints excluded: chain A residue 440 LYS Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 537 LYS Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 726 ILE Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 969 LYS Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain A residue 1014 ARG Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 104 LYS Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 68 ILE Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 113 LYS Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 122 ASN Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 132 GLU Chi-restraints excluded: chain D residue 198 TYR Chi-restraints excluded: chain D residue 206 THR Chi-restraints excluded: chain D residue 226 LEU Chi-restraints excluded: chain D residue 231 ILE Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 362 VAL Chi-restraints excluded: chain D residue 370 ASN Chi-restraints excluded: chain D residue 386 LYS Chi-restraints excluded: chain D residue 400 PHE Chi-restraints excluded: chain D residue 402 ILE Chi-restraints excluded: chain D residue 440 LYS Chi-restraints excluded: chain D residue 458 LYS Chi-restraints excluded: chain D residue 523 THR Chi-restraints excluded: chain D residue 528 LYS Chi-restraints excluded: chain D residue 549 THR Chi-restraints excluded: chain D residue 553 THR Chi-restraints excluded: chain D residue 556 ASN Chi-restraints excluded: chain D residue 588 THR Chi-restraints excluded: chain D residue 616 ASN Chi-restraints excluded: chain D residue 803 SER Chi-restraints excluded: chain D residue 811 LYS Chi-restraints excluded: chain D residue 851 CYS Chi-restraints excluded: chain D residue 859 THR Chi-restraints excluded: chain D residue 878 LEU Chi-restraints excluded: chain D residue 947 LYS Chi-restraints excluded: chain D residue 969 LYS Chi-restraints excluded: chain D residue 988 GLU Chi-restraints excluded: chain D residue 1041 ASP Chi-restraints excluded: chain D residue 1066 THR Chi-restraints excluded: chain D residue 1086 LYS Chi-restraints excluded: chain D residue 1104 VAL Chi-restraints excluded: chain D residue 1129 VAL Chi-restraints excluded: chain D residue 1141 LEU Chi-restraints excluded: chain E residue 1 GLU Chi-restraints excluded: chain E residue 52 THR Chi-restraints excluded: chain E residue 104 VAL Chi-restraints excluded: chain E residue 156 LYS Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain F residue 30 LYS Chi-restraints excluded: chain F residue 74 ILE Chi-restraints excluded: chain F residue 104 LYS Chi-restraints excluded: chain F residue 158 LYS Chi-restraints excluded: chain F residue 161 VAL Chi-restraints excluded: chain F residue 197 VAL Chi-restraints excluded: chain F residue 200 GLU Chi-restraints excluded: chain F residue 204 VAL Chi-restraints excluded: chain G residue 46 SER Chi-restraints excluded: chain G residue 62 VAL Chi-restraints excluded: chain G residue 100 ILE Chi-restraints excluded: chain G residue 102 ARG Chi-restraints excluded: chain G residue 117 LEU Chi-restraints excluded: chain G residue 128 ILE Chi-restraints excluded: chain G residue 131 CYS Chi-restraints excluded: chain G residue 203 SER Chi-restraints excluded: chain G residue 204 LYS Chi-restraints excluded: chain G residue 226 LEU Chi-restraints excluded: chain G residue 229 LEU Chi-restraints excluded: chain G residue 335 LEU Chi-restraints excluded: chain G residue 351 TYR Chi-restraints excluded: chain G residue 375 PHE Chi-restraints excluded: chain G residue 400 PHE Chi-restraints excluded: chain G residue 402 ILE Chi-restraints excluded: chain G residue 403 ARG Chi-restraints excluded: chain G residue 408 ARG Chi-restraints excluded: chain G residue 432 CYS Chi-restraints excluded: chain G residue 440 LYS Chi-restraints excluded: chain G residue 444 LYS Chi-restraints excluded: chain G residue 452 LEU Chi-restraints excluded: chain G residue 458 LYS Chi-restraints excluded: chain G residue 462 LYS Chi-restraints excluded: chain G residue 478 LYS Chi-restraints excluded: chain G residue 493 ARG Chi-restraints excluded: chain G residue 528 LYS Chi-restraints excluded: chain G residue 553 THR Chi-restraints excluded: chain G residue 569 ILE Chi-restraints excluded: chain G residue 588 THR Chi-restraints excluded: chain G residue 660 TYR Chi-restraints excluded: chain G residue 708 SER Chi-restraints excluded: chain G residue 791 THR Chi-restraints excluded: chain G residue 900 MET Chi-restraints excluded: chain G residue 947 LYS Chi-restraints excluded: chain G residue 950 ASP Chi-restraints excluded: chain G residue 960 ASN Chi-restraints excluded: chain G residue 975 SER Chi-restraints excluded: chain G residue 977 LEU Chi-restraints excluded: chain G residue 992 GLN Chi-restraints excluded: chain G residue 1041 ASP Chi-restraints excluded: chain G residue 1086 LYS Chi-restraints excluded: chain G residue 1104 VAL Chi-restraints excluded: chain G residue 1116 THR Chi-restraints excluded: chain G residue 1141 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 181 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 chunk 372 optimal weight: 0.9980 chunk 251 optimal weight: 30.0000 chunk 95 optimal weight: 0.6980 chunk 156 optimal weight: 4.9990 chunk 352 optimal weight: 0.6980 chunk 279 optimal weight: 0.0070 chunk 185 optimal weight: 2.9990 chunk 253 optimal weight: 4.9990 chunk 265 optimal weight: 10.0000 overall best weight: 0.8800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN ** A 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 957 GLN ** B 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 901 GLN ** G 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 542 ASN G 641 ASN ** G 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 960 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4334 r_free = 0.4334 target = 0.198190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.143922 restraints weight = 42426.906| |-----------------------------------------------------------------------------| r_work (start): 0.3610 rms_B_bonded: 2.59 r_work: 0.3470 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3304 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7486 moved from start: 0.3333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 30193 Z= 0.161 Angle : 0.589 11.262 41191 Z= 0.302 Chirality : 0.045 0.281 4712 Planarity : 0.005 0.101 5285 Dihedral : 7.218 79.657 4736 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.05 % Allowed : 9.27 % Favored : 90.68 % Rotamer: Outliers : 6.75 % Allowed : 15.94 % Favored : 77.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.48 % Twisted General : 0.09 % 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: -3.10 (0.13), residues: 3700 helix: -0.55 (0.21), residues: 668 sheet: -1.55 (0.17), residues: 879 loop : -2.92 (0.12), residues: 2153 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 237 TYR 0.024 0.001 TYR D1067 PHE 0.025 0.002 PHE A 541 TRP 0.016 0.001 TRP G 64 HIS 0.004 0.001 HIS G1088 Details of bonding type rmsd covalent geometry : bond 0.00378 (30124) covalent geometry : angle 0.57404 (41029) SS BOND : bond 0.00268 ( 45) SS BOND : angle 1.73515 ( 90) hydrogen bonds : bond 0.03683 ( 744) hydrogen bonds : angle 4.94062 ( 1980) link_NAG-ASN : bond 0.00255 ( 24) link_NAG-ASN : angle 2.67651 ( 72) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7400 Ramachandran restraints generated. 3700 Oldfield, 0 Emsley, 3700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7400 Ramachandran restraints generated. 3700 Oldfield, 0 Emsley, 3700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 741 residues out of total 3264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 217 poor density : 524 time to evaluate : 1.025 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 62 VAL cc_start: 0.8728 (t) cc_final: 0.8450 (m) REVERT: A 99 ASN cc_start: 0.7965 (OUTLIER) cc_final: 0.7573 (p0) REVERT: A 102 ARG cc_start: 0.7779 (mtm-85) cc_final: 0.7341 (ptp90) REVERT: A 132 GLU cc_start: 0.7708 (mt-10) cc_final: 0.7368 (mp0) REVERT: A 133 PHE cc_start: 0.8593 (m-80) cc_final: 0.8233 (m-80) REVERT: A 168 PHE cc_start: 0.8438 (OUTLIER) cc_final: 0.7677 (m-80) REVERT: A 188 ARG cc_start: 0.8463 (ptp90) cc_final: 0.8160 (mtt-85) REVERT: A 269 TYR cc_start: 0.8270 (m-80) cc_final: 0.8042 (m-80) REVERT: A 281 GLU cc_start: 0.7402 (OUTLIER) cc_final: 0.7101 (pp20) REVERT: A 316 SER cc_start: 0.8448 (t) cc_final: 0.7921 (p) REVERT: A 317 ASN cc_start: 0.7908 (m-40) cc_final: 0.7626 (m110) REVERT: A 324 GLU cc_start: 0.7033 (OUTLIER) cc_final: 0.6813 (tm-30) REVERT: A 325 SER cc_start: 0.8214 (m) cc_final: 0.7368 (t) REVERT: A 517 LEU cc_start: 0.3212 (OUTLIER) cc_final: 0.2831 (tm) REVERT: A 532 ASN cc_start: 0.8197 (t0) cc_final: 0.7996 (t0) REVERT: A 675 GLN cc_start: 0.7141 (mm-40) cc_final: 0.6844 (mm-40) REVERT: A 702 GLU cc_start: 0.7337 (tp30) cc_final: 0.6646 (tp30) REVERT: A 726 ILE cc_start: 0.8741 (OUTLIER) cc_final: 0.8532 (mp) REVERT: A 775 ASP cc_start: 0.7637 (m-30) cc_final: 0.7432 (m-30) REVERT: A 776 LYS cc_start: 0.8397 (ttpt) cc_final: 0.8066 (ttpt) REVERT: A 947 LYS cc_start: 0.8478 (mtpt) cc_final: 0.8254 (mtpp) REVERT: A 949 GLN cc_start: 0.8542 (mm-40) cc_final: 0.8239 (mm-40) REVERT: A 960 ASN cc_start: 0.8420 (t0) cc_final: 0.8181 (t0) REVERT: A 969 LYS cc_start: 0.8399 (OUTLIER) cc_final: 0.7644 (pptt) REVERT: A 1017 GLU cc_start: 0.8119 (tm-30) cc_final: 0.7754 (tm-30) REVERT: A 1073 LYS cc_start: 0.8390 (mtmt) cc_final: 0.8069 (mtpp) REVERT: D 41 LYS cc_start: 0.8633 (mttt) cc_final: 0.8327 (mtmm) REVERT: D 61 ASN cc_start: 0.7964 (m-40) cc_final: 0.7678 (p0) REVERT: D 83 VAL cc_start: 0.8308 (OUTLIER) cc_final: 0.8068 (p) REVERT: D 96 GLU cc_start: 0.6261 (OUTLIER) cc_final: 0.5759 (tt0) REVERT: D 105 ILE cc_start: 0.8301 (OUTLIER) cc_final: 0.7985 (mt) REVERT: D 169 GLU cc_start: 0.8290 (tm-30) cc_final: 0.7747 (tm-30) REVERT: D 188 ARG cc_start: 0.8354 (mtt-85) cc_final: 0.8092 (mtt-85) REVERT: D 206 THR cc_start: 0.8497 (OUTLIER) cc_final: 0.8246 (t) REVERT: D 239 GLN cc_start: 0.7789 (OUTLIER) cc_final: 0.7453 (tm-30) REVERT: D 290 ASP cc_start: 0.8069 (t70) cc_final: 0.7825 (t0) REVERT: D 303 LEU cc_start: 0.8414 (tp) cc_final: 0.8103 (mt) REVERT: D 319 ARG cc_start: 0.8099 (ttm170) cc_final: 0.7783 (ttm-80) REVERT: D 346 ARG cc_start: 0.8031 (mtt-85) cc_final: 0.7768 (mtt-85) REVERT: D 523 THR cc_start: 0.6020 (OUTLIER) cc_final: 0.5814 (p) REVERT: D 559 PHE cc_start: 0.8090 (m-80) cc_final: 0.7822 (m-10) REVERT: D 599 THR cc_start: 0.8344 (m) cc_final: 0.8052 (p) REVERT: D 692 ILE cc_start: 0.8384 (mm) cc_final: 0.8084 (mt) REVERT: D 705 VAL cc_start: 0.8670 (t) cc_final: 0.8410 (p) REVERT: D 730 SER cc_start: 0.8749 (t) cc_final: 0.8524 (m) REVERT: D 737 ASP cc_start: 0.7410 (t70) cc_final: 0.7073 (t0) REVERT: D 779 GLN cc_start: 0.8111 (OUTLIER) cc_final: 0.7755 (tm-30) REVERT: D 790 LYS cc_start: 0.8221 (mtpp) cc_final: 0.7994 (mtpp) REVERT: D 804 GLN cc_start: 0.8365 (mt0) cc_final: 0.7949 (mm-40) REVERT: D 816 SER cc_start: 0.8352 (p) cc_final: 0.7974 (t) REVERT: D 854 LYS cc_start: 0.8797 (ttmm) cc_final: 0.8516 (ttpp) REVERT: D 921 LYS cc_start: 0.8410 (tptp) cc_final: 0.8169 (tptp) REVERT: D 988 GLU cc_start: 0.7473 (OUTLIER) cc_final: 0.6733 (tm-30) REVERT: D 990 GLU cc_start: 0.8158 (mp0) cc_final: 0.7709 (mp0) REVERT: D 1086 LYS cc_start: 0.8526 (OUTLIER) cc_final: 0.8235 (pttt) REVERT: D 1118 ASP cc_start: 0.7946 (t0) cc_final: 0.7539 (t0) REVERT: F 200 GLU cc_start: 0.0795 (OUTLIER) cc_final: 0.0224 (pm20) REVERT: G 53 ASP cc_start: 0.7677 (m-30) cc_final: 0.7394 (m-30) REVERT: G 54 LEU cc_start: 0.8744 (mt) cc_final: 0.8537 (mp) REVERT: G 81 ASN cc_start: 0.7184 (OUTLIER) cc_final: 0.6649 (p0) REVERT: G 117 LEU cc_start: 0.7554 (OUTLIER) cc_final: 0.7340 (mt) REVERT: G 129 LYS cc_start: 0.8421 (mtmt) cc_final: 0.8021 (ptpt) REVERT: G 184 PHE cc_start: 0.8083 (m-80) cc_final: 0.7881 (m-10) REVERT: G 186 ASN cc_start: 0.7587 (OUTLIER) cc_final: 0.7095 (p0) REVERT: G 190 PHE cc_start: 0.8308 (m-80) cc_final: 0.8011 (m-80) REVERT: G 286 THR cc_start: 0.7862 (m) cc_final: 0.7590 (t) REVERT: G 293 LEU cc_start: 0.8870 (tp) cc_final: 0.8619 (tp) REVERT: G 340 GLU cc_start: 0.7537 (mm-30) cc_final: 0.7293 (mm-30) REVERT: G 364 ASP cc_start: 0.7842 (t70) cc_final: 0.7606 (t70) REVERT: G 453 TYR cc_start: 0.6216 (t80) cc_final: 0.5955 (t80) REVERT: G 478 LYS cc_start: 0.3513 (OUTLIER) cc_final: 0.3219 (tmmt) REVERT: G 493 ARG cc_start: 0.7018 (OUTLIER) cc_final: 0.6602 (mmp-170) REVERT: G 546 LEU cc_start: 0.8193 (tm) cc_final: 0.7951 (tt) REVERT: G 599 THR cc_start: 0.8836 (OUTLIER) cc_final: 0.8545 (p) REVERT: G 615 VAL cc_start: 0.7730 (OUTLIER) cc_final: 0.7403 (m) REVERT: G 655 TYR cc_start: 0.8459 (t80) cc_final: 0.8070 (t80) REVERT: G 663 ASP cc_start: 0.7459 (t70) cc_final: 0.7218 (t0) REVERT: G 697 MET cc_start: 0.8233 (mtp) cc_final: 0.8023 (mtm) REVERT: G 730 SER cc_start: 0.8676 (t) cc_final: 0.8384 (p) REVERT: G 745 ASP cc_start: 0.7384 (m-30) cc_final: 0.7174 (p0) REVERT: G 773 GLU cc_start: 0.7806 (tp30) cc_final: 0.7582 (tp30) REVERT: G 776 LYS cc_start: 0.8282 (ttpt) cc_final: 0.8020 (ttpt) REVERT: G 790 LYS cc_start: 0.7973 (mtmm) cc_final: 0.7752 (mtmm) REVERT: G 819 GLU cc_start: 0.7819 (mt-10) cc_final: 0.7485 (mt-10) REVERT: G 884 SER cc_start: 0.8472 (t) cc_final: 0.8105 (p) REVERT: G 964 LYS cc_start: 0.8476 (ttpp) cc_final: 0.8134 (ttpp) REVERT: G 970 PHE cc_start: 0.8237 (m-80) cc_final: 0.7746 (m-80) REVERT: G 1017 GLU cc_start: 0.7735 (tm-30) cc_final: 0.7332 (tm-30) REVERT: G 1019 ARG cc_start: 0.8066 (ttp-110) cc_final: 0.7836 (ttp80) REVERT: G 1107 ARG cc_start: 0.7593 (mtt180) cc_final: 0.7374 (mtt-85) outliers start: 217 outliers final: 146 residues processed: 680 average time/residue: 0.1910 time to fit residues: 204.5538 Evaluate side-chains 679 residues out of total 3264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 170 poor density : 509 time to evaluate : 0.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 99 ASN Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 158 ARG Chi-restraints excluded: chain A residue 168 PHE Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 370 ASN Chi-restraints excluded: chain A residue 386 LYS Chi-restraints excluded: chain A residue 400 PHE Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 403 ARG Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 440 LYS Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 726 ILE Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 795 LYS Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 969 LYS Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain A residue 1014 ARG Chi-restraints excluded: chain A residue 1038 LYS Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 107 ASP Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 104 LYS Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 68 ILE Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 87 ASN Chi-restraints excluded: chain D residue 96 GLU Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain D residue 113 LYS Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 122 ASN Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 132 GLU Chi-restraints excluded: chain D residue 206 THR Chi-restraints excluded: chain D residue 226 LEU Chi-restraints excluded: chain D residue 231 ILE Chi-restraints excluded: chain D residue 239 GLN Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 362 VAL Chi-restraints excluded: chain D residue 370 ASN Chi-restraints excluded: chain D residue 386 LYS Chi-restraints excluded: chain D residue 400 PHE Chi-restraints excluded: chain D residue 402 ILE Chi-restraints excluded: chain D residue 433 VAL Chi-restraints excluded: chain D residue 440 LYS Chi-restraints excluded: chain D residue 458 LYS Chi-restraints excluded: chain D residue 523 THR Chi-restraints excluded: chain D residue 528 LYS Chi-restraints excluded: chain D residue 553 THR Chi-restraints excluded: chain D residue 556 ASN Chi-restraints excluded: chain D residue 588 THR Chi-restraints excluded: chain D residue 649 CYS Chi-restraints excluded: chain D residue 725 GLU Chi-restraints excluded: chain D residue 779 GLN Chi-restraints excluded: chain D residue 803 SER Chi-restraints excluded: chain D residue 811 LYS Chi-restraints excluded: chain D residue 851 CYS Chi-restraints excluded: chain D residue 859 THR Chi-restraints excluded: chain D residue 878 LEU Chi-restraints excluded: chain D residue 988 GLU Chi-restraints excluded: chain D residue 1041 ASP Chi-restraints excluded: chain D residue 1066 THR Chi-restraints excluded: chain D residue 1073 LYS Chi-restraints excluded: chain D residue 1086 LYS Chi-restraints excluded: chain D residue 1100 THR Chi-restraints excluded: chain D residue 1104 VAL Chi-restraints excluded: chain D residue 1123 SER Chi-restraints excluded: chain D residue 1129 VAL Chi-restraints excluded: chain E residue 1 GLU Chi-restraints excluded: chain E residue 52 THR Chi-restraints excluded: chain E residue 104 VAL Chi-restraints excluded: chain E residue 121 LEU Chi-restraints excluded: chain E residue 151 LEU Chi-restraints excluded: chain E residue 156 LYS Chi-restraints excluded: chain E residue 164 THR Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain F residue 30 LYS Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain F residue 74 ILE Chi-restraints excluded: chain F residue 104 LYS Chi-restraints excluded: chain F residue 158 LYS Chi-restraints excluded: chain F residue 161 VAL Chi-restraints excluded: chain F residue 197 VAL Chi-restraints excluded: chain F residue 200 GLU Chi-restraints excluded: chain F residue 204 VAL Chi-restraints excluded: chain G residue 46 SER Chi-restraints excluded: chain G residue 47 VAL Chi-restraints excluded: chain G residue 81 ASN Chi-restraints excluded: chain G residue 100 ILE Chi-restraints excluded: chain G residue 102 ARG Chi-restraints excluded: chain G residue 117 LEU Chi-restraints excluded: chain G residue 128 ILE Chi-restraints excluded: chain G residue 131 CYS Chi-restraints excluded: chain G residue 171 VAL Chi-restraints excluded: chain G residue 186 ASN Chi-restraints excluded: chain G residue 187 LEU Chi-restraints excluded: chain G residue 203 SER Chi-restraints excluded: chain G residue 204 LYS Chi-restraints excluded: chain G residue 226 LEU Chi-restraints excluded: chain G residue 229 LEU Chi-restraints excluded: chain G residue 281 GLU Chi-restraints excluded: chain G residue 351 TYR Chi-restraints excluded: chain G residue 375 PHE Chi-restraints excluded: chain G residue 400 PHE Chi-restraints excluded: chain G residue 402 ILE Chi-restraints excluded: chain G residue 403 ARG Chi-restraints excluded: chain G residue 408 ARG Chi-restraints excluded: chain G residue 432 CYS Chi-restraints excluded: chain G residue 440 LYS Chi-restraints excluded: chain G residue 458 LYS Chi-restraints excluded: chain G residue 462 LYS Chi-restraints excluded: chain G residue 478 LYS Chi-restraints excluded: chain G residue 493 ARG Chi-restraints excluded: chain G residue 528 LYS Chi-restraints excluded: chain G residue 536 ASN Chi-restraints excluded: chain G residue 542 ASN Chi-restraints excluded: chain G residue 569 ILE Chi-restraints excluded: chain G residue 588 THR Chi-restraints excluded: chain G residue 599 THR Chi-restraints excluded: chain G residue 615 VAL Chi-restraints excluded: chain G residue 641 ASN Chi-restraints excluded: chain G residue 660 TYR Chi-restraints excluded: chain G residue 708 SER Chi-restraints excluded: chain G residue 791 THR Chi-restraints excluded: chain G residue 947 LYS Chi-restraints excluded: chain G residue 950 ASP Chi-restraints excluded: chain G residue 975 SER Chi-restraints excluded: chain G residue 977 LEU Chi-restraints excluded: chain G residue 991 VAL Chi-restraints excluded: chain G residue 1001 LEU Chi-restraints excluded: chain G residue 1041 ASP Chi-restraints excluded: chain G residue 1086 LYS Chi-restraints excluded: chain G residue 1116 THR Chi-restraints excluded: chain G residue 1130 ILE Chi-restraints excluded: chain G residue 1141 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 180 optimal weight: 0.1980 chunk 78 optimal weight: 1.9990 chunk 323 optimal weight: 1.9990 chunk 306 optimal weight: 1.9990 chunk 134 optimal weight: 6.9990 chunk 251 optimal weight: 30.0000 chunk 311 optimal weight: 20.0000 chunk 217 optimal weight: 0.9990 chunk 294 optimal weight: 0.7980 chunk 221 optimal weight: 0.9990 chunk 194 optimal weight: 0.6980 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 935 GLN A 957 GLN A1002 GLN ** B 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 30 ASN ** D 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 317 ASN D 872 GLN D 913 GLN D1002 GLN ** G 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 641 ASN G 913 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4341 r_free = 0.4341 target = 0.198731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.143007 restraints weight = 42684.198| |-----------------------------------------------------------------------------| r_work (start): 0.3594 rms_B_bonded: 2.36 r_work: 0.3471 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3308 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7463 moved from start: 0.3499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 30193 Z= 0.145 Angle : 0.575 11.450 41191 Z= 0.294 Chirality : 0.044 0.211 4712 Planarity : 0.005 0.100 5285 Dihedral : 6.956 79.686 4720 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.05 % Allowed : 9.24 % Favored : 90.70 % Rotamer: Outliers : 6.41 % Allowed : 16.90 % Favored : 76.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.48 % Twisted General : 0.09 % 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: -2.83 (0.13), residues: 3700 helix: -0.18 (0.21), residues: 665 sheet: -1.46 (0.16), residues: 901 loop : -2.75 (0.12), residues: 2134 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 237 TYR 0.023 0.001 TYR D1067 PHE 0.027 0.002 PHE A 855 TRP 0.022 0.001 TRP A 64 HIS 0.003 0.001 HIS A1088 Details of bonding type rmsd covalent geometry : bond 0.00342 (30124) covalent geometry : angle 0.56358 (41029) SS BOND : bond 0.00377 ( 45) SS BOND : angle 1.42942 ( 90) hydrogen bonds : bond 0.03447 ( 744) hydrogen bonds : angle 4.78108 ( 1980) link_NAG-ASN : bond 0.00310 ( 24) link_NAG-ASN : angle 2.32521 ( 72) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7400 Ramachandran restraints generated. 3700 Oldfield, 0 Emsley, 3700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7400 Ramachandran restraints generated. 3700 Oldfield, 0 Emsley, 3700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 721 residues out of total 3264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 206 poor density : 515 time to evaluate : 1.098 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: A 62 VAL cc_start: 0.8734 (t) cc_final: 0.8447 (m) REVERT: A 102 ARG cc_start: 0.7962 (mtm-85) cc_final: 0.7760 (ptp90) REVERT: A 132 GLU cc_start: 0.7627 (mt-10) cc_final: 0.7282 (mp0) REVERT: A 133 PHE cc_start: 0.8578 (m-80) cc_final: 0.8204 (m-80) REVERT: A 168 PHE cc_start: 0.8437 (OUTLIER) cc_final: 0.7683 (m-80) REVERT: A 188 ARG cc_start: 0.8497 (ptp90) cc_final: 0.8142 (mtt-85) REVERT: A 281 GLU cc_start: 0.7419 (OUTLIER) cc_final: 0.7149 (pp20) REVERT: A 316 SER cc_start: 0.8431 (t) cc_final: 0.7958 (p) REVERT: A 317 ASN cc_start: 0.7911 (m-40) cc_final: 0.7644 (m110) REVERT: A 324 GLU cc_start: 0.7004 (OUTLIER) cc_final: 0.6733 (tt0) REVERT: A 517 LEU cc_start: 0.3167 (OUTLIER) cc_final: 0.2778 (tm) REVERT: A 532 ASN cc_start: 0.8199 (t0) cc_final: 0.7987 (t0) REVERT: A 675 GLN cc_start: 0.7117 (mm-40) cc_final: 0.6821 (mm-40) REVERT: A 702 GLU cc_start: 0.7338 (tp30) cc_final: 0.6655 (tp30) REVERT: A 726 ILE cc_start: 0.8746 (OUTLIER) cc_final: 0.8530 (mp) REVERT: A 765 ARG cc_start: 0.8250 (ttm110) cc_final: 0.7905 (mtm-85) REVERT: A 776 LYS cc_start: 0.8385 (ttpt) cc_final: 0.8056 (ttpt) REVERT: A 804 GLN cc_start: 0.8429 (mm-40) cc_final: 0.7991 (mm-40) REVERT: A 947 LYS cc_start: 0.8427 (mtpt) cc_final: 0.8195 (mtpp) REVERT: A 949 GLN cc_start: 0.8521 (mm-40) cc_final: 0.8259 (mm-40) REVERT: A 960 ASN cc_start: 0.8402 (t0) cc_final: 0.8166 (t0) REVERT: A 969 LYS cc_start: 0.8393 (OUTLIER) cc_final: 0.7622 (pptt) REVERT: A 1017 GLU cc_start: 0.8055 (tm-30) cc_final: 0.7641 (tm-30) REVERT: A 1073 LYS cc_start: 0.8394 (mtmt) cc_final: 0.7996 (mtmm) REVERT: B 121 LEU cc_start: 0.2305 (OUTLIER) cc_final: 0.2061 (tt) REVERT: D 41 LYS cc_start: 0.8654 (mttt) cc_final: 0.8356 (mtmm) REVERT: D 61 ASN cc_start: 0.7944 (m-40) cc_final: 0.7684 (p0) REVERT: D 83 VAL cc_start: 0.8276 (OUTLIER) cc_final: 0.8053 (p) REVERT: D 96 GLU cc_start: 0.6276 (OUTLIER) cc_final: 0.5454 (tt0) REVERT: D 105 ILE cc_start: 0.8342 (OUTLIER) cc_final: 0.8033 (mt) REVERT: D 188 ARG cc_start: 0.8369 (mtt-85) cc_final: 0.8137 (mtt-85) REVERT: D 194 ASN cc_start: 0.7507 (m-40) cc_final: 0.7298 (m-40) REVERT: D 206 THR cc_start: 0.8471 (OUTLIER) cc_final: 0.8112 (t) REVERT: D 239 GLN cc_start: 0.7828 (OUTLIER) cc_final: 0.7524 (tm-30) REVERT: D 290 ASP cc_start: 0.8089 (t70) cc_final: 0.7737 (t0) REVERT: D 303 LEU cc_start: 0.8386 (tp) cc_final: 0.8083 (mt) REVERT: D 319 ARG cc_start: 0.8102 (ttm170) cc_final: 0.7795 (ttm-80) REVERT: D 346 ARG cc_start: 0.8044 (mtt-85) cc_final: 0.7801 (mtt-85) REVERT: D 599 THR cc_start: 0.8339 (m) cc_final: 0.8022 (p) REVERT: D 692 ILE cc_start: 0.8376 (mm) cc_final: 0.8092 (mt) REVERT: D 705 VAL cc_start: 0.8646 (t) cc_final: 0.8430 (p) REVERT: D 730 SER cc_start: 0.8736 (t) cc_final: 0.8500 (m) REVERT: D 737 ASP cc_start: 0.7349 (t70) cc_final: 0.7059 (t0) REVERT: D 752 LEU cc_start: 0.8366 (mt) cc_final: 0.7956 (mp) REVERT: D 753 LEU cc_start: 0.8007 (tp) cc_final: 0.7795 (tt) REVERT: D 779 GLN cc_start: 0.8095 (OUTLIER) cc_final: 0.7738 (tm-30) REVERT: D 790 LYS cc_start: 0.8237 (mtpp) cc_final: 0.8015 (mtpp) REVERT: D 804 GLN cc_start: 0.8380 (mt0) cc_final: 0.7991 (mm-40) REVERT: D 816 SER cc_start: 0.8365 (p) cc_final: 0.7978 (t) REVERT: D 854 LYS cc_start: 0.8682 (ttmm) cc_final: 0.8395 (ttpp) REVERT: D 921 LYS cc_start: 0.8390 (tptp) cc_final: 0.8155 (tptp) REVERT: D 988 GLU cc_start: 0.7386 (OUTLIER) cc_final: 0.6640 (tm-30) REVERT: D 990 GLU cc_start: 0.8067 (mp0) cc_final: 0.7644 (mp0) REVERT: D 1086 LYS cc_start: 0.8524 (OUTLIER) cc_final: 0.8240 (pttt) REVERT: D 1118 ASP cc_start: 0.7917 (t0) cc_final: 0.7449 (t0) REVERT: F 200 GLU cc_start: 0.0807 (OUTLIER) cc_final: 0.0184 (pm20) REVERT: G 47 VAL cc_start: 0.8664 (OUTLIER) cc_final: 0.8389 (t) REVERT: G 53 ASP cc_start: 0.7629 (m-30) cc_final: 0.7226 (m-30) REVERT: G 54 LEU cc_start: 0.8746 (mt) cc_final: 0.8533 (mp) REVERT: G 81 ASN cc_start: 0.7173 (OUTLIER) cc_final: 0.6650 (p0) REVERT: G 117 LEU cc_start: 0.7538 (OUTLIER) cc_final: 0.7322 (mt) REVERT: G 129 LYS cc_start: 0.8378 (mtmt) cc_final: 0.7834 (ptmm) REVERT: G 186 ASN cc_start: 0.7581 (OUTLIER) cc_final: 0.7096 (p0) REVERT: G 286 THR cc_start: 0.7857 (m) cc_final: 0.7602 (t) REVERT: G 293 LEU cc_start: 0.8895 (tp) cc_final: 0.8635 (tp) REVERT: G 340 GLU cc_start: 0.7555 (mm-30) cc_final: 0.7337 (mm-30) REVERT: G 453 TYR cc_start: 0.6265 (t80) cc_final: 0.5989 (t80) REVERT: G 478 LYS cc_start: 0.3569 (OUTLIER) cc_final: 0.3262 (tmmt) REVERT: G 493 ARG cc_start: 0.6992 (OUTLIER) cc_final: 0.6572 (mmp-170) REVERT: G 546 LEU cc_start: 0.8166 (tm) cc_final: 0.7927 (tt) REVERT: G 584 ILE cc_start: 0.7943 (tp) cc_final: 0.7742 (mm) REVERT: G 599 THR cc_start: 0.8835 (OUTLIER) cc_final: 0.8571 (p) REVERT: G 655 TYR cc_start: 0.8441 (t80) cc_final: 0.8067 (t80) REVERT: G 663 ASP cc_start: 0.7492 (t70) cc_final: 0.7232 (t0) REVERT: G 730 SER cc_start: 0.8664 (t) cc_final: 0.8382 (p) REVERT: G 773 GLU cc_start: 0.7787 (tp30) cc_final: 0.7577 (tp30) REVERT: G 776 LYS cc_start: 0.8290 (ttpt) cc_final: 0.8033 (ttpt) REVERT: G 790 LYS cc_start: 0.7956 (mtmm) cc_final: 0.7732 (mtmm) REVERT: G 803 SER cc_start: 0.8483 (m) cc_final: 0.8166 (p) REVERT: G 819 GLU cc_start: 0.7799 (mt-10) cc_final: 0.7464 (mt-10) REVERT: G 882 ILE cc_start: 0.8692 (pt) cc_final: 0.8270 (mt) REVERT: G 884 SER cc_start: 0.8463 (t) cc_final: 0.8147 (p) REVERT: G 964 LYS cc_start: 0.8450 (ttpp) cc_final: 0.8084 (ttpp) REVERT: G 1017 GLU cc_start: 0.7751 (tm-30) cc_final: 0.7348 (tm-30) REVERT: G 1019 ARG cc_start: 0.8042 (ttp-110) cc_final: 0.7830 (ttp80) outliers start: 206 outliers final: 152 residues processed: 664 average time/residue: 0.1975 time to fit residues: 205.2559 Evaluate side-chains 674 residues out of total 3264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 175 poor density : 499 time to evaluate : 0.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 158 ARG Chi-restraints excluded: chain A residue 168 PHE Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 370 ASN Chi-restraints excluded: chain A residue 386 LYS Chi-restraints excluded: chain A residue 400 PHE Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 403 ARG Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 440 LYS Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 726 ILE Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 795 LYS Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 935 GLN Chi-restraints excluded: chain A residue 969 LYS Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain A residue 1014 ARG Chi-restraints excluded: chain A residue 1038 LYS Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 104 LYS Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 68 ILE Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 96 GLU Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain D residue 111 ASP Chi-restraints excluded: chain D residue 113 LYS Chi-restraints excluded: chain D residue 122 ASN Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 132 GLU Chi-restraints excluded: chain D residue 195 ILE Chi-restraints excluded: chain D residue 206 THR Chi-restraints excluded: chain D residue 226 LEU Chi-restraints excluded: chain D residue 231 ILE Chi-restraints excluded: chain D residue 239 GLN Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 362 VAL Chi-restraints excluded: chain D residue 370 ASN Chi-restraints excluded: chain D residue 400 PHE Chi-restraints excluded: chain D residue 402 ILE Chi-restraints excluded: chain D residue 433 VAL Chi-restraints excluded: chain D residue 440 LYS Chi-restraints excluded: chain D residue 458 LYS Chi-restraints excluded: chain D residue 528 LYS Chi-restraints excluded: chain D residue 553 THR Chi-restraints excluded: chain D residue 556 ASN Chi-restraints excluded: chain D residue 588 THR Chi-restraints excluded: chain D residue 616 ASN Chi-restraints excluded: chain D residue 617 CYS Chi-restraints excluded: chain D residue 649 CYS Chi-restraints excluded: chain D residue 725 GLU Chi-restraints excluded: chain D residue 779 GLN Chi-restraints excluded: chain D residue 811 LYS Chi-restraints excluded: chain D residue 859 THR Chi-restraints excluded: chain D residue 878 LEU Chi-restraints excluded: chain D residue 900 MET Chi-restraints excluded: chain D residue 947 LYS Chi-restraints excluded: chain D residue 969 LYS Chi-restraints excluded: chain D residue 988 GLU Chi-restraints excluded: chain D residue 1041 ASP Chi-restraints excluded: chain D residue 1066 THR Chi-restraints excluded: chain D residue 1086 LYS Chi-restraints excluded: chain D residue 1100 THR Chi-restraints excluded: chain D residue 1104 VAL Chi-restraints excluded: chain D residue 1129 VAL Chi-restraints excluded: chain D residue 1141 LEU Chi-restraints excluded: chain E residue 1 GLU Chi-restraints excluded: chain E residue 52 THR Chi-restraints excluded: chain E residue 104 VAL Chi-restraints excluded: chain E residue 121 LEU Chi-restraints excluded: chain E residue 151 LEU Chi-restraints excluded: chain E residue 156 LYS Chi-restraints excluded: chain E residue 164 THR Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain F residue 30 LYS Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain F residue 74 ILE Chi-restraints excluded: chain F residue 104 LYS Chi-restraints excluded: chain F residue 158 LYS Chi-restraints excluded: chain F residue 161 VAL Chi-restraints excluded: chain F residue 197 VAL Chi-restraints excluded: chain F residue 200 GLU Chi-restraints excluded: chain F residue 204 VAL Chi-restraints excluded: chain G residue 46 SER Chi-restraints excluded: chain G residue 47 VAL Chi-restraints excluded: chain G residue 81 ASN Chi-restraints excluded: chain G residue 100 ILE Chi-restraints excluded: chain G residue 102 ARG Chi-restraints excluded: chain G residue 117 LEU Chi-restraints excluded: chain G residue 128 ILE Chi-restraints excluded: chain G residue 131 CYS Chi-restraints excluded: chain G residue 171 VAL Chi-restraints excluded: chain G residue 186 ASN Chi-restraints excluded: chain G residue 187 LEU Chi-restraints excluded: chain G residue 203 SER Chi-restraints excluded: chain G residue 204 LYS Chi-restraints excluded: chain G residue 226 LEU Chi-restraints excluded: chain G residue 229 LEU Chi-restraints excluded: chain G residue 231 ILE Chi-restraints excluded: chain G residue 281 GLU Chi-restraints excluded: chain G residue 335 LEU Chi-restraints excluded: chain G residue 351 TYR Chi-restraints excluded: chain G residue 375 PHE Chi-restraints excluded: chain G residue 400 PHE Chi-restraints excluded: chain G residue 402 ILE Chi-restraints excluded: chain G residue 403 ARG Chi-restraints excluded: chain G residue 408 ARG Chi-restraints excluded: chain G residue 432 CYS Chi-restraints excluded: chain G residue 440 LYS Chi-restraints excluded: chain G residue 441 LEU Chi-restraints excluded: chain G residue 452 LEU Chi-restraints excluded: chain G residue 458 LYS Chi-restraints excluded: chain G residue 462 LYS Chi-restraints excluded: chain G residue 478 LYS Chi-restraints excluded: chain G residue 493 ARG Chi-restraints excluded: chain G residue 528 LYS Chi-restraints excluded: chain G residue 553 THR Chi-restraints excluded: chain G residue 569 ILE Chi-restraints excluded: chain G residue 588 THR Chi-restraints excluded: chain G residue 599 THR Chi-restraints excluded: chain G residue 660 TYR Chi-restraints excluded: chain G residue 708 SER Chi-restraints excluded: chain G residue 754 LEU Chi-restraints excluded: chain G residue 791 THR Chi-restraints excluded: chain G residue 947 LYS Chi-restraints excluded: chain G residue 950 ASP Chi-restraints excluded: chain G residue 975 SER Chi-restraints excluded: chain G residue 977 LEU Chi-restraints excluded: chain G residue 993 ILE Chi-restraints excluded: chain G residue 1001 LEU Chi-restraints excluded: chain G residue 1041 ASP Chi-restraints excluded: chain G residue 1086 LYS Chi-restraints excluded: chain G residue 1116 THR Chi-restraints excluded: chain G residue 1130 ILE Chi-restraints excluded: chain G residue 1141 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 272 optimal weight: 2.9990 chunk 290 optimal weight: 1.9990 chunk 331 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 90 optimal weight: 0.8980 chunk 332 optimal weight: 0.8980 chunk 153 optimal weight: 0.9990 chunk 198 optimal weight: 0.9990 chunk 89 optimal weight: 0.7980 chunk 170 optimal weight: 5.9990 chunk 120 optimal weight: 50.0000 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 762 GLN A 965 GLN ** B 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 872 GLN D 901 GLN G 66 HIS ** G 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 542 ASN G 641 ASN G 762 GLN G1002 GLN G1005 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4330 r_free = 0.4330 target = 0.197920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.142073 restraints weight = 42384.098| |-----------------------------------------------------------------------------| r_work (start): 0.3582 rms_B_bonded: 2.36 r_work: 0.3457 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3282 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7490 moved from start: 0.3690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 30193 Z= 0.164 Angle : 0.583 10.126 41191 Z= 0.299 Chirality : 0.045 0.204 4712 Planarity : 0.005 0.098 5285 Dihedral : 6.834 79.652 4713 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.05 % Allowed : 9.57 % Favored : 90.38 % Rotamer: Outliers : 6.54 % Allowed : 17.43 % Favored : 76.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.48 % Twisted General : 0.09 % 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: -2.65 (0.13), residues: 3700 helix: 0.01 (0.21), residues: 651 sheet: -1.37 (0.17), residues: 893 loop : -2.61 (0.12), residues: 2156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 357 TYR 0.025 0.001 TYR D1067 PHE 0.026 0.002 PHE D 643 TRP 0.017 0.001 TRP G 64 HIS 0.004 0.001 HIS G1088 Details of bonding type rmsd covalent geometry : bond 0.00387 (30124) covalent geometry : angle 0.57282 (41029) SS BOND : bond 0.00305 ( 45) SS BOND : angle 1.48912 ( 90) hydrogen bonds : bond 0.03488 ( 744) hydrogen bonds : angle 4.73146 ( 1980) link_NAG-ASN : bond 0.00249 ( 24) link_NAG-ASN : angle 2.24078 ( 72) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7400 Ramachandran restraints generated. 3700 Oldfield, 0 Emsley, 3700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7400 Ramachandran restraints generated. 3700 Oldfield, 0 Emsley, 3700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 725 residues out of total 3264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 210 poor density : 515 time to evaluate : 1.030 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 62 VAL cc_start: 0.8740 (t) cc_final: 0.8470 (m) REVERT: A 102 ARG cc_start: 0.7991 (mtm-85) cc_final: 0.7714 (ptp90) REVERT: A 132 GLU cc_start: 0.7670 (mt-10) cc_final: 0.7196 (mp0) REVERT: A 188 ARG cc_start: 0.8513 (ptp90) cc_final: 0.8013 (mtt-85) REVERT: A 231 ILE cc_start: 0.8737 (tt) cc_final: 0.8350 (pt) REVERT: A 281 GLU cc_start: 0.7435 (OUTLIER) cc_final: 0.7168 (pp20) REVERT: A 316 SER cc_start: 0.8464 (t) cc_final: 0.8173 (p) REVERT: A 324 GLU cc_start: 0.7030 (OUTLIER) cc_final: 0.6817 (tt0) REVERT: A 517 LEU cc_start: 0.3237 (OUTLIER) cc_final: 0.2841 (tm) REVERT: A 537 LYS cc_start: 0.8429 (ttmt) cc_final: 0.8149 (ttmm) REVERT: A 675 GLN cc_start: 0.7143 (mm-40) cc_final: 0.6851 (mm-40) REVERT: A 702 GLU cc_start: 0.7452 (tp30) cc_final: 0.6834 (tp30) REVERT: A 726 ILE cc_start: 0.8759 (OUTLIER) cc_final: 0.8548 (mp) REVERT: A 776 LYS cc_start: 0.8371 (ttpt) cc_final: 0.8024 (ttpt) REVERT: A 804 GLN cc_start: 0.8364 (mm-40) cc_final: 0.8007 (mm-40) REVERT: A 947 LYS cc_start: 0.8443 (mtpt) cc_final: 0.8218 (mtpp) REVERT: A 949 GLN cc_start: 0.8519 (mm-40) cc_final: 0.8252 (mm-40) REVERT: A 960 ASN cc_start: 0.8441 (t0) cc_final: 0.8197 (t0) REVERT: A 969 LYS cc_start: 0.8402 (OUTLIER) cc_final: 0.7642 (pptt) REVERT: A 1017 GLU cc_start: 0.8125 (tm-30) cc_final: 0.7678 (tm-30) REVERT: A 1019 ARG cc_start: 0.7882 (ttp80) cc_final: 0.7669 (ttm110) REVERT: A 1073 LYS cc_start: 0.8386 (mtmt) cc_final: 0.8083 (mtpp) REVERT: B 121 LEU cc_start: 0.2372 (OUTLIER) cc_final: 0.2120 (tt) REVERT: D 41 LYS cc_start: 0.8647 (mttt) cc_final: 0.8335 (mtmm) REVERT: D 61 ASN cc_start: 0.7872 (m-40) cc_final: 0.7662 (p0) REVERT: D 96 GLU cc_start: 0.6284 (OUTLIER) cc_final: 0.5537 (tt0) REVERT: D 105 ILE cc_start: 0.8397 (mt) cc_final: 0.8097 (mt) REVERT: D 206 THR cc_start: 0.8218 (OUTLIER) cc_final: 0.7948 (p) REVERT: D 239 GLN cc_start: 0.7842 (OUTLIER) cc_final: 0.7463 (tm-30) REVERT: D 290 ASP cc_start: 0.8130 (t70) cc_final: 0.7772 (t0) REVERT: D 319 ARG cc_start: 0.8128 (ttm170) cc_final: 0.7843 (ttm-80) REVERT: D 346 ARG cc_start: 0.8033 (mtt-85) cc_final: 0.7771 (mtt-85) REVERT: D 599 THR cc_start: 0.8341 (m) cc_final: 0.8010 (p) REVERT: D 705 VAL cc_start: 0.8665 (t) cc_final: 0.8447 (p) REVERT: D 730 SER cc_start: 0.8743 (t) cc_final: 0.8506 (m) REVERT: D 737 ASP cc_start: 0.7321 (t70) cc_final: 0.7026 (t0) REVERT: D 752 LEU cc_start: 0.8384 (mt) cc_final: 0.8009 (mp) REVERT: D 779 GLN cc_start: 0.8101 (OUTLIER) cc_final: 0.7752 (tm-30) REVERT: D 790 LYS cc_start: 0.8216 (mtpp) cc_final: 0.7988 (mtpp) REVERT: D 804 GLN cc_start: 0.8402 (mt0) cc_final: 0.7993 (mm-40) REVERT: D 816 SER cc_start: 0.8353 (p) cc_final: 0.7964 (t) REVERT: D 854 LYS cc_start: 0.8698 (ttmm) cc_final: 0.8416 (ttpp) REVERT: D 921 LYS cc_start: 0.8359 (tptp) cc_final: 0.8109 (tptp) REVERT: D 988 GLU cc_start: 0.7261 (OUTLIER) cc_final: 0.6536 (tm-30) REVERT: D 990 GLU cc_start: 0.8116 (mp0) cc_final: 0.7701 (mp0) REVERT: D 1050 MET cc_start: 0.8355 (mtm) cc_final: 0.8121 (mtp) REVERT: D 1086 LYS cc_start: 0.8535 (OUTLIER) cc_final: 0.8229 (mtmm) REVERT: D 1118 ASP cc_start: 0.7911 (t0) cc_final: 0.7461 (t0) REVERT: F 200 GLU cc_start: 0.0852 (OUTLIER) cc_final: 0.0202 (pm20) REVERT: G 47 VAL cc_start: 0.8645 (OUTLIER) cc_final: 0.8371 (t) REVERT: G 53 ASP cc_start: 0.7703 (m-30) cc_final: 0.7407 (m-30) REVERT: G 54 LEU cc_start: 0.8751 (mt) cc_final: 0.8537 (mp) REVERT: G 81 ASN cc_start: 0.7218 (OUTLIER) cc_final: 0.6705 (p0) REVERT: G 117 LEU cc_start: 0.7728 (OUTLIER) cc_final: 0.7446 (mt) REVERT: G 129 LYS cc_start: 0.8396 (mtmt) cc_final: 0.7775 (ptmm) REVERT: G 186 ASN cc_start: 0.7644 (OUTLIER) cc_final: 0.7016 (p0) REVERT: G 286 THR cc_start: 0.7883 (m) cc_final: 0.7619 (t) REVERT: G 293 LEU cc_start: 0.8904 (tp) cc_final: 0.8649 (tp) REVERT: G 340 GLU cc_start: 0.7554 (mm-30) cc_final: 0.7336 (mm-30) REVERT: G 453 TYR cc_start: 0.6239 (t80) cc_final: 0.5963 (t80) REVERT: G 478 LYS cc_start: 0.3487 (OUTLIER) cc_final: 0.3190 (tmmt) REVERT: G 493 ARG cc_start: 0.6952 (OUTLIER) cc_final: 0.6466 (mmp-170) REVERT: G 546 LEU cc_start: 0.8093 (tm) cc_final: 0.7850 (tt) REVERT: G 599 THR cc_start: 0.8844 (OUTLIER) cc_final: 0.8577 (p) REVERT: G 615 VAL cc_start: 0.7845 (OUTLIER) cc_final: 0.7629 (m) REVERT: G 655 TYR cc_start: 0.8493 (t80) cc_final: 0.8117 (t80) REVERT: G 663 ASP cc_start: 0.7489 (t70) cc_final: 0.7230 (t0) REVERT: G 730 SER cc_start: 0.8692 (t) cc_final: 0.8392 (p) REVERT: G 773 GLU cc_start: 0.7843 (tp30) cc_final: 0.7611 (tp30) REVERT: G 776 LYS cc_start: 0.8288 (ttpt) cc_final: 0.8020 (ttpt) REVERT: G 790 LYS cc_start: 0.7945 (mtmm) cc_final: 0.7736 (mtmm) REVERT: G 803 SER cc_start: 0.8495 (m) cc_final: 0.8154 (p) REVERT: G 884 SER cc_start: 0.8463 (t) cc_final: 0.8156 (p) REVERT: G 964 LYS cc_start: 0.8511 (ttpp) cc_final: 0.8166 (ttpp) REVERT: G 1017 GLU cc_start: 0.7837 (tm-30) cc_final: 0.7421 (tm-30) REVERT: G 1107 ARG cc_start: 0.7450 (mtt-85) cc_final: 0.7035 (mtt-85) outliers start: 210 outliers final: 157 residues processed: 669 average time/residue: 0.1914 time to fit residues: 201.4119 Evaluate side-chains 680 residues out of total 3264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 178 poor density : 502 time to evaluate : 1.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 158 ARG Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 370 ASN Chi-restraints excluded: chain A residue 386 LYS Chi-restraints excluded: chain A residue 400 PHE Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 403 ARG Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 440 LYS Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 726 ILE Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 762 GLN Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 935 GLN Chi-restraints excluded: chain A residue 969 LYS Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain A residue 1014 ARG Chi-restraints excluded: chain A residue 1038 LYS Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 104 LYS Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 68 ILE Chi-restraints excluded: chain D residue 96 GLU Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain D residue 111 ASP Chi-restraints excluded: chain D residue 113 LYS Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 132 GLU Chi-restraints excluded: chain D residue 195 ILE Chi-restraints excluded: chain D residue 198 TYR Chi-restraints excluded: chain D residue 206 THR Chi-restraints excluded: chain D residue 226 LEU Chi-restraints excluded: chain D residue 231 ILE Chi-restraints excluded: chain D residue 239 GLN Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 362 VAL Chi-restraints excluded: chain D residue 370 ASN Chi-restraints excluded: chain D residue 400 PHE Chi-restraints excluded: chain D residue 402 ILE Chi-restraints excluded: chain D residue 433 VAL Chi-restraints excluded: chain D residue 440 LYS Chi-restraints excluded: chain D residue 458 LYS Chi-restraints excluded: chain D residue 528 LYS Chi-restraints excluded: chain D residue 553 THR Chi-restraints excluded: chain D residue 556 ASN Chi-restraints excluded: chain D residue 588 THR Chi-restraints excluded: chain D residue 616 ASN Chi-restraints excluded: chain D residue 617 CYS Chi-restraints excluded: chain D residue 725 GLU Chi-restraints excluded: chain D residue 779 GLN Chi-restraints excluded: chain D residue 803 SER Chi-restraints excluded: chain D residue 859 THR Chi-restraints excluded: chain D residue 878 LEU Chi-restraints excluded: chain D residue 900 MET Chi-restraints excluded: chain D residue 947 LYS Chi-restraints excluded: chain D residue 969 LYS Chi-restraints excluded: chain D residue 988 GLU Chi-restraints excluded: chain D residue 1041 ASP Chi-restraints excluded: chain D residue 1066 THR Chi-restraints excluded: chain D residue 1086 LYS Chi-restraints excluded: chain D residue 1100 THR Chi-restraints excluded: chain D residue 1104 VAL Chi-restraints excluded: chain D residue 1129 VAL Chi-restraints excluded: chain D residue 1141 LEU Chi-restraints excluded: chain E residue 1 GLU Chi-restraints excluded: chain E residue 52 THR Chi-restraints excluded: chain E residue 104 VAL Chi-restraints excluded: chain E residue 121 LEU Chi-restraints excluded: chain E residue 151 LEU Chi-restraints excluded: chain E residue 156 LYS Chi-restraints excluded: chain E residue 164 THR Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain F residue 30 LYS Chi-restraints excluded: chain F residue 74 ILE Chi-restraints excluded: chain F residue 104 LYS Chi-restraints excluded: chain F residue 158 LYS Chi-restraints excluded: chain F residue 161 VAL Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain F residue 197 VAL Chi-restraints excluded: chain F residue 200 GLU Chi-restraints excluded: chain F residue 204 VAL Chi-restraints excluded: chain G residue 46 SER Chi-restraints excluded: chain G residue 47 VAL Chi-restraints excluded: chain G residue 81 ASN Chi-restraints excluded: chain G residue 95 ILE Chi-restraints excluded: chain G residue 100 ILE Chi-restraints excluded: chain G residue 102 ARG Chi-restraints excluded: chain G residue 117 LEU Chi-restraints excluded: chain G residue 128 ILE Chi-restraints excluded: chain G residue 131 CYS Chi-restraints excluded: chain G residue 171 VAL Chi-restraints excluded: chain G residue 186 ASN Chi-restraints excluded: chain G residue 187 LEU Chi-restraints excluded: chain G residue 203 SER Chi-restraints excluded: chain G residue 204 LYS Chi-restraints excluded: chain G residue 229 LEU Chi-restraints excluded: chain G residue 231 ILE Chi-restraints excluded: chain G residue 281 GLU Chi-restraints excluded: chain G residue 335 LEU Chi-restraints excluded: chain G residue 351 TYR Chi-restraints excluded: chain G residue 375 PHE Chi-restraints excluded: chain G residue 400 PHE Chi-restraints excluded: chain G residue 402 ILE Chi-restraints excluded: chain G residue 403 ARG Chi-restraints excluded: chain G residue 408 ARG Chi-restraints excluded: chain G residue 432 CYS Chi-restraints excluded: chain G residue 440 LYS Chi-restraints excluded: chain G residue 441 LEU Chi-restraints excluded: chain G residue 452 LEU Chi-restraints excluded: chain G residue 458 LYS Chi-restraints excluded: chain G residue 462 LYS Chi-restraints excluded: chain G residue 478 LYS Chi-restraints excluded: chain G residue 493 ARG Chi-restraints excluded: chain G residue 528 LYS Chi-restraints excluded: chain G residue 536 ASN Chi-restraints excluded: chain G residue 542 ASN Chi-restraints excluded: chain G residue 553 THR Chi-restraints excluded: chain G residue 569 ILE Chi-restraints excluded: chain G residue 588 THR Chi-restraints excluded: chain G residue 599 THR Chi-restraints excluded: chain G residue 615 VAL Chi-restraints excluded: chain G residue 660 TYR Chi-restraints excluded: chain G residue 708 SER Chi-restraints excluded: chain G residue 746 SER Chi-restraints excluded: chain G residue 754 LEU Chi-restraints excluded: chain G residue 791 THR Chi-restraints excluded: chain G residue 947 LYS Chi-restraints excluded: chain G residue 950 ASP Chi-restraints excluded: chain G residue 973 ILE Chi-restraints excluded: chain G residue 975 SER Chi-restraints excluded: chain G residue 977 LEU Chi-restraints excluded: chain G residue 980 ILE Chi-restraints excluded: chain G residue 993 ILE Chi-restraints excluded: chain G residue 1001 LEU Chi-restraints excluded: chain G residue 1041 ASP Chi-restraints excluded: chain G residue 1086 LYS Chi-restraints excluded: chain G residue 1116 THR Chi-restraints excluded: chain G residue 1130 ILE Chi-restraints excluded: chain G residue 1141 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 313 optimal weight: 9.9990 chunk 261 optimal weight: 0.0570 chunk 287 optimal weight: 0.7980 chunk 214 optimal weight: 0.9980 chunk 138 optimal weight: 2.9990 chunk 168 optimal weight: 9.9990 chunk 123 optimal weight: 20.0000 chunk 39 optimal weight: 1.9990 chunk 320 optimal weight: 3.9990 chunk 196 optimal weight: 2.9990 chunk 61 optimal weight: 0.7980 overall best weight: 0.9300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 532 ASN A 957 GLN A 965 GLN ** B 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 644 GLN ** D 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 872 GLN D 901 GLN D 913 GLN ** G 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 542 ASN G 641 ASN G 690 GLN G1005 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4341 r_free = 0.4341 target = 0.198480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.143739 restraints weight = 42293.623| |-----------------------------------------------------------------------------| r_work (start): 0.3640 rms_B_bonded: 2.47 r_work: 0.3503 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3329 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7513 moved from start: 0.3822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 30193 Z= 0.165 Angle : 0.589 9.379 41191 Z= 0.301 Chirality : 0.045 0.201 4712 Planarity : 0.005 0.096 5285 Dihedral : 6.771 79.625 4708 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.05 % Allowed : 9.41 % Favored : 90.54 % Rotamer: Outliers : 6.38 % Allowed : 17.52 % Favored : 76.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.48 % Twisted General : 0.09 % 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: -2.50 (0.13), residues: 3700 helix: 0.20 (0.21), residues: 652 sheet: -1.26 (0.17), residues: 890 loop : -2.56 (0.13), residues: 2158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 237 TYR 0.025 0.001 TYR D1067 PHE 0.021 0.002 PHE A 541 TRP 0.042 0.001 TRP A 64 HIS 0.003 0.001 HIS A1088 Details of bonding type rmsd covalent geometry : bond 0.00390 (30124) covalent geometry : angle 0.57900 (41029) SS BOND : bond 0.00265 ( 45) SS BOND : angle 1.43896 ( 90) hydrogen bonds : bond 0.03448 ( 744) hydrogen bonds : angle 4.68915 ( 1980) link_NAG-ASN : bond 0.00235 ( 24) link_NAG-ASN : angle 2.21086 ( 72) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7400 Ramachandran restraints generated. 3700 Oldfield, 0 Emsley, 3700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7400 Ramachandran restraints generated. 3700 Oldfield, 0 Emsley, 3700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 716 residues out of total 3264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 205 poor density : 511 time to evaluate : 0.711 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: A 62 VAL cc_start: 0.8759 (t) cc_final: 0.8502 (m) REVERT: A 99 ASN cc_start: 0.7798 (p0) cc_final: 0.7287 (p0) REVERT: A 102 ARG cc_start: 0.8021 (mtm-85) cc_final: 0.7739 (ptp90) REVERT: A 132 GLU cc_start: 0.7657 (mt-10) cc_final: 0.7225 (mp0) REVERT: A 168 PHE cc_start: 0.8430 (OUTLIER) cc_final: 0.7659 (m-80) REVERT: A 188 ARG cc_start: 0.8509 (ptp90) cc_final: 0.7999 (mtt-85) REVERT: A 307 THR cc_start: 0.8586 (t) cc_final: 0.8352 (p) REVERT: A 316 SER cc_start: 0.8488 (t) cc_final: 0.8260 (p) REVERT: A 517 LEU cc_start: 0.3228 (OUTLIER) cc_final: 0.2855 (tm) REVERT: A 537 LYS cc_start: 0.8404 (ttmt) cc_final: 0.8099 (ttmm) REVERT: A 675 GLN cc_start: 0.7220 (mm-40) cc_final: 0.6938 (mm-40) REVERT: A 702 GLU cc_start: 0.7398 (tp30) cc_final: 0.6763 (tp30) REVERT: A 726 ILE cc_start: 0.8772 (OUTLIER) cc_final: 0.8545 (mp) REVERT: A 776 LYS cc_start: 0.8496 (ttpt) cc_final: 0.8137 (ttpt) REVERT: A 795 LYS cc_start: 0.8157 (OUTLIER) cc_final: 0.7929 (mptt) REVERT: A 947 LYS cc_start: 0.8341 (mtpt) cc_final: 0.8112 (mtpp) REVERT: A 949 GLN cc_start: 0.8547 (mm-40) cc_final: 0.8329 (mm-40) REVERT: A 960 ASN cc_start: 0.8413 (t0) cc_final: 0.8153 (t0) REVERT: A 969 LYS cc_start: 0.8505 (OUTLIER) cc_final: 0.7833 (pptt) REVERT: A 1017 GLU cc_start: 0.8153 (tm-30) cc_final: 0.7792 (tm-30) REVERT: A 1073 LYS cc_start: 0.8441 (mtmt) cc_final: 0.8157 (mtpp) REVERT: B 121 LEU cc_start: 0.2327 (OUTLIER) cc_final: 0.2061 (tt) REVERT: D 41 LYS cc_start: 0.8705 (mttt) cc_final: 0.8417 (mtmm) REVERT: D 96 GLU cc_start: 0.6391 (OUTLIER) cc_final: 0.5693 (tt0) REVERT: D 105 ILE cc_start: 0.8427 (mt) cc_final: 0.8096 (mt) REVERT: D 189 GLU cc_start: 0.7873 (mp0) cc_final: 0.7668 (mp0) REVERT: D 206 THR cc_start: 0.8331 (OUTLIER) cc_final: 0.8076 (t) REVERT: D 231 ILE cc_start: 0.7596 (OUTLIER) cc_final: 0.7319 (tp) REVERT: D 239 GLN cc_start: 0.7788 (tm-30) cc_final: 0.7420 (tm-30) REVERT: D 290 ASP cc_start: 0.7992 (t70) cc_final: 0.7728 (t0) REVERT: D 303 LEU cc_start: 0.8420 (tp) cc_final: 0.8122 (mt) REVERT: D 319 ARG cc_start: 0.8156 (ttm170) cc_final: 0.7892 (ttm-80) REVERT: D 346 ARG cc_start: 0.7979 (mtt-85) cc_final: 0.7712 (mtt-85) REVERT: D 377 PHE cc_start: 0.8212 (t80) cc_final: 0.7921 (t80) REVERT: D 524 VAL cc_start: 0.6418 (OUTLIER) cc_final: 0.6168 (p) REVERT: D 543 PHE cc_start: 0.8181 (m-10) cc_final: 0.7726 (m-10) REVERT: D 599 THR cc_start: 0.8338 (m) cc_final: 0.8027 (p) REVERT: D 737 ASP cc_start: 0.7314 (t70) cc_final: 0.7060 (t0) REVERT: D 752 LEU cc_start: 0.8370 (mt) cc_final: 0.7998 (mp) REVERT: D 779 GLN cc_start: 0.8080 (OUTLIER) cc_final: 0.7782 (tm-30) REVERT: D 790 LYS cc_start: 0.8272 (mtpp) cc_final: 0.8060 (mtpp) REVERT: D 804 GLN cc_start: 0.8352 (mt0) cc_final: 0.8022 (mm-40) REVERT: D 808 ASP cc_start: 0.7646 (t0) cc_final: 0.7005 (p0) REVERT: D 816 SER cc_start: 0.8482 (p) cc_final: 0.8167 (t) REVERT: D 854 LYS cc_start: 0.8723 (ttmm) cc_final: 0.8447 (ttpp) REVERT: D 921 LYS cc_start: 0.8453 (tptp) cc_final: 0.8210 (tptp) REVERT: D 988 GLU cc_start: 0.7090 (OUTLIER) cc_final: 0.6420 (tm-30) REVERT: D 990 GLU cc_start: 0.7937 (mp0) cc_final: 0.7576 (mp0) REVERT: D 1050 MET cc_start: 0.8320 (mtm) cc_final: 0.8102 (mtp) REVERT: D 1072 GLU cc_start: 0.8185 (pm20) cc_final: 0.7984 (pm20) REVERT: D 1086 LYS cc_start: 0.8535 (OUTLIER) cc_final: 0.8249 (mtmm) REVERT: D 1118 ASP cc_start: 0.8040 (t0) cc_final: 0.7618 (t0) REVERT: F 200 GLU cc_start: 0.0724 (OUTLIER) cc_final: 0.0158 (pm20) REVERT: G 53 ASP cc_start: 0.7661 (m-30) cc_final: 0.7397 (m-30) REVERT: G 54 LEU cc_start: 0.8766 (mt) cc_final: 0.8553 (mp) REVERT: G 81 ASN cc_start: 0.7167 (OUTLIER) cc_final: 0.6646 (p0) REVERT: G 117 LEU cc_start: 0.7762 (OUTLIER) cc_final: 0.7509 (mt) REVERT: G 129 LYS cc_start: 0.8418 (mtmt) cc_final: 0.7963 (ptmt) REVERT: G 186 ASN cc_start: 0.7590 (OUTLIER) cc_final: 0.7248 (p0) REVERT: G 188 ARG cc_start: 0.8858 (ptp90) cc_final: 0.8435 (mtt180) REVERT: G 286 THR cc_start: 0.7827 (m) cc_final: 0.7591 (t) REVERT: G 293 LEU cc_start: 0.8914 (tp) cc_final: 0.8654 (tp) REVERT: G 340 GLU cc_start: 0.7604 (mm-30) cc_final: 0.7366 (mm-30) REVERT: G 453 TYR cc_start: 0.6311 (t80) cc_final: 0.6048 (t80) REVERT: G 478 LYS cc_start: 0.3612 (OUTLIER) cc_final: 0.3277 (tmmt) REVERT: G 493 ARG cc_start: 0.7038 (OUTLIER) cc_final: 0.6537 (mmp-170) REVERT: G 528 LYS cc_start: 0.7059 (OUTLIER) cc_final: 0.6822 (mmmt) REVERT: G 599 THR cc_start: 0.8837 (OUTLIER) cc_final: 0.8582 (p) REVERT: G 655 TYR cc_start: 0.8469 (t80) cc_final: 0.8137 (t80) REVERT: G 663 ASP cc_start: 0.7480 (t70) cc_final: 0.7165 (t0) REVERT: G 730 SER cc_start: 0.8672 (t) cc_final: 0.8389 (p) REVERT: G 776 LYS cc_start: 0.8323 (ttpt) cc_final: 0.8061 (ttpt) REVERT: G 790 LYS cc_start: 0.7796 (mtmm) cc_final: 0.7587 (mtmm) REVERT: G 803 SER cc_start: 0.8528 (m) cc_final: 0.8219 (p) REVERT: G 884 SER cc_start: 0.8496 (t) cc_final: 0.8212 (p) REVERT: G 900 MET cc_start: 0.8284 (mmm) cc_final: 0.7973 (mmm) REVERT: G 964 LYS cc_start: 0.8488 (ttpp) cc_final: 0.8152 (ttpp) REVERT: G 1017 GLU cc_start: 0.7919 (tm-30) cc_final: 0.7549 (tm-30) REVERT: G 1107 ARG cc_start: 0.7436 (mtt-85) cc_final: 0.7128 (mtt-85) outliers start: 205 outliers final: 154 residues processed: 663 average time/residue: 0.1950 time to fit residues: 202.4092 Evaluate side-chains 671 residues out of total 3264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 175 poor density : 496 time to evaluate : 1.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 158 ARG Chi-restraints excluded: chain A residue 168 PHE Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 370 ASN Chi-restraints excluded: chain A residue 386 LYS Chi-restraints excluded: chain A residue 400 PHE Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 403 ARG Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 440 LYS Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 726 ILE Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 795 LYS Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 969 LYS Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain A residue 1014 ARG Chi-restraints excluded: chain A residue 1038 LYS Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 104 LYS Chi-restraints excluded: chain D residue 45 SER Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 68 ILE Chi-restraints excluded: chain D residue 87 ASN Chi-restraints excluded: chain D residue 96 GLU Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain D residue 111 ASP Chi-restraints excluded: chain D residue 113 LYS Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 132 GLU Chi-restraints excluded: chain D residue 195 ILE Chi-restraints excluded: chain D residue 206 THR Chi-restraints excluded: chain D residue 226 LEU Chi-restraints excluded: chain D residue 231 ILE Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 362 VAL Chi-restraints excluded: chain D residue 370 ASN Chi-restraints excluded: chain D residue 400 PHE Chi-restraints excluded: chain D residue 402 ILE Chi-restraints excluded: chain D residue 433 VAL Chi-restraints excluded: chain D residue 440 LYS Chi-restraints excluded: chain D residue 458 LYS Chi-restraints excluded: chain D residue 524 VAL Chi-restraints excluded: chain D residue 528 LYS Chi-restraints excluded: chain D residue 553 THR Chi-restraints excluded: chain D residue 556 ASN Chi-restraints excluded: chain D residue 569 ILE Chi-restraints excluded: chain D residue 588 THR Chi-restraints excluded: chain D residue 616 ASN Chi-restraints excluded: chain D residue 617 CYS Chi-restraints excluded: chain D residue 725 GLU Chi-restraints excluded: chain D residue 779 GLN Chi-restraints excluded: chain D residue 803 SER Chi-restraints excluded: chain D residue 849 LEU Chi-restraints excluded: chain D residue 859 THR Chi-restraints excluded: chain D residue 878 LEU Chi-restraints excluded: chain D residue 900 MET Chi-restraints excluded: chain D residue 947 LYS Chi-restraints excluded: chain D residue 969 LYS Chi-restraints excluded: chain D residue 988 GLU Chi-restraints excluded: chain D residue 1041 ASP Chi-restraints excluded: chain D residue 1066 THR Chi-restraints excluded: chain D residue 1086 LYS Chi-restraints excluded: chain D residue 1100 THR Chi-restraints excluded: chain D residue 1104 VAL Chi-restraints excluded: chain D residue 1129 VAL Chi-restraints excluded: chain D residue 1141 LEU Chi-restraints excluded: chain E residue 1 GLU Chi-restraints excluded: chain E residue 52 THR Chi-restraints excluded: chain E residue 104 VAL Chi-restraints excluded: chain E residue 121 LEU Chi-restraints excluded: chain E residue 151 LEU Chi-restraints excluded: chain E residue 156 LYS Chi-restraints excluded: chain E residue 164 THR Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain F residue 30 LYS Chi-restraints excluded: chain F residue 74 ILE Chi-restraints excluded: chain F residue 104 LYS Chi-restraints excluded: chain F residue 158 LYS Chi-restraints excluded: chain F residue 161 VAL Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain F residue 197 VAL Chi-restraints excluded: chain F residue 200 GLU Chi-restraints excluded: chain F residue 204 VAL Chi-restraints excluded: chain G residue 46 SER Chi-restraints excluded: chain G residue 47 VAL Chi-restraints excluded: chain G residue 81 ASN Chi-restraints excluded: chain G residue 95 ILE Chi-restraints excluded: chain G residue 100 ILE Chi-restraints excluded: chain G residue 102 ARG Chi-restraints excluded: chain G residue 117 LEU Chi-restraints excluded: chain G residue 128 ILE Chi-restraints excluded: chain G residue 131 CYS Chi-restraints excluded: chain G residue 171 VAL Chi-restraints excluded: chain G residue 186 ASN Chi-restraints excluded: chain G residue 187 LEU Chi-restraints excluded: chain G residue 203 SER Chi-restraints excluded: chain G residue 229 LEU Chi-restraints excluded: chain G residue 231 ILE Chi-restraints excluded: chain G residue 281 GLU Chi-restraints excluded: chain G residue 335 LEU Chi-restraints excluded: chain G residue 351 TYR Chi-restraints excluded: chain G residue 375 PHE Chi-restraints excluded: chain G residue 400 PHE Chi-restraints excluded: chain G residue 402 ILE Chi-restraints excluded: chain G residue 403 ARG Chi-restraints excluded: chain G residue 408 ARG Chi-restraints excluded: chain G residue 432 CYS Chi-restraints excluded: chain G residue 440 LYS Chi-restraints excluded: chain G residue 441 LEU Chi-restraints excluded: chain G residue 452 LEU Chi-restraints excluded: chain G residue 458 LYS Chi-restraints excluded: chain G residue 462 LYS Chi-restraints excluded: chain G residue 478 LYS Chi-restraints excluded: chain G residue 486 PHE Chi-restraints excluded: chain G residue 493 ARG Chi-restraints excluded: chain G residue 528 LYS Chi-restraints excluded: chain G residue 536 ASN Chi-restraints excluded: chain G residue 542 ASN Chi-restraints excluded: chain G residue 553 THR Chi-restraints excluded: chain G residue 569 ILE Chi-restraints excluded: chain G residue 588 THR Chi-restraints excluded: chain G residue 599 THR Chi-restraints excluded: chain G residue 660 TYR Chi-restraints excluded: chain G residue 708 SER Chi-restraints excluded: chain G residue 754 LEU Chi-restraints excluded: chain G residue 762 GLN Chi-restraints excluded: chain G residue 791 THR Chi-restraints excluded: chain G residue 947 LYS Chi-restraints excluded: chain G residue 973 ILE Chi-restraints excluded: chain G residue 975 SER Chi-restraints excluded: chain G residue 977 LEU Chi-restraints excluded: chain G residue 980 ILE Chi-restraints excluded: chain G residue 991 VAL Chi-restraints excluded: chain G residue 1041 ASP Chi-restraints excluded: chain G residue 1086 LYS Chi-restraints excluded: chain G residue 1116 THR Chi-restraints excluded: chain G residue 1130 ILE Chi-restraints excluded: chain G residue 1141 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 330 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 chunk 191 optimal weight: 1.9990 chunk 144 optimal weight: 3.9990 chunk 315 optimal weight: 3.9990 chunk 46 optimal weight: 4.9990 chunk 83 optimal weight: 0.7980 chunk 297 optimal weight: 3.9990 chunk 214 optimal weight: 1.9990 chunk 329 optimal weight: 0.5980 chunk 82 optimal weight: 0.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 99 ASN A 532 ASN A 965 GLN ** B 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 872 GLN D 901 GLN F 68 ASN ** G 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 542 ASN G 641 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4332 r_free = 0.4332 target = 0.197600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.142859 restraints weight = 42211.339| |-----------------------------------------------------------------------------| r_work (start): 0.3605 rms_B_bonded: 2.48 r_work: 0.3466 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3288 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 moved from start: 0.4004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 30193 Z= 0.210 Angle : 0.626 10.313 41191 Z= 0.319 Chirality : 0.046 0.212 4712 Planarity : 0.005 0.097 5285 Dihedral : 6.886 79.585 4708 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.05 % Allowed : 9.92 % Favored : 90.03 % Rotamer: Outliers : 5.82 % Allowed : 18.11 % Favored : 76.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.48 % Twisted General : 0.09 % 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: -2.44 (0.13), residues: 3700 helix: 0.22 (0.21), residues: 663 sheet: -1.22 (0.17), residues: 869 loop : -2.51 (0.13), residues: 2168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D1019 TYR 0.029 0.001 TYR D1067 PHE 0.033 0.002 PHE A 133 TRP 0.045 0.001 TRP A 64 HIS 0.005 0.001 HIS G1088 Details of bonding type rmsd covalent geometry : bond 0.00495 (30124) covalent geometry : angle 0.61551 (41029) SS BOND : bond 0.00304 ( 45) SS BOND : angle 1.60776 ( 90) hydrogen bonds : bond 0.03732 ( 744) hydrogen bonds : angle 4.75416 ( 1980) link_NAG-ASN : bond 0.00257 ( 24) link_NAG-ASN : angle 2.28819 ( 72) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7400 Ramachandran restraints generated. 3700 Oldfield, 0 Emsley, 3700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7400 Ramachandran restraints generated. 3700 Oldfield, 0 Emsley, 3700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 684 residues out of total 3264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 187 poor density : 497 time to evaluate : 1.003 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 62 VAL cc_start: 0.8752 (t) cc_final: 0.8509 (m) REVERT: A 99 ASN cc_start: 0.7672 (OUTLIER) cc_final: 0.7104 (p0) REVERT: A 101 ILE cc_start: 0.7898 (OUTLIER) cc_final: 0.7442 (tp) REVERT: A 102 ARG cc_start: 0.8041 (mtm-85) cc_final: 0.7757 (ptp90) REVERT: A 132 GLU cc_start: 0.7635 (mt-10) cc_final: 0.7197 (mp0) REVERT: A 188 ARG cc_start: 0.8503 (ptp90) cc_final: 0.8089 (mtt-85) REVERT: A 231 ILE cc_start: 0.8748 (tt) cc_final: 0.8437 (pt) REVERT: A 239 GLN cc_start: 0.7210 (tp40) cc_final: 0.6967 (tp40) REVERT: A 307 THR cc_start: 0.8577 (t) cc_final: 0.8372 (p) REVERT: A 316 SER cc_start: 0.8516 (t) cc_final: 0.8264 (p) REVERT: A 517 LEU cc_start: 0.3242 (OUTLIER) cc_final: 0.2878 (tm) REVERT: A 537 LYS cc_start: 0.8482 (ttmt) cc_final: 0.8155 (ttmm) REVERT: A 543 PHE cc_start: 0.7233 (m-10) cc_final: 0.7015 (m-80) REVERT: A 675 GLN cc_start: 0.7262 (mm-40) cc_final: 0.6970 (mm-40) REVERT: A 702 GLU cc_start: 0.7382 (tp30) cc_final: 0.6720 (tp30) REVERT: A 726 ILE cc_start: 0.8791 (OUTLIER) cc_final: 0.8562 (mp) REVERT: A 745 ASP cc_start: 0.7009 (p0) cc_final: 0.6791 (p0) REVERT: A 776 LYS cc_start: 0.8504 (ttpt) cc_final: 0.8144 (ttpt) REVERT: A 848 ASP cc_start: 0.7321 (p0) cc_final: 0.6981 (p0) REVERT: A 947 LYS cc_start: 0.8360 (mtpt) cc_final: 0.8138 (mtpp) REVERT: A 960 ASN cc_start: 0.8454 (t0) cc_final: 0.8206 (t0) REVERT: A 969 LYS cc_start: 0.8517 (OUTLIER) cc_final: 0.7866 (pptt) REVERT: A 1017 GLU cc_start: 0.8069 (tm-30) cc_final: 0.7754 (tm-30) REVERT: A 1073 LYS cc_start: 0.8456 (mtmt) cc_final: 0.8182 (mtpp) REVERT: B 121 LEU cc_start: 0.2252 (OUTLIER) cc_final: 0.1993 (tt) REVERT: D 92 PHE cc_start: 0.8311 (t80) cc_final: 0.8007 (t80) REVERT: D 96 GLU cc_start: 0.6525 (OUTLIER) cc_final: 0.6108 (tt0) REVERT: D 105 ILE cc_start: 0.8635 (mt) cc_final: 0.8264 (mt) REVERT: D 189 GLU cc_start: 0.7947 (mp0) cc_final: 0.7709 (mp0) REVERT: D 206 THR cc_start: 0.8341 (OUTLIER) cc_final: 0.8096 (t) REVERT: D 290 ASP cc_start: 0.8025 (t70) cc_final: 0.7763 (t0) REVERT: D 319 ARG cc_start: 0.8265 (ttm170) cc_final: 0.7996 (ttm-80) REVERT: D 346 ARG cc_start: 0.8026 (mtt-85) cc_final: 0.7724 (mtt-85) REVERT: D 377 PHE cc_start: 0.8162 (t80) cc_final: 0.7794 (t80) REVERT: D 543 PHE cc_start: 0.8212 (m-10) cc_final: 0.7738 (m-10) REVERT: D 599 THR cc_start: 0.8349 (m) cc_final: 0.8039 (p) REVERT: D 730 SER cc_start: 0.8693 (t) cc_final: 0.8462 (m) REVERT: D 737 ASP cc_start: 0.7406 (t70) cc_final: 0.7042 (t0) REVERT: D 779 GLN cc_start: 0.8177 (OUTLIER) cc_final: 0.7924 (tm-30) REVERT: D 790 LYS cc_start: 0.8254 (mtpp) cc_final: 0.8041 (mtpp) REVERT: D 808 ASP cc_start: 0.7700 (t0) cc_final: 0.7078 (p0) REVERT: D 816 SER cc_start: 0.8509 (p) cc_final: 0.8199 (t) REVERT: D 848 ASP cc_start: 0.7886 (p0) cc_final: 0.7636 (p0) REVERT: D 921 LYS cc_start: 0.8489 (tptp) cc_final: 0.8252 (tptp) REVERT: D 988 GLU cc_start: 0.7061 (OUTLIER) cc_final: 0.6340 (tm-30) REVERT: D 1086 LYS cc_start: 0.8536 (OUTLIER) cc_final: 0.8267 (mtmm) REVERT: D 1118 ASP cc_start: 0.8110 (t0) cc_final: 0.7579 (t0) REVERT: F 200 GLU cc_start: 0.0758 (OUTLIER) cc_final: 0.0194 (pm20) REVERT: G 53 ASP cc_start: 0.7743 (m-30) cc_final: 0.7469 (m-30) REVERT: G 81 ASN cc_start: 0.7164 (OUTLIER) cc_final: 0.6634 (p0) REVERT: G 117 LEU cc_start: 0.7961 (OUTLIER) cc_final: 0.7667 (mt) REVERT: G 121 ASN cc_start: 0.6934 (t0) cc_final: 0.6705 (t0) REVERT: G 129 LYS cc_start: 0.8409 (mtmt) cc_final: 0.7886 (ptmm) REVERT: G 186 ASN cc_start: 0.7645 (OUTLIER) cc_final: 0.7275 (p0) REVERT: G 188 ARG cc_start: 0.8847 (ptp90) cc_final: 0.8498 (mtt180) REVERT: G 286 THR cc_start: 0.7860 (m) cc_final: 0.7606 (t) REVERT: G 293 LEU cc_start: 0.8922 (tp) cc_final: 0.8659 (tp) REVERT: G 340 GLU cc_start: 0.7598 (mm-30) cc_final: 0.7332 (mm-30) REVERT: G 453 TYR cc_start: 0.6288 (t80) cc_final: 0.6054 (t80) REVERT: G 478 LYS cc_start: 0.3505 (OUTLIER) cc_final: 0.3217 (tmmt) REVERT: G 493 ARG cc_start: 0.6997 (OUTLIER) cc_final: 0.6507 (mmp-170) REVERT: G 505 HIS cc_start: 0.7531 (OUTLIER) cc_final: 0.7202 (t70) REVERT: G 528 LYS cc_start: 0.7052 (OUTLIER) cc_final: 0.6810 (mmmt) REVERT: G 599 THR cc_start: 0.8831 (OUTLIER) cc_final: 0.8572 (p) REVERT: G 663 ASP cc_start: 0.7466 (t70) cc_final: 0.7088 (t0) REVERT: G 730 SER cc_start: 0.8655 (t) cc_final: 0.8382 (p) REVERT: G 776 LYS cc_start: 0.8412 (ttpt) cc_final: 0.8085 (ttpt) REVERT: G 790 LYS cc_start: 0.7803 (mtmm) cc_final: 0.7577 (mtmm) REVERT: G 884 SER cc_start: 0.8529 (t) cc_final: 0.8233 (p) REVERT: G 900 MET cc_start: 0.8268 (mmm) cc_final: 0.7977 (mmm) REVERT: G 964 LYS cc_start: 0.8521 (ttpp) cc_final: 0.8201 (ttpp) REVERT: G 1017 GLU cc_start: 0.7939 (tm-30) cc_final: 0.7566 (tm-30) REVERT: G 1107 ARG cc_start: 0.7521 (mtt-85) cc_final: 0.7200 (mtt-85) outliers start: 187 outliers final: 151 residues processed: 635 average time/residue: 0.1915 time to fit residues: 190.3643 Evaluate side-chains 656 residues out of total 3264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 171 poor density : 485 time to evaluate : 0.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 99 ASN Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 158 ARG Chi-restraints excluded: chain A residue 168 PHE Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 370 ASN Chi-restraints excluded: chain A residue 386 LYS Chi-restraints excluded: chain A residue 400 PHE Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 403 ARG Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 440 LYS Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 726 ILE Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 969 LYS Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain A residue 1014 ARG Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 104 LYS Chi-restraints excluded: chain D residue 45 SER Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 68 ILE Chi-restraints excluded: chain D residue 87 ASN Chi-restraints excluded: chain D residue 96 GLU Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain D residue 111 ASP Chi-restraints excluded: chain D residue 113 LYS Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 171 VAL Chi-restraints excluded: chain D residue 195 ILE Chi-restraints excluded: chain D residue 206 THR Chi-restraints excluded: chain D residue 226 LEU Chi-restraints excluded: chain D residue 231 ILE Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 338 PHE Chi-restraints excluded: chain D residue 362 VAL Chi-restraints excluded: chain D residue 370 ASN Chi-restraints excluded: chain D residue 400 PHE Chi-restraints excluded: chain D residue 402 ILE Chi-restraints excluded: chain D residue 433 VAL Chi-restraints excluded: chain D residue 440 LYS Chi-restraints excluded: chain D residue 458 LYS Chi-restraints excluded: chain D residue 524 VAL Chi-restraints excluded: chain D residue 528 LYS Chi-restraints excluded: chain D residue 553 THR Chi-restraints excluded: chain D residue 569 ILE Chi-restraints excluded: chain D residue 588 THR Chi-restraints excluded: chain D residue 616 ASN Chi-restraints excluded: chain D residue 617 CYS Chi-restraints excluded: chain D residue 725 GLU Chi-restraints excluded: chain D residue 779 GLN Chi-restraints excluded: chain D residue 791 THR Chi-restraints excluded: chain D residue 803 SER Chi-restraints excluded: chain D residue 859 THR Chi-restraints excluded: chain D residue 878 LEU Chi-restraints excluded: chain D residue 900 MET Chi-restraints excluded: chain D residue 988 GLU Chi-restraints excluded: chain D residue 1041 ASP Chi-restraints excluded: chain D residue 1086 LYS Chi-restraints excluded: chain D residue 1100 THR Chi-restraints excluded: chain D residue 1104 VAL Chi-restraints excluded: chain D residue 1129 VAL Chi-restraints excluded: chain E residue 1 GLU Chi-restraints excluded: chain E residue 52 THR Chi-restraints excluded: chain E residue 104 VAL Chi-restraints excluded: chain E residue 121 LEU Chi-restraints excluded: chain E residue 151 LEU Chi-restraints excluded: chain E residue 156 LYS Chi-restraints excluded: chain E residue 164 THR Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain F residue 30 LYS Chi-restraints excluded: chain F residue 74 ILE Chi-restraints excluded: chain F residue 104 LYS Chi-restraints excluded: chain F residue 158 LYS Chi-restraints excluded: chain F residue 161 VAL Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain F residue 197 VAL Chi-restraints excluded: chain F residue 200 GLU Chi-restraints excluded: chain F residue 204 VAL Chi-restraints excluded: chain G residue 46 SER Chi-restraints excluded: chain G residue 47 VAL Chi-restraints excluded: chain G residue 81 ASN Chi-restraints excluded: chain G residue 100 ILE Chi-restraints excluded: chain G residue 102 ARG Chi-restraints excluded: chain G residue 117 LEU Chi-restraints excluded: chain G residue 128 ILE Chi-restraints excluded: chain G residue 131 CYS Chi-restraints excluded: chain G residue 171 VAL Chi-restraints excluded: chain G residue 186 ASN Chi-restraints excluded: chain G residue 187 LEU Chi-restraints excluded: chain G residue 203 SER Chi-restraints excluded: chain G residue 204 LYS Chi-restraints excluded: chain G residue 229 LEU Chi-restraints excluded: chain G residue 231 ILE Chi-restraints excluded: chain G residue 281 GLU Chi-restraints excluded: chain G residue 335 LEU Chi-restraints excluded: chain G residue 351 TYR Chi-restraints excluded: chain G residue 400 PHE Chi-restraints excluded: chain G residue 402 ILE Chi-restraints excluded: chain G residue 403 ARG Chi-restraints excluded: chain G residue 408 ARG Chi-restraints excluded: chain G residue 432 CYS Chi-restraints excluded: chain G residue 440 LYS Chi-restraints excluded: chain G residue 441 LEU Chi-restraints excluded: chain G residue 452 LEU Chi-restraints excluded: chain G residue 458 LYS Chi-restraints excluded: chain G residue 462 LYS Chi-restraints excluded: chain G residue 478 LYS Chi-restraints excluded: chain G residue 486 PHE Chi-restraints excluded: chain G residue 493 ARG Chi-restraints excluded: chain G residue 505 HIS Chi-restraints excluded: chain G residue 528 LYS Chi-restraints excluded: chain G residue 536 ASN Chi-restraints excluded: chain G residue 542 ASN Chi-restraints excluded: chain G residue 553 THR Chi-restraints excluded: chain G residue 569 ILE Chi-restraints excluded: chain G residue 588 THR Chi-restraints excluded: chain G residue 599 THR Chi-restraints excluded: chain G residue 660 TYR Chi-restraints excluded: chain G residue 708 SER Chi-restraints excluded: chain G residue 754 LEU Chi-restraints excluded: chain G residue 762 GLN Chi-restraints excluded: chain G residue 791 THR Chi-restraints excluded: chain G residue 947 LYS Chi-restraints excluded: chain G residue 973 ILE Chi-restraints excluded: chain G residue 975 SER Chi-restraints excluded: chain G residue 977 LEU Chi-restraints excluded: chain G residue 980 ILE Chi-restraints excluded: chain G residue 991 VAL Chi-restraints excluded: chain G residue 1001 LEU Chi-restraints excluded: chain G residue 1041 ASP Chi-restraints excluded: chain G residue 1086 LYS Chi-restraints excluded: chain G residue 1116 THR Chi-restraints excluded: chain G residue 1130 ILE Chi-restraints excluded: chain G residue 1141 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 45 optimal weight: 1.9990 chunk 203 optimal weight: 0.9980 chunk 163 optimal weight: 3.9990 chunk 270 optimal weight: 0.5980 chunk 358 optimal weight: 0.9980 chunk 285 optimal weight: 0.8980 chunk 118 optimal weight: 40.0000 chunk 131 optimal weight: 0.8980 chunk 170 optimal weight: 3.9990 chunk 181 optimal weight: 3.9990 chunk 334 optimal weight: 0.3980 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 532 ASN A1002 GLN D 61 ASN D 121 ASN ** D 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 872 GLN D 901 GLN D 935 GLN D1002 GLN ** G 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 641 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4345 r_free = 0.4345 target = 0.198782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.142940 restraints weight = 42139.842| |-----------------------------------------------------------------------------| r_work (start): 0.3595 rms_B_bonded: 2.40 r_work: 0.3460 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3293 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7526 moved from start: 0.4053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 30193 Z= 0.148 Angle : 0.602 10.106 41191 Z= 0.305 Chirality : 0.045 0.208 4712 Planarity : 0.005 0.101 5285 Dihedral : 6.738 79.616 4705 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.05 % Allowed : 9.32 % Favored : 90.62 % Rotamer: Outliers : 5.73 % Allowed : 18.27 % Favored : 76.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.48 % Twisted General : 0.09 % 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: -2.31 (0.13), residues: 3700 helix: 0.46 (0.21), residues: 662 sheet: -1.19 (0.17), residues: 885 loop : -2.45 (0.13), residues: 2153 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 273 TYR 0.023 0.001 TYR D1067 PHE 0.031 0.002 PHE A 133 TRP 0.046 0.001 TRP A 64 HIS 0.003 0.001 HIS A1088 Details of bonding type rmsd covalent geometry : bond 0.00349 (30124) covalent geometry : angle 0.59271 (41029) SS BOND : bond 0.00279 ( 45) SS BOND : angle 1.40356 ( 90) hydrogen bonds : bond 0.03395 ( 744) hydrogen bonds : angle 4.67040 ( 1980) link_NAG-ASN : bond 0.00203 ( 24) link_NAG-ASN : angle 2.16826 ( 72) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7400 Ramachandran restraints generated. 3700 Oldfield, 0 Emsley, 3700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7400 Ramachandran restraints generated. 3700 Oldfield, 0 Emsley, 3700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 670 residues out of total 3264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 184 poor density : 486 time to evaluate : 1.128 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 62 VAL cc_start: 0.8756 (t) cc_final: 0.8527 (m) REVERT: A 132 GLU cc_start: 0.7583 (mt-10) cc_final: 0.7175 (mp0) REVERT: A 188 ARG cc_start: 0.8490 (ptp90) cc_final: 0.8273 (mtt-85) REVERT: A 231 ILE cc_start: 0.8734 (tt) cc_final: 0.8411 (pt) REVERT: A 239 GLN cc_start: 0.7172 (tp40) cc_final: 0.6959 (tp40) REVERT: A 316 SER cc_start: 0.8483 (t) cc_final: 0.8223 (p) REVERT: A 517 LEU cc_start: 0.3183 (OUTLIER) cc_final: 0.2820 (tm) REVERT: A 537 LYS cc_start: 0.8484 (ttmt) cc_final: 0.8163 (ttmm) REVERT: A 675 GLN cc_start: 0.7239 (mm-40) cc_final: 0.6953 (mm-40) REVERT: A 702 GLU cc_start: 0.7394 (tp30) cc_final: 0.6710 (tp30) REVERT: A 726 ILE cc_start: 0.8789 (OUTLIER) cc_final: 0.8550 (mp) REVERT: A 765 ARG cc_start: 0.8195 (ttm110) cc_final: 0.7825 (mtm-85) REVERT: A 776 LYS cc_start: 0.8471 (ttpt) cc_final: 0.8114 (ttpt) REVERT: A 947 LYS cc_start: 0.8362 (mtpt) cc_final: 0.8124 (mtpp) REVERT: A 960 ASN cc_start: 0.8428 (t0) cc_final: 0.8167 (t0) REVERT: A 969 LYS cc_start: 0.8533 (OUTLIER) cc_final: 0.7837 (pptt) REVERT: A 1002 GLN cc_start: 0.7678 (OUTLIER) cc_final: 0.7477 (tt0) REVERT: A 1017 GLU cc_start: 0.8019 (tm-30) cc_final: 0.7694 (tm-30) REVERT: A 1073 LYS cc_start: 0.8452 (mtmt) cc_final: 0.8179 (mtpp) REVERT: B 121 LEU cc_start: 0.2285 (OUTLIER) cc_final: 0.2048 (tt) REVERT: D 54 LEU cc_start: 0.8010 (mm) cc_final: 0.7778 (mt) REVERT: D 96 GLU cc_start: 0.6492 (OUTLIER) cc_final: 0.5779 (tt0) REVERT: D 105 ILE cc_start: 0.8568 (mt) cc_final: 0.8219 (mt) REVERT: D 206 THR cc_start: 0.8356 (OUTLIER) cc_final: 0.8137 (t) REVERT: D 290 ASP cc_start: 0.7991 (t70) cc_final: 0.7737 (t0) REVERT: D 319 ARG cc_start: 0.8247 (ttm170) cc_final: 0.7985 (ttm-80) REVERT: D 346 ARG cc_start: 0.8061 (mtt-85) cc_final: 0.7758 (mtt-85) REVERT: D 377 PHE cc_start: 0.8129 (t80) cc_final: 0.7796 (t80) REVERT: D 524 VAL cc_start: 0.6475 (OUTLIER) cc_final: 0.6251 (p) REVERT: D 543 PHE cc_start: 0.8173 (m-10) cc_final: 0.7756 (m-10) REVERT: D 599 THR cc_start: 0.8323 (m) cc_final: 0.8004 (p) REVERT: D 730 SER cc_start: 0.8691 (t) cc_final: 0.8453 (m) REVERT: D 752 LEU cc_start: 0.8384 (mt) cc_final: 0.8005 (mp) REVERT: D 779 GLN cc_start: 0.8109 (OUTLIER) cc_final: 0.7860 (tm-30) REVERT: D 790 LYS cc_start: 0.8227 (mtpp) cc_final: 0.8018 (mtpp) REVERT: D 808 ASP cc_start: 0.7677 (t0) cc_final: 0.7092 (p0) REVERT: D 816 SER cc_start: 0.8515 (p) cc_final: 0.8246 (t) REVERT: D 848 ASP cc_start: 0.7902 (p0) cc_final: 0.7666 (p0) REVERT: D 921 LYS cc_start: 0.8442 (tptp) cc_final: 0.8210 (tptp) REVERT: D 1086 LYS cc_start: 0.8541 (OUTLIER) cc_final: 0.8322 (pttt) REVERT: D 1118 ASP cc_start: 0.7989 (t0) cc_final: 0.7480 (t0) REVERT: F 200 GLU cc_start: 0.0813 (OUTLIER) cc_final: 0.0367 (pm20) REVERT: G 53 ASP cc_start: 0.7710 (m-30) cc_final: 0.7442 (m-30) REVERT: G 81 ASN cc_start: 0.7078 (OUTLIER) cc_final: 0.6560 (p0) REVERT: G 117 LEU cc_start: 0.7856 (OUTLIER) cc_final: 0.7568 (mt) REVERT: G 121 ASN cc_start: 0.6922 (t0) cc_final: 0.6718 (t0) REVERT: G 129 LYS cc_start: 0.8403 (mtmt) cc_final: 0.7986 (ptmt) REVERT: G 186 ASN cc_start: 0.7637 (OUTLIER) cc_final: 0.7275 (p0) REVERT: G 188 ARG cc_start: 0.8816 (ptp90) cc_final: 0.8430 (mtt180) REVERT: G 286 THR cc_start: 0.7862 (m) cc_final: 0.7613 (t) REVERT: G 293 LEU cc_start: 0.8924 (tp) cc_final: 0.8649 (tp) REVERT: G 340 GLU cc_start: 0.7595 (mm-30) cc_final: 0.7354 (mm-30) REVERT: G 453 TYR cc_start: 0.6240 (t80) cc_final: 0.5993 (t80) REVERT: G 478 LYS cc_start: 0.3581 (OUTLIER) cc_final: 0.3274 (tmmt) REVERT: G 493 ARG cc_start: 0.6968 (OUTLIER) cc_final: 0.6475 (mmp-170) REVERT: G 505 HIS cc_start: 0.7493 (OUTLIER) cc_final: 0.7189 (t70) REVERT: G 588 THR cc_start: 0.8688 (OUTLIER) cc_final: 0.8388 (m) REVERT: G 599 THR cc_start: 0.8830 (OUTLIER) cc_final: 0.8586 (p) REVERT: G 663 ASP cc_start: 0.7483 (t70) cc_final: 0.7055 (t0) REVERT: G 730 SER cc_start: 0.8649 (t) cc_final: 0.8370 (p) REVERT: G 776 LYS cc_start: 0.8417 (ttpt) cc_final: 0.8061 (ttpt) REVERT: G 790 LYS cc_start: 0.7773 (mtmm) cc_final: 0.7549 (mtmm) REVERT: G 803 SER cc_start: 0.8511 (m) cc_final: 0.8219 (p) REVERT: G 884 SER cc_start: 0.8535 (t) cc_final: 0.8222 (p) REVERT: G 900 MET cc_start: 0.8279 (mmm) cc_final: 0.7987 (mmm) REVERT: G 964 LYS cc_start: 0.8523 (ttpp) cc_final: 0.8199 (ttpp) REVERT: G 1019 ARG cc_start: 0.8208 (ttp80) cc_final: 0.7993 (ttp-170) REVERT: G 1107 ARG cc_start: 0.7427 (mtt-85) cc_final: 0.7199 (mtt-85) outliers start: 184 outliers final: 146 residues processed: 622 average time/residue: 0.1954 time to fit residues: 190.3798 Evaluate side-chains 645 residues out of total 3264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 165 poor density : 480 time to evaluate : 1.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 158 ARG Chi-restraints excluded: chain A residue 168 PHE Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 370 ASN Chi-restraints excluded: chain A residue 386 LYS Chi-restraints excluded: chain A residue 400 PHE Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 403 ARG Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 440 LYS Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 532 ASN Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 726 ILE Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 969 LYS Chi-restraints excluded: chain A residue 1002 GLN Chi-restraints excluded: chain A residue 1014 ARG Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 104 LYS Chi-restraints excluded: chain D residue 45 SER Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 68 ILE Chi-restraints excluded: chain D residue 87 ASN Chi-restraints excluded: chain D residue 96 GLU Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain D residue 111 ASP Chi-restraints excluded: chain D residue 113 LYS Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 171 VAL Chi-restraints excluded: chain D residue 172 SER Chi-restraints excluded: chain D residue 195 ILE Chi-restraints excluded: chain D residue 206 THR Chi-restraints excluded: chain D residue 226 LEU Chi-restraints excluded: chain D residue 231 ILE Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 338 PHE Chi-restraints excluded: chain D residue 362 VAL Chi-restraints excluded: chain D residue 370 ASN Chi-restraints excluded: chain D residue 400 PHE Chi-restraints excluded: chain D residue 402 ILE Chi-restraints excluded: chain D residue 433 VAL Chi-restraints excluded: chain D residue 440 LYS Chi-restraints excluded: chain D residue 458 LYS Chi-restraints excluded: chain D residue 524 VAL Chi-restraints excluded: chain D residue 553 THR Chi-restraints excluded: chain D residue 569 ILE Chi-restraints excluded: chain D residue 588 THR Chi-restraints excluded: chain D residue 616 ASN Chi-restraints excluded: chain D residue 617 CYS Chi-restraints excluded: chain D residue 663 ASP Chi-restraints excluded: chain D residue 725 GLU Chi-restraints excluded: chain D residue 779 GLN Chi-restraints excluded: chain D residue 859 THR Chi-restraints excluded: chain D residue 878 LEU Chi-restraints excluded: chain D residue 900 MET Chi-restraints excluded: chain D residue 933 LYS Chi-restraints excluded: chain D residue 947 LYS Chi-restraints excluded: chain D residue 1041 ASP Chi-restraints excluded: chain D residue 1086 LYS Chi-restraints excluded: chain D residue 1100 THR Chi-restraints excluded: chain D residue 1104 VAL Chi-restraints excluded: chain D residue 1129 VAL Chi-restraints excluded: chain E residue 1 GLU Chi-restraints excluded: chain E residue 52 THR Chi-restraints excluded: chain E residue 104 VAL Chi-restraints excluded: chain E residue 121 LEU Chi-restraints excluded: chain E residue 151 LEU Chi-restraints excluded: chain E residue 156 LYS Chi-restraints excluded: chain E residue 164 THR Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain F residue 30 LYS Chi-restraints excluded: chain F residue 74 ILE Chi-restraints excluded: chain F residue 104 LYS Chi-restraints excluded: chain F residue 158 LYS Chi-restraints excluded: chain F residue 161 VAL Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain F residue 197 VAL Chi-restraints excluded: chain F residue 200 GLU Chi-restraints excluded: chain F residue 204 VAL Chi-restraints excluded: chain G residue 46 SER Chi-restraints excluded: chain G residue 47 VAL Chi-restraints excluded: chain G residue 62 VAL Chi-restraints excluded: chain G residue 81 ASN Chi-restraints excluded: chain G residue 100 ILE Chi-restraints excluded: chain G residue 102 ARG Chi-restraints excluded: chain G residue 117 LEU Chi-restraints excluded: chain G residue 128 ILE Chi-restraints excluded: chain G residue 131 CYS Chi-restraints excluded: chain G residue 171 VAL Chi-restraints excluded: chain G residue 186 ASN Chi-restraints excluded: chain G residue 187 LEU Chi-restraints excluded: chain G residue 203 SER Chi-restraints excluded: chain G residue 229 LEU Chi-restraints excluded: chain G residue 231 ILE Chi-restraints excluded: chain G residue 335 LEU Chi-restraints excluded: chain G residue 351 TYR Chi-restraints excluded: chain G residue 400 PHE Chi-restraints excluded: chain G residue 402 ILE Chi-restraints excluded: chain G residue 403 ARG Chi-restraints excluded: chain G residue 408 ARG Chi-restraints excluded: chain G residue 432 CYS Chi-restraints excluded: chain G residue 440 LYS Chi-restraints excluded: chain G residue 441 LEU Chi-restraints excluded: chain G residue 458 LYS Chi-restraints excluded: chain G residue 462 LYS Chi-restraints excluded: chain G residue 478 LYS Chi-restraints excluded: chain G residue 486 PHE Chi-restraints excluded: chain G residue 493 ARG Chi-restraints excluded: chain G residue 505 HIS Chi-restraints excluded: chain G residue 528 LYS Chi-restraints excluded: chain G residue 536 ASN Chi-restraints excluded: chain G residue 553 THR Chi-restraints excluded: chain G residue 569 ILE Chi-restraints excluded: chain G residue 588 THR Chi-restraints excluded: chain G residue 599 THR Chi-restraints excluded: chain G residue 641 ASN Chi-restraints excluded: chain G residue 660 TYR Chi-restraints excluded: chain G residue 708 SER Chi-restraints excluded: chain G residue 762 GLN Chi-restraints excluded: chain G residue 791 THR Chi-restraints excluded: chain G residue 947 LYS Chi-restraints excluded: chain G residue 973 ILE Chi-restraints excluded: chain G residue 975 SER Chi-restraints excluded: chain G residue 977 LEU Chi-restraints excluded: chain G residue 980 ILE Chi-restraints excluded: chain G residue 991 VAL Chi-restraints excluded: chain G residue 1001 LEU Chi-restraints excluded: chain G residue 1041 ASP Chi-restraints excluded: chain G residue 1086 LYS Chi-restraints excluded: chain G residue 1116 THR Chi-restraints excluded: chain G residue 1141 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 275 optimal weight: 0.0060 chunk 53 optimal weight: 1.9990 chunk 98 optimal weight: 0.5980 chunk 324 optimal weight: 0.7980 chunk 315 optimal weight: 3.9990 chunk 223 optimal weight: 0.8980 chunk 111 optimal weight: 30.0000 chunk 126 optimal weight: 0.5980 chunk 300 optimal weight: 0.4980 chunk 24 optimal weight: 0.6980 chunk 161 optimal weight: 10.0000 overall best weight: 0.4796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN A 532 ASN A 957 GLN A1002 GLN D 61 ASN D 81 ASN ** D 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 872 GLN D 901 GLN D 935 GLN ** G 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 542 ASN G 641 ASN G1005 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4357 r_free = 0.4357 target = 0.199924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.145470 restraints weight = 41972.286| |-----------------------------------------------------------------------------| r_work (start): 0.3652 rms_B_bonded: 2.46 r_work: 0.3510 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3343 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7474 moved from start: 0.4101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 30193 Z= 0.119 Angle : 0.589 11.500 41191 Z= 0.297 Chirality : 0.044 0.262 4712 Planarity : 0.005 0.101 5285 Dihedral : 6.517 79.615 4696 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.81 % Favored : 91.14 % Rotamer: Outliers : 5.45 % Allowed : 18.71 % Favored : 75.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.48 % Twisted General : 0.06 % 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: -2.16 (0.14), residues: 3700 helix: 0.63 (0.21), residues: 667 sheet: -1.06 (0.17), residues: 896 loop : -2.39 (0.13), residues: 2137 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 319 TYR 0.019 0.001 TYR D1067 PHE 0.030 0.001 PHE A 133 TRP 0.043 0.001 TRP A 64 HIS 0.003 0.000 HIS G1088 Details of bonding type rmsd covalent geometry : bond 0.00279 (30124) covalent geometry : angle 0.58110 (41029) SS BOND : bond 0.00256 ( 45) SS BOND : angle 1.19502 ( 90) hydrogen bonds : bond 0.03157 ( 744) hydrogen bonds : angle 4.58471 ( 1980) link_NAG-ASN : bond 0.00179 ( 24) link_NAG-ASN : angle 2.02799 ( 72) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7400 Ramachandran restraints generated. 3700 Oldfield, 0 Emsley, 3700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7400 Ramachandran restraints generated. 3700 Oldfield, 0 Emsley, 3700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 670 residues out of total 3264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 175 poor density : 495 time to evaluate : 1.146 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 62 VAL cc_start: 0.8746 (t) cc_final: 0.8509 (m) REVERT: A 102 ARG cc_start: 0.7896 (mtm-85) cc_final: 0.7668 (ptp90) REVERT: A 132 GLU cc_start: 0.7565 (mt-10) cc_final: 0.7140 (mp0) REVERT: A 168 PHE cc_start: 0.8385 (OUTLIER) cc_final: 0.7602 (m-80) REVERT: A 231 ILE cc_start: 0.8656 (tt) cc_final: 0.8286 (pt) REVERT: A 316 SER cc_start: 0.8488 (t) cc_final: 0.8251 (p) REVERT: A 517 LEU cc_start: 0.3244 (OUTLIER) cc_final: 0.2885 (tm) REVERT: A 558 LYS cc_start: 0.7919 (mmtt) cc_final: 0.7561 (mmmt) REVERT: A 675 GLN cc_start: 0.7248 (mm-40) cc_final: 0.6946 (mm-40) REVERT: A 702 GLU cc_start: 0.7384 (tp30) cc_final: 0.6702 (tp30) REVERT: A 726 ILE cc_start: 0.8774 (OUTLIER) cc_final: 0.8544 (mp) REVERT: A 765 ARG cc_start: 0.8134 (ttm110) cc_final: 0.7816 (mtm-85) REVERT: A 776 LYS cc_start: 0.8485 (ttpt) cc_final: 0.8098 (ttpt) REVERT: A 784 GLN cc_start: 0.8442 (mt0) cc_final: 0.8142 (mt0) REVERT: A 848 ASP cc_start: 0.7299 (p0) cc_final: 0.6932 (p0) REVERT: A 947 LYS cc_start: 0.8348 (mtpt) cc_final: 0.8122 (mtpp) REVERT: A 960 ASN cc_start: 0.8391 (t0) cc_final: 0.8129 (t0) REVERT: A 969 LYS cc_start: 0.8466 (OUTLIER) cc_final: 0.7762 (pptt) REVERT: A 1002 GLN cc_start: 0.7665 (OUTLIER) cc_final: 0.7445 (tt0) REVERT: A 1019 ARG cc_start: 0.7696 (ttm110) cc_final: 0.7483 (ttp80) REVERT: A 1073 LYS cc_start: 0.8451 (mtmt) cc_final: 0.8112 (mtmm) REVERT: B 121 LEU cc_start: 0.2127 (OUTLIER) cc_final: 0.1863 (tt) REVERT: D 54 LEU cc_start: 0.7997 (mm) cc_final: 0.7788 (mt) REVERT: D 105 ILE cc_start: 0.8507 (mt) cc_final: 0.8165 (mt) REVERT: D 206 THR cc_start: 0.8315 (OUTLIER) cc_final: 0.8107 (t) REVERT: D 290 ASP cc_start: 0.7947 (t70) cc_final: 0.7613 (t0) REVERT: D 303 LEU cc_start: 0.8384 (tp) cc_final: 0.8120 (mt) REVERT: D 319 ARG cc_start: 0.8230 (ttm170) cc_final: 0.7963 (ttm-80) REVERT: D 346 ARG cc_start: 0.8046 (mtt-85) cc_final: 0.7743 (mtt-85) REVERT: D 377 PHE cc_start: 0.8194 (t80) cc_final: 0.7917 (t80) REVERT: D 524 VAL cc_start: 0.6491 (OUTLIER) cc_final: 0.6280 (p) REVERT: D 599 THR cc_start: 0.8277 (m) cc_final: 0.7977 (p) REVERT: D 730 SER cc_start: 0.8687 (t) cc_final: 0.8445 (m) REVERT: D 752 LEU cc_start: 0.8336 (mt) cc_final: 0.7966 (mp) REVERT: D 779 GLN cc_start: 0.8103 (OUTLIER) cc_final: 0.7842 (tm-30) REVERT: D 790 LYS cc_start: 0.8222 (mtpp) cc_final: 0.8007 (mtpp) REVERT: D 816 SER cc_start: 0.8503 (p) cc_final: 0.8193 (t) REVERT: D 848 ASP cc_start: 0.7786 (p0) cc_final: 0.7541 (p0) REVERT: D 854 LYS cc_start: 0.8612 (ttmm) cc_final: 0.8347 (ttpp) REVERT: D 921 LYS cc_start: 0.8440 (tptp) cc_final: 0.8213 (tptp) REVERT: D 1086 LYS cc_start: 0.8518 (OUTLIER) cc_final: 0.8260 (pttt) REVERT: D 1118 ASP cc_start: 0.7953 (t0) cc_final: 0.7499 (t0) REVERT: F 200 GLU cc_start: 0.0447 (OUTLIER) cc_final: 0.0081 (pm20) REVERT: G 47 VAL cc_start: 0.8586 (OUTLIER) cc_final: 0.8306 (t) REVERT: G 53 ASP cc_start: 0.7644 (m-30) cc_final: 0.7401 (m-30) REVERT: G 81 ASN cc_start: 0.7060 (OUTLIER) cc_final: 0.6537 (p0) REVERT: G 117 LEU cc_start: 0.7763 (OUTLIER) cc_final: 0.7476 (mt) REVERT: G 129 LYS cc_start: 0.8398 (mtmt) cc_final: 0.7991 (ptmt) REVERT: G 186 ASN cc_start: 0.7578 (OUTLIER) cc_final: 0.7236 (p0) REVERT: G 188 ARG cc_start: 0.8712 (OUTLIER) cc_final: 0.8412 (mtt180) REVERT: G 286 THR cc_start: 0.7824 (m) cc_final: 0.7599 (t) REVERT: G 293 LEU cc_start: 0.8924 (tp) cc_final: 0.8648 (tp) REVERT: G 340 GLU cc_start: 0.7596 (mm-30) cc_final: 0.7370 (mm-30) REVERT: G 453 TYR cc_start: 0.6239 (t80) cc_final: 0.5964 (t80) REVERT: G 478 LYS cc_start: 0.3638 (OUTLIER) cc_final: 0.3319 (tmmt) REVERT: G 493 ARG cc_start: 0.6958 (OUTLIER) cc_final: 0.6453 (mmp-170) REVERT: G 588 THR cc_start: 0.8680 (OUTLIER) cc_final: 0.8387 (m) REVERT: G 663 ASP cc_start: 0.7475 (t70) cc_final: 0.7054 (t0) REVERT: G 730 SER cc_start: 0.8621 (t) cc_final: 0.8368 (p) REVERT: G 776 LYS cc_start: 0.8439 (ttpt) cc_final: 0.8057 (ttpt) REVERT: G 790 LYS cc_start: 0.7785 (mtmm) cc_final: 0.7555 (mtmm) REVERT: G 803 SER cc_start: 0.8489 (m) cc_final: 0.8205 (p) REVERT: G 884 SER cc_start: 0.8550 (t) cc_final: 0.8261 (p) REVERT: G 900 MET cc_start: 0.8257 (mmm) cc_final: 0.7957 (mmm) REVERT: G 964 LYS cc_start: 0.8479 (ttpp) cc_final: 0.8166 (ttpp) REVERT: G 1107 ARG cc_start: 0.7329 (mtt-85) cc_final: 0.7102 (mtt-85) outliers start: 175 outliers final: 143 residues processed: 621 average time/residue: 0.1886 time to fit residues: 183.8140 Evaluate side-chains 640 residues out of total 3264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 162 poor density : 478 time to evaluate : 0.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 99 ASN Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 158 ARG Chi-restraints excluded: chain A residue 168 PHE Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 370 ASN Chi-restraints excluded: chain A residue 386 LYS Chi-restraints excluded: chain A residue 400 PHE Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 403 ARG Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 440 LYS Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 532 ASN Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 726 ILE Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 969 LYS Chi-restraints excluded: chain A residue 1002 GLN Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 104 LYS Chi-restraints excluded: chain D residue 45 SER Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 68 ILE Chi-restraints excluded: chain D residue 87 ASN Chi-restraints excluded: chain D residue 96 GLU Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain D residue 111 ASP Chi-restraints excluded: chain D residue 113 LYS Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 126 VAL Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 206 THR Chi-restraints excluded: chain D residue 226 LEU Chi-restraints excluded: chain D residue 231 ILE Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 338 PHE Chi-restraints excluded: chain D residue 362 VAL Chi-restraints excluded: chain D residue 370 ASN Chi-restraints excluded: chain D residue 400 PHE Chi-restraints excluded: chain D residue 402 ILE Chi-restraints excluded: chain D residue 433 VAL Chi-restraints excluded: chain D residue 440 LYS Chi-restraints excluded: chain D residue 458 LYS Chi-restraints excluded: chain D residue 524 VAL Chi-restraints excluded: chain D residue 553 THR Chi-restraints excluded: chain D residue 556 ASN Chi-restraints excluded: chain D residue 569 ILE Chi-restraints excluded: chain D residue 588 THR Chi-restraints excluded: chain D residue 590 CYS Chi-restraints excluded: chain D residue 616 ASN Chi-restraints excluded: chain D residue 617 CYS Chi-restraints excluded: chain D residue 725 GLU Chi-restraints excluded: chain D residue 779 GLN Chi-restraints excluded: chain D residue 849 LEU Chi-restraints excluded: chain D residue 851 CYS Chi-restraints excluded: chain D residue 859 THR Chi-restraints excluded: chain D residue 878 LEU Chi-restraints excluded: chain D residue 900 MET Chi-restraints excluded: chain D residue 933 LYS Chi-restraints excluded: chain D residue 947 LYS Chi-restraints excluded: chain D residue 1041 ASP Chi-restraints excluded: chain D residue 1086 LYS Chi-restraints excluded: chain D residue 1100 THR Chi-restraints excluded: chain D residue 1104 VAL Chi-restraints excluded: chain D residue 1129 VAL Chi-restraints excluded: chain E residue 1 GLU Chi-restraints excluded: chain E residue 52 THR Chi-restraints excluded: chain E residue 104 VAL Chi-restraints excluded: chain E residue 121 LEU Chi-restraints excluded: chain E residue 151 LEU Chi-restraints excluded: chain E residue 156 LYS Chi-restraints excluded: chain E residue 164 THR Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain F residue 30 LYS Chi-restraints excluded: chain F residue 74 ILE Chi-restraints excluded: chain F residue 104 LYS Chi-restraints excluded: chain F residue 158 LYS Chi-restraints excluded: chain F residue 161 VAL Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain F residue 197 VAL Chi-restraints excluded: chain F residue 200 GLU Chi-restraints excluded: chain F residue 204 VAL Chi-restraints excluded: chain G residue 46 SER Chi-restraints excluded: chain G residue 47 VAL Chi-restraints excluded: chain G residue 62 VAL Chi-restraints excluded: chain G residue 81 ASN Chi-restraints excluded: chain G residue 100 ILE Chi-restraints excluded: chain G residue 102 ARG Chi-restraints excluded: chain G residue 117 LEU Chi-restraints excluded: chain G residue 128 ILE Chi-restraints excluded: chain G residue 131 CYS Chi-restraints excluded: chain G residue 171 VAL Chi-restraints excluded: chain G residue 186 ASN Chi-restraints excluded: chain G residue 187 LEU Chi-restraints excluded: chain G residue 188 ARG Chi-restraints excluded: chain G residue 203 SER Chi-restraints excluded: chain G residue 229 LEU Chi-restraints excluded: chain G residue 281 GLU Chi-restraints excluded: chain G residue 335 LEU Chi-restraints excluded: chain G residue 351 TYR Chi-restraints excluded: chain G residue 400 PHE Chi-restraints excluded: chain G residue 402 ILE Chi-restraints excluded: chain G residue 403 ARG Chi-restraints excluded: chain G residue 408 ARG Chi-restraints excluded: chain G residue 432 CYS Chi-restraints excluded: chain G residue 440 LYS Chi-restraints excluded: chain G residue 441 LEU Chi-restraints excluded: chain G residue 458 LYS Chi-restraints excluded: chain G residue 462 LYS Chi-restraints excluded: chain G residue 478 LYS Chi-restraints excluded: chain G residue 486 PHE Chi-restraints excluded: chain G residue 493 ARG Chi-restraints excluded: chain G residue 528 LYS Chi-restraints excluded: chain G residue 542 ASN Chi-restraints excluded: chain G residue 553 THR Chi-restraints excluded: chain G residue 569 ILE Chi-restraints excluded: chain G residue 588 THR Chi-restraints excluded: chain G residue 641 ASN Chi-restraints excluded: chain G residue 660 TYR Chi-restraints excluded: chain G residue 708 SER Chi-restraints excluded: chain G residue 791 THR Chi-restraints excluded: chain G residue 947 LYS Chi-restraints excluded: chain G residue 973 ILE Chi-restraints excluded: chain G residue 975 SER Chi-restraints excluded: chain G residue 991 VAL Chi-restraints excluded: chain G residue 1001 LEU Chi-restraints excluded: chain G residue 1041 ASP Chi-restraints excluded: chain G residue 1086 LYS Chi-restraints excluded: chain G residue 1116 THR Chi-restraints excluded: chain G residue 1141 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 282 optimal weight: 0.0010 chunk 239 optimal weight: 8.9990 chunk 111 optimal weight: 30.0000 chunk 303 optimal weight: 2.9990 chunk 50 optimal weight: 4.9990 chunk 294 optimal weight: 0.9990 chunk 102 optimal weight: 1.9990 chunk 263 optimal weight: 9.9990 chunk 173 optimal weight: 2.9990 chunk 129 optimal weight: 0.8980 chunk 207 optimal weight: 0.3980 overall best weight: 0.8590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 532 ASN A 762 GLN A 957 GLN A1002 GLN D 61 ASN ** D 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 317 ASN D 613 GLN ** D 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 872 GLN D 901 GLN D 914 ASN D 935 GLN ** D 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 66 HIS ** G 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 542 ASN G 641 ASN G1005 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4350 r_free = 0.4350 target = 0.199182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.144687 restraints weight = 41442.166| |-----------------------------------------------------------------------------| r_work (start): 0.3626 rms_B_bonded: 2.74 r_work: 0.3476 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3319 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7491 moved from start: 0.4130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 30193 Z= 0.156 Angle : 0.604 11.592 41191 Z= 0.305 Chirality : 0.045 0.287 4712 Planarity : 0.005 0.102 5285 Dihedral : 6.548 79.595 4696 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.05 % Allowed : 9.00 % Favored : 90.95 % Rotamer: Outliers : 5.48 % Allowed : 18.89 % Favored : 75.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.48 % Twisted General : 0.06 % 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: -2.15 (0.14), residues: 3700 helix: 0.61 (0.21), residues: 665 sheet: -1.04 (0.17), residues: 889 loop : -2.38 (0.13), residues: 2146 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG G1019 TYR 0.023 0.001 TYR D1067 PHE 0.046 0.002 PHE D 192 TRP 0.042 0.001 TRP A 64 HIS 0.004 0.001 HIS G 66 Details of bonding type rmsd covalent geometry : bond 0.00371 (30124) covalent geometry : angle 0.59622 (41029) SS BOND : bond 0.00279 ( 45) SS BOND : angle 1.34900 ( 90) hydrogen bonds : bond 0.03240 ( 744) hydrogen bonds : angle 4.60090 ( 1980) link_NAG-ASN : bond 0.00189 ( 24) link_NAG-ASN : angle 2.04045 ( 72) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10965.03 seconds wall clock time: 186 minutes 58.53 seconds (11218.53 seconds total)