Starting phenix.real_space_refine on Wed Jun 25 09:45:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wjy_32552/06_2025/7wjy_32552.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wjy_32552/06_2025/7wjy_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_32552/06_2025/7wjy_32552.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wjy_32552/06_2025/7wjy_32552.map" model { file = "/net/cci-nas-00/data/ceres_data/7wjy_32552/06_2025/7wjy_32552.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wjy_32552/06_2025/7wjy_32552.cif" } resolution = 3.24 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.89s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'GLN:plan1': 1, 'GLU:plan': 6, 'ARG:plan': 2, '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: {'GLN:plan1': 1, 'GLU:plan': 6, 'ARG:plan': 2, '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: {'GLN:plan1': 1, 'GLU:plan': 6, 'ARG:plan': 2, '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: 16.68, per 1000 atoms: 0.57 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: 6.68 Conformation dependent library (CDL) restraints added in 3.4 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: 3.50 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: 11.95 Time building geometry restraints manager: 7.94 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 1147 or resid 1301 thr \ ough 1307)) selection = (chain 'D' and (resid 26 through 1147 or resid 1301 through 1307)) selection = (chain 'G' and (resid 26 through 68 or resid 80 through 243 or resid 262 through \ 1147 or resid 1301 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: 2.600 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: 1.050 Check model and map are aligned: 0.190 Set scattering table: 0.240 Process input model: 63.380 Find NCS groups from input model: 1.580 Set up NCS constraints: 0.140 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:3.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 72.250 ------------------------------------------------------------------------------- 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 : 8.31 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.98 (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 TRP 0.007 0.001 TRP A 64 HIS 0.002 0.000 HIS E 213 PHE 0.023 0.001 PHE G 318 TYR 0.007 0.001 TYR G 202 ARG 0.002 0.000 ARG G 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00347 ( 24) link_NAG-ASN : angle 2.59304 ( 72) hydrogen bonds : bond 0.26321 ( 744) hydrogen bonds : angle 8.98290 ( 1980) SS BOND : bond 0.00697 ( 45) SS BOND : angle 0.78592 ( 90) covalent geometry : bond 0.00334 (30124) covalent geometry : angle 0.70076 (41029) *********************** 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 : 3.358 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: 0.8006 (p) REVERT: A 105 ILE cc_start: 0.8071 (mt) cc_final: 0.7748 (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: 0.6854 (m-80) REVERT: A 188 ARG cc_start: 0.7111 (ptp90) cc_final: 0.6868 (ptp90) REVERT: A 200 LYS cc_start: 0.7587 (mttm) cc_final: 0.7340 (mttm) REVERT: A 269 TYR cc_start: 0.7917 (m-80) cc_final: 0.7641 (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: 0.7669 (m) REVERT: A 532 ASN cc_start: 0.7162 (t0) cc_final: 0.6788 (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: 0.6165 (mm-40) REVERT: A 733 LYS cc_start: 0.8129 (mtmt) cc_final: 0.7809 (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: 0.6418 (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: 0.7466 (pptt) REVERT: A 979 ASP cc_start: 0.6392 (m-30) cc_final: 0.6173 (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 105 ILE cc_start: 0.7878 (mt) cc_final: 0.7555 (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: 0.6874 (mtt-85) REVERT: D 189 GLU cc_start: 0.6803 (mm-30) cc_final: 0.6524 (mm-30) REVERT: D 206 THR cc_start: 0.8291 (t) cc_final: 0.7915 (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: 0.7745 (p) REVERT: D 513 LEU cc_start: 0.7157 (mt) cc_final: 0.6935 (mt) REVERT: D 523 THR cc_start: 0.5854 (OUTLIER) cc_final: 0.5627 (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: 0.8034 (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: 0.7600 (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: 0.6702 (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: 0.6221 (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: -0.2091 (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: 0.6559 (p0) REVERT: G 187 LEU cc_start: 0.7600 (tp) cc_final: 0.7209 (tp) REVERT: G 189 GLU cc_start: 0.7114 (OUTLIER) cc_final: 0.6065 (mm-30) REVERT: G 269 TYR cc_start: 0.7588 (m-80) cc_final: 0.7239 (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: 0.6768 (t0) REVERT: G 576 VAL cc_start: 0.8700 (p) cc_final: 0.8386 (t) REVERT: G 655 TYR cc_start: 0.8267 (t80) cc_final: 0.7845 (t80) REVERT: G 663 ASP cc_start: 0.6948 (t70) cc_final: 0.6557 (t70) REVERT: G 673 SER cc_start: 0.8668 (p) cc_final: 0.8292 (m) REVERT: G 711 SER cc_start: 0.8113 (m) cc_final: 0.7877 (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: 0.7172 (ttpt) REVERT: G 790 LYS cc_start: 0.7557 (mtmm) cc_final: 0.7294 (mtmm) REVERT: G 821 LEU cc_start: 0.7902 (tt) cc_final: 0.7497 (mp) REVERT: G 855 PHE cc_start: 0.8121 (m-10) cc_final: 0.7902 (m-80) 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: 0.6784 (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: 0.8113 (OUTLIER) cc_final: 0.7767 (p) outliers start: 219 outliers final: 92 residues processed: 881 average time/residue: 0.4306 time to fit residues: 587.3342 Evaluate side-chains 661 residues out of total 3264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 550 time to evaluate : 3.194 ------------------------------------------------------------------------------- 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 314 optimal weight: 0.0060 chunk 282 optimal weight: 6.9990 chunk 156 optimal weight: 0.5980 chunk 96 optimal weight: 2.9990 chunk 190 optimal weight: 0.9980 chunk 151 optimal weight: 4.9990 chunk 292 optimal weight: 0.6980 chunk 113 optimal weight: 10.0000 chunk 177 optimal weight: 0.9990 chunk 217 optimal weight: 2.9990 chunk 338 optimal weight: 0.9980 overall best weight: 0.6596 ------------------------------------------------------------------------------- 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 183 ASN A 218 GLN A 388 ASN A 414 GLN A 448 ASN A 762 GLN A 774 GLN A 784 GLN A 901 GLN A 955 ASN A 965 GLN 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 88 GLN D 115 GLN ** D 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 173 GLN D 218 GLN D 317 ASN D 414 GLN ** D 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 450 ASN D 540 ASN D 564 GLN D 762 GLN ** D 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 804 GLN D 853 GLN D 895 GLN D 901 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 ** both conformations clash, **PLEASE CHECK MANUALLY** F 190 HIS 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 762 GLN G 784 GLN G 853 GLN G 901 GLN G 913 GLN G 960 ASN G 965 GLN G1010 GLN G1011 GLN G1048 HIS Total number of N/Q/H flips: 73 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4701 r_free = 0.4701 target = 0.240326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.4510 r_free = 0.4510 target = 0.215783 restraints weight = 48524.874| |-----------------------------------------------------------------------------| r_work (start): 0.4072 rms_B_bonded: 1.20 r_work: 0.3707 rms_B_bonded: 1.37 restraints_weight: 0.5000 r_work: 0.3600 rms_B_bonded: 2.34 restraints_weight: 0.2500 r_work (final): 0.3600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7176 moved from start: 0.2109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 30193 Z= 0.141 Angle : 0.585 8.311 41191 Z= 0.301 Chirality : 0.045 0.316 4712 Planarity : 0.005 0.089 5285 Dihedral : 7.673 80.153 4800 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.76 % Favored : 92.19 % Rotamer: Outliers : 6.29 % Allowed : 13.32 % Favored : 80.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.48 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.86 (0.12), residues: 3700 helix: -1.38 (0.19), residues: 629 sheet: -2.08 (0.16), residues: 888 loop : -3.30 (0.11), residues: 2183 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP E 53 HIS 0.004 0.001 HIS A 66 PHE 0.028 0.002 PHE A 133 TYR 0.023 0.001 TYR D1067 ARG 0.007 0.001 ARG G1107 Details of bonding type rmsd link_NAG-ASN : bond 0.00363 ( 24) link_NAG-ASN : angle 2.09071 ( 72) hydrogen bonds : bond 0.04214 ( 744) hydrogen bonds : angle 5.53123 ( 1980) SS BOND : bond 0.00430 ( 45) SS BOND : angle 1.49745 ( 90) covalent geometry : bond 0.00321 (30124) covalent geometry : angle 0.57516 (41029) *********************** 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 765 residues out of total 3264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 202 poor density : 563 time to evaluate : 3.079 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: A 104 TRP cc_start: 0.8211 (m-90) cc_final: 0.7499 (m-90) REVERT: A 127 VAL cc_start: 0.7903 (OUTLIER) cc_final: 0.7637 (p) REVERT: A 133 PHE cc_start: 0.8460 (m-80) cc_final: 0.8142 (m-80) REVERT: A 168 PHE cc_start: 0.7892 (OUTLIER) cc_final: 0.7278 (m-80) REVERT: A 324 GLU cc_start: 0.6625 (OUTLIER) cc_final: 0.6424 (tm-30) REVERT: A 325 SER cc_start: 0.8209 (m) cc_final: 0.7412 (m) REVERT: A 532 ASN cc_start: 0.7352 (t0) cc_final: 0.7008 (t0) REVERT: A 675 GLN cc_start: 0.6721 (mm-40) cc_final: 0.6447 (mm-40) REVERT: A 726 ILE cc_start: 0.8599 (OUTLIER) cc_final: 0.8311 (mp) REVERT: A 737 ASP cc_start: 0.6979 (t0) cc_final: 0.6767 (t0) REVERT: A 776 LYS cc_start: 0.8290 (ttpt) cc_final: 0.7932 (ttpt) REVERT: A 823 PHE cc_start: 0.7535 (m-80) cc_final: 0.7334 (m-80) REVERT: A 902 MET cc_start: 0.7935 (mmm) cc_final: 0.7698 (tpt) REVERT: A 949 GLN cc_start: 0.7968 (mm110) cc_final: 0.7670 (mm-40) REVERT: A 969 LYS cc_start: 0.8213 (OUTLIER) cc_final: 0.7653 (pptt) REVERT: A 1017 GLU cc_start: 0.7524 (tm-30) cc_final: 0.7153 (tm-30) REVERT: A 1127 ASP cc_start: 0.6496 (p0) cc_final: 0.6292 (p0) REVERT: A 1144 GLU cc_start: 0.7550 (tp30) cc_final: 0.7062 (tp30) REVERT: D 105 ILE cc_start: 0.8179 (mt) cc_final: 0.7777 (mt) REVERT: D 141 LEU cc_start: 0.4538 (OUTLIER) cc_final: 0.4254 (mt) REVERT: D 169 GLU cc_start: 0.7707 (tm-30) cc_final: 0.6724 (tm-30) REVERT: D 206 THR cc_start: 0.8239 (OUTLIER) cc_final: 0.7980 (t) REVERT: D 319 ARG cc_start: 0.7579 (ttm170) cc_final: 0.7263 (ttm-80) REVERT: D 692 ILE cc_start: 0.8278 (mm) cc_final: 0.8049 (mt) REVERT: D 705 VAL cc_start: 0.8626 (t) cc_final: 0.8322 (p) REVERT: D 755 GLN cc_start: 0.7790 (mm-40) cc_final: 0.7546 (mm-40) REVERT: D 759 PHE cc_start: 0.6591 (m-80) cc_final: 0.6215 (m-80) REVERT: D 804 GLN cc_start: 0.7947 (mt0) cc_final: 0.7605 (mm-40) REVERT: D 816 SER cc_start: 0.8510 (p) cc_final: 0.8212 (t) REVERT: D 854 LYS cc_start: 0.8632 (ttmm) cc_final: 0.8374 (ttpp) REVERT: D 955 ASN cc_start: 0.7907 (m-40) cc_final: 0.7538 (m110) REVERT: D 969 LYS cc_start: 0.8470 (OUTLIER) cc_final: 0.8180 (pttm) REVERT: D 978 ASN cc_start: 0.7846 (m-40) cc_final: 0.7474 (m110) REVERT: D 988 GLU cc_start: 0.7203 (OUTLIER) cc_final: 0.6683 (tm-30) REVERT: D 992 GLN cc_start: 0.7464 (mt0) cc_final: 0.7166 (mt0) REVERT: D 1019 ARG cc_start: 0.7835 (ttp80) cc_final: 0.7634 (ttp-110) REVERT: D 1029 MET cc_start: 0.8061 (ttm) cc_final: 0.7758 (ttm) REVERT: D 1072 GLU cc_start: 0.7985 (pm20) cc_final: 0.7657 (pm20) REVERT: D 1112 PRO cc_start: 0.8119 (Cg_exo) cc_final: 0.7869 (Cg_endo) REVERT: D 1118 ASP cc_start: 0.7107 (t0) cc_final: 0.6719 (t0) REVERT: F 200 GLU cc_start: 0.0272 (OUTLIER) cc_final: -0.0218 (pm20) REVERT: G 47 VAL cc_start: 0.8760 (OUTLIER) cc_final: 0.8514 (t) REVERT: G 130 VAL cc_start: 0.7741 (t) cc_final: 0.7377 (p) REVERT: G 186 ASN cc_start: 0.7114 (p0) cc_final: 0.6719 (p0) REVERT: G 327 VAL cc_start: 0.8663 (t) cc_final: 0.8411 (p) REVERT: G 357 ARG cc_start: 0.7072 (tpt170) cc_final: 0.6855 (tpt170) REVERT: G 422 ASN cc_start: 0.7377 (m-40) cc_final: 0.6969 (m-40) REVERT: G 453 TYR cc_start: 0.6019 (t80) cc_final: 0.5573 (t80) REVERT: G 493 ARG cc_start: 0.6910 (OUTLIER) cc_final: 0.6378 (mmp-170) REVERT: G 574 ASP cc_start: 0.7455 (t0) cc_final: 0.7216 (t0) REVERT: G 586 ASP cc_start: 0.7331 (t0) cc_final: 0.6937 (t0) REVERT: G 673 SER cc_start: 0.8676 (p) cc_final: 0.8448 (m) REVERT: G 675 GLN cc_start: 0.7281 (mm-40) cc_final: 0.7011 (mm-40) REVERT: G 764 LYS cc_start: 0.8020 (tttt) cc_final: 0.7752 (ttmm) REVERT: G 775 ASP cc_start: 0.7619 (m-30) cc_final: 0.7354 (m-30) REVERT: G 776 LYS cc_start: 0.8098 (ttpt) cc_final: 0.7882 (ttpt) REVERT: G 819 GLU cc_start: 0.7600 (mt-10) cc_final: 0.7263 (mt-10) REVERT: G 821 LEU cc_start: 0.8145 (tt) cc_final: 0.7681 (mp) REVERT: G 853 GLN cc_start: 0.7988 (mt0) cc_final: 0.7768 (mt0) REVERT: G 884 SER cc_start: 0.8327 (t) cc_final: 0.7963 (p) REVERT: G 921 LYS cc_start: 0.8026 (mmmt) cc_final: 0.7757 (mmmt) REVERT: G 949 GLN cc_start: 0.8259 (mm-40) cc_final: 0.8049 (mm-40) REVERT: G 977 LEU cc_start: 0.8190 (OUTLIER) cc_final: 0.7633 (mm) REVERT: G 993 ILE cc_start: 0.8502 (tp) cc_final: 0.8172 (tt) REVERT: G 998 THR cc_start: 0.8687 (t) cc_final: 0.8410 (p) REVERT: G 1017 GLU cc_start: 0.7282 (tm-30) cc_final: 0.7013 (tm-30) REVERT: G 1118 ASP cc_start: 0.7287 (t70) cc_final: 0.7023 (t70) REVERT: G 1125 ASN cc_start: 0.7925 (p0) cc_final: 0.7643 (p0) REVERT: G 1136 THR cc_start: 0.8201 (OUTLIER) cc_final: 0.7833 (p) outliers start: 202 outliers final: 124 residues processed: 723 average time/residue: 0.4468 time to fit residues: 505.1853 Evaluate side-chains 647 residues out of total 3264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 509 time to evaluate : 3.258 ------------------------------------------------------------------------------- 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 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 208 ILE Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 281 GLU 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 531 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 969 LYS 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 B residue 18 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 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 141 LEU Chi-restraints excluded: chain D residue 198 TYR Chi-restraints excluded: chain D residue 206 THR Chi-restraints excluded: chain D residue 229 LEU 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 803 SER 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 947 LYS Chi-restraints excluded: chain D residue 969 LYS Chi-restraints excluded: chain D residue 988 GLU Chi-restraints excluded: chain D residue 1038 LYS Chi-restraints excluded: chain D residue 1041 ASP Chi-restraints excluded: chain D residue 1073 LYS Chi-restraints excluded: chain D residue 1100 THR Chi-restraints excluded: chain D residue 1104 VAL Chi-restraints excluded: chain D residue 1127 ASP 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 128 GLN Chi-restraints excluded: chain F residue 158 LYS Chi-restraints excluded: chain F residue 161 VAL Chi-restraints excluded: chain F residue 190 HIS 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 62 VAL 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 127 VAL Chi-restraints excluded: chain G residue 131 CYS Chi-restraints excluded: chain G residue 189 GLU Chi-restraints excluded: chain G residue 229 LEU Chi-restraints excluded: chain G residue 317 ASN 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 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 511 VAL Chi-restraints excluded: chain G residue 517 LEU Chi-restraints excluded: chain G residue 528 LYS 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 746 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 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 1116 THR Chi-restraints excluded: chain G residue 1136 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 74 optimal weight: 0.0870 chunk 343 optimal weight: 0.7980 chunk 224 optimal weight: 0.0670 chunk 188 optimal weight: 1.9990 chunk 176 optimal weight: 0.7980 chunk 167 optimal weight: 8.9990 chunk 108 optimal weight: 0.6980 chunk 191 optimal weight: 1.9990 chunk 106 optimal weight: 40.0000 chunk 297 optimal weight: 5.9990 chunk 3 optimal weight: 1.9990 overall best weight: 0.4896 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 448 ASN A 957 GLN A 965 GLN A1108 ASN ** B 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 65 ASN ** D 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 186 ASN D 194 ASN ** D 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 271 GLN D 580 GLN D 774 GLN D 872 GLN D1106 GLN D1125 ASN ** F 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 190 HIS ** G 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 542 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4696 r_free = 0.4696 target = 0.239738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4502 r_free = 0.4502 target = 0.214917 restraints weight = 48486.051| |-----------------------------------------------------------------------------| r_work (start): 0.4065 rms_B_bonded: 1.20 r_work: 0.3700 rms_B_bonded: 1.39 restraints_weight: 0.5000 r_work: 0.3589 rms_B_bonded: 2.39 restraints_weight: 0.2500 r_work (final): 0.3589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7199 moved from start: 0.2574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 30193 Z= 0.119 Angle : 0.549 12.349 41191 Z= 0.281 Chirality : 0.044 0.246 4712 Planarity : 0.005 0.096 5285 Dihedral : 6.917 78.989 4744 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.95 % Favored : 92.00 % Rotamer: Outliers : 5.98 % Allowed : 15.62 % Favored : 78.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.48 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.33 (0.13), residues: 3700 helix: -0.63 (0.21), residues: 637 sheet: -1.77 (0.16), residues: 877 loop : -3.05 (0.11), residues: 2186 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP G 64 HIS 0.018 0.001 HIS F 190 PHE 0.025 0.001 PHE D 106 TYR 0.029 0.001 TYR D 265 ARG 0.007 0.000 ARG G1019 Details of bonding type rmsd link_NAG-ASN : bond 0.00277 ( 24) link_NAG-ASN : angle 2.34680 ( 72) hydrogen bonds : bond 0.03555 ( 744) hydrogen bonds : angle 5.01418 ( 1980) SS BOND : bond 0.00242 ( 45) SS BOND : angle 1.34810 ( 90) covalent geometry : bond 0.00276 (30124) covalent geometry : angle 0.53795 (41029) *********************** 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 695 residues out of total 3264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 192 poor density : 503 time to evaluate : 3.029 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: A 62 VAL cc_start: 0.8634 (t) cc_final: 0.8344 (m) REVERT: A 104 TRP cc_start: 0.8284 (m-90) cc_final: 0.7731 (m-90) REVERT: A 127 VAL cc_start: 0.7918 (OUTLIER) cc_final: 0.7700 (p) REVERT: A 133 PHE cc_start: 0.8514 (m-80) cc_final: 0.8279 (m-80) REVERT: A 168 PHE cc_start: 0.7882 (OUTLIER) cc_final: 0.7329 (m-80) REVERT: A 231 ILE cc_start: 0.8385 (mt) cc_final: 0.8180 (tt) REVERT: A 269 TYR cc_start: 0.8171 (m-80) cc_final: 0.7927 (m-80) REVERT: A 324 GLU cc_start: 0.6634 (tt0) cc_final: 0.6428 (tm-30) REVERT: A 325 SER cc_start: 0.8231 (m) cc_final: 0.7436 (m) REVERT: A 362 VAL cc_start: 0.6805 (OUTLIER) cc_final: 0.6550 (m) REVERT: A 517 LEU cc_start: 0.3111 (OUTLIER) cc_final: 0.2700 (tm) REVERT: A 532 ASN cc_start: 0.7456 (t0) cc_final: 0.7103 (t0) REVERT: A 675 GLN cc_start: 0.6687 (mm-40) cc_final: 0.6439 (mm-40) REVERT: A 776 LYS cc_start: 0.8282 (ttpt) cc_final: 0.7961 (ttpt) REVERT: A 787 GLN cc_start: 0.8293 (mm-40) cc_final: 0.7763 (mt0) REVERT: A 868 GLU cc_start: 0.7506 (tp30) cc_final: 0.7241 (tp30) REVERT: A 949 GLN cc_start: 0.7980 (mm110) cc_final: 0.7713 (mm-40) REVERT: A 960 ASN cc_start: 0.8021 (t0) cc_final: 0.7737 (t0) REVERT: A 969 LYS cc_start: 0.8197 (OUTLIER) cc_final: 0.7725 (pptt) REVERT: D 83 VAL cc_start: 0.7951 (OUTLIER) cc_final: 0.7563 (p) REVERT: D 105 ILE cc_start: 0.8195 (mt) cc_final: 0.7864 (mt) REVERT: D 169 GLU cc_start: 0.7799 (tm-30) cc_final: 0.7266 (tm-30) REVERT: D 188 ARG cc_start: 0.8068 (mtt90) cc_final: 0.7728 (mtt-85) REVERT: D 239 GLN cc_start: 0.7420 (OUTLIER) cc_final: 0.7114 (tm-30) REVERT: D 319 ARG cc_start: 0.7597 (ttm170) cc_final: 0.7229 (ttm-80) REVERT: D 705 VAL cc_start: 0.8623 (t) cc_final: 0.8354 (p) REVERT: D 804 GLN cc_start: 0.7993 (mt0) cc_final: 0.7628 (mm-40) REVERT: D 816 SER cc_start: 0.8580 (p) cc_final: 0.8264 (t) REVERT: D 854 LYS cc_start: 0.8550 (ttmm) cc_final: 0.8274 (ttpp) REVERT: D 969 LYS cc_start: 0.8424 (OUTLIER) cc_final: 0.8103 (pttm) REVERT: D 978 ASN cc_start: 0.7945 (m-40) cc_final: 0.7658 (m110) REVERT: D 988 GLU cc_start: 0.7188 (OUTLIER) cc_final: 0.6675 (tm-30) REVERT: D 990 GLU cc_start: 0.7796 (mp0) cc_final: 0.7402 (mp0) REVERT: D 992 GLN cc_start: 0.7531 (mt0) cc_final: 0.7218 (mt0) REVERT: D 1005 GLN cc_start: 0.7768 (tt0) cc_final: 0.7557 (tt0) REVERT: D 1029 MET cc_start: 0.7978 (ttm) cc_final: 0.7710 (ttm) REVERT: D 1072 GLU cc_start: 0.8018 (pm20) cc_final: 0.7772 (pm20) REVERT: D 1112 PRO cc_start: 0.8218 (Cg_exo) cc_final: 0.7986 (Cg_endo) REVERT: D 1118 ASP cc_start: 0.7093 (t0) cc_final: 0.6748 (t0) REVERT: F 200 GLU cc_start: 0.0175 (OUTLIER) cc_final: -0.0309 (pm20) REVERT: G 47 VAL cc_start: 0.8744 (OUTLIER) cc_final: 0.8523 (t) REVERT: G 63 THR cc_start: 0.8182 (OUTLIER) cc_final: 0.7343 (t) REVERT: G 81 ASN cc_start: 0.6844 (OUTLIER) cc_final: 0.6384 (p0) REVERT: G 130 VAL cc_start: 0.7790 (t) cc_final: 0.7332 (p) REVERT: G 186 ASN cc_start: 0.7159 (p0) cc_final: 0.6750 (p0) REVERT: G 453 TYR cc_start: 0.6042 (t80) cc_final: 0.5643 (t80) REVERT: G 478 LYS cc_start: 0.3668 (OUTLIER) cc_final: 0.3317 (tmmt) REVERT: G 493 ARG cc_start: 0.6835 (OUTLIER) cc_final: 0.6485 (mmp-170) REVERT: G 574 ASP cc_start: 0.7410 (t0) cc_final: 0.7139 (t0) REVERT: G 586 ASP cc_start: 0.7272 (t0) cc_final: 0.6864 (t0) REVERT: G 654 GLU cc_start: 0.7519 (pm20) cc_final: 0.7315 (pm20) REVERT: G 673 SER cc_start: 0.8671 (p) cc_final: 0.8326 (m) REVERT: G 675 GLN cc_start: 0.7285 (mm-40) cc_final: 0.6988 (mm-40) REVERT: G 764 LYS cc_start: 0.8068 (tttt) cc_final: 0.7801 (ttmm) REVERT: G 775 ASP cc_start: 0.7639 (m-30) cc_final: 0.7325 (m-30) REVERT: G 776 LYS cc_start: 0.8162 (ttpt) cc_final: 0.7950 (ttpt) REVERT: G 819 GLU cc_start: 0.7638 (mt-10) cc_final: 0.7324 (mt-10) REVERT: G 821 LEU cc_start: 0.8201 (tt) cc_final: 0.7655 (mp) REVERT: G 853 GLN cc_start: 0.7965 (mt0) cc_final: 0.7715 (mt0) REVERT: G 855 PHE cc_start: 0.8142 (m-10) cc_final: 0.7920 (m-10) REVERT: G 884 SER cc_start: 0.8382 (t) cc_final: 0.7998 (p) REVERT: G 949 GLN cc_start: 0.8295 (mm-40) cc_final: 0.7974 (mm-40) REVERT: G 979 ASP cc_start: 0.6905 (m-30) cc_final: 0.6704 (m-30) REVERT: G 993 ILE cc_start: 0.8462 (tp) cc_final: 0.8250 (tt) REVERT: G 1017 GLU cc_start: 0.7312 (tm-30) cc_final: 0.7017 (tm-30) REVERT: G 1118 ASP cc_start: 0.7363 (t70) cc_final: 0.7055 (t70) REVERT: G 1125 ASN cc_start: 0.7935 (p0) cc_final: 0.7658 (p0) outliers start: 192 outliers final: 128 residues processed: 647 average time/residue: 0.4286 time to fit residues: 432.9706 Evaluate side-chains 618 residues out of total 3264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 143 poor density : 475 time to evaluate : 3.068 ------------------------------------------------------------------------------- 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 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 206 THR Chi-restraints excluded: chain A residue 208 ILE 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 312 ILE 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 531 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 727 LEU Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 968 SER Chi-restraints excluded: chain A residue 969 LYS Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain A residue 1118 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 67 VAL Chi-restraints excluded: chain D residue 68 ILE Chi-restraints excluded: chain D residue 83 VAL 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 239 GLN Chi-restraints excluded: chain D residue 240 THR 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 616 ASN Chi-restraints excluded: chain D residue 803 SER 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 973 ILE 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 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 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 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 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 63 THR Chi-restraints excluded: chain G residue 68 ILE 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 128 ILE Chi-restraints excluded: chain G residue 131 CYS Chi-restraints excluded: chain G residue 189 GLU 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 312 ILE 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 383 SER Chi-restraints excluded: chain G residue 400 PHE 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 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 517 LEU Chi-restraints excluded: chain G residue 542 ASN Chi-restraints excluded: chain G residue 553 THR 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 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 54 optimal weight: 0.9990 chunk 365 optimal weight: 0.9990 chunk 35 optimal weight: 20.0000 chunk 128 optimal weight: 0.4980 chunk 215 optimal weight: 2.9990 chunk 194 optimal weight: 0.8980 chunk 290 optimal weight: 0.7980 chunk 311 optimal weight: 3.9990 chunk 33 optimal weight: 50.0000 chunk 31 optimal weight: 40.0000 chunk 21 optimal weight: 1.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 957 GLN A1002 GLN ** B 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 121 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 913 GLN ** F 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 394 ASN ** G 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4354 r_free = 0.4354 target = 0.200056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.144278 restraints weight = 43188.735| |-----------------------------------------------------------------------------| r_work (start): 0.3620 rms_B_bonded: 2.39 r_work: 0.3494 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3318 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7484 moved from start: 0.2977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 30193 Z= 0.153 Angle : 0.576 11.389 41191 Z= 0.294 Chirality : 0.045 0.300 4712 Planarity : 0.005 0.099 5285 Dihedral : 6.789 79.218 4729 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.54 % Favored : 91.38 % Rotamer: Outliers : 6.26 % Allowed : 15.84 % Favored : 77.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.48 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.98 (0.13), residues: 3700 helix: -0.26 (0.21), residues: 647 sheet: -1.52 (0.16), residues: 878 loop : -2.86 (0.12), residues: 2175 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP G 64 HIS 0.004 0.001 HIS G1088 PHE 0.026 0.002 PHE A 541 TYR 0.024 0.001 TYR D 265 ARG 0.005 0.000 ARG D 102 Details of bonding type rmsd link_NAG-ASN : bond 0.00215 ( 24) link_NAG-ASN : angle 2.39007 ( 72) hydrogen bonds : bond 0.03515 ( 744) hydrogen bonds : angle 4.84735 ( 1980) SS BOND : bond 0.00356 ( 45) SS BOND : angle 1.56827 ( 90) covalent geometry : bond 0.00360 (30124) covalent geometry : angle 0.56350 (41029) *********************** 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 702 residues out of total 3264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 201 poor density : 501 time to evaluate : 5.244 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: A 62 VAL cc_start: 0.8711 (t) cc_final: 0.8447 (m) REVERT: A 104 TRP cc_start: 0.8547 (m-90) cc_final: 0.8294 (m-90) REVERT: A 127 VAL cc_start: 0.8111 (OUTLIER) cc_final: 0.7900 (p) REVERT: A 133 PHE cc_start: 0.8589 (m-80) cc_final: 0.8311 (m-80) REVERT: A 168 PHE cc_start: 0.8292 (OUTLIER) cc_final: 0.7647 (m-80) REVERT: A 231 ILE cc_start: 0.8505 (mt) cc_final: 0.8280 (tt) REVERT: A 269 TYR cc_start: 0.8378 (m-80) cc_final: 0.8055 (m-80) REVERT: A 324 GLU cc_start: 0.7044 (OUTLIER) cc_final: 0.6834 (tm-30) REVERT: A 325 SER cc_start: 0.8354 (m) cc_final: 0.7548 (m) REVERT: A 517 LEU cc_start: 0.3226 (OUTLIER) cc_final: 0.2843 (tm) REVERT: A 532 ASN cc_start: 0.7892 (t0) cc_final: 0.7481 (t0) REVERT: A 578 ASP cc_start: 0.6878 (t0) cc_final: 0.6664 (t70) REVERT: A 605 SER cc_start: 0.8305 (p) cc_final: 0.8075 (t) REVERT: A 675 GLN cc_start: 0.7071 (mm-40) cc_final: 0.6792 (mm-40) REVERT: A 765 ARG cc_start: 0.8272 (ttp-110) cc_final: 0.7977 (mtm-85) REVERT: A 776 LYS cc_start: 0.8425 (ttpt) cc_final: 0.8086 (ttpt) REVERT: A 787 GLN cc_start: 0.8530 (mm-40) cc_final: 0.8051 (mt0) REVERT: A 795 LYS cc_start: 0.8029 (mptm) cc_final: 0.7668 (mptt) REVERT: A 949 GLN cc_start: 0.8316 (mm110) cc_final: 0.8077 (mm-40) REVERT: A 969 LYS cc_start: 0.8364 (OUTLIER) cc_final: 0.7833 (pptt) REVERT: A 979 ASP cc_start: 0.7232 (t0) cc_final: 0.7012 (t0) REVERT: B 121 LEU cc_start: 0.2276 (OUTLIER) cc_final: 0.2028 (tt) REVERT: D 83 VAL cc_start: 0.8228 (OUTLIER) cc_final: 0.7874 (p) REVERT: D 105 ILE cc_start: 0.8449 (mt) cc_final: 0.8093 (mt) REVERT: D 169 GLU cc_start: 0.8289 (tm-30) cc_final: 0.7932 (tm-30) REVERT: D 239 GLN cc_start: 0.7672 (OUTLIER) cc_final: 0.7382 (tm-30) REVERT: D 319 ARG cc_start: 0.8039 (ttm170) cc_final: 0.7735 (ttm-80) REVERT: D 523 THR cc_start: 0.5728 (OUTLIER) cc_final: 0.5504 (p) REVERT: D 599 THR cc_start: 0.8280 (m) cc_final: 0.8031 (p) REVERT: D 705 VAL cc_start: 0.8649 (t) cc_final: 0.8401 (p) REVERT: D 790 LYS cc_start: 0.8288 (mtpp) cc_final: 0.8075 (mtpp) REVERT: D 804 GLN cc_start: 0.8218 (mt0) cc_final: 0.7846 (mm-40) REVERT: D 816 SER cc_start: 0.8599 (p) cc_final: 0.8276 (t) REVERT: D 854 LYS cc_start: 0.8707 (ttmm) cc_final: 0.8394 (ttpp) REVERT: D 969 LYS cc_start: 0.8608 (OUTLIER) cc_final: 0.8391 (pttm) REVERT: D 978 ASN cc_start: 0.8319 (m-40) cc_final: 0.8116 (m-40) REVERT: D 988 GLU cc_start: 0.7419 (OUTLIER) cc_final: 0.6800 (tm-30) REVERT: D 990 GLU cc_start: 0.8069 (mp0) cc_final: 0.7580 (mp0) REVERT: D 992 GLN cc_start: 0.7808 (mt0) cc_final: 0.7421 (mt0) REVERT: D 1029 MET cc_start: 0.8227 (ttm) cc_final: 0.7957 (ttm) REVERT: D 1072 GLU cc_start: 0.8388 (pm20) cc_final: 0.8163 (pm20) REVERT: D 1118 ASP cc_start: 0.7749 (t0) cc_final: 0.7239 (t0) REVERT: F 200 GLU cc_start: 0.0750 (OUTLIER) cc_final: 0.0152 (pm20) REVERT: G 47 VAL cc_start: 0.8769 (OUTLIER) cc_final: 0.8522 (t) REVERT: G 63 THR cc_start: 0.8143 (OUTLIER) cc_final: 0.7933 (m) REVERT: G 81 ASN cc_start: 0.7293 (OUTLIER) cc_final: 0.6735 (p0) REVERT: G 130 VAL cc_start: 0.7415 (t) cc_final: 0.6896 (p) REVERT: G 184 PHE cc_start: 0.8004 (m-80) cc_final: 0.7720 (m-10) REVERT: G 186 ASN cc_start: 0.7492 (OUTLIER) cc_final: 0.6991 (p0) REVERT: G 286 THR cc_start: 0.7885 (p) cc_final: 0.7593 (t) REVERT: G 378 LYS cc_start: 0.7147 (OUTLIER) cc_final: 0.6824 (tptm) REVERT: G 453 TYR cc_start: 0.6097 (t80) cc_final: 0.5725 (t80) REVERT: G 478 LYS cc_start: 0.3384 (OUTLIER) cc_final: 0.3117 (tmmt) REVERT: G 493 ARG cc_start: 0.6900 (OUTLIER) cc_final: 0.6512 (mmp-170) REVERT: G 528 LYS cc_start: 0.7534 (OUTLIER) cc_final: 0.7315 (tmmt) REVERT: G 599 THR cc_start: 0.8822 (OUTLIER) cc_final: 0.8540 (p) REVERT: G 673 SER cc_start: 0.8710 (p) cc_final: 0.8446 (m) REVERT: G 745 ASP cc_start: 0.7169 (m-30) cc_final: 0.6913 (p0) REVERT: G 764 LYS cc_start: 0.8419 (tttt) cc_final: 0.8184 (ttmm) REVERT: G 803 SER cc_start: 0.8494 (m) cc_final: 0.8183 (p) REVERT: G 819 GLU cc_start: 0.7823 (mt-10) cc_final: 0.7351 (mt-10) REVERT: G 821 LEU cc_start: 0.8343 (tt) cc_final: 0.8056 (tp) REVERT: G 825 LYS cc_start: 0.8327 (mmmm) cc_final: 0.8026 (mmmm) REVERT: G 853 GLN cc_start: 0.8131 (mt0) cc_final: 0.7861 (mt0) REVERT: G 884 SER cc_start: 0.8401 (t) cc_final: 0.8008 (p) REVERT: G 949 GLN cc_start: 0.8588 (mm-40) cc_final: 0.8222 (mm-40) REVERT: G 993 ILE cc_start: 0.8364 (OUTLIER) cc_final: 0.7971 (mt) REVERT: G 994 ASP cc_start: 0.8172 (t70) cc_final: 0.7914 (t0) REVERT: G 1017 GLU cc_start: 0.7785 (tm-30) cc_final: 0.7416 (tm-30) REVERT: G 1107 ARG cc_start: 0.7260 (mtt-85) cc_final: 0.6857 (mtt180) outliers start: 201 outliers final: 147 residues processed: 652 average time/residue: 0.4689 time to fit residues: 481.7790 Evaluate side-chains 656 residues out of total 3264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 169 poor density : 487 time to evaluate : 3.346 ------------------------------------------------------------------------------- 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 127 VAL 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 206 THR Chi-restraints excluded: chain A residue 208 ILE 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 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 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 531 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 727 LEU Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 968 SER Chi-restraints excluded: chain A residue 969 LYS Chi-restraints excluded: chain A residue 990 GLU 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 B residue 121 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 51 THR 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 87 ASN 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 117 LEU Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 121 ASN Chi-restraints excluded: chain D residue 122 ASN Chi-restraints excluded: chain D residue 126 VAL Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 132 GLU Chi-restraints excluded: chain D residue 171 VAL Chi-restraints excluded: chain D residue 198 TYR Chi-restraints excluded: chain D residue 206 THR Chi-restraints excluded: chain D residue 239 GLN Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 274 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 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 569 ILE Chi-restraints excluded: chain D residue 588 THR Chi-restraints excluded: chain D residue 616 ASN Chi-restraints excluded: chain D residue 649 CYS 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 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 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 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 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 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 51 THR Chi-restraints excluded: chain G residue 62 VAL Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 68 ILE 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 128 ILE Chi-restraints excluded: chain G residue 171 VAL Chi-restraints excluded: chain G residue 186 ASN Chi-restraints excluded: chain G residue 189 GLU 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 305 SER 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 378 LYS Chi-restraints excluded: chain G residue 383 SER 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 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 615 VAL 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 935 GLN Chi-restraints excluded: chain G residue 947 LYS Chi-restraints excluded: chain G residue 950 ASP Chi-restraints excluded: chain G residue 993 ILE 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 282 optimal weight: 4.9990 chunk 27 optimal weight: 9.9990 chunk 271 optimal weight: 0.9990 chunk 234 optimal weight: 8.9990 chunk 69 optimal weight: 0.0870 chunk 117 optimal weight: 9.9990 chunk 331 optimal weight: 4.9990 chunk 142 optimal weight: 0.1980 chunk 10 optimal weight: 0.0970 chunk 247 optimal weight: 40.0000 chunk 123 optimal weight: 50.0000 overall best weight: 1.2760 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** A 949 GLN A1101 HIS ** B 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 30 ASN D 87 ASN D 121 ASN ** 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 872 GLN D 957 GLN D1106 GLN D1135 ASN ** F 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 641 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4332 r_free = 0.4332 target = 0.198243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.143233 restraints weight = 42481.972| |-----------------------------------------------------------------------------| r_work (start): 0.3594 rms_B_bonded: 2.57 r_work: 0.3455 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3287 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7465 moved from start: 0.3358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 30193 Z= 0.211 Angle : 0.611 11.114 41191 Z= 0.313 Chirality : 0.046 0.376 4712 Planarity : 0.005 0.101 5285 Dihedral : 6.913 79.373 4725 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.05 % Allowed : 9.05 % Favored : 90.89 % Rotamer: Outliers : 6.63 % Allowed : 16.31 % Favored : 77.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.48 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.79 (0.13), residues: 3700 helix: -0.21 (0.21), residues: 661 sheet: -1.34 (0.17), residues: 882 loop : -2.75 (0.12), residues: 2157 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP G 64 HIS 0.005 0.001 HIS G1088 PHE 0.037 0.002 PHE A 855 TYR 0.028 0.001 TYR D1067 ARG 0.008 0.000 ARG D1019 Details of bonding type rmsd link_NAG-ASN : bond 0.00245 ( 24) link_NAG-ASN : angle 2.40406 ( 72) hydrogen bonds : bond 0.03753 ( 744) hydrogen bonds : angle 4.83375 ( 1980) SS BOND : bond 0.00366 ( 45) SS BOND : angle 1.71875 ( 90) covalent geometry : bond 0.00495 (30124) covalent geometry : angle 0.59850 (41029) *********************** 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 733 residues out of total 3264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 213 poor density : 520 time to evaluate : 2.947 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: 0.8719 (t) cc_final: 0.8449 (m) REVERT: A 102 ARG cc_start: 0.7992 (mtm-85) cc_final: 0.7720 (ptp90) REVERT: A 132 GLU cc_start: 0.7738 (mt-10) cc_final: 0.7483 (mp0) REVERT: A 133 PHE cc_start: 0.8576 (m-80) cc_final: 0.8155 (m-80) REVERT: A 168 PHE cc_start: 0.8439 (OUTLIER) cc_final: 0.7700 (m-80) REVERT: A 177 MET cc_start: 0.4867 (ptp) cc_final: 0.4657 (ptp) REVERT: A 212 GLU cc_start: 0.7035 (OUTLIER) cc_final: 0.6684 (mm-30) REVERT: A 220 PHE cc_start: 0.8205 (t80) cc_final: 0.7904 (t80) REVERT: A 231 ILE cc_start: 0.8522 (mt) cc_final: 0.8308 (tt) REVERT: A 269 TYR cc_start: 0.8348 (m-80) cc_final: 0.7829 (m-80) REVERT: A 281 GLU cc_start: 0.7425 (OUTLIER) cc_final: 0.7126 (pp20) REVERT: A 307 THR cc_start: 0.8335 (m) cc_final: 0.8067 (t) REVERT: A 324 GLU cc_start: 0.7163 (tt0) cc_final: 0.6948 (tt0) REVERT: A 517 LEU cc_start: 0.3271 (OUTLIER) cc_final: 0.2895 (tm) REVERT: A 532 ASN cc_start: 0.8206 (t0) cc_final: 0.7618 (t0) REVERT: A 572 THR cc_start: 0.7807 (t) cc_final: 0.7373 (p) REVERT: A 578 ASP cc_start: 0.7030 (t0) cc_final: 0.6748 (t70) REVERT: A 675 GLN cc_start: 0.7155 (mm-40) cc_final: 0.6878 (mm-40) REVERT: A 765 ARG cc_start: 0.8246 (ttp-110) cc_final: 0.7942 (mtm-85) REVERT: A 776 LYS cc_start: 0.8396 (ttpt) cc_final: 0.8061 (ttpt) REVERT: A 787 GLN cc_start: 0.8568 (mm-40) cc_final: 0.8074 (mt0) REVERT: A 949 GLN cc_start: 0.8458 (mm-40) cc_final: 0.8190 (mm-40) REVERT: A 960 ASN cc_start: 0.8403 (t0) cc_final: 0.8189 (t0) REVERT: A 969 LYS cc_start: 0.8461 (OUTLIER) cc_final: 0.7796 (pptt) REVERT: A 979 ASP cc_start: 0.7317 (t0) cc_final: 0.6944 (t0) REVERT: A 1073 LYS cc_start: 0.8409 (mtmt) cc_final: 0.8063 (mtpp) REVERT: B 121 LEU cc_start: 0.2252 (OUTLIER) cc_final: 0.1984 (tt) REVERT: D 83 VAL cc_start: 0.8236 (OUTLIER) cc_final: 0.7915 (p) REVERT: D 105 ILE cc_start: 0.8468 (OUTLIER) cc_final: 0.8096 (mt) REVERT: D 239 GLN cc_start: 0.7802 (OUTLIER) cc_final: 0.7530 (tm-30) REVERT: D 290 ASP cc_start: 0.8159 (t70) cc_final: 0.7804 (t0) REVERT: D 319 ARG cc_start: 0.8078 (ttm170) cc_final: 0.7783 (ttm-80) REVERT: D 346 ARG cc_start: 0.7816 (OUTLIER) cc_final: 0.7514 (mtp180) REVERT: D 543 PHE cc_start: 0.8332 (m-10) cc_final: 0.7994 (m-10) REVERT: D 599 THR cc_start: 0.8339 (m) cc_final: 0.8014 (p) REVERT: D 705 VAL cc_start: 0.8647 (t) cc_final: 0.8426 (p) REVERT: D 737 ASP cc_start: 0.7571 (t0) cc_final: 0.7266 (t0) REVERT: D 790 LYS cc_start: 0.8277 (mtpp) cc_final: 0.8052 (mtpp) REVERT: D 804 GLN cc_start: 0.8281 (mt0) cc_final: 0.8028 (mm-40) REVERT: D 816 SER cc_start: 0.8548 (p) cc_final: 0.8230 (t) REVERT: D 854 LYS cc_start: 0.8731 (ttmm) cc_final: 0.8426 (ttpp) REVERT: D 988 GLU cc_start: 0.7359 (OUTLIER) cc_final: 0.6586 (tm-30) REVERT: D 990 GLU cc_start: 0.8045 (mp0) cc_final: 0.7596 (mp0) REVERT: D 992 GLN cc_start: 0.7751 (mt0) cc_final: 0.7364 (mt0) REVERT: D 1029 MET cc_start: 0.8342 (ttm) cc_final: 0.8110 (ttm) REVERT: D 1118 ASP cc_start: 0.7895 (t0) cc_final: 0.7415 (t0) REVERT: D 1139 ASP cc_start: 0.7984 (p0) cc_final: 0.7604 (p0) REVERT: D 1141 LEU cc_start: 0.8585 (OUTLIER) cc_final: 0.8188 (mp) REVERT: F 200 GLU cc_start: 0.0533 (OUTLIER) cc_final: -0.0031 (pm20) REVERT: G 47 VAL cc_start: 0.8738 (OUTLIER) cc_final: 0.8467 (t) REVERT: G 54 LEU cc_start: 0.8719 (mp) cc_final: 0.8475 (mt) REVERT: G 63 THR cc_start: 0.8047 (OUTLIER) cc_final: 0.7809 (m) REVERT: G 81 ASN cc_start: 0.7256 (OUTLIER) cc_final: 0.6689 (p0) REVERT: G 129 LYS cc_start: 0.8390 (ptpt) cc_final: 0.7744 (pttp) REVERT: G 186 ASN cc_start: 0.7567 (OUTLIER) cc_final: 0.7047 (p0) REVERT: G 286 THR cc_start: 0.7808 (p) cc_final: 0.7586 (t) REVERT: G 453 TYR cc_start: 0.5895 (t80) cc_final: 0.5610 (t80) REVERT: G 478 LYS cc_start: 0.3416 (OUTLIER) cc_final: 0.3145 (tmmt) REVERT: G 493 ARG cc_start: 0.6842 (OUTLIER) cc_final: 0.6384 (mmp-170) REVERT: G 528 LYS cc_start: 0.7299 (OUTLIER) cc_final: 0.7097 (tmmt) REVERT: G 599 THR cc_start: 0.8846 (OUTLIER) cc_final: 0.8568 (p) REVERT: G 641 ASN cc_start: 0.8047 (OUTLIER) cc_final: 0.7826 (p0) REVERT: G 654 GLU cc_start: 0.7831 (pm20) cc_final: 0.7564 (pm20) REVERT: G 745 ASP cc_start: 0.7322 (m-30) cc_final: 0.7028 (p0) REVERT: G 764 LYS cc_start: 0.8529 (tttt) cc_final: 0.8228 (ttmm) REVERT: G 819 GLU cc_start: 0.7830 (mt-10) cc_final: 0.7452 (mt-10) REVERT: G 851 CYS cc_start: 0.8521 (t) cc_final: 0.8256 (t) REVERT: G 945 LEU cc_start: 0.8463 (OUTLIER) cc_final: 0.8242 (mp) REVERT: G 949 GLN cc_start: 0.8618 (mm-40) cc_final: 0.8264 (mm-40) REVERT: G 970 PHE cc_start: 0.8214 (m-80) cc_final: 0.7669 (m-80) REVERT: G 993 ILE cc_start: 0.8309 (OUTLIER) cc_final: 0.7946 (mt) REVERT: G 1017 GLU cc_start: 0.7819 (tm-30) cc_final: 0.7397 (tm-30) outliers start: 213 outliers final: 144 residues processed: 670 average time/residue: 0.4172 time to fit residues: 439.4474 Evaluate side-chains 661 residues out of total 3264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 168 poor density : 493 time to evaluate : 2.935 ------------------------------------------------------------------------------- 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 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 206 THR Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 212 GLU 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 301 CYS Chi-restraints excluded: chain A residue 312 ILE 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 705 VAL 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 934 ILE Chi-restraints excluded: chain A residue 968 SER Chi-restraints excluded: chain A residue 969 LYS Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain A residue 1118 ASP 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 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 120 VAL Chi-restraints excluded: chain D residue 121 ASN 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 141 LEU Chi-restraints excluded: chain D residue 198 TYR Chi-restraints excluded: chain D residue 239 GLN Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 274 THR Chi-restraints excluded: chain D residue 346 ARG 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 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 697 MET 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 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 988 GLU Chi-restraints excluded: chain D residue 1041 ASP Chi-restraints excluded: chain D residue 1050 MET Chi-restraints excluded: chain D residue 1066 THR Chi-restraints excluded: chain D residue 1081 ILE 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 128 GLN 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 51 THR Chi-restraints excluded: chain G residue 62 VAL Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 81 ASN Chi-restraints excluded: chain G residue 100 ILE Chi-restraints excluded: chain G residue 128 ILE Chi-restraints excluded: chain G residue 186 ASN Chi-restraints excluded: chain G residue 189 GLU Chi-restraints excluded: chain G residue 204 LYS Chi-restraints excluded: chain G residue 229 LEU Chi-restraints excluded: chain G residue 240 THR Chi-restraints excluded: chain G residue 305 SER Chi-restraints excluded: chain G residue 351 TYR Chi-restraints excluded: chain G residue 375 PHE Chi-restraints excluded: chain G residue 383 SER 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 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 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 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 935 GLN Chi-restraints excluded: chain G residue 945 LEU Chi-restraints excluded: chain G residue 947 LYS Chi-restraints excluded: chain G residue 950 ASP Chi-restraints excluded: chain G residue 976 VAL 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 1136 THR 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 222 optimal weight: 0.6980 chunk 33 optimal weight: 9.9990 chunk 359 optimal weight: 0.5980 chunk 350 optimal weight: 0.5980 chunk 27 optimal weight: 4.9990 chunk 285 optimal weight: 0.6980 chunk 338 optimal weight: 0.9990 chunk 72 optimal weight: 2.9990 chunk 241 optimal weight: 0.0370 chunk 38 optimal weight: 50.0000 chunk 147 optimal weight: 0.7980 overall best weight: 0.5258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 580 GLN ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 949 GLN A1101 HIS ** B 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 121 ASN ** 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 804 GLN D 872 GLN D 935 GLN ** F 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 66 HIS ** 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 = 0.4353 r_free = 0.4353 target = 0.200086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.145784 restraints weight = 42724.777| |-----------------------------------------------------------------------------| r_work (start): 0.3621 rms_B_bonded: 2.58 r_work: 0.3478 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3315 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7458 moved from start: 0.3471 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= 0.120 Angle : 0.565 9.866 41191 Z= 0.287 Chirality : 0.044 0.321 4712 Planarity : 0.005 0.097 5285 Dihedral : 6.615 79.530 4715 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.43 % Favored : 91.51 % Rotamer: Outliers : 5.91 % Allowed : 17.62 % Favored : 76.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.48 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.50 (0.13), residues: 3700 helix: 0.18 (0.21), residues: 662 sheet: -1.15 (0.17), residues: 863 loop : -2.60 (0.12), residues: 2175 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP G 64 HIS 0.004 0.001 HIS G1088 PHE 0.022 0.001 PHE A 541 TYR 0.020 0.001 TYR D1067 ARG 0.009 0.000 ARG G1019 Details of bonding type rmsd link_NAG-ASN : bond 0.00183 ( 24) link_NAG-ASN : angle 2.27174 ( 72) hydrogen bonds : bond 0.03190 ( 744) hydrogen bonds : angle 4.64143 ( 1980) SS BOND : bond 0.00360 ( 45) SS BOND : angle 1.44838 ( 90) covalent geometry : bond 0.00286 (30124) covalent geometry : angle 0.55400 (41029) *********************** 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 694 residues out of total 3264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 190 poor density : 504 time to evaluate : 3.302 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: 0.8728 (t) cc_final: 0.8483 (m) REVERT: A 99 ASN cc_start: 0.7902 (p0) cc_final: 0.7698 (p0) REVERT: A 132 GLU cc_start: 0.7636 (mt-10) cc_final: 0.7407 (mp0) REVERT: A 133 PHE cc_start: 0.8625 (m-80) cc_final: 0.8266 (m-80) REVERT: A 177 MET cc_start: 0.4884 (ptp) cc_final: 0.4680 (ptp) REVERT: A 212 GLU cc_start: 0.7074 (OUTLIER) cc_final: 0.6541 (mm-30) REVERT: A 220 PHE cc_start: 0.8203 (t80) cc_final: 0.7735 (t80) REVERT: A 269 TYR cc_start: 0.8294 (m-80) cc_final: 0.7859 (m-80) REVERT: A 281 GLU cc_start: 0.7378 (OUTLIER) cc_final: 0.7113 (pp20) REVERT: A 307 THR cc_start: 0.8178 (m) cc_final: 0.7929 (t) REVERT: A 325 SER cc_start: 0.8405 (m) cc_final: 0.8090 (t) REVERT: A 517 LEU cc_start: 0.3255 (OUTLIER) cc_final: 0.2901 (tm) REVERT: A 572 THR cc_start: 0.7869 (t) cc_final: 0.7419 (p) REVERT: A 675 GLN cc_start: 0.7089 (mm-40) cc_final: 0.6810 (mm-40) REVERT: A 745 ASP cc_start: 0.6543 (p0) cc_final: 0.6285 (p0) REVERT: A 765 ARG cc_start: 0.8244 (ttp-110) cc_final: 0.7964 (mtm-85) REVERT: A 776 LYS cc_start: 0.8444 (ttpt) cc_final: 0.8112 (ttpt) REVERT: A 787 GLN cc_start: 0.8566 (mm-40) cc_final: 0.8106 (mt0) REVERT: A 949 GLN cc_start: 0.8392 (mm110) cc_final: 0.8165 (mm-40) REVERT: A 960 ASN cc_start: 0.8380 (t0) cc_final: 0.8152 (t0) REVERT: A 969 LYS cc_start: 0.8424 (OUTLIER) cc_final: 0.7780 (pptt) REVERT: A 979 ASP cc_start: 0.7393 (t0) cc_final: 0.7125 (t0) REVERT: A 1017 GLU cc_start: 0.8031 (tm-30) cc_final: 0.7739 (tm-30) REVERT: A 1073 LYS cc_start: 0.8468 (mtmt) cc_final: 0.8058 (mtmm) REVERT: D 83 VAL cc_start: 0.8261 (OUTLIER) cc_final: 0.7993 (p) REVERT: D 105 ILE cc_start: 0.8486 (OUTLIER) cc_final: 0.8105 (mt) REVERT: D 169 GLU cc_start: 0.8256 (tm-30) cc_final: 0.7784 (tm-30) REVERT: D 188 ARG cc_start: 0.8347 (OUTLIER) cc_final: 0.8147 (mtt-85) REVERT: D 239 GLN cc_start: 0.7685 (OUTLIER) cc_final: 0.7470 (tm-30) REVERT: D 290 ASP cc_start: 0.8009 (t70) cc_final: 0.7691 (t0) REVERT: D 319 ARG cc_start: 0.8128 (ttm170) cc_final: 0.7841 (ttm-80) REVERT: D 346 ARG cc_start: 0.7814 (OUTLIER) cc_final: 0.7533 (mtp180) REVERT: D 599 THR cc_start: 0.8286 (m) cc_final: 0.7987 (p) REVERT: D 705 VAL cc_start: 0.8613 (t) cc_final: 0.8372 (p) REVERT: D 737 ASP cc_start: 0.7504 (t0) cc_final: 0.7100 (t0) REVERT: D 753 LEU cc_start: 0.8093 (tp) cc_final: 0.7889 (tt) REVERT: D 790 LYS cc_start: 0.8264 (mtpp) cc_final: 0.8056 (mtpp) REVERT: D 804 GLN cc_start: 0.8266 (mt0) cc_final: 0.8044 (mm-40) REVERT: D 816 SER cc_start: 0.8528 (p) cc_final: 0.8201 (t) REVERT: D 988 GLU cc_start: 0.7255 (OUTLIER) cc_final: 0.6614 (tm-30) REVERT: D 990 GLU cc_start: 0.8019 (mp0) cc_final: 0.7585 (mp0) REVERT: D 1118 ASP cc_start: 0.7870 (t0) cc_final: 0.7378 (t0) REVERT: D 1139 ASP cc_start: 0.7965 (p0) cc_final: 0.7593 (p0) REVERT: F 200 GLU cc_start: 0.0639 (OUTLIER) cc_final: 0.0018 (pm20) REVERT: G 47 VAL cc_start: 0.8800 (OUTLIER) cc_final: 0.8500 (t) REVERT: G 63 THR cc_start: 0.8110 (OUTLIER) cc_final: 0.7173 (t) REVERT: G 81 ASN cc_start: 0.7178 (OUTLIER) cc_final: 0.6607 (p0) REVERT: G 129 LYS cc_start: 0.8357 (ptpt) cc_final: 0.7814 (pttp) REVERT: G 130 VAL cc_start: 0.7574 (t) cc_final: 0.7120 (p) REVERT: G 186 ASN cc_start: 0.7485 (OUTLIER) cc_final: 0.7031 (p0) REVERT: G 286 THR cc_start: 0.7792 (p) cc_final: 0.7582 (t) REVERT: G 357 ARG cc_start: 0.7858 (tpt-90) cc_final: 0.7649 (ttt-90) REVERT: G 453 TYR cc_start: 0.6135 (t80) cc_final: 0.5755 (t80) REVERT: G 478 LYS cc_start: 0.3469 (OUTLIER) cc_final: 0.3187 (tmmt) REVERT: G 493 ARG cc_start: 0.6877 (OUTLIER) cc_final: 0.6502 (mmp-170) REVERT: G 505 HIS cc_start: 0.7472 (OUTLIER) cc_final: 0.7254 (t70) REVERT: G 599 THR cc_start: 0.8834 (OUTLIER) cc_final: 0.8563 (p) REVERT: G 745 ASP cc_start: 0.7221 (m-30) cc_final: 0.7004 (p0) REVERT: G 764 LYS cc_start: 0.8430 (tttt) cc_final: 0.8194 (ttmt) REVERT: G 779 GLN cc_start: 0.8678 (tt0) cc_final: 0.8448 (tt0) REVERT: G 803 SER cc_start: 0.8521 (m) cc_final: 0.8210 (p) REVERT: G 825 LYS cc_start: 0.8370 (mmmm) cc_final: 0.8141 (mmmm) REVERT: G 853 GLN cc_start: 0.8094 (mt0) cc_final: 0.7872 (mt0) REVERT: G 949 GLN cc_start: 0.8609 (mm-40) cc_final: 0.8299 (mm-40) REVERT: G 1017 GLU cc_start: 0.7795 (tm-30) cc_final: 0.7419 (tm-30) outliers start: 190 outliers final: 138 residues processed: 642 average time/residue: 0.4864 time to fit residues: 495.6681 Evaluate side-chains 647 residues out of total 3264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 157 poor density : 490 time to evaluate : 3.273 ------------------------------------------------------------------------------- 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 212 GLU 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 301 CYS Chi-restraints excluded: chain A residue 312 ILE 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 537 LYS Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 705 VAL 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 934 ILE Chi-restraints excluded: chain A residue 957 GLN Chi-restraints excluded: chain A residue 968 SER Chi-restraints excluded: chain A residue 969 LYS Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain B residue 18 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 87 ASN 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 120 VAL 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 188 ARG 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 274 THR Chi-restraints excluded: chain D residue 346 ARG 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 528 LYS 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 725 GLU 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 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 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 128 GLN 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 63 THR 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 171 VAL Chi-restraints excluded: chain G residue 186 ASN Chi-restraints excluded: chain G residue 189 GLU 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 240 THR Chi-restraints excluded: chain G residue 375 PHE Chi-restraints excluded: chain G residue 383 SER 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 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 754 LEU Chi-restraints excluded: chain G residue 791 THR Chi-restraints excluded: chain G residue 935 GLN Chi-restraints excluded: chain G residue 947 LYS Chi-restraints excluded: chain G residue 950 ASP Chi-restraints excluded: chain G residue 976 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 1136 THR 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 212 optimal weight: 1.9990 chunk 236 optimal weight: 10.0000 chunk 22 optimal weight: 2.9990 chunk 111 optimal weight: 50.0000 chunk 187 optimal weight: 0.8980 chunk 123 optimal weight: 20.0000 chunk 109 optimal weight: 6.9990 chunk 303 optimal weight: 3.9990 chunk 147 optimal weight: 1.9990 chunk 182 optimal weight: 0.7980 chunk 193 optimal weight: 0.0770 overall best weight: 1.1542 ------------------------------------------------------------------------------- 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 762 GLN A 935 GLN A 949 GLN ** B 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 121 ASN ** D 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 205 HIS ** D 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 641 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4349 r_free = 0.4349 target = 0.199068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.144268 restraints weight = 42383.146| |-----------------------------------------------------------------------------| r_work (start): 0.3608 rms_B_bonded: 2.56 r_work: 0.3463 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3289 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7508 moved from start: 0.3700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 30193 Z= 0.195 Angle : 0.611 10.755 41191 Z= 0.312 Chirality : 0.046 0.318 4712 Planarity : 0.005 0.100 5285 Dihedral : 6.597 79.543 4707 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.05 % Allowed : 9.32 % Favored : 90.62 % Rotamer: Outliers : 6.04 % Allowed : 17.46 % Favored : 76.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.48 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.44 (0.13), residues: 3700 helix: 0.13 (0.21), residues: 661 sheet: -1.08 (0.17), residues: 867 loop : -2.54 (0.13), residues: 2172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP A 64 HIS 0.005 0.001 HIS G1088 PHE 0.026 0.002 PHE G 329 TYR 0.027 0.001 TYR D1067 ARG 0.008 0.000 ARG G1019 Details of bonding type rmsd link_NAG-ASN : bond 0.00331 ( 24) link_NAG-ASN : angle 2.05542 ( 72) hydrogen bonds : bond 0.03608 ( 744) hydrogen bonds : angle 4.70183 ( 1980) SS BOND : bond 0.00330 ( 45) SS BOND : angle 1.78516 ( 90) covalent geometry : bond 0.00460 (30124) covalent geometry : angle 0.59983 (41029) *********************** 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 691 residues out of total 3264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 194 poor density : 497 time to evaluate : 2.939 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 VAL cc_start: 0.8728 (t) cc_final: 0.8464 (m) REVERT: A 105 ILE cc_start: 0.8400 (mt) cc_final: 0.8195 (mm) REVERT: A 133 PHE cc_start: 0.8590 (m-80) cc_final: 0.8123 (m-80) REVERT: A 168 PHE cc_start: 0.8445 (OUTLIER) cc_final: 0.7876 (m-80) REVERT: A 212 GLU cc_start: 0.6980 (OUTLIER) cc_final: 0.6474 (mm-30) REVERT: A 220 PHE cc_start: 0.8212 (t80) cc_final: 0.7797 (t80) REVERT: A 231 ILE cc_start: 0.8677 (tt) cc_final: 0.8325 (pt) REVERT: A 269 TYR cc_start: 0.8353 (m-80) cc_final: 0.7988 (m-80) REVERT: A 281 GLU cc_start: 0.7436 (OUTLIER) cc_final: 0.7217 (pp20) REVERT: A 307 THR cc_start: 0.8304 (m) cc_final: 0.8063 (t) REVERT: A 317 ASN cc_start: 0.8005 (m-40) cc_final: 0.7680 (m110) REVERT: A 325 SER cc_start: 0.8373 (m) cc_final: 0.8009 (t) REVERT: A 517 LEU cc_start: 0.3267 (OUTLIER) cc_final: 0.2897 (tm) REVERT: A 572 THR cc_start: 0.7948 (t) cc_final: 0.7440 (p) REVERT: A 643 PHE cc_start: 0.8282 (t80) cc_final: 0.8040 (t80) REVERT: A 675 GLN cc_start: 0.7206 (mm-40) cc_final: 0.6917 (mm-40) REVERT: A 745 ASP cc_start: 0.6844 (p0) cc_final: 0.6572 (p0) REVERT: A 765 ARG cc_start: 0.8223 (ttp-110) cc_final: 0.7958 (mtm-85) REVERT: A 776 LYS cc_start: 0.8514 (ttpt) cc_final: 0.8208 (ttpt) REVERT: A 787 GLN cc_start: 0.8526 (mm-40) cc_final: 0.8069 (mt0) REVERT: A 949 GLN cc_start: 0.8554 (mm-40) cc_final: 0.8315 (mm-40) REVERT: A 960 ASN cc_start: 0.8416 (t0) cc_final: 0.8186 (t0) REVERT: A 969 LYS cc_start: 0.8453 (OUTLIER) cc_final: 0.7792 (pptt) REVERT: A 979 ASP cc_start: 0.7345 (t0) cc_final: 0.7071 (t0) REVERT: A 1017 GLU cc_start: 0.8114 (tm-30) cc_final: 0.7739 (tm-30) REVERT: A 1073 LYS cc_start: 0.8502 (mtmt) cc_final: 0.8186 (mtpp) REVERT: B 121 LEU cc_start: 0.2166 (OUTLIER) cc_final: 0.1906 (tt) REVERT: D 34 ARG cc_start: 0.8281 (OUTLIER) cc_final: 0.8075 (ttm110) REVERT: D 83 VAL cc_start: 0.8259 (OUTLIER) cc_final: 0.8021 (p) REVERT: D 105 ILE cc_start: 0.8556 (OUTLIER) cc_final: 0.8164 (mt) REVERT: D 106 PHE cc_start: 0.7479 (m-80) cc_final: 0.7272 (m-80) REVERT: D 169 GLU cc_start: 0.8262 (tm-30) cc_final: 0.7968 (tm-30) REVERT: D 239 GLN cc_start: 0.7862 (OUTLIER) cc_final: 0.7609 (tm-30) REVERT: D 290 ASP cc_start: 0.7998 (t70) cc_final: 0.7655 (t0) REVERT: D 319 ARG cc_start: 0.8203 (ttm170) cc_final: 0.7910 (ttm-80) REVERT: D 346 ARG cc_start: 0.7752 (OUTLIER) cc_final: 0.7468 (mtp180) REVERT: D 524 VAL cc_start: 0.6087 (OUTLIER) cc_final: 0.5846 (p) REVERT: D 599 THR cc_start: 0.8340 (m) cc_final: 0.8047 (p) REVERT: D 704 SER cc_start: 0.8776 (t) cc_final: 0.8560 (p) REVERT: D 705 VAL cc_start: 0.8649 (t) cc_final: 0.8413 (p) REVERT: D 790 LYS cc_start: 0.8288 (mtpp) cc_final: 0.8067 (mtpp) REVERT: D 804 GLN cc_start: 0.8327 (mt0) cc_final: 0.8125 (mm-40) REVERT: D 816 SER cc_start: 0.8526 (p) cc_final: 0.8204 (t) REVERT: D 988 GLU cc_start: 0.7189 (mm-30) cc_final: 0.6477 (tm-30) REVERT: D 992 GLN cc_start: 0.7848 (mt0) cc_final: 0.7647 (mt0) REVERT: D 1118 ASP cc_start: 0.7979 (t0) cc_final: 0.7524 (t0) REVERT: D 1139 ASP cc_start: 0.8051 (p0) cc_final: 0.7678 (p0) REVERT: D 1141 LEU cc_start: 0.8640 (OUTLIER) cc_final: 0.8228 (mp) REVERT: F 200 GLU cc_start: 0.0413 (OUTLIER) cc_final: -0.0173 (pm20) REVERT: G 47 VAL cc_start: 0.8658 (OUTLIER) cc_final: 0.8393 (t) REVERT: G 63 THR cc_start: 0.8067 (OUTLIER) cc_final: 0.7048 (t) REVERT: G 81 ASN cc_start: 0.7157 (OUTLIER) cc_final: 0.6603 (p0) REVERT: G 129 LYS cc_start: 0.8378 (ptpt) cc_final: 0.7827 (pttp) REVERT: G 186 ASN cc_start: 0.7597 (OUTLIER) cc_final: 0.7178 (p0) REVERT: G 286 THR cc_start: 0.7810 (p) cc_final: 0.7599 (t) REVERT: G 453 TYR cc_start: 0.6078 (t80) cc_final: 0.5797 (t80) REVERT: G 478 LYS cc_start: 0.3533 (OUTLIER) cc_final: 0.3224 (tmmt) REVERT: G 493 ARG cc_start: 0.6606 (OUTLIER) cc_final: 0.6339 (mmp-170) REVERT: G 505 HIS cc_start: 0.7510 (OUTLIER) cc_final: 0.7298 (t70) REVERT: G 599 THR cc_start: 0.8818 (OUTLIER) cc_final: 0.8555 (p) REVERT: G 764 LYS cc_start: 0.8459 (tttt) cc_final: 0.8243 (ttmt) REVERT: G 819 GLU cc_start: 0.7812 (mt-10) cc_final: 0.7473 (mt-10) REVERT: G 825 LYS cc_start: 0.8299 (mmmm) cc_final: 0.7809 (mtpp) REVERT: G 882 ILE cc_start: 0.8737 (pt) cc_final: 0.8336 (mt) REVERT: G 884 SER cc_start: 0.8441 (t) cc_final: 0.8096 (p) REVERT: G 900 MET cc_start: 0.8302 (mmm) cc_final: 0.7987 (mmm) REVERT: G 949 GLN cc_start: 0.8655 (mm-40) cc_final: 0.8356 (mm-40) REVERT: G 970 PHE cc_start: 0.8280 (m-80) cc_final: 0.7713 (m-80) REVERT: G 977 LEU cc_start: 0.8112 (OUTLIER) cc_final: 0.7712 (mm) REVERT: G 1017 GLU cc_start: 0.7913 (tm-30) cc_final: 0.7530 (tm-30) outliers start: 194 outliers final: 141 residues processed: 640 average time/residue: 0.4295 time to fit residues: 429.5353 Evaluate side-chains 651 residues out of total 3264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 164 poor density : 487 time to evaluate : 3.251 ------------------------------------------------------------------------------- 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 212 GLU 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 301 CYS Chi-restraints excluded: chain A residue 312 ILE 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 599 THR Chi-restraints excluded: chain A residue 705 VAL 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 934 ILE Chi-restraints excluded: chain A residue 957 GLN Chi-restraints excluded: chain A residue 968 SER Chi-restraints excluded: chain A residue 969 LYS Chi-restraints excluded: chain A residue 990 GLU 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 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 34 ARG 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 105 ILE Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain D residue 113 LYS Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 121 ASN 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 239 GLN Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 274 THR Chi-restraints excluded: chain D residue 346 ARG 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 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 725 GLU 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 1041 ASP Chi-restraints excluded: chain D residue 1066 THR 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 128 GLN 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 63 THR 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 171 VAL Chi-restraints excluded: chain G residue 186 ASN 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 281 GLU Chi-restraints excluded: chain G residue 375 PHE Chi-restraints excluded: chain G residue 383 SER 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 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 732 THR Chi-restraints excluded: chain G residue 754 LEU Chi-restraints excluded: chain G residue 791 THR Chi-restraints excluded: chain G residue 935 GLN Chi-restraints excluded: chain G residue 947 LYS Chi-restraints excluded: chain G residue 950 ASP Chi-restraints excluded: chain G residue 976 VAL Chi-restraints excluded: chain G residue 977 LEU Chi-restraints excluded: chain G residue 980 ILE Chi-restraints excluded: chain G residue 1001 LEU Chi-restraints excluded: chain G residue 1041 ASP Chi-restraints excluded: chain G residue 1082 CYS Chi-restraints excluded: chain G residue 1086 LYS Chi-restraints excluded: chain G residue 1116 THR Chi-restraints excluded: chain G residue 1136 THR 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 25 optimal weight: 4.9990 chunk 330 optimal weight: 0.9990 chunk 352 optimal weight: 2.9990 chunk 207 optimal weight: 2.9990 chunk 65 optimal weight: 5.9990 chunk 273 optimal weight: 0.7980 chunk 179 optimal weight: 1.9990 chunk 224 optimal weight: 1.9990 chunk 169 optimal weight: 0.0060 chunk 151 optimal weight: 1.9990 chunk 354 optimal weight: 1.9990 overall best weight: 1.1602 ------------------------------------------------------------------------------- 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 965 GLN ** B 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 121 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 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 122 ASN ** G 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 641 ASN G 762 GLN G1005 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4345 r_free = 0.4345 target = 0.198811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.142275 restraints weight = 41261.215| |-----------------------------------------------------------------------------| r_work (start): 0.3605 rms_B_bonded: 2.52 r_work: 0.3464 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3297 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7507 moved from start: 0.3890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 30193 Z= 0.195 Angle : 0.631 11.122 41191 Z= 0.320 Chirality : 0.046 0.415 4712 Planarity : 0.005 0.098 5285 Dihedral : 6.572 79.679 4701 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.05 % Allowed : 9.65 % Favored : 90.30 % Rotamer: Outliers : 5.85 % Allowed : 18.05 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.37 (0.13), residues: 3700 helix: 0.25 (0.21), residues: 664 sheet: -1.11 (0.17), residues: 892 loop : -2.50 (0.13), residues: 2144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.001 TRP A 64 HIS 0.005 0.001 HIS G1088 PHE 0.029 0.002 PHE D 192 TYR 0.027 0.001 TYR D1067 ARG 0.008 0.000 ARG D1019 Details of bonding type rmsd link_NAG-ASN : bond 0.00299 ( 24) link_NAG-ASN : angle 2.08377 ( 72) hydrogen bonds : bond 0.03575 ( 744) hydrogen bonds : angle 4.72011 ( 1980) SS BOND : bond 0.00391 ( 45) SS BOND : angle 1.88933 ( 90) covalent geometry : bond 0.00461 (30124) covalent geometry : angle 0.62020 (41029) *********************** 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 701 residues out of total 3264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 188 poor density : 513 time to evaluate : 2.865 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: 0.8741 (t) cc_final: 0.8486 (m) REVERT: A 212 GLU cc_start: 0.6921 (OUTLIER) cc_final: 0.6449 (mm-30) REVERT: A 220 PHE cc_start: 0.8208 (t80) cc_final: 0.7907 (t80) REVERT: A 269 TYR cc_start: 0.8361 (m-80) cc_final: 0.8007 (m-80) REVERT: A 317 ASN cc_start: 0.7939 (m-40) cc_final: 0.7612 (m110) REVERT: A 324 GLU cc_start: 0.6648 (tm-30) cc_final: 0.6186 (tm-30) REVERT: A 325 SER cc_start: 0.8237 (m) cc_final: 0.6955 (t) REVERT: A 517 LEU cc_start: 0.3248 (OUTLIER) cc_final: 0.2862 (tm) REVERT: A 571 ASP cc_start: 0.6691 (t70) cc_final: 0.6472 (t0) REVERT: A 572 THR cc_start: 0.7926 (t) cc_final: 0.7405 (p) REVERT: A 675 GLN cc_start: 0.7205 (mm-40) cc_final: 0.6920 (mm-40) REVERT: A 745 ASP cc_start: 0.6986 (p0) cc_final: 0.6708 (p0) REVERT: A 765 ARG cc_start: 0.8229 (ttp-110) cc_final: 0.7954 (mtm-85) REVERT: A 773 GLU cc_start: 0.7873 (tt0) cc_final: 0.7663 (tt0) REVERT: A 776 LYS cc_start: 0.8491 (ttpt) cc_final: 0.8133 (ttpt) REVERT: A 787 GLN cc_start: 0.8498 (mm-40) cc_final: 0.8042 (mt0) REVERT: A 795 LYS cc_start: 0.8227 (OUTLIER) cc_final: 0.7928 (mptt) REVERT: A 949 GLN cc_start: 0.8577 (mm-40) cc_final: 0.8335 (mm-40) REVERT: A 960 ASN cc_start: 0.8407 (t0) cc_final: 0.8165 (t0) REVERT: A 969 LYS cc_start: 0.8453 (OUTLIER) cc_final: 0.7741 (pptt) REVERT: A 979 ASP cc_start: 0.7366 (t0) cc_final: 0.7055 (t0) REVERT: A 1017 GLU cc_start: 0.7919 (tm-30) cc_final: 0.7709 (tm-30) REVERT: A 1019 ARG cc_start: 0.8043 (ttm110) cc_final: 0.7794 (ttp80) REVERT: A 1073 LYS cc_start: 0.8486 (mtmt) cc_final: 0.8178 (mtpp) REVERT: B 121 LEU cc_start: 0.2061 (OUTLIER) cc_final: 0.1798 (tt) REVERT: D 34 ARG cc_start: 0.8398 (OUTLIER) cc_final: 0.8126 (ttm110) REVERT: D 92 PHE cc_start: 0.8262 (t80) cc_final: 0.7999 (t80) REVERT: D 96 GLU cc_start: 0.6819 (tt0) cc_final: 0.6441 (tt0) REVERT: D 104 TRP cc_start: 0.7090 (m-90) cc_final: 0.6858 (m-90) REVERT: D 105 ILE cc_start: 0.8565 (OUTLIER) cc_final: 0.8189 (mt) REVERT: D 169 GLU cc_start: 0.8232 (tm-30) cc_final: 0.7973 (tm-30) REVERT: D 290 ASP cc_start: 0.8026 (t70) cc_final: 0.7662 (t0) REVERT: D 319 ARG cc_start: 0.8226 (ttm170) cc_final: 0.7952 (ttm-80) REVERT: D 346 ARG cc_start: 0.7801 (OUTLIER) cc_final: 0.7488 (mtp180) REVERT: D 599 THR cc_start: 0.8337 (m) cc_final: 0.8028 (p) REVERT: D 704 SER cc_start: 0.8767 (t) cc_final: 0.8555 (p) REVERT: D 705 VAL cc_start: 0.8649 (t) cc_final: 0.8441 (p) REVERT: D 790 LYS cc_start: 0.8274 (mtpp) cc_final: 0.8052 (mtpp) REVERT: D 816 SER cc_start: 0.8526 (p) cc_final: 0.8194 (t) REVERT: D 848 ASP cc_start: 0.7875 (p0) cc_final: 0.7624 (p0) REVERT: D 988 GLU cc_start: 0.7098 (mm-30) cc_final: 0.6376 (tm-30) REVERT: D 1118 ASP cc_start: 0.8028 (t0) cc_final: 0.7558 (t0) REVERT: D 1139 ASP cc_start: 0.8075 (p0) cc_final: 0.7702 (p0) REVERT: F 200 GLU cc_start: 0.0398 (OUTLIER) cc_final: -0.0200 (pm20) REVERT: G 47 VAL cc_start: 0.8656 (OUTLIER) cc_final: 0.8372 (t) REVERT: G 63 THR cc_start: 0.8034 (OUTLIER) cc_final: 0.7047 (t) REVERT: G 81 ASN cc_start: 0.7149 (OUTLIER) cc_final: 0.6595 (p0) REVERT: G 96 GLU cc_start: 0.7384 (pm20) cc_final: 0.7072 (pm20) REVERT: G 129 LYS cc_start: 0.8407 (ptpt) cc_final: 0.7857 (ptmm) REVERT: G 186 ASN cc_start: 0.7549 (OUTLIER) cc_final: 0.7073 (p0) REVERT: G 187 LEU cc_start: 0.8150 (tp) cc_final: 0.7942 (tt) REVERT: G 286 THR cc_start: 0.7806 (p) cc_final: 0.7599 (t) REVERT: G 370 ASN cc_start: 0.7004 (OUTLIER) cc_final: 0.6747 (p0) REVERT: G 453 TYR cc_start: 0.5877 (t80) cc_final: 0.5633 (t80) REVERT: G 478 LYS cc_start: 0.3495 (OUTLIER) cc_final: 0.2940 (tmmt) REVERT: G 486 PHE cc_start: 0.3687 (OUTLIER) cc_final: 0.3356 (p90) REVERT: G 493 ARG cc_start: 0.6580 (OUTLIER) cc_final: 0.6265 (mmp-170) REVERT: G 591 SER cc_start: 0.8762 (t) cc_final: 0.8544 (m) REVERT: G 599 THR cc_start: 0.8816 (OUTLIER) cc_final: 0.8562 (p) REVERT: G 615 VAL cc_start: 0.8196 (t) cc_final: 0.7976 (m) REVERT: G 752 LEU cc_start: 0.8359 (pp) cc_final: 0.8133 (tt) REVERT: G 764 LYS cc_start: 0.8431 (tttt) cc_final: 0.8211 (ttmt) REVERT: G 884 SER cc_start: 0.8475 (t) cc_final: 0.8178 (p) REVERT: G 900 MET cc_start: 0.8252 (mmm) cc_final: 0.7940 (mmm) REVERT: G 949 GLN cc_start: 0.8619 (mm-40) cc_final: 0.8309 (mm-40) REVERT: G 1107 ARG cc_start: 0.7667 (mtt180) cc_final: 0.7270 (mtt-85) outliers start: 188 outliers final: 145 residues processed: 651 average time/residue: 0.4288 time to fit residues: 437.6362 Evaluate side-chains 655 residues out of total 3264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 163 poor density : 492 time to evaluate : 3.809 ------------------------------------------------------------------------------- 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 212 GLU 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 301 CYS Chi-restraints excluded: chain A residue 312 ILE 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 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 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 934 ILE Chi-restraints excluded: chain A residue 957 GLN Chi-restraints excluded: chain A residue 968 SER Chi-restraints excluded: chain A residue 969 LYS Chi-restraints excluded: chain A residue 1041 ASP 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 34 ARG 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 105 ILE Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain D residue 113 LYS Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 121 ASN Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 132 GLU Chi-restraints excluded: chain D residue 229 LEU Chi-restraints excluded: chain D residue 231 ILE Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 274 THR Chi-restraints excluded: chain D residue 346 ARG 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 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 725 GLU Chi-restraints excluded: chain D residue 803 SER 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 1041 ASP Chi-restraints excluded: chain D residue 1066 THR 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 128 GLN 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 63 THR 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 128 ILE Chi-restraints excluded: chain G residue 171 VAL Chi-restraints excluded: chain G residue 186 ASN Chi-restraints excluded: chain G residue 203 SER Chi-restraints excluded: chain G residue 229 LEU Chi-restraints excluded: chain G residue 240 THR Chi-restraints excluded: chain G residue 281 GLU Chi-restraints excluded: chain G residue 353 TRP Chi-restraints excluded: chain G residue 370 ASN Chi-restraints excluded: chain G residue 375 PHE Chi-restraints excluded: chain G residue 383 SER 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 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 590 CYS 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 732 THR Chi-restraints excluded: chain G residue 754 LEU Chi-restraints excluded: chain G residue 791 THR Chi-restraints excluded: chain G residue 935 GLN Chi-restraints excluded: chain G residue 947 LYS Chi-restraints excluded: chain G residue 950 ASP Chi-restraints excluded: chain G residue 976 VAL Chi-restraints excluded: chain G residue 977 LEU Chi-restraints excluded: chain G residue 980 ILE Chi-restraints excluded: chain G residue 1001 LEU Chi-restraints excluded: chain G residue 1041 ASP Chi-restraints excluded: chain G residue 1082 CYS Chi-restraints excluded: chain G residue 1086 LYS Chi-restraints excluded: chain G residue 1097 SER Chi-restraints excluded: chain G residue 1116 THR Chi-restraints excluded: chain G residue 1136 THR 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 60 optimal weight: 2.9990 chunk 111 optimal weight: 30.0000 chunk 95 optimal weight: 0.4980 chunk 324 optimal weight: 0.5980 chunk 179 optimal weight: 0.8980 chunk 120 optimal weight: 6.9990 chunk 370 optimal weight: 0.9980 chunk 273 optimal weight: 1.9990 chunk 86 optimal weight: 0.0030 chunk 35 optimal weight: 40.0000 chunk 38 optimal weight: 9.9990 overall best weight: 0.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 532 ASN A 965 GLN ** B 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 81 ASN ** D 121 ASN ** 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 239 GLN ** D 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 913 GLN D 935 GLN ** D 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 66 HIS ** G 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 641 ASN G1005 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4360 r_free = 0.4360 target = 0.200135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.143316 restraints weight = 41046.769| |-----------------------------------------------------------------------------| r_work (start): 0.3616 rms_B_bonded: 2.64 r_work: 0.3485 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3324 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7495 moved from start: 0.3963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 30193 Z= 0.131 Angle : 0.616 15.455 41191 Z= 0.312 Chirality : 0.045 0.365 4712 Planarity : 0.005 0.103 5285 Dihedral : 6.426 79.736 4691 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.05 % Allowed : 9.14 % Favored : 90.81 % Rotamer: Outliers : 5.51 % Allowed : 18.64 % Favored : 75.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.48 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.22 (0.14), residues: 3700 helix: 0.57 (0.22), residues: 658 sheet: -1.09 (0.17), residues: 883 loop : -2.42 (0.13), residues: 2159 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.001 TRP A 64 HIS 0.004 0.001 HIS G 66 PHE 0.036 0.001 PHE A 133 TYR 0.035 0.001 TYR G 351 ARG 0.007 0.000 ARG D1019 Details of bonding type rmsd link_NAG-ASN : bond 0.00180 ( 24) link_NAG-ASN : angle 1.99785 ( 72) hydrogen bonds : bond 0.03240 ( 744) hydrogen bonds : angle 4.57305 ( 1980) SS BOND : bond 0.00338 ( 45) SS BOND : angle 2.17855 ( 90) covalent geometry : bond 0.00310 (30124) covalent geometry : angle 0.60339 (41029) *********************** 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 667 residues out of total 3264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 177 poor density : 490 time to evaluate : 2.858 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 VAL cc_start: 0.8756 (t) cc_final: 0.8532 (m) REVERT: A 220 PHE cc_start: 0.8254 (t80) cc_final: 0.7820 (t80) REVERT: A 269 TYR cc_start: 0.8349 (m-80) cc_final: 0.8023 (m-80) REVERT: A 317 ASN cc_start: 0.7921 (m-40) cc_final: 0.7609 (m110) REVERT: A 325 SER cc_start: 0.8194 (m) cc_final: 0.7921 (t) REVERT: A 517 LEU cc_start: 0.3327 (OUTLIER) cc_final: 0.2970 (tm) REVERT: A 558 LYS cc_start: 0.7819 (mmtm) cc_final: 0.7404 (mmmt) REVERT: A 572 THR cc_start: 0.7938 (t) cc_final: 0.7472 (p) REVERT: A 675 GLN cc_start: 0.7147 (mm-40) cc_final: 0.6865 (mm-40) REVERT: A 745 ASP cc_start: 0.6981 (p0) cc_final: 0.6697 (p0) REVERT: A 765 ARG cc_start: 0.8151 (ttp-110) cc_final: 0.7882 (mtm-85) REVERT: A 776 LYS cc_start: 0.8485 (ttpt) cc_final: 0.8108 (ttpt) REVERT: A 787 GLN cc_start: 0.8488 (mm-40) cc_final: 0.8053 (mt0) REVERT: A 795 LYS cc_start: 0.8236 (mptm) cc_final: 0.7927 (mptt) REVERT: A 804 GLN cc_start: 0.8230 (mm-40) cc_final: 0.7881 (mm-40) REVERT: A 949 GLN cc_start: 0.8538 (mm-40) cc_final: 0.8322 (mm-40) REVERT: A 960 ASN cc_start: 0.8394 (t0) cc_final: 0.8151 (t0) REVERT: A 969 LYS cc_start: 0.8401 (OUTLIER) cc_final: 0.7680 (pptt) REVERT: A 979 ASP cc_start: 0.7387 (t0) cc_final: 0.7067 (t0) REVERT: A 1017 GLU cc_start: 0.8111 (tm-30) cc_final: 0.7856 (tm-30) REVERT: A 1019 ARG cc_start: 0.8022 (ttm110) cc_final: 0.7745 (ttp80) REVERT: A 1038 LYS cc_start: 0.8618 (OUTLIER) cc_final: 0.8358 (mtmt) REVERT: A 1073 LYS cc_start: 0.8469 (mtmt) cc_final: 0.8118 (mtmm) REVERT: B 121 LEU cc_start: 0.2134 (OUTLIER) cc_final: 0.1881 (tt) REVERT: D 92 PHE cc_start: 0.8311 (t80) cc_final: 0.8021 (t80) REVERT: D 96 GLU cc_start: 0.6565 (tt0) cc_final: 0.6002 (tt0) REVERT: D 105 ILE cc_start: 0.8549 (OUTLIER) cc_final: 0.8199 (mt) REVERT: D 169 GLU cc_start: 0.8269 (tm-30) cc_final: 0.7967 (tm-30) REVERT: D 290 ASP cc_start: 0.7973 (t70) cc_final: 0.7647 (t0) REVERT: D 319 ARG cc_start: 0.8238 (ttm170) cc_final: 0.7967 (ttm-80) REVERT: D 346 ARG cc_start: 0.7773 (OUTLIER) cc_final: 0.7451 (mtp180) REVERT: D 524 VAL cc_start: 0.6073 (OUTLIER) cc_final: 0.5852 (p) REVERT: D 599 THR cc_start: 0.8287 (m) cc_final: 0.7973 (p) REVERT: D 704 SER cc_start: 0.8736 (t) cc_final: 0.8525 (p) REVERT: D 705 VAL cc_start: 0.8616 (t) cc_final: 0.8388 (p) REVERT: D 790 LYS cc_start: 0.8272 (mtpp) cc_final: 0.8051 (mtpp) REVERT: D 808 ASP cc_start: 0.7636 (t0) cc_final: 0.7037 (p0) REVERT: D 816 SER cc_start: 0.8506 (p) cc_final: 0.8235 (t) REVERT: D 848 ASP cc_start: 0.7843 (p0) cc_final: 0.7611 (p0) REVERT: D 947 LYS cc_start: 0.8628 (OUTLIER) cc_final: 0.8370 (mtpt) REVERT: D 988 GLU cc_start: 0.7189 (mm-30) cc_final: 0.6511 (tm-30) REVERT: D 990 GLU cc_start: 0.8011 (mp0) cc_final: 0.7564 (mp0) REVERT: D 1118 ASP cc_start: 0.7991 (t0) cc_final: 0.7584 (t0) REVERT: D 1139 ASP cc_start: 0.8060 (p0) cc_final: 0.7693 (p0) REVERT: F 200 GLU cc_start: 0.0606 (OUTLIER) cc_final: 0.0164 (pm20) REVERT: G 47 VAL cc_start: 0.8659 (OUTLIER) cc_final: 0.8375 (t) REVERT: G 54 LEU cc_start: 0.8742 (mp) cc_final: 0.8483 (mt) REVERT: G 63 THR cc_start: 0.8028 (OUTLIER) cc_final: 0.6976 (t) REVERT: G 81 ASN cc_start: 0.7141 (OUTLIER) cc_final: 0.6553 (p0) REVERT: G 129 LYS cc_start: 0.8296 (ptpt) cc_final: 0.7724 (ptmm) REVERT: G 186 ASN cc_start: 0.7445 (OUTLIER) cc_final: 0.6954 (p0) REVERT: G 239 GLN cc_start: 0.7777 (tp-100) cc_final: 0.7197 (tp-100) REVERT: G 478 LYS cc_start: 0.3493 (OUTLIER) cc_final: 0.2968 (tmmt) REVERT: G 486 PHE cc_start: 0.3597 (OUTLIER) cc_final: 0.3280 (p90) REVERT: G 493 ARG cc_start: 0.6418 (OUTLIER) cc_final: 0.6160 (mmp-170) REVERT: G 591 SER cc_start: 0.8713 (t) cc_final: 0.8506 (m) REVERT: G 655 TYR cc_start: 0.8316 (t80) cc_final: 0.7875 (t80) REVERT: G 803 SER cc_start: 0.8522 (m) cc_final: 0.8242 (p) REVERT: G 884 SER cc_start: 0.8490 (t) cc_final: 0.8193 (p) REVERT: G 900 MET cc_start: 0.8255 (mmm) cc_final: 0.7937 (mmm) REVERT: G 949 GLN cc_start: 0.8618 (mm-40) cc_final: 0.8314 (mm-40) REVERT: G 1107 ARG cc_start: 0.7612 (mtt180) cc_final: 0.7196 (mtt-85) REVERT: G 1136 THR cc_start: 0.8331 (OUTLIER) cc_final: 0.8051 (p) outliers start: 177 outliers final: 136 residues processed: 617 average time/residue: 0.4561 time to fit residues: 439.0322 Evaluate side-chains 627 residues out of total 3264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 153 poor density : 474 time to evaluate : 3.248 ------------------------------------------------------------------------------- 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 229 LEU Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 312 ILE 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 705 VAL 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 934 ILE Chi-restraints excluded: chain A residue 968 SER Chi-restraints excluded: chain A residue 969 LYS 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 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 87 ASN 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 127 VAL Chi-restraints excluded: chain D residue 132 GLU Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 188 ARG 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 274 THR Chi-restraints excluded: chain D residue 346 ARG 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 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 725 GLU 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 947 LYS Chi-restraints excluded: chain D residue 1041 ASP Chi-restraints excluded: chain D residue 1066 THR 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 128 GLN 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 63 THR 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 128 ILE Chi-restraints excluded: chain G residue 171 VAL Chi-restraints excluded: chain G residue 186 ASN Chi-restraints excluded: chain G residue 203 SER Chi-restraints excluded: chain G residue 229 LEU Chi-restraints excluded: chain G residue 240 THR Chi-restraints excluded: chain G residue 281 GLU Chi-restraints excluded: chain G residue 298 GLU Chi-restraints excluded: chain G residue 351 TYR Chi-restraints excluded: chain G residue 353 TRP Chi-restraints excluded: chain G residue 375 PHE Chi-restraints excluded: chain G residue 383 SER Chi-restraints excluded: chain G residue 400 PHE 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 553 THR Chi-restraints excluded: chain G residue 569 ILE Chi-restraints excluded: chain G residue 588 THR Chi-restraints excluded: chain G residue 590 CYS 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 856 LYS Chi-restraints excluded: chain G residue 935 GLN Chi-restraints excluded: chain G residue 947 LYS Chi-restraints excluded: chain G residue 950 ASP Chi-restraints excluded: chain G residue 964 LYS Chi-restraints excluded: chain G residue 976 VAL Chi-restraints excluded: chain G residue 980 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 1136 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 319 optimal weight: 0.9990 chunk 100 optimal weight: 2.9990 chunk 159 optimal weight: 0.8980 chunk 147 optimal weight: 0.0470 chunk 119 optimal weight: 10.0000 chunk 328 optimal weight: 0.7980 chunk 46 optimal weight: 2.9990 chunk 308 optimal weight: 3.9990 chunk 273 optimal weight: 0.5980 chunk 165 optimal weight: 2.9990 chunk 85 optimal weight: 3.9990 overall best weight: 0.6680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 532 ASN A 965 GLN ** B 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 121 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 935 GLN ** D 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1125 ASN ** F 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 641 ASN G1005 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4360 r_free = 0.4360 target = 0.200094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.144668 restraints weight = 41137.698| |-----------------------------------------------------------------------------| r_work (start): 0.3638 rms_B_bonded: 2.72 r_work: 0.3495 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3336 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7486 moved from start: 0.4035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 30193 Z= 0.140 Angle : 0.625 13.839 41191 Z= 0.315 Chirality : 0.045 0.371 4712 Planarity : 0.005 0.103 5285 Dihedral : 6.455 79.670 4691 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.05 % Allowed : 9.19 % Favored : 90.76 % Rotamer: Outliers : 5.10 % Allowed : 19.39 % Favored : 75.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.48 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.15 (0.14), residues: 3700 helix: 0.65 (0.22), residues: 651 sheet: -1.09 (0.17), residues: 876 loop : -2.35 (0.13), residues: 2173 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.001 TRP A 64 HIS 0.003 0.001 HIS G1088 PHE 0.061 0.002 PHE D 192 TYR 0.035 0.001 TYR G 351 ARG 0.006 0.000 ARG D1019 Details of bonding type rmsd link_NAG-ASN : bond 0.00455 ( 24) link_NAG-ASN : angle 2.84607 ( 72) hydrogen bonds : bond 0.03260 ( 744) hydrogen bonds : angle 4.56013 ( 1980) SS BOND : bond 0.00303 ( 45) SS BOND : angle 2.00271 ( 90) covalent geometry : bond 0.00332 (30124) covalent geometry : angle 0.60730 (41029) ********************** 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 643 residues out of total 3264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 164 poor density : 479 time to evaluate : 3.269 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 VAL cc_start: 0.8755 (t) cc_final: 0.8522 (m) REVERT: A 116 SER cc_start: 0.8480 (t) cc_final: 0.8170 (p) REVERT: A 212 GLU cc_start: 0.6923 (OUTLIER) cc_final: 0.6399 (mm-30) REVERT: A 220 PHE cc_start: 0.8206 (t80) cc_final: 0.7808 (t80) REVERT: A 269 TYR cc_start: 0.8322 (m-80) cc_final: 0.7998 (m-80) REVERT: A 290 ASP cc_start: 0.7584 (t70) cc_final: 0.7374 (t0) REVERT: A 317 ASN cc_start: 0.7907 (m-40) cc_final: 0.7596 (m110) REVERT: A 324 GLU cc_start: 0.6908 (tm-30) cc_final: 0.6354 (tm-30) REVERT: A 325 SER cc_start: 0.8183 (m) cc_final: 0.7068 (t) REVERT: A 517 LEU cc_start: 0.3247 (OUTLIER) cc_final: 0.2876 (tm) REVERT: A 558 LYS cc_start: 0.7832 (mmtm) cc_final: 0.7413 (mmmt) REVERT: A 572 THR cc_start: 0.7912 (t) cc_final: 0.7495 (p) REVERT: A 675 GLN cc_start: 0.7118 (mm-40) cc_final: 0.6780 (mm-40) REVERT: A 762 GLN cc_start: 0.8225 (mt0) cc_final: 0.7960 (mt0) REVERT: A 765 ARG cc_start: 0.8131 (ttp-110) cc_final: 0.7861 (mtm-85) REVERT: A 776 LYS cc_start: 0.8503 (ttpt) cc_final: 0.8118 (ttpt) REVERT: A 787 GLN cc_start: 0.8485 (mm-40) cc_final: 0.8047 (mt0) REVERT: A 795 LYS cc_start: 0.8234 (mptm) cc_final: 0.7917 (mptt) REVERT: A 949 GLN cc_start: 0.8512 (mm-40) cc_final: 0.8301 (mm-40) REVERT: A 960 ASN cc_start: 0.8357 (t0) cc_final: 0.8116 (t0) REVERT: A 969 LYS cc_start: 0.8409 (OUTLIER) cc_final: 0.7681 (pptt) REVERT: A 1017 GLU cc_start: 0.8050 (tm-30) cc_final: 0.7804 (tm-30) REVERT: A 1019 ARG cc_start: 0.7737 (ttm110) cc_final: 0.7504 (ttp80) REVERT: A 1038 LYS cc_start: 0.8596 (OUTLIER) cc_final: 0.8344 (mtmt) REVERT: A 1073 LYS cc_start: 0.8459 (mtmt) cc_final: 0.8118 (mtmm) REVERT: B 121 LEU cc_start: 0.2168 (OUTLIER) cc_final: 0.1913 (tt) REVERT: D 92 PHE cc_start: 0.8290 (t80) cc_final: 0.8007 (t80) REVERT: D 96 GLU cc_start: 0.6431 (tt0) cc_final: 0.5857 (tt0) REVERT: D 105 ILE cc_start: 0.8558 (OUTLIER) cc_final: 0.8196 (mt) REVERT: D 290 ASP cc_start: 0.7954 (t70) cc_final: 0.7641 (t0) REVERT: D 319 ARG cc_start: 0.8218 (ttm170) cc_final: 0.7939 (ttm-80) REVERT: D 346 ARG cc_start: 0.7748 (OUTLIER) cc_final: 0.7434 (mtp180) REVERT: D 524 VAL cc_start: 0.6122 (OUTLIER) cc_final: 0.5910 (p) REVERT: D 599 THR cc_start: 0.8283 (m) cc_final: 0.7970 (p) REVERT: D 704 SER cc_start: 0.8711 (t) cc_final: 0.8498 (p) REVERT: D 705 VAL cc_start: 0.8613 (t) cc_final: 0.8384 (p) REVERT: D 730 SER cc_start: 0.8685 (t) cc_final: 0.8471 (m) REVERT: D 790 LYS cc_start: 0.8260 (mtpp) cc_final: 0.8039 (mtpp) REVERT: D 808 ASP cc_start: 0.7628 (t0) cc_final: 0.7021 (p0) REVERT: D 816 SER cc_start: 0.8510 (p) cc_final: 0.8234 (t) REVERT: D 848 ASP cc_start: 0.7789 (p0) cc_final: 0.7554 (p0) REVERT: D 947 LYS cc_start: 0.8610 (OUTLIER) cc_final: 0.8346 (mtpt) REVERT: D 988 GLU cc_start: 0.7149 (OUTLIER) cc_final: 0.6446 (tm-30) REVERT: D 990 GLU cc_start: 0.7974 (mp0) cc_final: 0.7534 (mp0) REVERT: D 1118 ASP cc_start: 0.8017 (t0) cc_final: 0.7596 (t0) REVERT: D 1139 ASP cc_start: 0.8017 (p0) cc_final: 0.7647 (p0) REVERT: F 200 GLU cc_start: 0.0704 (OUTLIER) cc_final: 0.0255 (pm20) REVERT: G 47 VAL cc_start: 0.8568 (OUTLIER) cc_final: 0.8331 (t) REVERT: G 63 THR cc_start: 0.8011 (OUTLIER) cc_final: 0.6968 (t) REVERT: G 81 ASN cc_start: 0.7066 (OUTLIER) cc_final: 0.6506 (p0) REVERT: G 129 LYS cc_start: 0.8321 (ptpt) cc_final: 0.7710 (ptmm) REVERT: G 186 ASN cc_start: 0.7402 (OUTLIER) cc_final: 0.6987 (p0) REVERT: G 239 GLN cc_start: 0.7710 (tp-100) cc_final: 0.7118 (tp-100) REVERT: G 370 ASN cc_start: 0.6954 (OUTLIER) cc_final: 0.6663 (p0) REVERT: G 478 LYS cc_start: 0.3600 (OUTLIER) cc_final: 0.3073 (tmmt) REVERT: G 486 PHE cc_start: 0.3650 (OUTLIER) cc_final: 0.3339 (p90) REVERT: G 493 ARG cc_start: 0.6388 (OUTLIER) cc_final: 0.6139 (mmp-170) REVERT: G 655 TYR cc_start: 0.8262 (t80) cc_final: 0.7829 (t80) REVERT: G 752 LEU cc_start: 0.8311 (pp) cc_final: 0.8103 (tt) REVERT: G 803 SER cc_start: 0.8510 (m) cc_final: 0.8227 (p) REVERT: G 855 PHE cc_start: 0.7738 (OUTLIER) cc_final: 0.7074 (t80) REVERT: G 856 LYS cc_start: 0.8455 (OUTLIER) cc_final: 0.8041 (mttp) REVERT: G 884 SER cc_start: 0.8501 (t) cc_final: 0.8215 (p) REVERT: G 900 MET cc_start: 0.8249 (mmm) cc_final: 0.7928 (mmm) REVERT: G 949 GLN cc_start: 0.8603 (mm-40) cc_final: 0.8287 (mm-40) REVERT: G 1107 ARG cc_start: 0.7591 (mtt180) cc_final: 0.7176 (mtt-85) REVERT: G 1136 THR cc_start: 0.8338 (OUTLIER) cc_final: 0.8063 (p) outliers start: 164 outliers final: 135 residues processed: 595 average time/residue: 0.4575 time to fit residues: 430.6567 Evaluate side-chains 627 residues out of total 3264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 157 poor density : 470 time to evaluate : 2.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 63 THR 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 212 GLU 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 301 CYS Chi-restraints excluded: chain A residue 312 ILE 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 569 ILE Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 705 VAL 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 934 ILE Chi-restraints excluded: chain A residue 957 GLN Chi-restraints excluded: chain A residue 968 SER Chi-restraints excluded: chain A residue 969 LYS 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 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 87 ASN 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 121 ASN Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 188 ARG Chi-restraints excluded: chain D residue 210 VAL Chi-restraints excluded: chain D residue 231 ILE Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 274 THR Chi-restraints excluded: chain D residue 346 ARG 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 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 725 GLU 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 935 GLN Chi-restraints excluded: chain D residue 947 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 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 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 128 GLN 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 63 THR 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 128 ILE Chi-restraints excluded: chain G residue 171 VAL Chi-restraints excluded: chain G residue 186 ASN Chi-restraints excluded: chain G residue 203 SER Chi-restraints excluded: chain G residue 229 LEU Chi-restraints excluded: chain G residue 240 THR Chi-restraints excluded: chain G residue 281 GLU Chi-restraints excluded: chain G residue 298 GLU Chi-restraints excluded: chain G residue 370 ASN Chi-restraints excluded: chain G residue 375 PHE Chi-restraints excluded: chain G residue 383 SER Chi-restraints excluded: chain G residue 400 PHE 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 588 THR Chi-restraints excluded: chain G residue 590 CYS 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 855 PHE Chi-restraints excluded: chain G residue 856 LYS Chi-restraints excluded: chain G residue 935 GLN Chi-restraints excluded: chain G residue 947 LYS Chi-restraints excluded: chain G residue 950 ASP Chi-restraints excluded: chain G residue 964 LYS Chi-restraints excluded: chain G residue 976 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 1136 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 207 optimal weight: 3.9990 chunk 100 optimal weight: 2.9990 chunk 64 optimal weight: 0.8980 chunk 185 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 300 optimal weight: 7.9990 chunk 229 optimal weight: 0.9980 chunk 333 optimal weight: 0.5980 chunk 283 optimal weight: 5.9990 chunk 289 optimal weight: 4.9990 chunk 280 optimal weight: 0.4980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 532 ASN ** B 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 115 GLN D 121 ASN ** D 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 66 HIS ** G 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 641 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4352 r_free = 0.4352 target = 0.199264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.144241 restraints weight = 41128.091| |-----------------------------------------------------------------------------| r_work (start): 0.3633 rms_B_bonded: 2.74 r_work: 0.3480 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3321 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7490 moved from start: 0.4103 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= 0.175 Angle : 0.642 13.636 41191 Z= 0.323 Chirality : 0.046 0.384 4712 Planarity : 0.005 0.103 5285 Dihedral : 6.436 79.640 4688 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.03 % Allowed : 9.70 % Favored : 90.27 % Rotamer: Outliers : 5.42 % Allowed : 19.30 % Favored : 75.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.48 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.15 (0.14), residues: 3700 helix: 0.59 (0.22), residues: 658 sheet: -1.04 (0.17), residues: 874 loop : -2.35 (0.13), residues: 2168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.001 TRP A 64 HIS 0.004 0.001 HIS G1088 PHE 0.038 0.002 PHE A 592 TYR 0.033 0.001 TYR D 170 ARG 0.014 0.000 ARG A 319 Details of bonding type rmsd link_NAG-ASN : bond 0.00412 ( 24) link_NAG-ASN : angle 2.86192 ( 72) hydrogen bonds : bond 0.03374 ( 744) hydrogen bonds : angle 4.58682 ( 1980) SS BOND : bond 0.00323 ( 45) SS BOND : angle 2.00083 ( 90) covalent geometry : bond 0.00414 (30124) covalent geometry : angle 0.62486 (41029) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 27910.47 seconds wall clock time: 489 minutes 25.46 seconds (29365.46 seconds total)