Starting phenix.real_space_refine on Sun Aug 9 12:13:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9v2v_64741/08_2026/9v2v_64741.cif Found real_map, /net/cci-nas-00/data/ceres_data/9v2v_64741/08_2026/9v2v_64741.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9v2v_64741/08_2026/9v2v_64741.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9v2v_64741/08_2026/9v2v_64741.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9v2v_64741/08_2026/9v2v_64741.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9v2v_64741/08_2026/9v2v_64741.map" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.009 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: 6 Type Number sf(0) Gaussians Zn 1 6.06 5 P 308 5.49 5 S 113 5.16 5 C 20731 2.51 5 N 6095 2.21 5 O 6993 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 98 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 34241 Number of models: 1 Model: "" Number of chains: 22 Chain: "A" Number of atoms: 4734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 562, 4734 Classifications: {'peptide': 562} Link IDs: {'PTRANS': 13, 'TRANS': 548} Chain breaks: 6 Chain: "B" Number of atoms: 3824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 456, 3824 Classifications: {'peptide': 456} Link IDs: {'PTRANS': 8, 'TRANS': 447} Chain breaks: 7 Chain: "C" Number of atoms: 3054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 385, 3054 Classifications: {'peptide': 385} Link IDs: {'PTRANS': 18, 'TRANS': 366} Chain: "D" Number of atoms: 2929 Number of conformers: 1 Conformer: "" Number of residues, atoms: 369, 2929 Classifications: {'peptide': 369} Link IDs: {'PTRANS': 15, 'TRANS': 353} Chain: "E" Number of atoms: 1022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 1022 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 1, 'TRANS': 117} Chain: "F" Number of atoms: 1392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 1392 Classifications: {'peptide': 166} Link IDs: {'PTRANS': 6, 'TRANS': 159} Chain breaks: 1 Chain: "G" Number of atoms: 1021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 1021 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 5, 'TRANS': 115} Chain: "H" Number of atoms: 1438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1438 Classifications: {'peptide': 180} Link IDs: {'PTRANS': 14, 'TRANS': 165} Chain breaks: 2 Chain: "I" Number of atoms: 864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 864 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 3, 'TRANS': 101} Chain: "J" Number of atoms: 1293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1293 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 7, 'TRANS': 149} Chain breaks: 2 Chain: "K" Number of atoms: 340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 340 Classifications: {'peptide': 40} Link IDs: {'TRANS': 39} Chain breaks: 1 Chain: "O" Number of atoms: 825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 825 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "P" Number of atoms: 730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 730 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "Q" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 811 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 4, 'TRANS': 93} Chain: "R" Number of atoms: 637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 637 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 1, 'TRANS': 77} Chain: "S" Number of atoms: 825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 825 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "T" Number of atoms: 715 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 715 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 2, 'TRANS': 88} Chain: "U" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 800 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 4, 'TRANS': 92} Chain: "V" Number of atoms: 637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 637 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 1, 'TRANS': 77} Chain: "X" Number of atoms: 3195 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 3195 Classifications: {'DNA': 155} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 154} Chain: "Y" Number of atoms: 3154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 3154 Classifications: {'DNA': 155} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 154} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.77, per 1000 atoms: 0.17 Number of scatterers: 34241 At special positions: 0 Unit cell: (136.32, 176.79, 232.88, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 1 29.99 S 113 16.00 P 308 15.00 O 6993 8.00 N 6095 7.00 C 20731 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.55 Conformation dependent library (CDL) restraints added in 853.0 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN C 501 " pdb="ZN ZN C 501 " - pdb=" ND1 HIS C 188 " 6670 Ramachandran restraints generated. 3335 Oldfield, 0 Emsley, 3335 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6498 Finding SS restraints... Secondary structure from input PDB file: 142 helices and 17 sheets defined 56.6% alpha, 3.2% beta 120 base pairs and 272 stacking pairs defined. Time for finding SS restraints: 4.31 Creating SS restraints... Processing helix chain 'A' and resid 663 through 674 Processing helix chain 'A' and resid 678 through 694 removed outlier: 3.766A pdb=" N TYR A 682 " --> pdb=" O ASN A 678 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LEU A 686 " --> pdb=" O TYR A 682 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LYS A 687 " --> pdb=" O THR A 683 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ILE A 688 " --> pdb=" O GLU A 684 " (cutoff:3.500A) Processing helix chain 'A' and resid 698 through 711 removed outlier: 3.938A pdb=" N ASP A 707 " --> pdb=" O VAL A 703 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N PHE A 708 " --> pdb=" O GLU A 704 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N TYR A 709 " --> pdb=" O LYS A 705 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLY A 711 " --> pdb=" O ASP A 707 " (cutoff:3.500A) Processing helix chain 'A' and resid 803 through 839 removed outlier: 3.699A pdb=" N TYR A 820 " --> pdb=" O GLU A 816 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N THR A 833 " --> pdb=" O GLN A 829 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N ILE A 834 " --> pdb=" O CYS A 830 " (cutoff:3.500A) Processing helix chain 'A' and resid 842 through 847 Processing helix chain 'A' and resid 861 through 871 Processing helix chain 'A' and resid 875 through 886 removed outlier: 3.572A pdb=" N ILE A 879 " --> pdb=" O ARG A 875 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 922 removed outlier: 3.547A pdb=" N ALA A 891 " --> pdb=" O PRO A 887 " (cutoff:3.500A) Proline residue: A 892 - end of helix removed outlier: 3.890A pdb=" N ARG A 897 " --> pdb=" O VAL A 893 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLU A 911 " --> pdb=" O ARG A 907 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LYS A 914 " --> pdb=" O ARG A 910 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N VAL A 915 " --> pdb=" O GLU A 911 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLU A 918 " --> pdb=" O LYS A 914 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LYS A 922 " --> pdb=" O GLU A 918 " (cutoff:3.500A) Processing helix chain 'A' and resid 923 through 928 Processing helix chain 'A' and resid 929 through 934 removed outlier: 4.187A pdb=" N THR A 934 " --> pdb=" O HIS A 930 " (cutoff:3.500A) Processing helix chain 'A' and resid 934 through 943 removed outlier: 3.661A pdb=" N LYS A 941 " --> pdb=" O GLN A 937 " (cutoff:3.500A) Processing helix chain 'A' and resid 982 through 997 removed outlier: 4.166A pdb=" N TYR A 986 " --> pdb=" O LYS A 982 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N THR A 994 " --> pdb=" O CYS A 990 " (cutoff:3.500A) Processing helix chain 'A' and resid 1003 through 1023 removed outlier: 3.647A pdb=" N ILE A1018 " --> pdb=" O LEU A1014 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LEU A1020 " --> pdb=" O TYR A1016 " (cutoff:3.500A) Processing helix chain 'A' and resid 1075 through 1080 Processing helix chain 'A' and resid 1144 through 1163 removed outlier: 3.523A pdb=" N GLU A1160 " --> pdb=" O GLU A1156 " (cutoff:3.500A) Processing helix chain 'A' and resid 1164 through 1174 removed outlier: 3.529A pdb=" N GLU A1171 " --> pdb=" O ARG A1167 " (cutoff:3.500A) Processing helix chain 'A' and resid 1178 through 1183 Processing helix chain 'A' and resid 1189 through 1194 Processing helix chain 'A' and resid 1202 through 1217 Processing helix chain 'A' and resid 1220 through 1231 Processing helix chain 'A' and resid 1236 through 1240 removed outlier: 3.680A pdb=" N LEU A1239 " --> pdb=" O ALA A1236 " (cutoff:3.500A) Processing helix chain 'A' and resid 1241 through 1259 removed outlier: 3.694A pdb=" N LEU A1256 " --> pdb=" O HIS A1252 " (cutoff:3.500A) Processing helix chain 'A' and resid 1259 through 1274 Processing helix chain 'A' and resid 1280 through 1294 removed outlier: 3.557A pdb=" N LEU A1288 " --> pdb=" O ILE A1284 " (cutoff:3.500A) Processing helix chain 'A' and resid 1330 through 1343 removed outlier: 3.675A pdb=" N TRP A1334 " --> pdb=" O ASP A1330 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N TYR A1336 " --> pdb=" O ASP A1332 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N THR A1339 " --> pdb=" O LYS A1335 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEU A1343 " --> pdb=" O THR A1339 " (cutoff:3.500A) Processing helix chain 'B' and resid 803 through 814 removed outlier: 4.069A pdb=" N GLU B 812 " --> pdb=" O PHE B 808 " (cutoff:3.500A) Processing helix chain 'B' and resid 815 through 825 removed outlier: 3.648A pdb=" N PHE B 819 " --> pdb=" O HIS B 815 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ILE B 821 " --> pdb=" O TYR B 817 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N GLU B 822 " --> pdb=" O ASP B 818 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ASN B 824 " --> pdb=" O TYR B 820 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LEU B 825 " --> pdb=" O ILE B 821 " (cutoff:3.500A) Processing helix chain 'B' and resid 827 through 839 removed outlier: 3.706A pdb=" N THR B 833 " --> pdb=" O GLN B 829 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N ILE B 834 " --> pdb=" O CYS B 830 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N VAL B 835 " --> pdb=" O LEU B 831 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ASN B 836 " --> pdb=" O GLU B 832 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N LYS B 837 " --> pdb=" O THR B 833 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ILE B 838 " --> pdb=" O ILE B 834 " (cutoff:3.500A) Processing helix chain 'B' and resid 857 through 861 Processing helix chain 'B' and resid 862 through 871 removed outlier: 3.630A pdb=" N ARG B 868 " --> pdb=" O LYS B 864 " (cutoff:3.500A) Processing helix chain 'B' and resid 874 through 876 No H-bonds generated for 'chain 'B' and resid 874 through 876' Processing helix chain 'B' and resid 877 through 886 removed outlier: 3.904A pdb=" N ASP B 881 " --> pdb=" O PHE B 877 " (cutoff:3.500A) Processing helix chain 'B' and resid 890 through 915 removed outlier: 4.131A pdb=" N LEU B 895 " --> pdb=" O ALA B 891 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N LYS B 896 " --> pdb=" O PRO B 892 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N ARG B 897 " --> pdb=" O VAL B 893 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLN B 900 " --> pdb=" O LYS B 896 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLU B 911 " --> pdb=" O ARG B 907 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL B 915 " --> pdb=" O GLU B 911 " (cutoff:3.500A) Processing helix chain 'B' and resid 915 through 920 Processing helix chain 'B' and resid 932 through 942 Processing helix chain 'B' and resid 948 through 952 removed outlier: 3.752A pdb=" N GLU B 951 " --> pdb=" O LEU B 948 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N ILE B 952 " --> pdb=" O ILE B 949 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 948 through 952' Processing helix chain 'B' and resid 953 through 961 removed outlier: 4.118A pdb=" N VAL B 957 " --> pdb=" O SER B 953 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N ASP B 958 " --> pdb=" O SER B 954 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N GLN B 959 " --> pdb=" O ILE B 955 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR B 960 " --> pdb=" O LYS B 956 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ASN B 961 " --> pdb=" O VAL B 957 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 953 through 961' Processing helix chain 'B' and resid 986 through 996 removed outlier: 4.940A pdb=" N THR B 994 " --> pdb=" O CYS B 990 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N PHE B 995 " --> pdb=" O LEU B 991 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ILE B 996 " --> pdb=" O ALA B 992 " (cutoff:3.500A) Processing helix chain 'B' and resid 1004 through 1007 Processing helix chain 'B' and resid 1008 through 1013 Processing helix chain 'B' and resid 1028 through 1032 Processing helix chain 'B' and resid 1141 through 1146 Processing helix chain 'B' and resid 1146 through 1156 removed outlier: 4.021A pdb=" N HIS B1150 " --> pdb=" O ILE B1146 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N THR B1152 " --> pdb=" O PHE B1148 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N TYR B1155 " --> pdb=" O TRP B1151 " (cutoff:3.500A) Processing helix chain 'B' and resid 1164 through 1174 removed outlier: 4.123A pdb=" N THR B1169 " --> pdb=" O ASN B1165 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N LYS B1170 " --> pdb=" O GLU B1166 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLU B1171 " --> pdb=" O ARG B1167 " (cutoff:3.500A) Processing helix chain 'B' and resid 1188 through 1193 removed outlier: 3.730A pdb=" N GLU B1193 " --> pdb=" O GLN B1190 " (cutoff:3.500A) Processing helix chain 'B' and resid 1202 through 1213 removed outlier: 3.938A pdb=" N GLN B1206 " --> pdb=" O ASP B1202 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N VAL B1207 " --> pdb=" O ALA B1203 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ARG B1213 " --> pdb=" O ARG B1209 " (cutoff:3.500A) Processing helix chain 'B' and resid 1226 through 1232 removed outlier: 3.975A pdb=" N GLN B1230 " --> pdb=" O GLU B1226 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA B1231 " --> pdb=" O SER B1227 " (cutoff:3.500A) Processing helix chain 'B' and resid 1251 through 1256 Processing helix chain 'C' and resid 28 through 32 removed outlier: 3.896A pdb=" N TYR C 32 " --> pdb=" O VAL C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 55 removed outlier: 4.040A pdb=" N ARG C 46 " --> pdb=" O PRO C 42 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU C 51 " --> pdb=" O MET C 47 " (cutoff:3.500A) Processing helix chain 'C' and resid 70 through 75 Processing helix chain 'C' and resid 79 through 87 Processing helix chain 'C' and resid 93 through 97 Processing helix chain 'C' and resid 98 through 103 removed outlier: 3.780A pdb=" N VAL C 102 " --> pdb=" O LYS C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 115 through 136 Processing helix chain 'C' and resid 164 through 174 Processing helix chain 'C' and resid 192 through 197 Processing helix chain 'C' and resid 243 through 260 removed outlier: 3.920A pdb=" N VAL C 250 " --> pdb=" O THR C 246 " (cutoff:3.500A) Proline residue: C 253 - end of helix Processing helix chain 'C' and resid 287 through 300 removed outlier: 3.930A pdb=" N CYS C 294 " --> pdb=" O GLY C 290 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N VAL C 295 " --> pdb=" O HIS C 291 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N VAL C 298 " --> pdb=" O CYS C 294 " (cutoff:3.500A) Processing helix chain 'C' and resid 314 through 330 removed outlier: 3.898A pdb=" N ARG C 320 " --> pdb=" O ARG C 316 " (cutoff:3.500A) Processing helix chain 'C' and resid 343 through 347 Processing helix chain 'C' and resid 365 through 381 removed outlier: 3.618A pdb=" N ASN C 379 " --> pdb=" O ASN C 375 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLU C 381 " --> pdb=" O PHE C 377 " (cutoff:3.500A) Processing helix chain 'C' and resid 382 through 384 No H-bonds generated for 'chain 'C' and resid 382 through 384' Processing helix chain 'D' and resid 42 through 49 removed outlier: 4.072A pdb=" N ARG D 46 " --> pdb=" O PRO D 42 " (cutoff:3.500A) Processing helix chain 'D' and resid 50 through 56 Processing helix chain 'D' and resid 70 through 74 removed outlier: 3.559A pdb=" N GLU D 73 " --> pdb=" O THR D 70 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N MET D 74 " --> pdb=" O LYS D 71 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 70 through 74' Processing helix chain 'D' and resid 79 through 87 removed outlier: 3.650A pdb=" N PHE D 85 " --> pdb=" O GLU D 81 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 103 Processing helix chain 'D' and resid 115 through 136 removed outlier: 3.707A pdb=" N SER D 121 " --> pdb=" O TYR D 117 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N SER D 123 " --> pdb=" O TYR D 119 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU D 134 " --> pdb=" O GLY D 130 " (cutoff:3.500A) Processing helix chain 'D' and resid 165 through 173 removed outlier: 3.600A pdb=" N ILE D 171 " --> pdb=" O VAL D 167 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLU D 172 " --> pdb=" O LEU D 168 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LEU D 173 " --> pdb=" O GLY D 169 " (cutoff:3.500A) Processing helix chain 'D' and resid 247 through 259 removed outlier: 3.916A pdb=" N PHE D 251 " --> pdb=" O TYR D 247 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLU D 252 " --> pdb=" O ARG D 248 " (cutoff:3.500A) Proline residue: D 253 - end of helix removed outlier: 3.503A pdb=" N LYS D 256 " --> pdb=" O GLU D 252 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LYS D 257 " --> pdb=" O PRO D 253 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 300 removed outlier: 5.137A pdb=" N CYS D 294 " --> pdb=" O GLY D 290 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N VAL D 295 " --> pdb=" O HIS D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 317 through 330 removed outlier: 3.795A pdb=" N PHE D 324 " --> pdb=" O ARG D 320 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLY D 327 " --> pdb=" O CYS D 323 " (cutoff:3.500A) Processing helix chain 'D' and resid 343 through 348 removed outlier: 3.671A pdb=" N TYR D 347 " --> pdb=" O TYR D 344 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N GLY D 348 " --> pdb=" O GLU D 345 " (cutoff:3.500A) Processing helix chain 'D' and resid 365 through 379 removed outlier: 4.032A pdb=" N LYS D 371 " --> pdb=" O GLU D 367 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N VAL D 372 " --> pdb=" O TYR D 368 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N MET D 373 " --> pdb=" O LEU D 369 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N THR D 374 " --> pdb=" O ASP D 370 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ASN D 375 " --> pdb=" O LYS D 371 " (cutoff:3.500A) Processing helix chain 'D' and resid 380 through 384 removed outlier: 3.794A pdb=" N THR D 383 " --> pdb=" O LEU D 380 " (cutoff:3.500A) Processing helix chain 'E' and resid 178 through 211 removed outlier: 3.830A pdb=" N LEU E 183 " --> pdb=" O ARG E 179 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ILE E 186 " --> pdb=" O ALA E 182 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N ILE E 189 " --> pdb=" O GLU E 185 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ARG E 197 " --> pdb=" O PHE E 193 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLN E 198 " --> pdb=" O ALA E 194 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ARG E 207 " --> pdb=" O ASN E 203 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU E 208 " --> pdb=" O GLN E 204 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N THR E 210 " --> pdb=" O VAL E 206 " (cutoff:3.500A) Processing helix chain 'E' and resid 213 through 218 removed outlier: 3.616A pdb=" N GLY E 218 " --> pdb=" O MET E 214 " (cutoff:3.500A) Processing helix chain 'E' and resid 226 through 283 removed outlier: 4.314A pdb=" N ALA E 232 " --> pdb=" O SER E 228 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N TYR E 236 " --> pdb=" O ALA E 232 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N THR E 259 " --> pdb=" O GLU E 255 " (cutoff:3.500A) Processing helix chain 'E' and resid 284 through 294 removed outlier: 3.669A pdb=" N ASP E 288 " --> pdb=" O GLN E 284 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ILE E 289 " --> pdb=" O THR E 285 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N ASN E 290 " --> pdb=" O TRP E 286 " (cutoff:3.500A) Processing helix chain 'F' and resid 14 through 16 No H-bonds generated for 'chain 'F' and resid 14 through 16' Processing helix chain 'F' and resid 17 through 35 removed outlier: 3.747A pdb=" N SER F 23 " --> pdb=" O PHE F 19 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ILE F 28 " --> pdb=" O LYS F 24 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N TYR F 29 " --> pdb=" O VAL F 25 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N SER F 34 " --> pdb=" O GLN F 30 " (cutoff:3.500A) Processing helix chain 'F' and resid 35 through 52 removed outlier: 3.668A pdb=" N ARG F 43 " --> pdb=" O GLN F 39 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N LEU F 44 " --> pdb=" O TYR F 40 " (cutoff:3.500A) Processing helix chain 'F' and resid 61 through 123 removed outlier: 3.527A pdb=" N ILE F 121 " --> pdb=" O LEU F 117 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLN F 123 " --> pdb=" O SER F 119 " (cutoff:3.500A) Processing helix chain 'F' and resid 123 through 141 removed outlier: 3.568A pdb=" N LYS F 127 " --> pdb=" O GLN F 123 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLU F 130 " --> pdb=" O LYS F 126 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N MET F 135 " --> pdb=" O GLU F 131 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ASP F 136 " --> pdb=" O ARG F 132 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N VAL F 137 " --> pdb=" O LEU F 133 " (cutoff:3.500A) Processing helix chain 'F' and resid 300 through 315 removed outlier: 3.787A pdb=" N GLU F 306 " --> pdb=" O ASP F 302 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ARG F 312 " --> pdb=" O ILE F 308 " (cutoff:3.500A) Processing helix chain 'G' and resid 73 through 88 removed outlier: 3.745A pdb=" N GLN G 77 " --> pdb=" O THR G 73 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N TYR G 79 " --> pdb=" O ALA G 75 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ASN G 82 " --> pdb=" O GLN G 78 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU G 83 " --> pdb=" O TYR G 79 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ILE G 84 " --> pdb=" O ILE G 80 " (cutoff:3.500A) Processing helix chain 'G' and resid 108 through 120 removed outlier: 3.802A pdb=" N LEU G 112 " --> pdb=" O THR G 108 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ASP G 117 " --> pdb=" O ARG G 113 " (cutoff:3.500A) Processing helix chain 'G' and resid 128 through 133 Processing helix chain 'G' and resid 138 through 142 Processing helix chain 'G' and resid 158 through 171 removed outlier: 4.436A pdb=" N VAL G 165 " --> pdb=" O ASP G 161 " (cutoff:3.500A) Processing helix chain 'H' and resid 70 through 76 removed outlier: 3.855A pdb=" N PHE H 75 " --> pdb=" O SER H 71 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N THR H 76 " --> pdb=" O VAL H 72 " (cutoff:3.500A) Processing helix chain 'H' and resid 144 through 153 removed outlier: 4.034A pdb=" N ILE H 148 " --> pdb=" O THR H 144 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ASN H 153 " --> pdb=" O GLN H 149 " (cutoff:3.500A) Processing helix chain 'H' and resid 179 through 184 Processing helix chain 'H' and resid 192 through 197 removed outlier: 4.251A pdb=" N SER H 195 " --> pdb=" O SER H 192 " (cutoff:3.500A) Processing helix chain 'I' and resid 13 through 15 No H-bonds generated for 'chain 'I' and resid 13 through 15' Processing helix chain 'I' and resid 16 through 28 Proline residue: I 22 - end of helix removed outlier: 3.773A pdb=" N TYR I 28 " --> pdb=" O ALA I 24 " (cutoff:3.500A) Processing helix chain 'I' and resid 30 through 40 removed outlier: 3.800A pdb=" N GLU I 34 " --> pdb=" O THR I 30 " (cutoff:3.500A) Processing helix chain 'I' and resid 42 through 55 removed outlier: 3.601A pdb=" N LYS I 55 " --> pdb=" O ASP I 51 " (cutoff:3.500A) Processing helix chain 'I' and resid 62 through 115 removed outlier: 3.655A pdb=" N LEU I 68 " --> pdb=" O THR I 64 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LEU I 69 " --> pdb=" O GLN I 65 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N LYS I 74 " --> pdb=" O ASN I 70 " (cutoff:3.500A) Proline residue: I 81 - end of helix removed outlier: 3.575A pdb=" N SER I 91 " --> pdb=" O MET I 87 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N ARG I 99 " --> pdb=" O ASP I 95 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL I 110 " --> pdb=" O LEU I 106 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ILE I 112 " --> pdb=" O TYR I 108 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N LYS I 113 " --> pdb=" O GLU I 109 " (cutoff:3.500A) Processing helix chain 'J' and resid 188 through 219 removed outlier: 3.637A pdb=" N ALA J 194 " --> pdb=" O LEU J 190 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N SER J 207 " --> pdb=" O LYS J 203 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ARG J 210 " --> pdb=" O MET J 206 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N VAL J 217 " --> pdb=" O GLN J 213 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N PHE J 218 " --> pdb=" O PHE J 214 " (cutoff:3.500A) Processing helix chain 'J' and resid 227 through 232 removed outlier: 3.898A pdb=" N ASN J 232 " --> pdb=" O GLU J 228 " (cutoff:3.500A) Processing helix chain 'J' and resid 286 through 290 Processing helix chain 'J' and resid 330 through 384 removed outlier: 3.904A pdb=" N LEU J 334 " --> pdb=" O GLU J 330 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ASN J 335 " --> pdb=" O GLN J 331 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N GLU J 336 " --> pdb=" O GLN J 332 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLU J 337 " --> pdb=" O GLN J 333 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLU J 339 " --> pdb=" O ASN J 335 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N SER J 340 " --> pdb=" O GLU J 336 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU J 377 " --> pdb=" O ARG J 373 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ASN J 378 " --> pdb=" O GLY J 374 " (cutoff:3.500A) Processing helix chain 'K' and resid 244 through 252 removed outlier: 3.517A pdb=" N GLU K 249 " --> pdb=" O MET K 245 " (cutoff:3.500A) Processing helix chain 'K' and resid 463 through 479 removed outlier: 3.703A pdb=" N VAL K 467 " --> pdb=" O ASN K 463 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLU K 468 " --> pdb=" O GLN K 464 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N VAL K 470 " --> pdb=" O PHE K 466 " (cutoff:3.500A) Processing helix chain 'O' and resid 16 through 21 Processing helix chain 'O' and resid 26 through 36 Processing helix chain 'O' and resid 46 through 73 Processing helix chain 'O' and resid 79 through 90 removed outlier: 3.616A pdb=" N ASN O 89 " --> pdb=" O LEU O 85 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ASP O 90 " --> pdb=" O ALA O 86 " (cutoff:3.500A) Processing helix chain 'O' and resid 90 through 97 Processing helix chain 'O' and resid 112 through 116 Processing helix chain 'P' and resid 34 through 46 removed outlier: 3.601A pdb=" N GLN P 44 " --> pdb=" O LYS P 40 " (cutoff:3.500A) Processing helix chain 'P' and resid 52 through 81 removed outlier: 3.660A pdb=" N ILE P 58 " --> pdb=" O LYS P 54 " (cutoff:3.500A) Processing helix chain 'P' and resid 87 through 99 Processing helix chain 'P' and resid 100 through 120 removed outlier: 3.755A pdb=" N SER P 120 " --> pdb=" O THR P 116 " (cutoff:3.500A) Processing helix chain 'Q' and resid 44 through 56 Processing helix chain 'Q' and resid 63 through 77 removed outlier: 3.728A pdb=" N ASP Q 77 " --> pdb=" O GLU Q 73 " (cutoff:3.500A) Processing helix chain 'Q' and resid 85 through 114 Processing helix chain 'Q' and resid 120 through 131 removed outlier: 3.916A pdb=" N ILE Q 124 " --> pdb=" O MET Q 120 " (cutoff:3.500A) Processing helix chain 'R' and resid 25 through 29 Processing helix chain 'R' and resid 30 through 41 Processing helix chain 'R' and resid 50 through 76 removed outlier: 3.724A pdb=" N ASN R 64 " --> pdb=" O VAL R 60 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ARG R 67 " --> pdb=" O GLU R 63 " (cutoff:3.500A) Processing helix chain 'R' and resid 82 through 92 Processing helix chain 'S' and resid 16 through 22 Processing helix chain 'S' and resid 26 through 36 Processing helix chain 'S' and resid 46 through 65 Processing helix chain 'S' and resid 65 through 73 Processing helix chain 'S' and resid 79 through 90 removed outlier: 3.563A pdb=" N LEU S 83 " --> pdb=" O ILE S 79 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ASN S 89 " --> pdb=" O LEU S 85 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ASP S 90 " --> pdb=" O ALA S 86 " (cutoff:3.500A) Processing helix chain 'S' and resid 92 through 97 Processing helix chain 'T' and resid 34 through 46 removed outlier: 3.998A pdb=" N GLN T 44 " --> pdb=" O LYS T 40 " (cutoff:3.500A) Processing helix chain 'T' and resid 52 through 81 removed outlier: 3.513A pdb=" N ILE T 70 " --> pdb=" O VAL T 66 " (cutoff:3.500A) Processing helix chain 'T' and resid 87 through 99 Processing helix chain 'T' and resid 101 through 118 removed outlier: 3.507A pdb=" N SER T 109 " --> pdb=" O LYS T 105 " (cutoff:3.500A) Processing helix chain 'U' and resid 44 through 56 removed outlier: 3.684A pdb=" N LYS U 56 " --> pdb=" O ARG U 52 " (cutoff:3.500A) Processing helix chain 'U' and resid 63 through 76 Processing helix chain 'U' and resid 85 through 114 removed outlier: 3.508A pdb=" N ALA U 98 " --> pdb=" O GLU U 94 " (cutoff:3.500A) Processing helix chain 'U' and resid 120 through 132 removed outlier: 3.704A pdb=" N ILE U 124 " --> pdb=" O MET U 120 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ARG U 131 " --> pdb=" O ALA U 127 " (cutoff:3.500A) Processing helix chain 'V' and resid 25 through 29 Processing helix chain 'V' and resid 30 through 41 Processing helix chain 'V' and resid 50 through 76 removed outlier: 3.724A pdb=" N ASN V 64 " --> pdb=" O VAL V 60 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ARG V 67 " --> pdb=" O GLU V 63 " (cutoff:3.500A) Processing helix chain 'V' and resid 82 through 92 Processing sheet with id=AA1, first strand: chain 'A' and resid 977 through 978 removed outlier: 3.699A pdb=" N MET A1300 " --> pdb=" O ILE A1317 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 1300 through 1303 removed outlier: 3.562A pdb=" N MET B1300 " --> pdb=" O ILE B1317 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLN B1315 " --> pdb=" O ARG B1302 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 21 through 23 Processing sheet with id=AA4, first strand: chain 'C' and resid 234 through 238 removed outlier: 7.466A pdb=" N VAL C 234 " --> pdb=" O VAL C 203 " (cutoff:3.500A) removed outlier: 5.793A pdb=" N THR C 205 " --> pdb=" O VAL C 234 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N VAL C 236 " --> pdb=" O THR C 205 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N SER C 207 " --> pdb=" O VAL C 236 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N LEU C 238 " --> pdb=" O SER C 207 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N HIS C 209 " --> pdb=" O LEU C 238 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N LEU C 181 " --> pdb=" O VAL C 268 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N GLN C 270 " --> pdb=" O LEU C 181 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N ILE C 183 " --> pdb=" O GLN C 270 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N VAL C 267 " --> pdb=" O MET C 306 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N VAL C 308 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N LEU C 269 " --> pdb=" O VAL C 308 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 62 through 64 removed outlier: 6.157A pdb=" N VAL D 21 " --> pdb=" O GLU D 62 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N TYR D 64 " --> pdb=" O VAL D 21 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N TYR D 23 " --> pdb=" O TYR D 64 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N ALA D 142 " --> pdb=" O VAL D 307 " (cutoff:3.500A) removed outlier: 5.749A pdb=" N VAL D 267 " --> pdb=" O MET D 306 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N VAL D 308 " --> pdb=" O VAL D 267 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N ILE D 183 " --> pdb=" O VAL D 268 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N VAL D 180 " --> pdb=" O MET D 204 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N CYS D 206 " --> pdb=" O VAL D 180 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N TYR D 182 " --> pdb=" O CYS D 206 " (cutoff:3.500A) removed outlier: 8.203A pdb=" N PHE D 208 " --> pdb=" O TYR D 182 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N VAL D 236 " --> pdb=" O SER D 207 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N HIS D 209 " --> pdb=" O VAL D 236 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'G' and resid 125 through 126 removed outlier: 5.974A pdb=" N ASP G 125 " --> pdb=" O ILE G 157 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'H' and resid 140 through 141 removed outlier: 3.695A pdb=" N VAL H 228 " --> pdb=" O LEU H 141 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'O' and resid 42 through 43 removed outlier: 7.128A pdb=" N ARG O 42 " --> pdb=" O ILE P 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'O' and resid 77 through 78 Processing sheet with id=AB1, first strand: chain 'O' and resid 100 through 102 Processing sheet with id=AB2, first strand: chain 'Q' and resid 83 through 84 removed outlier: 6.856A pdb=" N ARG Q 83 " --> pdb=" O VAL R 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'Q' and resid 118 through 119 Processing sheet with id=AB4, first strand: chain 'R' and resid 96 through 98 Processing sheet with id=AB5, first strand: chain 'S' and resid 42 through 43 removed outlier: 6.939A pdb=" N ARG S 42 " --> pdb=" O ILE T 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'S' and resid 77 through 78 Processing sheet with id=AB7, first strand: chain 'U' and resid 83 through 84 removed outlier: 6.752A pdb=" N ARG U 83 " --> pdb=" O VAL V 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'U' and resid 118 through 119 1206 hydrogen bonds defined for protein. 3528 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 287 hydrogen bonds 510 hydrogen bond angles 0 basepair planarities 120 basepair parallelities 272 stacking parallelities Total time for adding SS restraints: 9.19 Time building geometry restraints manager: 3.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 6669 1.32 - 1.45: 10852 1.45 - 1.57: 17281 1.57 - 1.69: 567 1.69 - 1.82: 187 Bond restraints: 35556 Sorted by residual: bond pdb=" C1' DC Y 8 " pdb=" N1 DC Y 8 " ideal model delta sigma weight residual 1.468 1.350 0.118 1.40e-02 5.10e+03 7.14e+01 bond pdb=" C3' DA X -13 " pdb=" O3' DA X -13 " ideal model delta sigma weight residual 1.435 1.331 0.104 1.30e-02 5.92e+03 6.43e+01 bond pdb=" C3' DC Y -4 " pdb=" O3' DC Y -4 " ideal model delta sigma weight residual 1.435 1.333 0.102 1.30e-02 5.92e+03 6.19e+01 bond pdb=" C3' DC X 7 " pdb=" O3' DC X 7 " ideal model delta sigma weight residual 1.435 1.333 0.102 1.30e-02 5.92e+03 6.13e+01 bond pdb=" C3' DG X 8 " pdb=" O3' DG X 8 " ideal model delta sigma weight residual 1.435 1.334 0.101 1.30e-02 5.92e+03 6.00e+01 ... (remaining 35551 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.16: 45467 2.16 - 4.31: 3309 4.31 - 6.47: 419 6.47 - 8.62: 83 8.62 - 10.78: 24 Bond angle restraints: 49302 Sorted by residual: angle pdb=" N ALA B1275 " pdb=" CA ALA B1275 " pdb=" C ALA B1275 " ideal model delta sigma weight residual 114.75 104.13 10.62 1.26e+00 6.30e-01 7.10e+01 angle pdb=" N VAL T 41 " pdb=" CA VAL T 41 " pdb=" C VAL T 41 " ideal model delta sigma weight residual 113.42 104.38 9.04 1.17e+00 7.31e-01 5.96e+01 angle pdb=" N ASN A1143 " pdb=" CA ASN A1143 " pdb=" C ASN A1143 " ideal model delta sigma weight residual 114.75 105.17 9.58 1.26e+00 6.30e-01 5.78e+01 angle pdb=" N HIS G 153 " pdb=" CA HIS G 153 " pdb=" C HIS G 153 " ideal model delta sigma weight residual 114.64 104.06 10.58 1.52e+00 4.33e-01 4.84e+01 angle pdb=" N HIS A 857 " pdb=" CA HIS A 857 " pdb=" C HIS A 857 " ideal model delta sigma weight residual 114.56 106.22 8.34 1.27e+00 6.20e-01 4.32e+01 ... (remaining 49297 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.52: 19067 35.52 - 71.03: 1574 71.03 - 106.55: 24 106.55 - 142.06: 1 142.06 - 177.58: 1 Dihedral angle restraints: 20667 sinusoidal: 10628 harmonic: 10039 Sorted by residual: dihedral pdb=" CA TYR C 347 " pdb=" C TYR C 347 " pdb=" N GLY C 348 " pdb=" CA GLY C 348 " ideal model delta harmonic sigma weight residual 180.00 150.80 29.20 0 5.00e+00 4.00e-02 3.41e+01 dihedral pdb=" CA LEU J 170 " pdb=" C LEU J 170 " pdb=" N SER J 171 " pdb=" CA SER J 171 " ideal model delta harmonic sigma weight residual -180.00 -151.77 -28.23 0 5.00e+00 4.00e-02 3.19e+01 dihedral pdb=" CA LEU E 216 " pdb=" C LEU E 216 " pdb=" N GLU E 217 " pdb=" CA GLU E 217 " ideal model delta harmonic sigma weight residual -180.00 -152.73 -27.27 0 5.00e+00 4.00e-02 2.98e+01 ... (remaining 20664 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.094: 4339 0.094 - 0.189: 998 0.189 - 0.283: 100 0.283 - 0.378: 5 0.378 - 0.472: 1 Chirality restraints: 5443 Sorted by residual: chirality pdb=" CB ILE C 242 " pdb=" CA ILE C 242 " pdb=" CG1 ILE C 242 " pdb=" CG2 ILE C 242 " both_signs ideal model delta sigma weight residual False 2.64 2.17 0.47 2.00e-01 2.50e+01 5.58e+00 chirality pdb=" CB VAL T 66 " pdb=" CA VAL T 66 " pdb=" CG1 VAL T 66 " pdb=" CG2 VAL T 66 " both_signs ideal model delta sigma weight residual False -2.63 -2.29 -0.34 2.00e-01 2.50e+01 2.87e+00 chirality pdb=" CB ILE T 51 " pdb=" CA ILE T 51 " pdb=" CG1 ILE T 51 " pdb=" CG2 ILE T 51 " both_signs ideal model delta sigma weight residual False 2.64 2.31 0.34 2.00e-01 2.50e+01 2.86e+00 ... (remaining 5440 not shown) Planarity restraints: 5219 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG G 156 " -0.457 9.50e-02 1.11e+02 2.05e-01 2.57e+01 pdb=" NE ARG G 156 " 0.026 2.00e-02 2.50e+03 pdb=" CZ ARG G 156 " 0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG G 156 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG G 156 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 770 " 0.443 9.50e-02 1.11e+02 1.99e-01 2.42e+01 pdb=" NE ARG B 770 " -0.026 2.00e-02 2.50e+03 pdb=" CZ ARG B 770 " -0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG B 770 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG B 770 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE S 25 " -0.024 2.00e-02 2.50e+03 2.56e-02 1.14e+01 pdb=" CG PHE S 25 " 0.059 2.00e-02 2.50e+03 pdb=" CD1 PHE S 25 " -0.019 2.00e-02 2.50e+03 pdb=" CD2 PHE S 25 " -0.008 2.00e-02 2.50e+03 pdb=" CE1 PHE S 25 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE S 25 " -0.009 2.00e-02 2.50e+03 pdb=" CZ PHE S 25 " -0.001 2.00e-02 2.50e+03 ... (remaining 5216 not shown) Histogram of nonbonded interaction distances: 1.55 - 2.22: 3 2.22 - 2.89: 12924 2.89 - 3.56: 50825 3.56 - 4.23: 94351 4.23 - 4.90: 145171 Nonbonded interactions: 303274 Sorted by model distance: nonbonded pdb=" OD2 ASP C 186 " pdb="ZN ZN C 501 " model vdw 1.548 2.230 nonbonded pdb=" CB ARG F 67 " pdb=" NH2 ARG G 156 " model vdw 1.909 3.520 nonbonded pdb=" N2 DG X 21 " pdb=" O2 DC Y -21 " model vdw 2.215 3.120 nonbonded pdb=" O6 DG X -8 " pdb=" N4 DC Y 8 " model vdw 2.223 3.120 nonbonded pdb=" N4 DC X -9 " pdb=" O6 DG Y 9 " model vdw 2.226 3.120 ... (remaining 303269 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 'C' and resid 16 through 384) selection = chain 'D' } ncs_group { reference = chain 'O' selection = chain 'S' } ncs_group { reference = (chain 'P' and resid 29 through 119) selection = chain 'T' } ncs_group { reference = (chain 'Q' and resid 37 through 133) selection = chain 'U' } ncs_group { reference = chain 'R' selection = chain 'V' } 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: 18.390 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: 0.030 Extract box with map and model: 0.880 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 36.100 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.090 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: 0.000 Load rotamer database and sin/cos tables:8.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 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 : 0.017 0.405 35557 Z= 0.969 Angle : 1.232 10.777 49302 Z= 0.805 Chirality : 0.077 0.472 5443 Planarity : 0.008 0.205 5219 Dihedral : 19.668 177.577 14169 Min Nonbonded Distance : 1.548 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.45 % Allowed : 6.63 % Favored : 92.92 % Rotamer: Outliers : 0.95 % Allowed : 3.84 % Favored : 95.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.31 (0.10), residues: 3335 helix: -3.87 (0.06), residues: 1848 sheet: -2.95 (0.39), residues: 148 loop : -2.80 (0.14), residues: 1339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.002 ARG C 202 TYR 0.057 0.004 TYR C 343 PHE 0.059 0.004 PHE S 25 TRP 0.024 0.003 TRP A1223 HIS 0.020 0.003 HIS C 78 Details of bonding type rmsd/Z covalent geometry : bond 0.01716 / 0.97 (35556) covalent geometry : angle 1.23229 / 0.81 (49302) hydrogen bonds : bond 0.28552 / 18.35 ( 1493) hydrogen bonds : angle 10.30900 / 7.01 ( 4038) metal coordination : bond 0.40516 / 21.32 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6670 Ramachandran restraints generated. 3335 Oldfield, 0 Emsley, 3335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6670 Ramachandran restraints generated. 3335 Oldfield, 0 Emsley, 3335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 720 residues out of total 3044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 691 time to evaluate : 1.175 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1076 LYS cc_start: 0.8785 (mmtp) cc_final: 0.8509 (mmpt) REVERT: A 1261 LYS cc_start: 0.7761 (mmtt) cc_final: 0.7470 (tptp) REVERT: B 881 ASP cc_start: 0.8528 (t0) cc_final: 0.8131 (p0) REVERT: B 1234 ASN cc_start: 0.8737 (t0) cc_final: 0.8476 (t0) REVERT: B 1294 MET cc_start: 0.7929 (ptp) cc_final: 0.7589 (tpp) REVERT: B 1317 ILE cc_start: 0.8050 (mm) cc_final: 0.7638 (mm) REVERT: C 94 LEU cc_start: 0.9083 (tp) cc_final: 0.8880 (tm) REVERT: C 136 ARG cc_start: 0.7844 (mtm110) cc_final: 0.7609 (mtp85) REVERT: D 47 MET cc_start: 0.8635 (mtp) cc_final: 0.8351 (mtp) REVERT: D 197 PHE cc_start: 0.8729 (m-80) cc_final: 0.8339 (m-80) REVERT: D 247 TYR cc_start: 0.8825 (t80) cc_final: 0.8594 (t80) REVERT: D 251 PHE cc_start: 0.8219 (p90) cc_final: 0.7673 (p90) REVERT: D 297 TYR cc_start: 0.8342 (t80) cc_final: 0.7929 (t80) REVERT: D 305 MET cc_start: 0.8497 (ttp) cc_final: 0.7902 (mtt) REVERT: D 306 MET cc_start: 0.7502 (mtp) cc_final: 0.7077 (mtp) REVERT: D 320 ARG cc_start: 0.8771 (mtt180) cc_final: 0.8485 (mtt180) REVERT: D 322 TRP cc_start: 0.9008 (m-10) cc_final: 0.8673 (m-10) REVERT: D 347 TYR cc_start: 0.9160 (m-80) cc_final: 0.8860 (m-80) REVERT: E 233 ILE cc_start: 0.9413 (tp) cc_final: 0.9191 (tp) REVERT: E 266 ASP cc_start: 0.8191 (t0) cc_final: 0.7733 (t0) REVERT: E 270 LYS cc_start: 0.9010 (mttm) cc_final: 0.8578 (mttm) REVERT: F 50 ASP cc_start: 0.8610 (m-30) cc_final: 0.8361 (m-30) REVERT: F 61 GLN cc_start: 0.8651 (tp-100) cc_final: 0.8282 (tm-30) REVERT: G 190 ASN cc_start: 0.2118 (m-40) cc_final: 0.1782 (m110) REVERT: I 33 HIS cc_start: 0.8736 (m-70) cc_final: 0.8212 (m-70) REVERT: I 76 TYR cc_start: 0.8447 (m-80) cc_final: 0.8113 (m-80) REVERT: I 78 GLU cc_start: 0.8512 (pt0) cc_final: 0.7829 (tm-30) REVERT: I 96 ASN cc_start: 0.8310 (t0) cc_final: 0.7233 (t0) REVERT: J 192 ASN cc_start: 0.8357 (p0) cc_final: 0.7868 (t0) REVERT: J 237 ASN cc_start: 0.5918 (m-40) cc_final: 0.5716 (m-40) REVERT: J 350 GLN cc_start: 0.8206 (tt0) cc_final: 0.7688 (tt0) REVERT: J 357 ARG cc_start: 0.8744 (ttp-170) cc_final: 0.8400 (ttp80) REVERT: J 358 ASN cc_start: 0.8232 (m110) cc_final: 0.7917 (m110) REVERT: J 361 LYS cc_start: 0.9399 (mtpp) cc_final: 0.9184 (mtpt) REVERT: K 483 MET cc_start: 0.3422 (tpt) cc_final: 0.3172 (mmm) REVERT: O 15 LYS cc_start: 0.7390 (tmtt) cc_final: 0.7163 (tmmm) REVERT: O 61 GLU cc_start: 0.7818 (mm-30) cc_final: 0.7612 (mm-30) REVERT: O 91 GLU cc_start: 0.7892 (tm-30) cc_final: 0.7515 (tm-30) REVERT: P 31 LYS cc_start: 0.7748 (tptt) cc_final: 0.7213 (tttp) REVERT: P 54 LYS cc_start: 0.8823 (tptt) cc_final: 0.8609 (tppp) REVERT: S 19 SER cc_start: 0.8870 (p) cc_final: 0.8489 (p) REVERT: S 36 LYS cc_start: 0.8561 (mmtm) cc_final: 0.8197 (mmmm) REVERT: S 72 ASP cc_start: 0.8379 (m-30) cc_final: 0.8111 (m-30) REVERT: S 73 ASN cc_start: 0.8312 (m110) cc_final: 0.7921 (m-40) REVERT: U 52 ARG cc_start: 0.7872 (mtt90) cc_final: 0.7578 (mtm110) REVERT: V 93 GLN cc_start: 0.8327 (mt0) cc_final: 0.8084 (mt0) outliers start: 29 outliers final: 13 residues processed: 713 average time/residue: 0.7575 time to fit residues: 632.9471 Evaluate side-chains 468 residues out of total 3044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 455 time to evaluate : 1.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 996 ILE Chi-restraints excluded: chain A residue 1243 ASP Chi-restraints excluded: chain B residue 765 MET Chi-restraints excluded: chain B residue 767 CYS Chi-restraints excluded: chain B residue 771 ASP Chi-restraints excluded: chain B residue 774 CYS Chi-restraints excluded: chain B residue 775 TRP Chi-restraints excluded: chain B residue 1145 TYR Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain D residue 109 ASP Chi-restraints excluded: chain D residue 317 ASN Chi-restraints excluded: chain R residue 96 THR Chi-restraints excluded: chain V residue 96 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 197 optimal weight: 7.9990 chunk 215 optimal weight: 0.0470 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 0.5980 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 0.7980 chunk 207 optimal weight: 0.8980 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 0.0060 chunk 183 optimal weight: 0.7980 chunk 298 optimal weight: 0.7980 overall best weight: 0.4494 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 678 ASN ** A 815 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 836 ASN A 844 ASN A 983 ASN A1252 HIS B 798 HIS B 801 ASN ** B 815 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1247 GLN C 105 ASN C 231 ASN C 317 ASN C 331 ASN ** D 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 54 ASN D 76 GLN D 105 ASN ** D 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 189 HIS D 231 ASN D 375 ASN D 379 ASN E 204 GLN E 209 GLN E 220 HIS E 253 ASN E 280 ASN F 20 ASN F 317 GLN G 82 ASN G 92 HIS G 100 HIS G 126 ASN G 158 HIS H 86 ASN H 149 GLN ** H 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 205 ASN H 209 GLN ** I 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 196 GLN J 213 GLN ** J 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 331 GLN ** J 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 463 ASN O 104 GLN O 110 ASN Q 68 GLN Q 108 ASN ** Q 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 46 HIS Total number of N/Q/H flips: 44 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4332 r_free = 0.4332 target = 0.136135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.097208 restraints weight = 90836.611| |-----------------------------------------------------------------------------| r_work (start): 0.3548 rms_B_bonded: 2.69 r_work: 0.3293 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.2438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 35557 Z= 0.191 Angle : 0.798 11.515 49302 Z= 0.429 Chirality : 0.049 0.265 5443 Planarity : 0.006 0.063 5219 Dihedral : 25.065 177.282 7172 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.43 % Favored : 94.48 % Rotamer: Outliers : 3.02 % Allowed : 11.50 % Favored : 85.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.60 (0.12), residues: 3335 helix: -2.20 (0.09), residues: 1883 sheet: -2.83 (0.37), residues: 156 loop : -2.39 (0.15), residues: 1296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B1273 TYR 0.029 0.002 TYR D 117 PHE 0.027 0.002 PHE B1269 TRP 0.029 0.002 TRP A 912 HIS 0.015 0.001 HIS H 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.19 (35556) covalent geometry : angle 0.79775 / 0.43 (49302) hydrogen bonds : bond 0.08192 / 5.21 ( 1493) hydrogen bonds : angle 5.34944 / 3.62 ( 4038) metal coordination : bond 0.02094 / 1.10 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6670 Ramachandran restraints generated. 3335 Oldfield, 0 Emsley, 3335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6670 Ramachandran restraints generated. 3335 Oldfield, 0 Emsley, 3335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 622 residues out of total 3044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 530 time to evaluate : 1.175 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 986 TYR cc_start: 0.7682 (t80) cc_final: 0.6715 (m-80) REVERT: A 1146 ILE cc_start: 0.8928 (pt) cc_final: 0.8591 (mt) REVERT: A 1156 GLU cc_start: 0.8309 (tp30) cc_final: 0.7914 (tp30) REVERT: A 1261 LYS cc_start: 0.7762 (mmtt) cc_final: 0.7512 (tptp) REVERT: A 1301 PHE cc_start: 0.8708 (m-80) cc_final: 0.8216 (m-80) REVERT: B 774 CYS cc_start: 0.3584 (OUTLIER) cc_final: 0.3377 (p) REVERT: B 881 ASP cc_start: 0.8901 (t0) cc_final: 0.8352 (p0) REVERT: B 916 TRP cc_start: 0.8171 (m-10) cc_final: 0.7556 (m-10) REVERT: B 1257 MET cc_start: 0.7978 (ptp) cc_final: 0.7687 (ppp) REVERT: B 1317 ILE cc_start: 0.7869 (mm) cc_final: 0.7645 (mm) REVERT: C 94 LEU cc_start: 0.9143 (tp) cc_final: 0.8930 (tm) REVERT: C 100 GLU cc_start: 0.8433 (mp0) cc_final: 0.8100 (mp0) REVERT: D 232 TYR cc_start: 0.6601 (m-10) cc_final: 0.6333 (m-10) REVERT: D 247 TYR cc_start: 0.8981 (t80) cc_final: 0.8650 (t80) REVERT: D 251 PHE cc_start: 0.8392 (p90) cc_final: 0.8074 (p90) REVERT: D 259 MET cc_start: 0.8765 (mtp) cc_final: 0.8532 (ptm) REVERT: D 297 TYR cc_start: 0.8359 (t80) cc_final: 0.8012 (t80) REVERT: D 305 MET cc_start: 0.8432 (ttp) cc_final: 0.7934 (mtt) REVERT: D 306 MET cc_start: 0.7806 (mtp) cc_final: 0.7403 (mtp) REVERT: D 322 TRP cc_start: 0.8957 (m-10) cc_final: 0.8528 (m-10) REVERT: D 344 TYR cc_start: 0.8483 (t80) cc_final: 0.8135 (t80) REVERT: D 347 TYR cc_start: 0.9162 (m-80) cc_final: 0.8883 (m-80) REVERT: D 369 LEU cc_start: 0.9165 (mt) cc_final: 0.8776 (pp) REVERT: D 376 ILE cc_start: 0.9439 (mp) cc_final: 0.9214 (mp) REVERT: E 226 TYR cc_start: 0.8430 (p90) cc_final: 0.7859 (p90) REVERT: E 227 TYR cc_start: 0.9098 (m-10) cc_final: 0.8798 (m-10) REVERT: F 50 ASP cc_start: 0.8794 (m-30) cc_final: 0.8590 (m-30) REVERT: F 61 GLN cc_start: 0.8506 (tp-100) cc_final: 0.8116 (tm-30) REVERT: F 85 GLU cc_start: 0.8718 (OUTLIER) cc_final: 0.8332 (mp0) REVERT: F 135 MET cc_start: 0.3136 (mpm) cc_final: 0.2820 (mpm) REVERT: G 168 ARG cc_start: 0.8116 (ptm-80) cc_final: 0.7639 (ptm-80) REVERT: G 183 GLN cc_start: 0.6898 (mm110) cc_final: 0.6693 (mm-40) REVERT: I 78 GLU cc_start: 0.8394 (pt0) cc_final: 0.8063 (pp20) REVERT: I 84 GLU cc_start: 0.8769 (tm-30) cc_final: 0.8489 (tp30) REVERT: I 87 MET cc_start: 0.8409 (ttp) cc_final: 0.7804 (ttp) REVERT: J 228 GLU cc_start: 0.7356 (OUTLIER) cc_final: 0.6605 (tp30) REVERT: J 357 ARG cc_start: 0.9053 (ttp-170) cc_final: 0.8732 (ttp80) REVERT: J 358 ASN cc_start: 0.8305 (m110) cc_final: 0.7956 (m110) REVERT: O 15 LYS cc_start: 0.7525 (tmtt) cc_final: 0.7247 (ttpp) REVERT: P 31 LYS cc_start: 0.7691 (tptt) cc_final: 0.7075 (tttp) REVERT: Q 133 GLU cc_start: 0.8051 (OUTLIER) cc_final: 0.7780 (mt-10) REVERT: S 36 LYS cc_start: 0.8697 (mmtm) cc_final: 0.8319 (mmmm) REVERT: S 71 ARG cc_start: 0.8108 (mtm110) cc_final: 0.7810 (mtt-85) REVERT: S 72 ASP cc_start: 0.8501 (m-30) cc_final: 0.8266 (m-30) REVERT: S 73 ASN cc_start: 0.8267 (m110) cc_final: 0.7919 (m-40) REVERT: T 83 ARG cc_start: 0.8708 (OUTLIER) cc_final: 0.7509 (mtt-85) REVERT: U 42 ARG cc_start: 0.7996 (mtm-85) cc_final: 0.7254 (mtt-85) REVERT: U 52 ARG cc_start: 0.8351 (mtt90) cc_final: 0.7966 (mtm110) REVERT: U 94 GLU cc_start: 0.8671 (mm-30) cc_final: 0.8354 (mm-30) REVERT: V 50 ILE cc_start: 0.8450 (tt) cc_final: 0.8163 (tt) REVERT: V 59 LYS cc_start: 0.8932 (tttm) cc_final: 0.8729 (ttpt) outliers start: 92 outliers final: 27 residues processed: 574 average time/residue: 0.6379 time to fit residues: 437.5088 Evaluate side-chains 467 residues out of total 3044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 435 time to evaluate : 0.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1180 PHE Chi-restraints excluded: chain B residue 771 ASP Chi-restraints excluded: chain B residue 774 CYS Chi-restraints excluded: chain B residue 775 TRP Chi-restraints excluded: chain B residue 912 TRP Chi-restraints excluded: chain B residue 1024 ILE Chi-restraints excluded: chain D residue 108 ASP Chi-restraints excluded: chain D residue 123 SER Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain D residue 199 THR Chi-restraints excluded: chain D residue 249 SER Chi-restraints excluded: chain D residue 267 VAL Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain E residue 233 ILE Chi-restraints excluded: chain F residue 85 GLU Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain I residue 20 GLU Chi-restraints excluded: chain I residue 39 CYS Chi-restraints excluded: chain J residue 228 GLU Chi-restraints excluded: chain J residue 286 ASP Chi-restraints excluded: chain P residue 75 SER Chi-restraints excluded: chain P residue 110 GLU Chi-restraints excluded: chain Q residue 68 GLN Chi-restraints excluded: chain Q residue 133 GLU Chi-restraints excluded: chain R residue 49 LEU Chi-restraints excluded: chain R residue 96 THR Chi-restraints excluded: chain T residue 81 ASN Chi-restraints excluded: chain T residue 83 ARG Chi-restraints excluded: chain T residue 87 THR Chi-restraints excluded: chain T residue 102 GLU Chi-restraints excluded: chain U residue 58 THR Chi-restraints excluded: chain V residue 31 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 69 optimal weight: 1.9990 chunk 275 optimal weight: 0.5980 chunk 247 optimal weight: 3.9990 chunk 249 optimal weight: 0.7980 chunk 234 optimal weight: 0.7980 chunk 115 optimal weight: 3.9990 chunk 206 optimal weight: 0.9990 chunk 4 optimal weight: 8.9990 chunk 45 optimal weight: 0.0470 chunk 280 optimal weight: 4.9990 chunk 86 optimal weight: 9.9990 overall best weight: 0.6480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 829 GLN A1222 GLN ** B1137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 43 HIS ** D 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 359 ASN ** I 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 178 HIS J 196 GLN J 331 GLN ** J 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 350 GLN J 360 GLN P 46 HIS ** Q 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 44 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.135894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.095208 restraints weight = 90642.688| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 2.68 r_work: 0.3265 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.2943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 35557 Z= 0.169 Angle : 0.698 9.348 49302 Z= 0.377 Chirality : 0.045 0.265 5443 Planarity : 0.005 0.050 5219 Dihedral : 25.006 176.330 7156 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 11.89 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.67 % Favored : 94.30 % Rotamer: Outliers : 2.83 % Allowed : 14.13 % Favored : 83.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.56 (0.13), residues: 3335 helix: -1.18 (0.11), residues: 1869 sheet: -2.61 (0.37), residues: 166 loop : -2.21 (0.15), residues: 1300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG Q 72 TYR 0.024 0.002 TYR D 55 PHE 0.029 0.002 PHE B1269 TRP 0.022 0.001 TRP A 912 HIS 0.012 0.001 HIS C 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.17 (35556) covalent geometry : angle 0.69772 / 0.38 (49302) hydrogen bonds : bond 0.07256 / 4.65 ( 1493) hydrogen bonds : angle 4.76370 / 3.21 ( 4038) metal coordination : bond 0.00055 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6670 Ramachandran restraints generated. 3335 Oldfield, 0 Emsley, 3335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6670 Ramachandran restraints generated. 3335 Oldfield, 0 Emsley, 3335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 569 residues out of total 3044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 483 time to evaluate : 0.853 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: A 757 ARG cc_start: 0.7910 (tpt-90) cc_final: 0.7628 (tpt-90) REVERT: A 811 GLU cc_start: 0.8430 (tt0) cc_final: 0.7912 (tt0) REVERT: A 986 TYR cc_start: 0.7569 (t80) cc_final: 0.6639 (m-80) REVERT: A 1016 TYR cc_start: 0.6907 (m-10) cc_final: 0.6676 (m-80) REVERT: A 1156 GLU cc_start: 0.8290 (tp30) cc_final: 0.7858 (tp30) REVERT: A 1222 GLN cc_start: 0.8403 (OUTLIER) cc_final: 0.8200 (pt0) REVERT: A 1261 LYS cc_start: 0.7731 (mmtt) cc_final: 0.7509 (tptp) REVERT: A 1301 PHE cc_start: 0.8655 (m-80) cc_final: 0.8262 (m-80) REVERT: A 1316 TYR cc_start: 0.7645 (p90) cc_final: 0.7273 (p90) REVERT: B 821 ILE cc_start: 0.8358 (OUTLIER) cc_final: 0.8016 (tp) REVERT: B 881 ASP cc_start: 0.8852 (t0) cc_final: 0.8334 (p0) REVERT: B 895 LEU cc_start: 0.8897 (OUTLIER) cc_final: 0.8694 (mp) REVERT: B 916 TRP cc_start: 0.8287 (m-10) cc_final: 0.7550 (m-10) REVERT: B 1150 HIS cc_start: 0.7786 (m170) cc_final: 0.7493 (m-70) REVERT: B 1232 TYR cc_start: 0.7718 (t80) cc_final: 0.7459 (t80) REVERT: B 1257 MET cc_start: 0.7900 (ptp) cc_final: 0.7535 (ppp) REVERT: B 1317 ILE cc_start: 0.7756 (mm) cc_final: 0.7265 (mm) REVERT: C 100 GLU cc_start: 0.8508 (mp0) cc_final: 0.8167 (mp0) REVERT: D 40 MET cc_start: 0.3903 (mmm) cc_final: 0.3527 (tpp) REVERT: D 232 TYR cc_start: 0.6477 (m-10) cc_final: 0.6272 (m-10) REVERT: D 247 TYR cc_start: 0.9018 (t80) cc_final: 0.8313 (t80) REVERT: D 251 PHE cc_start: 0.8349 (p90) cc_final: 0.7989 (p90) REVERT: D 255 ILE cc_start: 0.9520 (mm) cc_final: 0.9136 (mt) REVERT: D 259 MET cc_start: 0.8779 (mtp) cc_final: 0.8566 (ptm) REVERT: D 288 MET cc_start: 0.8789 (ptt) cc_final: 0.8527 (ptt) REVERT: D 297 TYR cc_start: 0.8448 (t80) cc_final: 0.7986 (t80) REVERT: D 305 MET cc_start: 0.8429 (ttp) cc_final: 0.7959 (mtt) REVERT: D 344 TYR cc_start: 0.8461 (t80) cc_final: 0.8109 (t80) REVERT: D 347 TYR cc_start: 0.9140 (m-80) cc_final: 0.8910 (m-80) REVERT: D 376 ILE cc_start: 0.9415 (mp) cc_final: 0.9180 (mp) REVERT: E 226 TYR cc_start: 0.8488 (p90) cc_final: 0.8214 (p90) REVERT: E 227 TYR cc_start: 0.9058 (m-10) cc_final: 0.8787 (m-10) REVERT: E 270 LYS cc_start: 0.8803 (mttp) cc_final: 0.8512 (mtmt) REVERT: E 286 TRP cc_start: 0.7778 (OUTLIER) cc_final: 0.7003 (t60) REVERT: F 50 ASP cc_start: 0.8728 (m-30) cc_final: 0.8425 (m-30) REVERT: F 65 GLN cc_start: 0.9106 (mt0) cc_final: 0.8889 (mt0) REVERT: F 85 GLU cc_start: 0.8780 (OUTLIER) cc_final: 0.8356 (mp0) REVERT: G 168 ARG cc_start: 0.8140 (ptm-80) cc_final: 0.7777 (ptm-80) REVERT: I 84 GLU cc_start: 0.8821 (tm-30) cc_final: 0.8499 (tp30) REVERT: J 206 MET cc_start: 0.8643 (OUTLIER) cc_final: 0.8253 (mmm) REVERT: J 346 GLN cc_start: 0.8197 (tm-30) cc_final: 0.7959 (tm-30) REVERT: J 351 ARG cc_start: 0.8270 (mtt180) cc_final: 0.8029 (mtt90) REVERT: J 357 ARG cc_start: 0.9056 (ttp-170) cc_final: 0.8739 (ttp80) REVERT: J 378 ASN cc_start: 0.8633 (m-40) cc_final: 0.7885 (p0) REVERT: O 74 LYS cc_start: 0.8842 (mmtt) cc_final: 0.8608 (tppt) REVERT: O 91 GLU cc_start: 0.8502 (tm-30) cc_final: 0.8223 (tm-30) REVERT: P 31 LYS cc_start: 0.7687 (tptt) cc_final: 0.7070 (tttp) REVERT: Q 133 GLU cc_start: 0.8086 (OUTLIER) cc_final: 0.7795 (mt-10) REVERT: S 36 LYS cc_start: 0.8732 (mmtm) cc_final: 0.8365 (mmmm) REVERT: S 71 ARG cc_start: 0.8091 (mtm110) cc_final: 0.7756 (mtt-85) REVERT: S 72 ASP cc_start: 0.8449 (m-30) cc_final: 0.8206 (m-30) REVERT: S 91 GLU cc_start: 0.7712 (pp20) cc_final: 0.7247 (pm20) REVERT: T 83 ARG cc_start: 0.8737 (OUTLIER) cc_final: 0.7590 (mtt-85) REVERT: U 42 ARG cc_start: 0.7933 (mtm-85) cc_final: 0.7124 (mtt-85) REVERT: U 52 ARG cc_start: 0.8306 (mtt90) cc_final: 0.8058 (mtp180) REVERT: V 50 ILE cc_start: 0.8431 (tt) cc_final: 0.8109 (tt) REVERT: V 59 LYS cc_start: 0.8916 (tttm) cc_final: 0.8703 (ttpt) outliers start: 86 outliers final: 34 residues processed: 524 average time/residue: 0.6339 time to fit residues: 398.9290 Evaluate side-chains 470 residues out of total 3044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 428 time to evaluate : 0.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 773 MET Chi-restraints excluded: chain A residue 861 THR Chi-restraints excluded: chain A residue 996 ILE Chi-restraints excluded: chain A residue 1144 ILE Chi-restraints excluded: chain A residue 1222 GLN Chi-restraints excluded: chain B residue 771 ASP Chi-restraints excluded: chain B residue 775 TRP Chi-restraints excluded: chain B residue 821 ILE Chi-restraints excluded: chain B residue 895 LEU Chi-restraints excluded: chain B residue 912 TRP Chi-restraints excluded: chain B residue 1204 TYR Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 370 ASP Chi-restraints excluded: chain D residue 108 ASP Chi-restraints excluded: chain D residue 168 LEU Chi-restraints excluded: chain D residue 199 THR Chi-restraints excluded: chain D residue 249 SER Chi-restraints excluded: chain D residue 267 VAL Chi-restraints excluded: chain D residue 268 VAL Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain E residue 205 LEU Chi-restraints excluded: chain E residue 229 LYS Chi-restraints excluded: chain E residue 286 TRP Chi-restraints excluded: chain F residue 85 GLU Chi-restraints excluded: chain G residue 82 ASN Chi-restraints excluded: chain G residue 175 ILE Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain I residue 39 CYS Chi-restraints excluded: chain J residue 206 MET Chi-restraints excluded: chain J residue 286 ASP Chi-restraints excluded: chain O residue 113 SER Chi-restraints excluded: chain Q residue 133 GLU Chi-restraints excluded: chain R residue 49 LEU Chi-restraints excluded: chain R residue 96 THR Chi-restraints excluded: chain S residue 114 VAL Chi-restraints excluded: chain T residue 81 ASN Chi-restraints excluded: chain T residue 83 ARG Chi-restraints excluded: chain T residue 87 THR Chi-restraints excluded: chain T residue 102 GLU Chi-restraints excluded: chain U residue 58 THR Chi-restraints excluded: chain V residue 31 LYS Chi-restraints excluded: chain V residue 96 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 249 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 69.2844 > 50:) chunk 276 optimal weight: 1.9990 chunk 246 optimal weight: 0.9990 chunk 35 optimal weight: 5.9990 chunk 3 optimal weight: 9.9990 chunk 169 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 83 optimal weight: 7.9990 chunk 281 optimal weight: 0.8980 chunk 226 optimal weight: 50.0000 chunk 164 optimal weight: 9.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 998 HIS ** A1150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1222 GLN B1137 ASN B1141 ASN ** B1221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 92 HIS G 173 HIS ** I 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 196 GLN J 331 GLN ** J 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 360 GLN Q 68 GLN ** Q 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4301 r_free = 0.4301 target = 0.134882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.093967 restraints weight = 90506.083| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 2.70 r_work: 0.3225 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.3184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 35557 Z= 0.215 Angle : 0.705 9.232 49302 Z= 0.376 Chirality : 0.045 0.267 5443 Planarity : 0.005 0.047 5219 Dihedral : 25.084 175.638 7155 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 12.69 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.67 % Favored : 94.30 % Rotamer: Outliers : 3.25 % Allowed : 15.11 % Favored : 81.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.03 (0.13), residues: 3335 helix: -0.68 (0.11), residues: 1868 sheet: -2.55 (0.38), residues: 162 loop : -2.07 (0.16), residues: 1305 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG J 293 TYR 0.019 0.002 TYR K 252 PHE 0.025 0.002 PHE B1269 TRP 0.024 0.001 TRP A 912 HIS 0.009 0.001 HIS A1252 Details of bonding type rmsd/Z covalent geometry : bond 0.00462 / 0.21 (35556) covalent geometry : angle 0.70464 / 0.38 (49302) hydrogen bonds : bond 0.06766 / 4.36 ( 1493) hydrogen bonds : angle 4.56236 / 3.07 ( 4038) metal coordination : bond 0.00276 / 0.15 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6670 Ramachandran restraints generated. 3335 Oldfield, 0 Emsley, 3335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6670 Ramachandran restraints generated. 3335 Oldfield, 0 Emsley, 3335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 568 residues out of total 3044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 469 time to evaluate : 1.099 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 811 GLU cc_start: 0.8485 (tt0) cc_final: 0.8028 (tt0) REVERT: A 986 TYR cc_start: 0.7586 (t80) cc_final: 0.6661 (m-80) REVERT: A 1016 TYR cc_start: 0.6773 (m-10) cc_final: 0.6452 (m-10) REVERT: A 1146 ILE cc_start: 0.8942 (OUTLIER) cc_final: 0.8702 (mt) REVERT: A 1156 GLU cc_start: 0.8295 (tp30) cc_final: 0.7894 (tp30) REVERT: A 1261 LYS cc_start: 0.7790 (mmtt) cc_final: 0.7552 (tptp) REVERT: A 1273 ARG cc_start: 0.8804 (mmm-85) cc_final: 0.8121 (tpt-90) REVERT: A 1301 PHE cc_start: 0.8676 (m-80) cc_final: 0.8304 (m-80) REVERT: B 821 ILE cc_start: 0.8383 (OUTLIER) cc_final: 0.7934 (tp) REVERT: B 881 ASP cc_start: 0.8853 (t0) cc_final: 0.8368 (p0) REVERT: B 912 TRP cc_start: 0.7926 (OUTLIER) cc_final: 0.7597 (t-100) REVERT: B 916 TRP cc_start: 0.8477 (m-10) cc_final: 0.8181 (m-10) REVERT: B 1257 MET cc_start: 0.7902 (ptp) cc_final: 0.7503 (ppp) REVERT: C 61 MET cc_start: 0.8805 (ptt) cc_final: 0.8605 (ptt) REVERT: C 100 GLU cc_start: 0.8565 (mp0) cc_final: 0.8264 (mp0) REVERT: D 40 MET cc_start: 0.4484 (mmm) cc_final: 0.4037 (mmm) REVERT: D 41 LYS cc_start: 0.7102 (tppp) cc_final: 0.6755 (tppp) REVERT: D 49 HIS cc_start: 0.9331 (t-170) cc_final: 0.9095 (t-170) REVERT: D 232 TYR cc_start: 0.6503 (m-10) cc_final: 0.6234 (m-10) REVERT: D 247 TYR cc_start: 0.9001 (t80) cc_final: 0.8399 (t80) REVERT: D 251 PHE cc_start: 0.8319 (p90) cc_final: 0.8018 (p90) REVERT: D 255 ILE cc_start: 0.9528 (mm) cc_final: 0.9282 (mt) REVERT: D 305 MET cc_start: 0.8416 (ttp) cc_final: 0.7965 (mtt) REVERT: D 306 MET cc_start: 0.7611 (tmm) cc_final: 0.7133 (tmm) REVERT: D 322 TRP cc_start: 0.9120 (m-10) cc_final: 0.8531 (m-10) REVERT: D 344 TYR cc_start: 0.8486 (t80) cc_final: 0.8185 (t80) REVERT: D 347 TYR cc_start: 0.9263 (m-80) cc_final: 0.8936 (m-80) REVERT: D 353 LEU cc_start: 0.8674 (OUTLIER) cc_final: 0.8448 (pt) REVERT: D 369 LEU cc_start: 0.9304 (mt) cc_final: 0.8902 (pp) REVERT: E 227 TYR cc_start: 0.9004 (m-10) cc_final: 0.8783 (m-10) REVERT: E 286 TRP cc_start: 0.7821 (OUTLIER) cc_final: 0.7000 (t60) REVERT: F 50 ASP cc_start: 0.8738 (m-30) cc_final: 0.8435 (m-30) REVERT: F 61 GLN cc_start: 0.8497 (tp-100) cc_final: 0.8230 (tp40) REVERT: F 72 GLU cc_start: 0.8659 (tt0) cc_final: 0.8427 (tt0) REVERT: F 85 GLU cc_start: 0.8800 (OUTLIER) cc_final: 0.8376 (mp0) REVERT: I 43 MET cc_start: 0.8345 (ttm) cc_final: 0.8097 (mmt) REVERT: I 84 GLU cc_start: 0.8808 (tm-30) cc_final: 0.8550 (tp30) REVERT: I 87 MET cc_start: 0.8736 (OUTLIER) cc_final: 0.8054 (ttp) REVERT: J 206 MET cc_start: 0.8628 (OUTLIER) cc_final: 0.8233 (mmm) REVERT: J 332 GLN cc_start: 0.8542 (tp40) cc_final: 0.7718 (pm20) REVERT: J 346 GLN cc_start: 0.8212 (tm-30) cc_final: 0.7941 (tm-30) REVERT: J 350 GLN cc_start: 0.8322 (mt0) cc_final: 0.8107 (mt0) REVERT: J 357 ARG cc_start: 0.9047 (ttp-170) cc_final: 0.8657 (ttp80) REVERT: J 378 ASN cc_start: 0.8683 (m-40) cc_final: 0.7964 (p0) REVERT: O 74 LYS cc_start: 0.8915 (mmtt) cc_final: 0.8645 (tppt) REVERT: O 91 GLU cc_start: 0.8543 (tm-30) cc_final: 0.8332 (tm-30) REVERT: P 31 LYS cc_start: 0.7724 (tptt) cc_final: 0.7108 (tttp) REVERT: Q 133 GLU cc_start: 0.8128 (OUTLIER) cc_final: 0.7820 (mt-10) REVERT: S 15 LYS cc_start: 0.7220 (OUTLIER) cc_final: 0.6547 (mttt) REVERT: S 36 LYS cc_start: 0.8761 (mmtm) cc_final: 0.8406 (mmmm) REVERT: S 71 ARG cc_start: 0.8100 (mtm110) cc_final: 0.7765 (mtt-85) REVERT: S 72 ASP cc_start: 0.8495 (m-30) cc_final: 0.8269 (m-30) REVERT: T 83 ARG cc_start: 0.8739 (OUTLIER) cc_final: 0.7739 (mtt-85) REVERT: U 42 ARG cc_start: 0.7956 (mtm-85) cc_final: 0.7423 (mtm-85) REVERT: U 52 ARG cc_start: 0.8382 (mtt90) cc_final: 0.8084 (mtp180) REVERT: V 50 ILE cc_start: 0.8594 (tt) cc_final: 0.8268 (tt) REVERT: V 59 LYS cc_start: 0.8938 (tttm) cc_final: 0.8720 (ttpt) outliers start: 99 outliers final: 36 residues processed: 520 average time/residue: 0.6286 time to fit residues: 391.4126 Evaluate side-chains 469 residues out of total 3044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 422 time to evaluate : 1.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 773 MET Chi-restraints excluded: chain A residue 861 THR Chi-restraints excluded: chain A residue 934 THR Chi-restraints excluded: chain A residue 1144 ILE Chi-restraints excluded: chain A residue 1146 ILE Chi-restraints excluded: chain A residue 1177 THR Chi-restraints excluded: chain A residue 1180 PHE Chi-restraints excluded: chain A residue 1250 VAL Chi-restraints excluded: chain A residue 1309 THR Chi-restraints excluded: chain B residue 771 ASP Chi-restraints excluded: chain B residue 774 CYS Chi-restraints excluded: chain B residue 775 TRP Chi-restraints excluded: chain B residue 821 ILE Chi-restraints excluded: chain B residue 912 TRP Chi-restraints excluded: chain B residue 1219 LEU Chi-restraints excluded: chain D residue 168 LEU Chi-restraints excluded: chain D residue 199 THR Chi-restraints excluded: chain D residue 246 THR Chi-restraints excluded: chain D residue 249 SER Chi-restraints excluded: chain D residue 276 LEU Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain D residue 353 LEU Chi-restraints excluded: chain E residue 205 LEU Chi-restraints excluded: chain E residue 233 ILE Chi-restraints excluded: chain E residue 286 TRP Chi-restraints excluded: chain F residue 85 GLU Chi-restraints excluded: chain F residue 292 THR Chi-restraints excluded: chain G residue 82 ASN Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain I residue 39 CYS Chi-restraints excluded: chain I residue 87 MET Chi-restraints excluded: chain J residue 206 MET Chi-restraints excluded: chain J residue 217 VAL Chi-restraints excluded: chain J residue 286 ASP Chi-restraints excluded: chain Q residue 58 THR Chi-restraints excluded: chain Q residue 133 GLU Chi-restraints excluded: chain R residue 49 LEU Chi-restraints excluded: chain R residue 96 THR Chi-restraints excluded: chain S residue 15 LYS Chi-restraints excluded: chain S residue 114 VAL Chi-restraints excluded: chain T residue 81 ASN Chi-restraints excluded: chain T residue 83 ARG Chi-restraints excluded: chain T residue 87 THR Chi-restraints excluded: chain T residue 102 GLU Chi-restraints excluded: chain U residue 58 THR Chi-restraints excluded: chain V residue 31 LYS Chi-restraints excluded: chain V residue 96 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 95 optimal weight: 20.0000 chunk 236 optimal weight: 9.9990 chunk 233 optimal weight: 0.0980 chunk 98 optimal weight: 5.9990 chunk 254 optimal weight: 0.7980 chunk 91 optimal weight: 6.9990 chunk 245 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 141 optimal weight: 6.9990 chunk 286 optimal weight: 0.5980 chunk 115 optimal weight: 3.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 815 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1206 GLN A1222 GLN B1252 HIS C 235 ASN D 38 HIS ** D 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 375 ASN E 220 HIS F 61 GLN F 65 GLN ** I 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 222 HIS J 230 ASN J 331 GLN ** J 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 360 GLN O 38 ASN O 110 ASN Q 68 GLN ** Q 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 104 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4300 r_free = 0.4300 target = 0.134758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.093770 restraints weight = 90626.550| |-----------------------------------------------------------------------------| r_work (start): 0.3456 rms_B_bonded: 2.71 r_work: 0.3209 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.3379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 35557 Z= 0.223 Angle : 0.700 9.910 49302 Z= 0.372 Chirality : 0.045 0.269 5443 Planarity : 0.004 0.048 5219 Dihedral : 25.102 174.232 7155 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 12.49 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.85 % Favored : 94.12 % Rotamer: Outliers : 2.86 % Allowed : 16.52 % Favored : 80.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.75 (0.14), residues: 3335 helix: -0.42 (0.11), residues: 1873 sheet: -2.35 (0.39), residues: 161 loop : -2.01 (0.16), residues: 1301 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG J 293 TYR 0.024 0.002 TYR B1232 PHE 0.026 0.002 PHE B1269 TRP 0.024 0.001 TRP A 912 HIS 0.015 0.001 HIS B1293 Details of bonding type rmsd/Z covalent geometry : bond 0.00483 / 0.22 (35556) covalent geometry : angle 0.69959 / 0.37 (49302) hydrogen bonds : bond 0.06605 / 4.26 ( 1493) hydrogen bonds : angle 4.46604 / 3.01 ( 4038) metal coordination : bond 0.00317 / 0.17 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6670 Ramachandran restraints generated. 3335 Oldfield, 0 Emsley, 3335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6670 Ramachandran restraints generated. 3335 Oldfield, 0 Emsley, 3335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 543 residues out of total 3044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 456 time to evaluate : 0.835 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 811 GLU cc_start: 0.8530 (tt0) cc_final: 0.8079 (tt0) REVERT: A 986 TYR cc_start: 0.7657 (t80) cc_final: 0.6698 (m-80) REVERT: A 1016 TYR cc_start: 0.6788 (m-10) cc_final: 0.6463 (m-10) REVERT: A 1146 ILE cc_start: 0.8911 (OUTLIER) cc_final: 0.8621 (mm) REVERT: A 1156 GLU cc_start: 0.8336 (tp30) cc_final: 0.7925 (tp30) REVERT: A 1261 LYS cc_start: 0.7782 (mmtt) cc_final: 0.7496 (mptp) REVERT: A 1273 ARG cc_start: 0.8765 (mmm-85) cc_final: 0.7884 (tpt-90) REVERT: A 1301 PHE cc_start: 0.8677 (m-80) cc_final: 0.8314 (m-80) REVERT: B 821 ILE cc_start: 0.8410 (OUTLIER) cc_final: 0.8087 (tp) REVERT: B 881 ASP cc_start: 0.8906 (t0) cc_final: 0.8436 (p0) REVERT: B 912 TRP cc_start: 0.8001 (OUTLIER) cc_final: 0.7689 (t-100) REVERT: B 916 TRP cc_start: 0.8647 (m-10) cc_final: 0.8191 (m-10) REVERT: B 1257 MET cc_start: 0.7886 (ptp) cc_final: 0.7518 (ppp) REVERT: C 61 MET cc_start: 0.8825 (ptt) cc_final: 0.8538 (ptt) REVERT: C 100 GLU cc_start: 0.8596 (mp0) cc_final: 0.8252 (mp0) REVERT: C 153 LYS cc_start: 0.9242 (OUTLIER) cc_final: 0.8914 (mttp) REVERT: C 370 ASP cc_start: 0.8582 (t0) cc_final: 0.8317 (t0) REVERT: D 40 MET cc_start: 0.4901 (mmm) cc_final: 0.4574 (mmm) REVERT: D 61 MET cc_start: 0.7987 (ppp) cc_final: 0.7784 (pp-130) REVERT: D 232 TYR cc_start: 0.6544 (m-10) cc_final: 0.6221 (m-10) REVERT: D 247 TYR cc_start: 0.9017 (t80) cc_final: 0.8254 (t80) REVERT: D 251 PHE cc_start: 0.8304 (p90) cc_final: 0.7995 (p90) REVERT: D 259 MET cc_start: 0.8770 (mtp) cc_final: 0.8472 (ptm) REVERT: D 288 MET cc_start: 0.8889 (ptt) cc_final: 0.8545 (ptt) REVERT: D 297 TYR cc_start: 0.8436 (t80) cc_final: 0.8011 (t80) REVERT: D 305 MET cc_start: 0.8416 (ttp) cc_final: 0.8007 (mtt) REVERT: D 306 MET cc_start: 0.7631 (tmm) cc_final: 0.7170 (tmm) REVERT: D 322 TRP cc_start: 0.9125 (m-10) cc_final: 0.8591 (m-10) REVERT: D 344 TYR cc_start: 0.8527 (t80) cc_final: 0.8212 (t80) REVERT: D 347 TYR cc_start: 0.9278 (m-80) cc_final: 0.8966 (m-80) REVERT: D 376 ILE cc_start: 0.9392 (mp) cc_final: 0.9068 (mp) REVERT: E 227 TYR cc_start: 0.9023 (m-10) cc_final: 0.8780 (m-10) REVERT: E 284 GLN cc_start: 0.8500 (tm-30) cc_final: 0.8178 (tm-30) REVERT: E 286 TRP cc_start: 0.7886 (OUTLIER) cc_final: 0.7062 (t60) REVERT: F 50 ASP cc_start: 0.8729 (m-30) cc_final: 0.8447 (m-30) REVERT: F 61 GLN cc_start: 0.8586 (tp40) cc_final: 0.8359 (tp-100) REVERT: F 72 GLU cc_start: 0.8681 (tt0) cc_final: 0.8432 (tt0) REVERT: F 85 GLU cc_start: 0.8828 (OUTLIER) cc_final: 0.8405 (mp0) REVERT: G 175 ILE cc_start: 0.8098 (OUTLIER) cc_final: 0.7768 (pp) REVERT: I 43 MET cc_start: 0.8357 (ttm) cc_final: 0.8089 (mmt) REVERT: I 79 LEU cc_start: 0.8706 (tm) cc_final: 0.8271 (tp) REVERT: J 206 MET cc_start: 0.8670 (OUTLIER) cc_final: 0.8320 (mmm) REVERT: J 332 GLN cc_start: 0.8554 (tp40) cc_final: 0.7774 (pm20) REVERT: J 342 ARG cc_start: 0.7346 (OUTLIER) cc_final: 0.6898 (ttp-110) REVERT: J 346 GLN cc_start: 0.8197 (tm-30) cc_final: 0.7940 (tm-30) REVERT: J 350 GLN cc_start: 0.8340 (mt0) cc_final: 0.8070 (mt0) REVERT: J 351 ARG cc_start: 0.8403 (OUTLIER) cc_final: 0.8133 (mmt90) REVERT: J 357 ARG cc_start: 0.9009 (ttp-170) cc_final: 0.8525 (ttm170) REVERT: J 358 ASN cc_start: 0.8542 (m110) cc_final: 0.8214 (m110) REVERT: J 378 ASN cc_start: 0.8686 (m-40) cc_final: 0.7979 (p0) REVERT: O 74 LYS cc_start: 0.8945 (mmtt) cc_final: 0.8656 (tppt) REVERT: P 31 LYS cc_start: 0.7743 (tptt) cc_final: 0.7111 (tttp) REVERT: Q 133 GLU cc_start: 0.8131 (OUTLIER) cc_final: 0.7815 (mt-10) REVERT: S 15 LYS cc_start: 0.7269 (OUTLIER) cc_final: 0.6624 (mmtt) REVERT: S 36 LYS cc_start: 0.8779 (mmtm) cc_final: 0.8385 (mmmm) REVERT: S 71 ARG cc_start: 0.8129 (mtm110) cc_final: 0.7792 (mtt-85) REVERT: S 72 ASP cc_start: 0.8494 (m-30) cc_final: 0.8287 (m-30) REVERT: T 83 ARG cc_start: 0.8754 (OUTLIER) cc_final: 0.7788 (mtt-85) REVERT: U 42 ARG cc_start: 0.7930 (mtm-85) cc_final: 0.7026 (mtt-85) REVERT: U 52 ARG cc_start: 0.8415 (mtt90) cc_final: 0.8100 (mtp180) REVERT: U 94 GLU cc_start: 0.8719 (mm-30) cc_final: 0.8360 (mm-30) REVERT: V 50 ILE cc_start: 0.8677 (tt) cc_final: 0.8322 (tt) outliers start: 87 outliers final: 37 residues processed: 500 average time/residue: 0.6110 time to fit residues: 366.8206 Evaluate side-chains 473 residues out of total 3044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 423 time to evaluate : 0.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 702 LEU Chi-restraints excluded: chain A residue 773 MET Chi-restraints excluded: chain A residue 861 THR Chi-restraints excluded: chain A residue 934 THR Chi-restraints excluded: chain A residue 1144 ILE Chi-restraints excluded: chain A residue 1146 ILE Chi-restraints excluded: chain A residue 1180 PHE Chi-restraints excluded: chain A residue 1250 VAL Chi-restraints excluded: chain A residue 1309 THR Chi-restraints excluded: chain B residue 765 MET Chi-restraints excluded: chain B residue 771 ASP Chi-restraints excluded: chain B residue 775 TRP Chi-restraints excluded: chain B residue 821 ILE Chi-restraints excluded: chain B residue 912 TRP Chi-restraints excluded: chain B residue 1219 LEU Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 153 LYS Chi-restraints excluded: chain D residue 199 THR Chi-restraints excluded: chain D residue 249 SER Chi-restraints excluded: chain D residue 267 VAL Chi-restraints excluded: chain D residue 276 LEU Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain E residue 205 LEU Chi-restraints excluded: chain E residue 226 TYR Chi-restraints excluded: chain E residue 286 TRP Chi-restraints excluded: chain F residue 85 GLU Chi-restraints excluded: chain F residue 99 ILE Chi-restraints excluded: chain F residue 292 THR Chi-restraints excluded: chain G residue 82 ASN Chi-restraints excluded: chain G residue 106 GLU Chi-restraints excluded: chain G residue 175 ILE Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain I residue 39 CYS Chi-restraints excluded: chain J residue 206 MET Chi-restraints excluded: chain J residue 217 VAL Chi-restraints excluded: chain J residue 342 ARG Chi-restraints excluded: chain J residue 351 ARG Chi-restraints excluded: chain Q residue 58 THR Chi-restraints excluded: chain Q residue 133 GLU Chi-restraints excluded: chain R residue 49 LEU Chi-restraints excluded: chain R residue 96 THR Chi-restraints excluded: chain S residue 15 LYS Chi-restraints excluded: chain S residue 114 VAL Chi-restraints excluded: chain T residue 81 ASN Chi-restraints excluded: chain T residue 83 ARG Chi-restraints excluded: chain T residue 87 THR Chi-restraints excluded: chain T residue 102 GLU Chi-restraints excluded: chain U residue 58 THR Chi-restraints excluded: chain V residue 31 LYS Chi-restraints excluded: chain V residue 96 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 169 optimal weight: 0.9990 chunk 189 optimal weight: 3.9990 chunk 116 optimal weight: 0.9980 chunk 245 optimal weight: 0.9980 chunk 250 optimal weight: 5.9990 chunk 296 optimal weight: 1.9990 chunk 47 optimal weight: 0.9990 chunk 335 optimal weight: 9.9990 chunk 74 optimal weight: 7.9990 chunk 238 optimal weight: 5.9990 chunk 206 optimal weight: 0.8980 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 815 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 38 HIS ** D 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 375 ASN E 220 HIS ** G 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 331 GLN ** J 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 370 ASN P 92 GLN Q 68 GLN ** Q 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.135274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.095007 restraints weight = 89907.995| |-----------------------------------------------------------------------------| r_work (start): 0.3477 rms_B_bonded: 2.57 r_work: 0.3256 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.3593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 35557 Z= 0.178 Angle : 0.678 9.923 49302 Z= 0.361 Chirality : 0.044 0.265 5443 Planarity : 0.004 0.063 5219 Dihedral : 25.059 172.875 7155 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.64 % Favored : 94.33 % Rotamer: Outliers : 2.56 % Allowed : 17.64 % Favored : 79.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.52 (0.14), residues: 3335 helix: -0.20 (0.12), residues: 1882 sheet: -2.09 (0.42), residues: 152 loop : -2.01 (0.16), residues: 1301 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG J 293 TYR 0.076 0.002 TYR E 226 PHE 0.024 0.002 PHE G 111 TRP 0.028 0.001 TRP A 912 HIS 0.013 0.001 HIS B1293 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.18 (35556) covalent geometry : angle 0.67843 / 0.36 (49302) hydrogen bonds : bond 0.06481 / 4.17 ( 1493) hydrogen bonds : angle 4.32593 / 2.92 ( 4038) metal coordination : bond 0.00217 / 0.11 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6670 Ramachandran restraints generated. 3335 Oldfield, 0 Emsley, 3335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6670 Ramachandran restraints generated. 3335 Oldfield, 0 Emsley, 3335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 542 residues out of total 3044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 464 time to evaluate : 1.169 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: A 811 GLU cc_start: 0.8446 (tt0) cc_final: 0.8046 (tt0) REVERT: A 986 TYR cc_start: 0.7585 (t80) cc_final: 0.6653 (m-80) REVERT: A 1016 TYR cc_start: 0.6689 (m-10) cc_final: 0.6350 (m-10) REVERT: A 1146 ILE cc_start: 0.8872 (OUTLIER) cc_final: 0.8670 (mm) REVERT: A 1156 GLU cc_start: 0.8218 (tp30) cc_final: 0.7805 (tp30) REVERT: A 1261 LYS cc_start: 0.7762 (mmtt) cc_final: 0.7468 (mptp) REVERT: A 1273 ARG cc_start: 0.8765 (mmm-85) cc_final: 0.7793 (tpt-90) REVERT: A 1301 PHE cc_start: 0.8619 (m-80) cc_final: 0.8306 (m-80) REVERT: B 821 ILE cc_start: 0.8367 (OUTLIER) cc_final: 0.7979 (tp) REVERT: B 881 ASP cc_start: 0.8868 (t0) cc_final: 0.8421 (p0) REVERT: B 912 TRP cc_start: 0.8020 (OUTLIER) cc_final: 0.6944 (t-100) REVERT: B 1257 MET cc_start: 0.7857 (ptp) cc_final: 0.7004 (ppp) REVERT: C 100 GLU cc_start: 0.8542 (mp0) cc_final: 0.8244 (mp0) REVERT: C 370 ASP cc_start: 0.8484 (t0) cc_final: 0.8241 (t0) REVERT: D 40 MET cc_start: 0.5139 (mmm) cc_final: 0.4545 (mmm) REVERT: D 41 LYS cc_start: 0.7069 (tppp) cc_final: 0.6823 (tppp) REVERT: D 247 TYR cc_start: 0.8939 (t80) cc_final: 0.8540 (t80) REVERT: D 259 MET cc_start: 0.8717 (mtp) cc_final: 0.8431 (ptm) REVERT: D 297 TYR cc_start: 0.8389 (t80) cc_final: 0.7954 (t80) REVERT: D 305 MET cc_start: 0.8364 (ttp) cc_final: 0.7985 (mtt) REVERT: D 306 MET cc_start: 0.7567 (tmm) cc_final: 0.7095 (tmm) REVERT: D 322 TRP cc_start: 0.9107 (m-10) cc_final: 0.8601 (m-10) REVERT: D 344 TYR cc_start: 0.8488 (t80) cc_final: 0.8169 (t80) REVERT: D 347 TYR cc_start: 0.9170 (m-80) cc_final: 0.8901 (m-80) REVERT: D 369 LEU cc_start: 0.9314 (mt) cc_final: 0.8862 (pp) REVERT: E 227 TYR cc_start: 0.8883 (m-10) cc_final: 0.8618 (m-80) REVERT: E 286 TRP cc_start: 0.7877 (OUTLIER) cc_final: 0.7048 (t60) REVERT: E 288 ASP cc_start: 0.8073 (m-30) cc_final: 0.7801 (m-30) REVERT: F 50 ASP cc_start: 0.8705 (m-30) cc_final: 0.8421 (m-30) REVERT: F 61 GLN cc_start: 0.8532 (tp40) cc_final: 0.8293 (tp-100) REVERT: F 85 GLU cc_start: 0.8755 (OUTLIER) cc_final: 0.8336 (mp0) REVERT: G 168 ARG cc_start: 0.8280 (ptp-170) cc_final: 0.7815 (ptm-80) REVERT: G 175 ILE cc_start: 0.8150 (OUTLIER) cc_final: 0.7789 (pp) REVERT: I 43 MET cc_start: 0.8220 (ttm) cc_final: 0.7916 (mmp) REVERT: I 77 GLU cc_start: 0.8302 (mm-30) cc_final: 0.8066 (mm-30) REVERT: I 79 LEU cc_start: 0.8717 (tm) cc_final: 0.8185 (tp) REVERT: J 206 MET cc_start: 0.8605 (OUTLIER) cc_final: 0.8286 (mmm) REVERT: J 332 GLN cc_start: 0.8587 (tp40) cc_final: 0.7773 (pm20) REVERT: J 346 GLN cc_start: 0.8178 (tm-30) cc_final: 0.7938 (tm-30) REVERT: J 357 ARG cc_start: 0.8996 (ttp-170) cc_final: 0.8648 (ttp80) REVERT: J 358 ASN cc_start: 0.8503 (m110) cc_final: 0.8154 (m110) REVERT: J 378 ASN cc_start: 0.8675 (m-40) cc_final: 0.8017 (p0) REVERT: P 31 LYS cc_start: 0.7707 (tptt) cc_final: 0.7100 (tttp) REVERT: Q 133 GLU cc_start: 0.8064 (OUTLIER) cc_final: 0.7754 (mt-10) REVERT: S 15 LYS cc_start: 0.7152 (OUTLIER) cc_final: 0.6561 (mttm) REVERT: S 36 LYS cc_start: 0.8731 (mmtm) cc_final: 0.8381 (mmmm) REVERT: S 71 ARG cc_start: 0.8092 (mtm110) cc_final: 0.7771 (mtt-85) REVERT: S 72 ASP cc_start: 0.8475 (m-30) cc_final: 0.8258 (m-30) REVERT: T 83 ARG cc_start: 0.8732 (OUTLIER) cc_final: 0.7674 (mtt-85) REVERT: U 42 ARG cc_start: 0.7992 (mtm-85) cc_final: 0.7052 (mtt-85) REVERT: U 52 ARG cc_start: 0.8370 (mtt90) cc_final: 0.8102 (mtp180) REVERT: U 94 GLU cc_start: 0.8640 (mm-30) cc_final: 0.8295 (mm-30) REVERT: V 50 ILE cc_start: 0.8604 (tt) cc_final: 0.8232 (tt) outliers start: 78 outliers final: 36 residues processed: 503 average time/residue: 0.6310 time to fit residues: 381.0309 Evaluate side-chains 470 residues out of total 3044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 424 time to evaluate : 1.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 698 ASP Chi-restraints excluded: chain A residue 702 LEU Chi-restraints excluded: chain A residue 861 THR Chi-restraints excluded: chain A residue 934 THR Chi-restraints excluded: chain A residue 996 ILE Chi-restraints excluded: chain A residue 1144 ILE Chi-restraints excluded: chain A residue 1146 ILE Chi-restraints excluded: chain A residue 1177 THR Chi-restraints excluded: chain A residue 1250 VAL Chi-restraints excluded: chain B residue 771 ASP Chi-restraints excluded: chain B residue 775 TRP Chi-restraints excluded: chain B residue 821 ILE Chi-restraints excluded: chain B residue 912 TRP Chi-restraints excluded: chain B residue 1219 LEU Chi-restraints excluded: chain D residue 38 HIS Chi-restraints excluded: chain D residue 123 SER Chi-restraints excluded: chain D residue 168 LEU Chi-restraints excluded: chain D residue 249 SER Chi-restraints excluded: chain D residue 276 LEU Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain D residue 326 THR Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain E residue 205 LEU Chi-restraints excluded: chain E residue 286 TRP Chi-restraints excluded: chain F residue 85 GLU Chi-restraints excluded: chain F residue 99 ILE Chi-restraints excluded: chain F residue 292 THR Chi-restraints excluded: chain G residue 82 ASN Chi-restraints excluded: chain G residue 106 GLU Chi-restraints excluded: chain G residue 175 ILE Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain I residue 39 CYS Chi-restraints excluded: chain J residue 206 MET Chi-restraints excluded: chain J residue 217 VAL Chi-restraints excluded: chain Q residue 58 THR Chi-restraints excluded: chain Q residue 68 GLN Chi-restraints excluded: chain Q residue 133 GLU Chi-restraints excluded: chain R residue 49 LEU Chi-restraints excluded: chain R residue 96 THR Chi-restraints excluded: chain S residue 15 LYS Chi-restraints excluded: chain S residue 114 VAL Chi-restraints excluded: chain T residue 81 ASN Chi-restraints excluded: chain T residue 83 ARG Chi-restraints excluded: chain T residue 87 THR Chi-restraints excluded: chain T residue 102 GLU Chi-restraints excluded: chain V residue 96 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 15 optimal weight: 0.5980 chunk 360 optimal weight: 40.0000 chunk 19 optimal weight: 0.8980 chunk 342 optimal weight: 9.9990 chunk 345 optimal weight: 40.0000 chunk 294 optimal weight: 0.5980 chunk 221 optimal weight: 7.9990 chunk 48 optimal weight: 2.9990 chunk 171 optimal weight: 3.9990 chunk 97 optimal weight: 3.9990 chunk 187 optimal weight: 6.9990 overall best weight: 1.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 815 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1143 ASN ** A1150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 38 HIS ** D 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 220 HIS G 91 ASN ** G 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 331 GLN ** J 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 370 ASN Q 68 GLN ** Q 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.134362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.091846 restraints weight = 90370.177| |-----------------------------------------------------------------------------| r_work (start): 0.3432 rms_B_bonded: 2.36 r_work: 0.3244 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.3646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.075 35557 Z= 0.251 Angle : 0.715 11.196 49302 Z= 0.378 Chirality : 0.046 0.270 5443 Planarity : 0.004 0.071 5219 Dihedral : 25.101 172.336 7155 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 12.58 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.88 % Favored : 94.09 % Rotamer: Outliers : 2.53 % Allowed : 18.23 % Favored : 79.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.44 (0.14), residues: 3335 helix: -0.17 (0.12), residues: 1894 sheet: -2.02 (0.42), residues: 151 loop : -1.94 (0.16), residues: 1290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG V 36 TYR 0.024 0.002 TYR B1232 PHE 0.025 0.002 PHE B1269 TRP 0.029 0.002 TRP A 912 HIS 0.011 0.001 HIS B1293 Details of bonding type rmsd/Z covalent geometry : bond 0.00550 / 0.25 (35556) covalent geometry : angle 0.71535 / 0.38 (49302) hydrogen bonds : bond 0.06439 / 4.16 ( 1493) hydrogen bonds : angle 4.38071 / 2.96 ( 4038) metal coordination : bond 0.00447 / 0.24 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6670 Ramachandran restraints generated. 3335 Oldfield, 0 Emsley, 3335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6670 Ramachandran restraints generated. 3335 Oldfield, 0 Emsley, 3335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 519 residues out of total 3044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 442 time to evaluate : 1.138 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 811 GLU cc_start: 0.8424 (tt0) cc_final: 0.8045 (tt0) REVERT: A 947 GLN cc_start: 0.8922 (tm-30) cc_final: 0.8667 (tm-30) REVERT: A 986 TYR cc_start: 0.7584 (t80) cc_final: 0.6623 (m-80) REVERT: A 1016 TYR cc_start: 0.6679 (m-10) cc_final: 0.6345 (m-10) REVERT: A 1261 LYS cc_start: 0.7763 (mmtt) cc_final: 0.7473 (mptp) REVERT: A 1273 ARG cc_start: 0.8786 (mmm-85) cc_final: 0.7784 (tpt-90) REVERT: B 881 ASP cc_start: 0.8788 (t0) cc_final: 0.8384 (p0) REVERT: B 912 TRP cc_start: 0.8065 (OUTLIER) cc_final: 0.7001 (t-100) REVERT: B 1257 MET cc_start: 0.7816 (ptp) cc_final: 0.7464 (ppp) REVERT: C 100 GLU cc_start: 0.8564 (mp0) cc_final: 0.8255 (mp0) REVERT: C 153 LYS cc_start: 0.9233 (OUTLIER) cc_final: 0.8517 (mttp) REVERT: C 370 ASP cc_start: 0.8519 (t0) cc_final: 0.8302 (t0) REVERT: D 40 MET cc_start: 0.5324 (mmm) cc_final: 0.4833 (mmm) REVERT: D 47 MET cc_start: 0.8870 (mpt) cc_final: 0.8619 (mpt) REVERT: D 247 TYR cc_start: 0.8930 (t80) cc_final: 0.8010 (t80) REVERT: D 251 PHE cc_start: 0.8346 (p90) cc_final: 0.7553 (p90) REVERT: D 288 MET cc_start: 0.8858 (ptt) cc_final: 0.8571 (mpp) REVERT: D 297 TYR cc_start: 0.8457 (t80) cc_final: 0.8038 (t80) REVERT: D 305 MET cc_start: 0.8371 (ttp) cc_final: 0.8019 (mtt) REVERT: D 306 MET cc_start: 0.7541 (tmm) cc_final: 0.6940 (tmm) REVERT: D 315 MET cc_start: 0.6111 (OUTLIER) cc_final: 0.5124 (tpt) REVERT: D 316 ARG cc_start: 0.8322 (ttm-80) cc_final: 0.8045 (ttm-80) REVERT: D 322 TRP cc_start: 0.9197 (m-10) cc_final: 0.8650 (m-10) REVERT: D 347 TYR cc_start: 0.9217 (m-80) cc_final: 0.8994 (m-80) REVERT: D 369 LEU cc_start: 0.9351 (mt) cc_final: 0.8898 (pp) REVERT: E 226 TYR cc_start: 0.8190 (p90) cc_final: 0.7826 (p90) REVERT: E 227 TYR cc_start: 0.8985 (m-10) cc_final: 0.8672 (m-80) REVERT: E 235 ASP cc_start: 0.8559 (OUTLIER) cc_final: 0.8322 (p0) REVERT: E 286 TRP cc_start: 0.7840 (OUTLIER) cc_final: 0.7216 (t60) REVERT: E 288 ASP cc_start: 0.7938 (m-30) cc_final: 0.7676 (m-30) REVERT: F 50 ASP cc_start: 0.8705 (m-30) cc_final: 0.8437 (m-30) REVERT: F 61 GLN cc_start: 0.8555 (tp40) cc_final: 0.8320 (tp-100) REVERT: F 85 GLU cc_start: 0.8749 (OUTLIER) cc_final: 0.8330 (mp0) REVERT: G 168 ARG cc_start: 0.8274 (ptp-170) cc_final: 0.7739 (ptm-80) REVERT: G 175 ILE cc_start: 0.8140 (OUTLIER) cc_final: 0.7789 (pp) REVERT: I 43 MET cc_start: 0.8256 (ttm) cc_final: 0.7994 (mmp) REVERT: I 79 LEU cc_start: 0.8713 (tm) cc_final: 0.8184 (tp) REVERT: J 205 GLN cc_start: 0.8562 (tp40) cc_final: 0.8092 (tp40) REVERT: J 206 MET cc_start: 0.8615 (OUTLIER) cc_final: 0.8283 (mmm) REVERT: J 228 GLU cc_start: 0.7874 (OUTLIER) cc_final: 0.7670 (tt0) REVERT: J 332 GLN cc_start: 0.8613 (tp40) cc_final: 0.7782 (pm20) REVERT: J 346 GLN cc_start: 0.8186 (tm-30) cc_final: 0.7933 (tm-30) REVERT: J 357 ARG cc_start: 0.8953 (ttp-170) cc_final: 0.8648 (ttp80) REVERT: J 358 ASN cc_start: 0.8592 (m110) cc_final: 0.8222 (m110) REVERT: J 378 ASN cc_start: 0.8684 (m-40) cc_final: 0.8044 (p0) REVERT: P 31 LYS cc_start: 0.7764 (tptt) cc_final: 0.7161 (tttp) REVERT: Q 133 GLU cc_start: 0.8095 (OUTLIER) cc_final: 0.7776 (mt-10) REVERT: S 15 LYS cc_start: 0.7217 (OUTLIER) cc_final: 0.6679 (mttt) REVERT: S 36 LYS cc_start: 0.8785 (mmtm) cc_final: 0.8389 (mmmm) REVERT: S 71 ARG cc_start: 0.8108 (mtm110) cc_final: 0.7798 (mtt-85) REVERT: S 91 GLU cc_start: 0.7823 (OUTLIER) cc_final: 0.7217 (pp20) REVERT: T 83 ARG cc_start: 0.8730 (OUTLIER) cc_final: 0.7869 (mtt-85) REVERT: U 42 ARG cc_start: 0.7988 (mtm-85) cc_final: 0.7532 (mtm-85) REVERT: U 52 ARG cc_start: 0.8379 (mtt90) cc_final: 0.8059 (mtp180) REVERT: U 59 GLU cc_start: 0.8421 (OUTLIER) cc_final: 0.7751 (pm20) REVERT: U 94 GLU cc_start: 0.8665 (mm-30) cc_final: 0.8307 (mm-30) REVERT: V 59 LYS cc_start: 0.8911 (OUTLIER) cc_final: 0.8649 (tttm) outliers start: 77 outliers final: 32 residues processed: 480 average time/residue: 0.6978 time to fit residues: 402.0668 Evaluate side-chains 465 residues out of total 3044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 418 time to evaluate : 1.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 702 LEU Chi-restraints excluded: chain A residue 861 THR Chi-restraints excluded: chain A residue 934 THR Chi-restraints excluded: chain A residue 1144 ILE Chi-restraints excluded: chain A residue 1177 THR Chi-restraints excluded: chain A residue 1250 VAL Chi-restraints excluded: chain B residue 771 ASP Chi-restraints excluded: chain B residue 775 TRP Chi-restraints excluded: chain B residue 912 TRP Chi-restraints excluded: chain B residue 1219 LEU Chi-restraints excluded: chain C residue 153 LYS Chi-restraints excluded: chain C residue 279 ASP Chi-restraints excluded: chain D residue 249 SER Chi-restraints excluded: chain D residue 267 VAL Chi-restraints excluded: chain D residue 276 LEU Chi-restraints excluded: chain D residue 315 MET Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain E residue 205 LEU Chi-restraints excluded: chain E residue 235 ASP Chi-restraints excluded: chain E residue 286 TRP Chi-restraints excluded: chain F residue 85 GLU Chi-restraints excluded: chain F residue 99 ILE Chi-restraints excluded: chain F residue 292 THR Chi-restraints excluded: chain G residue 106 GLU Chi-restraints excluded: chain G residue 175 ILE Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain I residue 39 CYS Chi-restraints excluded: chain J residue 206 MET Chi-restraints excluded: chain J residue 217 VAL Chi-restraints excluded: chain J residue 228 GLU Chi-restraints excluded: chain J residue 344 LEU Chi-restraints excluded: chain O residue 113 SER Chi-restraints excluded: chain Q residue 58 THR Chi-restraints excluded: chain Q residue 133 GLU Chi-restraints excluded: chain R residue 49 LEU Chi-restraints excluded: chain R residue 96 THR Chi-restraints excluded: chain S residue 15 LYS Chi-restraints excluded: chain S residue 91 GLU Chi-restraints excluded: chain S residue 114 VAL Chi-restraints excluded: chain T residue 81 ASN Chi-restraints excluded: chain T residue 83 ARG Chi-restraints excluded: chain T residue 87 THR Chi-restraints excluded: chain T residue 102 GLU Chi-restraints excluded: chain U residue 59 GLU Chi-restraints excluded: chain V residue 31 LYS Chi-restraints excluded: chain V residue 59 LYS Chi-restraints excluded: chain V residue 96 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 192 optimal weight: 0.6980 chunk 32 optimal weight: 0.5980 chunk 285 optimal weight: 0.6980 chunk 262 optimal weight: 0.9990 chunk 280 optimal weight: 4.9990 chunk 81 optimal weight: 0.0370 chunk 50 optimal weight: 0.0170 chunk 150 optimal weight: 10.0000 chunk 214 optimal weight: 40.0000 chunk 273 optimal weight: 0.8980 chunk 266 optimal weight: 0.5980 overall best weight: 0.3896 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 815 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1150 HIS ** B1221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 31 ASN ** D 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 375 ASN E 220 HIS G 82 ASN ** G 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 331 GLN ** J 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 360 GLN J 370 ASN O 110 ASN Q 68 GLN ** Q 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4321 r_free = 0.4321 target = 0.136104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.095898 restraints weight = 90573.905| |-----------------------------------------------------------------------------| r_work (start): 0.3493 rms_B_bonded: 2.69 r_work: 0.3275 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.3868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.099 35557 Z= 0.142 Angle : 0.678 13.644 49302 Z= 0.359 Chirality : 0.043 0.267 5443 Planarity : 0.004 0.056 5219 Dihedral : 24.982 171.038 7155 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.46 % Favored : 94.51 % Rotamer: Outliers : 2.17 % Allowed : 18.89 % Favored : 78.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.27 (0.14), residues: 3335 helix: -0.01 (0.12), residues: 1897 sheet: -1.89 (0.43), residues: 150 loop : -1.91 (0.16), residues: 1288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG J 293 TYR 0.023 0.001 TYR C 313 PHE 0.029 0.001 PHE G 111 TRP 0.033 0.002 TRP A 912 HIS 0.011 0.001 HIS I 41 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.14 (35556) covalent geometry : angle 0.67769 / 0.36 (49302) hydrogen bonds : bond 0.06466 / 4.15 ( 1493) hydrogen bonds : angle 4.24821 / 2.87 ( 4038) metal coordination : bond 0.00020 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6670 Ramachandran restraints generated. 3335 Oldfield, 0 Emsley, 3335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6670 Ramachandran restraints generated. 3335 Oldfield, 0 Emsley, 3335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 528 residues out of total 3044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 462 time to evaluate : 1.007 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 811 GLU cc_start: 0.8482 (tt0) cc_final: 0.8096 (tt0) REVERT: A 947 GLN cc_start: 0.8939 (tm-30) cc_final: 0.8693 (tm-30) REVERT: A 986 TYR cc_start: 0.7597 (t80) cc_final: 0.6663 (m-80) REVERT: A 1016 TYR cc_start: 0.6595 (m-10) cc_final: 0.6231 (m-10) REVERT: A 1156 GLU cc_start: 0.8213 (tp30) cc_final: 0.7825 (tp30) REVERT: A 1261 LYS cc_start: 0.7727 (mmtt) cc_final: 0.7439 (mptp) REVERT: A 1273 ARG cc_start: 0.8750 (mmm-85) cc_final: 0.8546 (tpt90) REVERT: A 1300 MET cc_start: 0.6973 (ttp) cc_final: 0.6332 (ttm) REVERT: A 1301 PHE cc_start: 0.8597 (m-80) cc_final: 0.8282 (m-80) REVERT: A 1316 TYR cc_start: 0.7708 (p90) cc_final: 0.7299 (p90) REVERT: B 834 ILE cc_start: 0.8256 (OUTLIER) cc_final: 0.7753 (tt) REVERT: B 881 ASP cc_start: 0.8919 (t0) cc_final: 0.8475 (p0) REVERT: B 912 TRP cc_start: 0.8022 (OUTLIER) cc_final: 0.6969 (t-100) REVERT: B 1257 MET cc_start: 0.7793 (ptp) cc_final: 0.7043 (ppp) REVERT: C 94 LEU cc_start: 0.9182 (tp) cc_final: 0.8974 (tm) REVERT: C 153 LYS cc_start: 0.9196 (OUTLIER) cc_final: 0.8451 (mttp) REVERT: C 370 ASP cc_start: 0.8534 (t0) cc_final: 0.8300 (t0) REVERT: D 40 MET cc_start: 0.5810 (mmm) cc_final: 0.5377 (mmm) REVERT: D 76 GLN cc_start: 0.7452 (pm20) cc_final: 0.7093 (mp10) REVERT: D 128 MET cc_start: 0.8760 (mmm) cc_final: 0.8520 (mpm) REVERT: D 247 TYR cc_start: 0.8936 (t80) cc_final: 0.7970 (t80) REVERT: D 251 PHE cc_start: 0.8291 (p90) cc_final: 0.7564 (p90) REVERT: D 259 MET cc_start: 0.8737 (mtp) cc_final: 0.8491 (ptm) REVERT: D 288 MET cc_start: 0.8786 (ptt) cc_final: 0.8331 (mpp) REVERT: D 297 TYR cc_start: 0.8417 (t80) cc_final: 0.8024 (t80) REVERT: D 305 MET cc_start: 0.8296 (ttp) cc_final: 0.7987 (mtt) REVERT: D 306 MET cc_start: 0.7495 (tmm) cc_final: 0.6999 (tmm) REVERT: D 316 ARG cc_start: 0.8336 (ttm-80) cc_final: 0.8096 (ttm-80) REVERT: D 322 TRP cc_start: 0.9147 (m-10) cc_final: 0.8651 (m-10) REVERT: D 344 TYR cc_start: 0.8463 (t80) cc_final: 0.8112 (t80) REVERT: D 369 LEU cc_start: 0.9357 (mt) cc_final: 0.8924 (pp) REVERT: E 226 TYR cc_start: 0.8170 (p90) cc_final: 0.7769 (p90) REVERT: E 227 TYR cc_start: 0.8915 (m-10) cc_final: 0.8585 (m-80) REVERT: E 235 ASP cc_start: 0.8586 (OUTLIER) cc_final: 0.8326 (p0) REVERT: E 286 TRP cc_start: 0.7732 (OUTLIER) cc_final: 0.6997 (t60) REVERT: F 50 ASP cc_start: 0.8688 (m-30) cc_final: 0.8463 (m-30) REVERT: F 61 GLN cc_start: 0.8508 (tp40) cc_final: 0.8277 (tp-100) REVERT: F 72 GLU cc_start: 0.8617 (tt0) cc_final: 0.8385 (tt0) REVERT: F 85 GLU cc_start: 0.8796 (OUTLIER) cc_final: 0.8359 (mp0) REVERT: G 113 ARG cc_start: 0.8430 (mtp180) cc_final: 0.8143 (mtt90) REVERT: G 126 ASN cc_start: 0.8006 (t0) cc_final: 0.7088 (p0) REVERT: G 168 ARG cc_start: 0.8267 (ptp-170) cc_final: 0.7779 (ptm-80) REVERT: G 175 ILE cc_start: 0.8122 (OUTLIER) cc_final: 0.7744 (pp) REVERT: H 244 ARG cc_start: 0.7777 (tpt170) cc_final: 0.7392 (ttm170) REVERT: I 16 ASP cc_start: 0.8713 (p0) cc_final: 0.8435 (p0) REVERT: I 43 MET cc_start: 0.8241 (ttm) cc_final: 0.7933 (mmp) REVERT: I 79 LEU cc_start: 0.8656 (tm) cc_final: 0.8176 (tp) REVERT: J 206 MET cc_start: 0.8617 (OUTLIER) cc_final: 0.8247 (mmm) REVERT: J 228 GLU cc_start: 0.7778 (OUTLIER) cc_final: 0.7518 (tt0) REVERT: J 332 GLN cc_start: 0.8520 (tp40) cc_final: 0.7721 (pm20) REVERT: J 346 GLN cc_start: 0.8125 (tm-30) cc_final: 0.7854 (tm-30) REVERT: J 357 ARG cc_start: 0.8924 (ttp-170) cc_final: 0.8674 (ttp80) REVERT: J 358 ASN cc_start: 0.8528 (m110) cc_final: 0.8183 (m110) REVERT: J 375 ARG cc_start: 0.8387 (mmm160) cc_final: 0.7992 (mtp85) REVERT: P 31 LYS cc_start: 0.7687 (tptt) cc_final: 0.7070 (tttp) REVERT: P 53 SER cc_start: 0.9058 (p) cc_final: 0.8786 (p) REVERT: Q 133 GLU cc_start: 0.8064 (OUTLIER) cc_final: 0.7844 (mt-10) REVERT: S 15 LYS cc_start: 0.7211 (OUTLIER) cc_final: 0.6647 (mttm) REVERT: S 36 LYS cc_start: 0.8724 (mmtm) cc_final: 0.8326 (mmmm) REVERT: S 71 ARG cc_start: 0.8086 (mtm110) cc_final: 0.7765 (mtt-85) REVERT: S 72 ASP cc_start: 0.8459 (m-30) cc_final: 0.8228 (m-30) REVERT: S 91 GLU cc_start: 0.7810 (pp20) cc_final: 0.7432 (pp20) REVERT: T 48 ASP cc_start: 0.7936 (m-30) cc_final: 0.7489 (t70) REVERT: T 83 ARG cc_start: 0.8737 (OUTLIER) cc_final: 0.7685 (mtt-85) REVERT: U 42 ARG cc_start: 0.7985 (mtm-85) cc_final: 0.7391 (mtm-85) REVERT: U 52 ARG cc_start: 0.8359 (mtt90) cc_final: 0.8094 (mtp180) REVERT: U 94 GLU cc_start: 0.8670 (mm-30) cc_final: 0.8303 (mm-30) outliers start: 66 outliers final: 28 residues processed: 498 average time/residue: 0.6302 time to fit residues: 377.7093 Evaluate side-chains 459 residues out of total 3044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 419 time to evaluate : 1.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 861 THR Chi-restraints excluded: chain A residue 934 THR Chi-restraints excluded: chain A residue 1144 ILE Chi-restraints excluded: chain A residue 1146 ILE Chi-restraints excluded: chain B residue 771 ASP Chi-restraints excluded: chain B residue 772 ASP Chi-restraints excluded: chain B residue 775 TRP Chi-restraints excluded: chain B residue 834 ILE Chi-restraints excluded: chain B residue 912 TRP Chi-restraints excluded: chain B residue 1219 LEU Chi-restraints excluded: chain C residue 153 LYS Chi-restraints excluded: chain D residue 249 SER Chi-restraints excluded: chain D residue 276 LEU Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain E residue 205 LEU Chi-restraints excluded: chain E residue 235 ASP Chi-restraints excluded: chain E residue 286 TRP Chi-restraints excluded: chain F residue 85 GLU Chi-restraints excluded: chain F residue 292 THR Chi-restraints excluded: chain G residue 106 GLU Chi-restraints excluded: chain G residue 175 ILE Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain I residue 39 CYS Chi-restraints excluded: chain J residue 206 MET Chi-restraints excluded: chain J residue 228 GLU Chi-restraints excluded: chain J residue 344 LEU Chi-restraints excluded: chain O residue 113 SER Chi-restraints excluded: chain Q residue 58 THR Chi-restraints excluded: chain Q residue 68 GLN Chi-restraints excluded: chain Q residue 133 GLU Chi-restraints excluded: chain R residue 49 LEU Chi-restraints excluded: chain R residue 96 THR Chi-restraints excluded: chain S residue 15 LYS Chi-restraints excluded: chain S residue 114 VAL Chi-restraints excluded: chain T residue 81 ASN Chi-restraints excluded: chain T residue 83 ARG Chi-restraints excluded: chain T residue 87 THR Chi-restraints excluded: chain T residue 102 GLU Chi-restraints excluded: chain V residue 96 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 318 optimal weight: 0.1980 chunk 107 optimal weight: 0.6980 chunk 70 optimal weight: 7.9990 chunk 12 optimal weight: 0.6980 chunk 32 optimal weight: 0.5980 chunk 86 optimal weight: 10.0000 chunk 262 optimal weight: 0.7980 chunk 57 optimal weight: 0.9990 chunk 226 optimal weight: 50.0000 chunk 15 optimal weight: 0.3980 chunk 248 optimal weight: 0.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 815 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 886 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 331 ASN D 375 ASN E 220 HIS ** E 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 183 GLN ** I 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 205 GLN J 331 GLN J 370 ASN J 378 ASN Q 68 GLN ** Q 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4322 r_free = 0.4322 target = 0.136168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.095972 restraints weight = 90091.651| |-----------------------------------------------------------------------------| r_work (start): 0.3497 rms_B_bonded: 2.75 r_work: 0.3263 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.3965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 35557 Z= 0.145 Angle : 0.684 12.072 49302 Z= 0.361 Chirality : 0.043 0.310 5443 Planarity : 0.004 0.069 5219 Dihedral : 24.912 170.480 7155 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 12.32 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.61 % Favored : 94.36 % Rotamer: Outliers : 1.61 % Allowed : 20.11 % Favored : 78.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.17 (0.14), residues: 3335 helix: 0.08 (0.12), residues: 1892 sheet: -1.83 (0.42), residues: 149 loop : -1.88 (0.16), residues: 1294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG J 293 TYR 0.031 0.001 TYR D 347 PHE 0.026 0.001 PHE D 197 TRP 0.035 0.002 TRP A 912 HIS 0.014 0.001 HIS B1293 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.14 (35556) covalent geometry : angle 0.68377 / 0.36 (49302) hydrogen bonds : bond 0.06348 / 4.08 ( 1493) hydrogen bonds : angle 4.22529 / 2.85 ( 4038) metal coordination : bond 0.00165 / 0.09 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6670 Ramachandran restraints generated. 3335 Oldfield, 0 Emsley, 3335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6670 Ramachandran restraints generated. 3335 Oldfield, 0 Emsley, 3335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 496 residues out of total 3044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 447 time to evaluate : 1.250 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 811 GLU cc_start: 0.8474 (tt0) cc_final: 0.8055 (tt0) REVERT: A 947 GLN cc_start: 0.8956 (tm-30) cc_final: 0.8714 (tm-30) REVERT: A 986 TYR cc_start: 0.7580 (t80) cc_final: 0.6688 (m-80) REVERT: A 1012 ASP cc_start: 0.8345 (m-30) cc_final: 0.8125 (t0) REVERT: A 1016 TYR cc_start: 0.6628 (m-10) cc_final: 0.6066 (m-10) REVERT: A 1261 LYS cc_start: 0.7758 (mmtt) cc_final: 0.7475 (mptp) REVERT: A 1273 ARG cc_start: 0.8746 (mmm-85) cc_final: 0.8518 (tpt90) REVERT: A 1300 MET cc_start: 0.6991 (ttp) cc_final: 0.6357 (ttm) REVERT: A 1301 PHE cc_start: 0.8588 (m-80) cc_final: 0.8244 (m-80) REVERT: A 1316 TYR cc_start: 0.7712 (p90) cc_final: 0.7294 (p90) REVERT: B 773 MET cc_start: 0.4694 (mmt) cc_final: 0.4411 (mpm) REVERT: B 834 ILE cc_start: 0.8235 (OUTLIER) cc_final: 0.7710 (tt) REVERT: B 881 ASP cc_start: 0.8917 (t0) cc_final: 0.8509 (p0) REVERT: B 912 TRP cc_start: 0.8040 (OUTLIER) cc_final: 0.7709 (t-100) REVERT: B 916 TRP cc_start: 0.8648 (m-10) cc_final: 0.8120 (m-10) REVERT: B 1257 MET cc_start: 0.7883 (ptp) cc_final: 0.7639 (ppp) REVERT: C 94 LEU cc_start: 0.9190 (tp) cc_final: 0.8979 (tm) REVERT: C 99 ARG cc_start: 0.8299 (ppt170) cc_final: 0.8058 (ppt170) REVERT: C 100 GLU cc_start: 0.8719 (mp0) cc_final: 0.8361 (mp0) REVERT: C 370 ASP cc_start: 0.8523 (t0) cc_final: 0.8296 (t0) REVERT: D 40 MET cc_start: 0.5911 (mmm) cc_final: 0.5509 (mmm) REVERT: D 128 MET cc_start: 0.8701 (mmm) cc_final: 0.8491 (mpm) REVERT: D 247 TYR cc_start: 0.8878 (t80) cc_final: 0.7934 (t80) REVERT: D 251 PHE cc_start: 0.8290 (p90) cc_final: 0.7545 (p90) REVERT: D 259 MET cc_start: 0.8727 (mtp) cc_final: 0.8471 (ptm) REVERT: D 288 MET cc_start: 0.8799 (ptt) cc_final: 0.8352 (mpp) REVERT: D 305 MET cc_start: 0.8332 (ttp) cc_final: 0.8025 (mtt) REVERT: D 306 MET cc_start: 0.7511 (tmm) cc_final: 0.6955 (tmm) REVERT: D 315 MET cc_start: 0.6430 (tpp) cc_final: 0.6158 (tpt) REVERT: D 322 TRP cc_start: 0.9157 (m-10) cc_final: 0.8699 (m-10) REVERT: D 344 TYR cc_start: 0.8523 (t80) cc_final: 0.8224 (t80) REVERT: D 369 LEU cc_start: 0.9314 (mt) cc_final: 0.8875 (pp) REVERT: E 235 ASP cc_start: 0.8613 (OUTLIER) cc_final: 0.8341 (p0) REVERT: E 286 TRP cc_start: 0.7784 (OUTLIER) cc_final: 0.7088 (t60) REVERT: E 288 ASP cc_start: 0.7921 (m-30) cc_final: 0.7240 (m-30) REVERT: F 50 ASP cc_start: 0.8673 (m-30) cc_final: 0.8427 (m-30) REVERT: F 61 GLN cc_start: 0.8508 (tp40) cc_final: 0.8277 (tp-100) REVERT: F 72 GLU cc_start: 0.8604 (tt0) cc_final: 0.8385 (tt0) REVERT: F 85 GLU cc_start: 0.8794 (OUTLIER) cc_final: 0.8383 (mp0) REVERT: G 126 ASN cc_start: 0.8004 (t0) cc_final: 0.7108 (p0) REVERT: G 168 ARG cc_start: 0.8234 (ptp-170) cc_final: 0.7754 (ptm-80) REVERT: G 175 ILE cc_start: 0.8114 (OUTLIER) cc_final: 0.7736 (pp) REVERT: H 244 ARG cc_start: 0.7877 (tpt170) cc_final: 0.7464 (ttm170) REVERT: I 16 ASP cc_start: 0.8755 (p0) cc_final: 0.8476 (p0) REVERT: I 43 MET cc_start: 0.8212 (ttm) cc_final: 0.7929 (mmp) REVERT: I 79 LEU cc_start: 0.8651 (tm) cc_final: 0.8125 (tp) REVERT: J 177 ASN cc_start: 0.7642 (p0) cc_final: 0.6793 (t0) REVERT: J 205 GLN cc_start: 0.8539 (tp-100) cc_final: 0.8148 (tp40) REVERT: J 206 MET cc_start: 0.8619 (OUTLIER) cc_final: 0.8343 (mmm) REVERT: J 228 GLU cc_start: 0.7800 (OUTLIER) cc_final: 0.7561 (tt0) REVERT: J 332 GLN cc_start: 0.8539 (tp40) cc_final: 0.7722 (pm20) REVERT: J 346 GLN cc_start: 0.8139 (tm-30) cc_final: 0.7869 (tm-30) REVERT: J 357 ARG cc_start: 0.9032 (ttp-170) cc_final: 0.8671 (ttp80) REVERT: J 358 ASN cc_start: 0.8573 (m110) cc_final: 0.8189 (m110) REVERT: J 361 LYS cc_start: 0.9435 (mtpt) cc_final: 0.9187 (mtpt) REVERT: J 375 ARG cc_start: 0.8390 (mmm160) cc_final: 0.7517 (mtp85) REVERT: J 378 ASN cc_start: 0.8631 (m-40) cc_final: 0.7987 (p0) REVERT: P 31 LYS cc_start: 0.7708 (tptt) cc_final: 0.7109 (tttp) REVERT: P 53 SER cc_start: 0.9050 (p) cc_final: 0.8782 (p) REVERT: Q 133 GLU cc_start: 0.8078 (OUTLIER) cc_final: 0.7860 (mt-10) REVERT: S 15 LYS cc_start: 0.7162 (OUTLIER) cc_final: 0.6607 (mttm) REVERT: S 36 LYS cc_start: 0.8714 (mmtm) cc_final: 0.8341 (mmmm) REVERT: S 71 ARG cc_start: 0.8112 (mtm110) cc_final: 0.7809 (mtm-85) REVERT: S 72 ASP cc_start: 0.8478 (m-30) cc_final: 0.8239 (m-30) REVERT: S 91 GLU cc_start: 0.7826 (pp20) cc_final: 0.7393 (pp20) REVERT: T 48 ASP cc_start: 0.7958 (m-30) cc_final: 0.7509 (t70) REVERT: T 85 THR cc_start: 0.8922 (t) cc_final: 0.8711 (p) REVERT: U 42 ARG cc_start: 0.8011 (mtm-85) cc_final: 0.7405 (mtm-85) REVERT: U 52 ARG cc_start: 0.8400 (mtt90) cc_final: 0.8091 (mtp180) REVERT: U 59 GLU cc_start: 0.8465 (pm20) cc_final: 0.7998 (pm20) REVERT: U 94 GLU cc_start: 0.8664 (mm-30) cc_final: 0.8319 (mm-30) REVERT: U 120 MET cc_start: 0.9074 (mmm) cc_final: 0.8822 (mtm) outliers start: 49 outliers final: 26 residues processed: 477 average time/residue: 0.6614 time to fit residues: 379.8118 Evaluate side-chains 460 residues out of total 3044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 424 time to evaluate : 1.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 861 THR Chi-restraints excluded: chain A residue 934 THR Chi-restraints excluded: chain A residue 1144 ILE Chi-restraints excluded: chain A residue 1146 ILE Chi-restraints excluded: chain A residue 1177 THR Chi-restraints excluded: chain B residue 775 TRP Chi-restraints excluded: chain B residue 834 ILE Chi-restraints excluded: chain B residue 912 TRP Chi-restraints excluded: chain D residue 249 SER Chi-restraints excluded: chain D residue 276 LEU Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain E residue 205 LEU Chi-restraints excluded: chain E residue 235 ASP Chi-restraints excluded: chain E residue 286 TRP Chi-restraints excluded: chain F residue 85 GLU Chi-restraints excluded: chain F residue 292 THR Chi-restraints excluded: chain G residue 106 GLU Chi-restraints excluded: chain G residue 175 ILE Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain I residue 39 CYS Chi-restraints excluded: chain J residue 206 MET Chi-restraints excluded: chain J residue 228 GLU Chi-restraints excluded: chain J residue 344 LEU Chi-restraints excluded: chain O residue 113 SER Chi-restraints excluded: chain Q residue 58 THR Chi-restraints excluded: chain Q residue 68 GLN Chi-restraints excluded: chain Q residue 133 GLU Chi-restraints excluded: chain R residue 49 LEU Chi-restraints excluded: chain R residue 96 THR Chi-restraints excluded: chain S residue 15 LYS Chi-restraints excluded: chain S residue 114 VAL Chi-restraints excluded: chain T residue 81 ASN Chi-restraints excluded: chain T residue 87 THR Chi-restraints excluded: chain T residue 102 GLU Chi-restraints excluded: chain V residue 96 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 55 optimal weight: 9.9990 chunk 100 optimal weight: 0.8980 chunk 52 optimal weight: 0.9990 chunk 284 optimal weight: 1.9990 chunk 302 optimal weight: 0.9980 chunk 252 optimal weight: 0.9980 chunk 70 optimal weight: 1.9990 chunk 348 optimal weight: 20.0000 chunk 139 optimal weight: 8.9990 chunk 261 optimal weight: 4.9990 chunk 182 optimal weight: 0.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 815 HIS ** B 886 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 930 HIS ** C 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 330 ASN ** D 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 220 HIS ** E 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 370 ASN Q 68 GLN ** Q 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.135870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.093871 restraints weight = 90539.746| |-----------------------------------------------------------------------------| r_work (start): 0.3473 rms_B_bonded: 2.42 r_work: 0.3286 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.4034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 35557 Z= 0.175 Angle : 0.704 13.233 49302 Z= 0.370 Chirality : 0.044 0.298 5443 Planarity : 0.004 0.075 5219 Dihedral : 24.882 169.965 7153 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 12.57 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.64 % Favored : 94.33 % Rotamer: Outliers : 1.48 % Allowed : 20.89 % Favored : 77.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.11 (0.14), residues: 3335 helix: 0.12 (0.12), residues: 1899 sheet: -1.84 (0.42), residues: 149 loop : -1.84 (0.16), residues: 1287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG J 293 TYR 0.022 0.001 TYR K 252 PHE 0.029 0.002 PHE G 111 TRP 0.041 0.002 TRP A 912 HIS 0.011 0.001 HIS B1293 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.18 (35556) covalent geometry : angle 0.70442 / 0.37 (49302) hydrogen bonds : bond 0.06227 / 4.01 ( 1493) hydrogen bonds : angle 4.23672 / 2.86 ( 4038) metal coordination : bond 0.00260 / 0.14 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6670 Ramachandran restraints generated. 3335 Oldfield, 0 Emsley, 3335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6670 Ramachandran restraints generated. 3335 Oldfield, 0 Emsley, 3335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 477 residues out of total 3044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 432 time to evaluate : 1.156 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 811 GLU cc_start: 0.8391 (tt0) cc_final: 0.8009 (tt0) REVERT: A 947 GLN cc_start: 0.8949 (tm-30) cc_final: 0.8714 (tm-30) REVERT: A 986 TYR cc_start: 0.7544 (t80) cc_final: 0.6653 (m-80) REVERT: A 1016 TYR cc_start: 0.6575 (m-10) cc_final: 0.6217 (m-10) REVERT: A 1156 GLU cc_start: 0.8146 (tp30) cc_final: 0.7725 (tp30) REVERT: A 1261 LYS cc_start: 0.7731 (mmtt) cc_final: 0.7460 (mptp) REVERT: A 1273 ARG cc_start: 0.8760 (mmm-85) cc_final: 0.8524 (tpt90) REVERT: A 1300 MET cc_start: 0.7076 (ttp) cc_final: 0.6434 (ttm) REVERT: A 1301 PHE cc_start: 0.8591 (m-80) cc_final: 0.8217 (m-80) REVERT: A 1316 TYR cc_start: 0.7654 (p90) cc_final: 0.7239 (p90) REVERT: B 821 ILE cc_start: 0.8322 (OUTLIER) cc_final: 0.7855 (tp) REVERT: B 834 ILE cc_start: 0.8066 (OUTLIER) cc_final: 0.7517 (tt) REVERT: B 881 ASP cc_start: 0.8795 (t0) cc_final: 0.8439 (p0) REVERT: B 912 TRP cc_start: 0.8042 (OUTLIER) cc_final: 0.6992 (t-100) REVERT: B 1257 MET cc_start: 0.7770 (ptp) cc_final: 0.7106 (ppp) REVERT: C 99 ARG cc_start: 0.8349 (ppt170) cc_final: 0.8065 (ppt170) REVERT: C 100 GLU cc_start: 0.8687 (mp0) cc_final: 0.8330 (mp0) REVERT: C 370 ASP cc_start: 0.8505 (t0) cc_final: 0.8276 (t0) REVERT: D 40 MET cc_start: 0.6125 (mmm) cc_final: 0.5843 (mmm) REVERT: D 128 MET cc_start: 0.8698 (mmm) cc_final: 0.8485 (mpm) REVERT: D 247 TYR cc_start: 0.8878 (t80) cc_final: 0.7947 (t80) REVERT: D 251 PHE cc_start: 0.8336 (p90) cc_final: 0.7580 (p90) REVERT: D 259 MET cc_start: 0.8701 (mtp) cc_final: 0.8432 (ptm) REVERT: D 288 MET cc_start: 0.8760 (ptt) cc_final: 0.8350 (mpp) REVERT: D 305 MET cc_start: 0.8326 (ttp) cc_final: 0.7981 (mtt) REVERT: D 306 MET cc_start: 0.7457 (tmm) cc_final: 0.6889 (tmm) REVERT: D 315 MET cc_start: 0.6254 (tpp) cc_final: 0.5998 (tpt) REVERT: D 322 TRP cc_start: 0.9185 (m-10) cc_final: 0.8734 (m-10) REVERT: D 344 TYR cc_start: 0.8527 (t80) cc_final: 0.8239 (t80) REVERT: D 369 LEU cc_start: 0.9306 (mt) cc_final: 0.8869 (pp) REVERT: E 227 TYR cc_start: 0.8790 (m-80) cc_final: 0.8585 (m-80) REVERT: E 235 ASP cc_start: 0.8605 (OUTLIER) cc_final: 0.8317 (p0) REVERT: E 286 TRP cc_start: 0.7745 (OUTLIER) cc_final: 0.7042 (t60) REVERT: F 50 ASP cc_start: 0.8640 (m-30) cc_final: 0.8395 (m-30) REVERT: F 61 GLN cc_start: 0.8492 (tp40) cc_final: 0.8259 (tp-100) REVERT: F 85 GLU cc_start: 0.8752 (OUTLIER) cc_final: 0.8342 (mp0) REVERT: G 168 ARG cc_start: 0.8214 (ptp-170) cc_final: 0.7842 (ptm-80) REVERT: G 175 ILE cc_start: 0.8133 (OUTLIER) cc_final: 0.7788 (pp) REVERT: H 244 ARG cc_start: 0.7740 (tpt170) cc_final: 0.7406 (ttm170) REVERT: I 16 ASP cc_start: 0.8762 (p0) cc_final: 0.8466 (p0) REVERT: I 43 MET cc_start: 0.8212 (ttm) cc_final: 0.7871 (mmp) REVERT: I 79 LEU cc_start: 0.8641 (tm) cc_final: 0.8140 (tp) REVERT: I 91 SER cc_start: 0.9423 (m) cc_final: 0.9156 (p) REVERT: J 177 ASN cc_start: 0.7506 (p0) cc_final: 0.6616 (t0) REVERT: J 206 MET cc_start: 0.8533 (OUTLIER) cc_final: 0.8251 (mmm) REVERT: J 228 GLU cc_start: 0.7805 (OUTLIER) cc_final: 0.7563 (tt0) REVERT: J 332 GLN cc_start: 0.8557 (tp40) cc_final: 0.7734 (pm20) REVERT: J 346 GLN cc_start: 0.8132 (tm-30) cc_final: 0.7865 (tm-30) REVERT: J 357 ARG cc_start: 0.8906 (ttp-170) cc_final: 0.8625 (ttp80) REVERT: J 358 ASN cc_start: 0.8612 (m110) cc_final: 0.8333 (m110) REVERT: J 361 LYS cc_start: 0.9415 (mtpt) cc_final: 0.9088 (mtpt) REVERT: J 375 ARG cc_start: 0.8398 (mmm160) cc_final: 0.7538 (mtp85) REVERT: J 378 ASN cc_start: 0.8598 (m-40) cc_final: 0.7995 (p0) REVERT: P 31 LYS cc_start: 0.7715 (tptt) cc_final: 0.7139 (tttp) REVERT: P 53 SER cc_start: 0.9050 (p) cc_final: 0.8778 (p) REVERT: Q 133 GLU cc_start: 0.8076 (OUTLIER) cc_final: 0.7857 (mt-10) REVERT: S 15 LYS cc_start: 0.7172 (OUTLIER) cc_final: 0.6632 (mttm) REVERT: S 36 LYS cc_start: 0.8708 (mmtm) cc_final: 0.8329 (mmmm) REVERT: S 71 ARG cc_start: 0.8030 (mtm110) cc_final: 0.7746 (mtm-85) REVERT: S 72 ASP cc_start: 0.8473 (m-30) cc_final: 0.8230 (m-30) REVERT: S 91 GLU cc_start: 0.7766 (pp20) cc_final: 0.7318 (pp20) REVERT: T 48 ASP cc_start: 0.7898 (m-30) cc_final: 0.7482 (t70) REVERT: U 42 ARG cc_start: 0.8045 (mtm-85) cc_final: 0.7448 (mtm-85) REVERT: U 52 ARG cc_start: 0.8355 (mtt90) cc_final: 0.8060 (mtp180) REVERT: U 94 GLU cc_start: 0.8634 (mm-30) cc_final: 0.8290 (mm-30) REVERT: U 120 MET cc_start: 0.9047 (mmm) cc_final: 0.8790 (mtm) outliers start: 45 outliers final: 23 residues processed: 455 average time/residue: 0.6609 time to fit residues: 360.6790 Evaluate side-chains 454 residues out of total 3044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 420 time to evaluate : 0.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 861 THR Chi-restraints excluded: chain A residue 934 THR Chi-restraints excluded: chain A residue 1177 THR Chi-restraints excluded: chain B residue 775 TRP Chi-restraints excluded: chain B residue 821 ILE Chi-restraints excluded: chain B residue 834 ILE Chi-restraints excluded: chain B residue 912 TRP Chi-restraints excluded: chain D residue 249 SER Chi-restraints excluded: chain D residue 276 LEU Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain E residue 205 LEU Chi-restraints excluded: chain E residue 235 ASP Chi-restraints excluded: chain E residue 286 TRP Chi-restraints excluded: chain F residue 85 GLU Chi-restraints excluded: chain F residue 292 THR Chi-restraints excluded: chain G residue 106 GLU Chi-restraints excluded: chain G residue 175 ILE Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain I residue 39 CYS Chi-restraints excluded: chain J residue 206 MET Chi-restraints excluded: chain J residue 228 GLU Chi-restraints excluded: chain J residue 344 LEU Chi-restraints excluded: chain O residue 113 SER Chi-restraints excluded: chain Q residue 58 THR Chi-restraints excluded: chain Q residue 68 GLN Chi-restraints excluded: chain Q residue 133 GLU Chi-restraints excluded: chain R residue 49 LEU Chi-restraints excluded: chain R residue 96 THR Chi-restraints excluded: chain S residue 15 LYS Chi-restraints excluded: chain S residue 114 VAL Chi-restraints excluded: chain T residue 81 ASN Chi-restraints excluded: chain T residue 87 THR Chi-restraints excluded: chain T residue 102 GLU Chi-restraints excluded: chain V residue 96 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 353 optimal weight: 6.9990 chunk 132 optimal weight: 0.8980 chunk 332 optimal weight: 40.0000 chunk 330 optimal weight: 0.9980 chunk 251 optimal weight: 0.8980 chunk 123 optimal weight: 0.8980 chunk 199 optimal weight: 0.9990 chunk 235 optimal weight: 1.9990 chunk 247 optimal weight: 0.8980 chunk 140 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B1221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 38 HIS ** D 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 220 HIS ** E 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 205 GLN ** J 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 370 ASN Q 68 GLN ** Q 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 104 GLN ** T 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.135940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.094061 restraints weight = 90373.862| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 2.39 r_work: 0.3295 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.4107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 35557 Z= 0.170 Angle : 0.697 12.992 49302 Z= 0.367 Chirality : 0.044 0.289 5443 Planarity : 0.004 0.074 5219 Dihedral : 24.867 169.248 7153 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 12.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 1.45 % Allowed : 20.86 % Favored : 77.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.07 (0.14), residues: 3335 helix: 0.15 (0.12), residues: 1901 sheet: -1.86 (0.42), residues: 149 loop : -1.82 (0.16), residues: 1285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG J 293 TYR 0.032 0.002 TYR D 297 PHE 0.030 0.002 PHE D 197 TRP 0.041 0.002 TRP A 912 HIS 0.012 0.001 HIS B1293 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.17 (35556) covalent geometry : angle 0.69746 / 0.37 (49302) hydrogen bonds : bond 0.06190 / 3.99 ( 1493) hydrogen bonds : angle 4.21697 / 2.85 ( 4038) metal coordination : bond 0.00242 / 0.13 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13390.78 seconds wall clock time: 228 minutes 25.30 seconds (13705.30 seconds total)