Starting phenix.real_space_refine on Mon Jul 6 10:59:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9v2v_64741/07_2026/9v2v_64741.cif Found real_map, /net/cci-nas-00/data/ceres_data/9v2v_64741/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9v2v_64741/07_2026/9v2v_64741.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9v2v_64741/07_2026/9v2v_64741.map" model { file = "/net/cci-nas-00/data/ceres_data/9v2v_64741/07_2026/9v2v_64741.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9v2v_64741/07_2026/9v2v_64741.cif" } 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-dev-6108/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: 6.02, per 1000 atoms: 0.18 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: 2.98 Conformation dependent library (CDL) restraints added in 1.3 seconds 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: 4.64 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: 7.73 Time building geometry restraints manager: 3.99 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: 45475 2.16 - 4.31: 3301 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: 19.820 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.010 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.790 Check model and map are aligned: 0.110 Set scattering table: 0.090 Process input model: 36.720 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.500 ------------------------------------------------------------------------------- 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= 0.968 Angle : 1.231 10.777 49302 Z= 0.804 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 / 0.96 (35556) covalent geometry : angle 1.23101 / 0.80 (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 : 1.115 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 940 LYS cc_start: 0.8963 (tppp) cc_final: 0.8682 (tttm) 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: 0.8488 (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: 0.8029 time to fit residues: 668.5035 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 : 1.237 ------------------------------------------------------------------------------- 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 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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** ** I 114 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 Q 68 GLN Q 108 ASN ** Q 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 44 GLN T 46 HIS Total number of N/Q/H flips: 44 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4335 r_free = 0.4335 target = 0.136362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.097334 restraints weight = 90888.194| |-----------------------------------------------------------------------------| r_work (start): 0.3551 rms_B_bonded: 2.66 r_work: 0.3304 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.2515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 35557 Z= 0.189 Angle : 0.789 12.292 49302 Z= 0.426 Chirality : 0.048 0.241 5443 Planarity : 0.006 0.060 5219 Dihedral : 25.168 176.339 7172 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 12.31 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.34 % Favored : 94.57 % Rotamer: Outliers : 2.96 % Allowed : 11.33 % Favored : 85.71 % 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: -3.56 (0.12), residues: 3335 helix: -2.17 (0.09), residues: 1882 sheet: -2.83 (0.37), residues: 156 loop : -2.37 (0.15), residues: 1297 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.035 0.001 ARG B1273 TYR 0.029 0.002 TYR D 117 PHE 0.026 0.002 PHE G 119 TRP 0.027 0.002 TRP A 912 HIS 0.015 0.001 HIS H 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.19 (35556) covalent geometry : angle 0.78913 / 0.43 (49302) hydrogen bonds : bond 0.08075 / 5.12 ( 1493) hydrogen bonds : angle 5.28916 / 3.58 ( 4038) metal coordination : bond 0.02195 / 1.16 ( 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 626 residues out of total 3044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 536 time to evaluate : 1.139 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 811 GLU cc_start: 0.8401 (tt0) cc_final: 0.7878 (tt0) REVERT: A 986 TYR cc_start: 0.7624 (t80) cc_final: 0.6713 (m-80) REVERT: A 1146 ILE cc_start: 0.8922 (pt) cc_final: 0.8595 (mt) REVERT: A 1156 GLU cc_start: 0.8246 (tp30) cc_final: 0.7874 (tp30) REVERT: A 1261 LYS cc_start: 0.7749 (mmtt) cc_final: 0.7489 (tptp) REVERT: A 1301 PHE cc_start: 0.8688 (m-80) cc_final: 0.8208 (m-80) REVERT: B 881 ASP cc_start: 0.8824 (t0) cc_final: 0.8282 (p0) REVERT: B 916 TRP cc_start: 0.8152 (m-10) cc_final: 0.7545 (m-10) REVERT: B 1257 MET cc_start: 0.7998 (ptp) cc_final: 0.7708 (ppp) REVERT: B 1294 MET cc_start: 0.7773 (ptp) cc_final: 0.7432 (tpp) REVERT: B 1317 ILE cc_start: 0.7825 (mm) cc_final: 0.7612 (mm) REVERT: C 94 LEU cc_start: 0.9138 (tp) cc_final: 0.8933 (tm) REVERT: C 100 GLU cc_start: 0.8404 (mp0) cc_final: 0.8095 (mp0) REVERT: D 232 TYR cc_start: 0.6570 (m-10) cc_final: 0.6335 (m-10) REVERT: D 247 TYR cc_start: 0.8888 (t80) cc_final: 0.8598 (t80) REVERT: D 305 MET cc_start: 0.8425 (ttp) cc_final: 0.7932 (mtt) REVERT: D 306 MET cc_start: 0.7794 (mtp) cc_final: 0.7423 (mtp) REVERT: D 322 TRP cc_start: 0.8902 (m-10) cc_final: 0.8480 (m-10) REVERT: D 344 TYR cc_start: 0.8499 (t80) cc_final: 0.8123 (t80) REVERT: D 347 TYR cc_start: 0.9148 (m-80) cc_final: 0.8920 (m-80) REVERT: D 369 LEU cc_start: 0.9143 (mt) cc_final: 0.8803 (pp) REVERT: D 371 LYS cc_start: 0.9238 (ptpt) cc_final: 0.9031 (ptpt) REVERT: D 376 ILE cc_start: 0.9429 (mp) cc_final: 0.9209 (mp) REVERT: E 226 TYR cc_start: 0.8438 (p90) cc_final: 0.7876 (p90) REVERT: E 227 TYR cc_start: 0.9101 (m-10) cc_final: 0.8798 (m-10) REVERT: F 61 GLN cc_start: 0.8484 (tp-100) cc_final: 0.8123 (tm-30) REVERT: F 85 GLU cc_start: 0.8653 (OUTLIER) cc_final: 0.8288 (mp0) REVERT: F 135 MET cc_start: 0.3111 (mpm) cc_final: 0.2809 (mpm) REVERT: G 168 ARG cc_start: 0.8110 (ptm-80) cc_final: 0.7635 (ptm-80) REVERT: G 183 GLN cc_start: 0.6858 (mm110) cc_final: 0.6596 (mm-40) REVERT: I 78 GLU cc_start: 0.8372 (pt0) cc_final: 0.8054 (pp20) REVERT: I 84 GLU cc_start: 0.8798 (tm-30) cc_final: 0.8472 (tp30) REVERT: I 87 MET cc_start: 0.8394 (ttp) cc_final: 0.7846 (ttp) REVERT: J 179 LYS cc_start: 0.3803 (mttt) cc_final: 0.3554 (mttt) REVERT: J 228 GLU cc_start: 0.7331 (OUTLIER) cc_final: 0.6589 (tp30) REVERT: J 357 ARG cc_start: 0.9056 (ttp-170) cc_final: 0.8786 (ttp80) REVERT: J 358 ASN cc_start: 0.8287 (m110) cc_final: 0.7967 (m110) REVERT: O 15 LYS cc_start: 0.7502 (tmtt) cc_final: 0.7264 (ttpp) REVERT: P 31 LYS cc_start: 0.7692 (tptt) cc_final: 0.7114 (tttp) REVERT: Q 133 GLU cc_start: 0.8036 (OUTLIER) cc_final: 0.7777 (mt-10) REVERT: S 36 LYS cc_start: 0.8683 (mmtm) cc_final: 0.8321 (mmmm) REVERT: S 71 ARG cc_start: 0.8120 (mtm110) cc_final: 0.7862 (mtm-85) REVERT: S 91 GLU cc_start: 0.7735 (pp20) cc_final: 0.7258 (pm20) REVERT: T 83 ARG cc_start: 0.8695 (OUTLIER) cc_final: 0.7560 (mtt-85) REVERT: U 42 ARG cc_start: 0.7686 (mtm-85) cc_final: 0.7058 (mtt-85) REVERT: U 52 ARG cc_start: 0.8335 (mtt90) cc_final: 0.7975 (mtm110) REVERT: U 94 GLU cc_start: 0.8648 (mm-30) cc_final: 0.8342 (mm-30) REVERT: V 50 ILE cc_start: 0.8430 (tt) cc_final: 0.8135 (tt) outliers start: 90 outliers final: 27 residues processed: 580 average time/residue: 0.6959 time to fit residues: 482.6220 Evaluate side-chains 465 residues out of total 3044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 434 time to evaluate : 1.105 ------------------------------------------------------------------------------- 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 775 TRP Chi-restraints excluded: chain B residue 828 ILE Chi-restraints excluded: chain B residue 912 TRP Chi-restraints excluded: chain B residue 1204 TYR 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 229 LYS 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 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: 0.8980 chunk 275 optimal weight: 0.6980 chunk 247 optimal weight: 3.9990 chunk 249 optimal weight: 2.9990 chunk 234 optimal weight: 0.8980 chunk 115 optimal weight: 3.9990 chunk 206 optimal weight: 0.5980 chunk 4 optimal weight: 10.0000 chunk 45 optimal weight: 0.0980 chunk 280 optimal weight: 4.9990 chunk 86 optimal weight: 8.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 359 ASN ** E 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 178 HIS J 196 GLN J 331 GLN J 350 GLN P 46 HIS ** Q 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.135910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.093774 restraints weight = 90734.902| |-----------------------------------------------------------------------------| r_work (start): 0.3480 rms_B_bonded: 2.38 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: 0.8349 moved from start: 0.2970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 35557 Z= 0.169 Angle : 0.694 9.479 49302 Z= 0.377 Chirality : 0.045 0.244 5443 Planarity : 0.005 0.050 5219 Dihedral : 25.061 175.606 7155 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.85 % Favored : 94.12 % Rotamer: Outliers : 2.92 % Allowed : 14.16 % Favored : 82.92 % 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: -2.55 (0.13), residues: 3335 helix: -1.16 (0.11), residues: 1870 sheet: -2.58 (0.37), residues: 168 loop : -2.21 (0.15), residues: 1297 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG Q 72 TYR 0.030 0.002 TYR D 297 PHE 0.028 0.002 PHE B1269 TRP 0.023 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 0.69418 / 0.38 (49302) hydrogen bonds : bond 0.07271 / 4.67 ( 1493) hydrogen bonds : angle 4.75915 / 3.20 ( 4038) metal coordination : bond 0.00071 / 0.04 ( 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 573 residues out of total 3044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 484 time to evaluate : 1.297 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: A 757 ARG cc_start: 0.7889 (tpt-90) cc_final: 0.7608 (tpt-90) REVERT: A 811 GLU cc_start: 0.8408 (tt0) cc_final: 0.7934 (tt0) REVERT: A 940 LYS cc_start: 0.9104 (tttm) cc_final: 0.8635 (ttpt) REVERT: A 986 TYR cc_start: 0.7487 (t80) cc_final: 0.6584 (m-80) REVERT: A 1016 TYR cc_start: 0.6877 (m-10) cc_final: 0.6643 (m-80) REVERT: A 1156 GLU cc_start: 0.8190 (tp30) cc_final: 0.7764 (tp30) REVERT: A 1261 LYS cc_start: 0.7714 (mmtt) cc_final: 0.7487 (tptp) REVERT: A 1301 PHE cc_start: 0.8633 (m-80) cc_final: 0.8250 (m-80) REVERT: A 1316 TYR cc_start: 0.7620 (p90) cc_final: 0.7248 (p90) REVERT: B 821 ILE cc_start: 0.8259 (OUTLIER) cc_final: 0.7788 (tp) REVERT: B 881 ASP cc_start: 0.8699 (t0) cc_final: 0.8224 (p0) REVERT: B 916 TRP cc_start: 0.8238 (m-10) cc_final: 0.7512 (m-10) REVERT: B 1150 HIS cc_start: 0.7685 (m170) cc_final: 0.7431 (m-70) REVERT: B 1232 TYR cc_start: 0.7587 (t80) cc_final: 0.7381 (t80) REVERT: B 1257 MET cc_start: 0.7839 (ptp) cc_final: 0.7473 (ppp) REVERT: C 73 GLU cc_start: 0.8653 (mt-10) cc_final: 0.8425 (mt-10) REVERT: C 100 GLU cc_start: 0.8460 (mp0) cc_final: 0.8137 (mp0) REVERT: D 232 TYR cc_start: 0.6324 (m-10) cc_final: 0.6123 (m-10) REVERT: D 247 TYR cc_start: 0.8986 (t80) cc_final: 0.8704 (t80) REVERT: D 251 PHE cc_start: 0.8600 (p90) cc_final: 0.8311 (p90) REVERT: D 259 MET cc_start: 0.8413 (ptm) cc_final: 0.7618 (ppp) REVERT: D 288 MET cc_start: 0.8753 (ptt) cc_final: 0.8539 (ptt) REVERT: D 344 TYR cc_start: 0.8447 (t80) cc_final: 0.8097 (t80) REVERT: D 347 TYR cc_start: 0.9118 (m-80) cc_final: 0.8869 (m-80) REVERT: D 376 ILE cc_start: 0.9387 (mp) cc_final: 0.9141 (mp) REVERT: E 226 TYR cc_start: 0.8512 (p90) cc_final: 0.8280 (p90) REVERT: E 227 TYR cc_start: 0.9058 (m-10) cc_final: 0.8790 (m-10) REVERT: E 270 LYS cc_start: 0.8761 (mttp) cc_final: 0.8477 (mtmt) REVERT: E 286 TRP cc_start: 0.7771 (OUTLIER) cc_final: 0.6983 (t60) REVERT: F 50 ASP cc_start: 0.8578 (m-30) cc_final: 0.8325 (m-30) REVERT: F 61 GLN cc_start: 0.8496 (tp-100) cc_final: 0.8295 (tp-100) REVERT: F 65 GLN cc_start: 0.9089 (mt0) cc_final: 0.8871 (mt0) REVERT: F 85 GLU cc_start: 0.8718 (OUTLIER) cc_final: 0.8300 (mp0) REVERT: J 206 MET cc_start: 0.8570 (OUTLIER) cc_final: 0.8232 (mmm) REVERT: J 351 ARG cc_start: 0.8282 (mtt180) cc_final: 0.8071 (mmt90) REVERT: J 357 ARG cc_start: 0.9045 (ttp-170) cc_final: 0.8726 (ttp80) REVERT: J 378 ASN cc_start: 0.8653 (m-40) cc_final: 0.7903 (p0) REVERT: O 74 LYS cc_start: 0.8848 (mmtt) cc_final: 0.8643 (tppt) REVERT: O 91 GLU cc_start: 0.8421 (tm-30) cc_final: 0.8162 (tm-30) REVERT: P 31 LYS cc_start: 0.7699 (tptt) cc_final: 0.7095 (tttp) REVERT: Q 133 GLU cc_start: 0.8075 (OUTLIER) cc_final: 0.7786 (mt-10) REVERT: S 36 LYS cc_start: 0.8694 (mmtm) cc_final: 0.8320 (mmmm) REVERT: S 71 ARG cc_start: 0.8063 (mtm110) cc_final: 0.7753 (mtt-85) REVERT: S 72 ASP cc_start: 0.8458 (m-30) cc_final: 0.8203 (m-30) REVERT: S 91 GLU cc_start: 0.7692 (OUTLIER) cc_final: 0.7239 (pm20) REVERT: T 83 ARG cc_start: 0.8708 (OUTLIER) cc_final: 0.7556 (mtt-85) REVERT: U 42 ARG cc_start: 0.7634 (mtm-85) cc_final: 0.7354 (mtm-85) REVERT: U 52 ARG cc_start: 0.8273 (mtt90) cc_final: 0.8033 (mtp180) REVERT: U 59 GLU cc_start: 0.8380 (OUTLIER) cc_final: 0.8153 (pt0) REVERT: U 94 GLU cc_start: 0.8622 (mm-30) cc_final: 0.8279 (mm-30) REVERT: V 50 ILE cc_start: 0.8404 (tt) cc_final: 0.8091 (tt) outliers start: 89 outliers final: 36 residues processed: 523 average time/residue: 0.7083 time to fit residues: 442.6647 Evaluate side-chains 480 residues out of total 3044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 436 time to evaluate : 1.233 ------------------------------------------------------------------------------- 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 996 ILE Chi-restraints excluded: chain A residue 1144 ILE 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 C residue 122 ILE Chi-restraints excluded: chain C residue 370 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 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 P residue 110 GLU 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 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 58 THR Chi-restraints excluded: chain U residue 59 GLU 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 optimal weight: 2.9990 chunk 276 optimal weight: 2.9990 chunk 246 optimal weight: 2.9990 chunk 35 optimal weight: 4.9990 chunk 3 optimal weight: 6.9990 chunk 169 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 83 optimal weight: 10.0000 chunk 281 optimal weight: 0.6980 chunk 226 optimal weight: 5.9990 chunk 164 optimal weight: 9.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1137 ASN ** B1252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 43 HIS ** 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 360 GLN O 38 ASN Q 68 GLN Q 108 ASN ** Q 113 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 = 0.4293 r_free = 0.4293 target = 0.134292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.093187 restraints weight = 90388.319| |-----------------------------------------------------------------------------| r_work (start): 0.3440 rms_B_bonded: 2.62 r_work: 0.3221 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.3112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 35557 Z= 0.267 Angle : 0.715 9.266 49302 Z= 0.383 Chirality : 0.046 0.248 5443 Planarity : 0.005 0.045 5219 Dihedral : 25.195 175.322 7155 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 13.08 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.94 % Favored : 94.03 % Rotamer: Outliers : 3.15 % Allowed : 15.64 % Favored : 81.21 % 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: -2.11 (0.13), residues: 3335 helix: -0.75 (0.11), residues: 1873 sheet: -2.51 (0.38), residues: 166 loop : -2.09 (0.16), residues: 1296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG J 293 TYR 0.022 0.002 TYR D 297 PHE 0.024 0.002 PHE B1269 TRP 0.023 0.001 TRP A 912 HIS 0.013 0.001 HIS A1252 Details of bonding type rmsd/Z covalent geometry : bond 0.00584 / 0.27 (35556) covalent geometry : angle 0.71509 / 0.38 (49302) hydrogen bonds : bond 0.06830 / 4.41 ( 1493) hydrogen bonds : angle 4.62216 / 3.11 ( 4038) metal coordination : bond 0.00433 / 0.23 ( 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 559 residues out of total 3044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 463 time to evaluate : 1.227 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: A 811 GLU cc_start: 0.8472 (tt0) cc_final: 0.8017 (tt0) REVERT: A 947 GLN cc_start: 0.8891 (tm-30) cc_final: 0.8643 (tm-30) REVERT: A 986 TYR cc_start: 0.7610 (t80) cc_final: 0.6688 (m-80) REVERT: A 1016 TYR cc_start: 0.6779 (m-10) cc_final: 0.6485 (m-10) REVERT: A 1146 ILE cc_start: 0.8931 (OUTLIER) cc_final: 0.8691 (mt) REVERT: A 1156 GLU cc_start: 0.8236 (tp30) cc_final: 0.7844 (tp30) REVERT: A 1261 LYS cc_start: 0.7817 (mmtt) cc_final: 0.7574 (tptp) REVERT: A 1273 ARG cc_start: 0.8781 (mmm-85) cc_final: 0.8049 (tpt-90) REVERT: A 1316 TYR cc_start: 0.7574 (p90) cc_final: 0.7176 (p90) REVERT: B 881 ASP cc_start: 0.8864 (t0) cc_final: 0.8350 (p0) REVERT: B 912 TRP cc_start: 0.7921 (OUTLIER) cc_final: 0.7604 (t-100) REVERT: B 916 TRP cc_start: 0.8484 (m-10) cc_final: 0.8144 (m-10) REVERT: B 1150 HIS cc_start: 0.7842 (m170) cc_final: 0.7538 (m-70) REVERT: B 1194 MET cc_start: 0.2371 (ptt) cc_final: 0.2128 (ptt) REVERT: B 1257 MET cc_start: 0.7961 (ptp) cc_final: 0.7404 (ppp) REVERT: B 1317 ILE cc_start: 0.7578 (mm) cc_final: 0.7357 (mm) REVERT: C 100 GLU cc_start: 0.8546 (mp0) cc_final: 0.8250 (mp0) REVERT: D 49 HIS cc_start: 0.9342 (t-170) cc_final: 0.9074 (t-170) REVERT: D 232 TYR cc_start: 0.6416 (m-10) cc_final: 0.6177 (m-10) REVERT: D 251 PHE cc_start: 0.8589 (p90) cc_final: 0.8336 (p90) REVERT: D 305 MET cc_start: 0.8479 (ttp) cc_final: 0.8018 (mtt) REVERT: D 322 TRP cc_start: 0.9135 (m-10) cc_final: 0.8563 (m-10) REVERT: D 344 TYR cc_start: 0.8496 (t80) cc_final: 0.8183 (t80) REVERT: D 347 TYR cc_start: 0.9267 (m-80) cc_final: 0.8969 (m-80) REVERT: D 353 LEU cc_start: 0.8698 (OUTLIER) cc_final: 0.8472 (pt) REVERT: D 369 LEU cc_start: 0.9331 (mt) cc_final: 0.8916 (pp) REVERT: D 376 ILE cc_start: 0.9424 (mp) cc_final: 0.9222 (mp) REVERT: E 227 TYR cc_start: 0.9028 (m-10) cc_final: 0.8785 (m-10) REVERT: E 286 TRP cc_start: 0.7801 (OUTLIER) cc_final: 0.6953 (t60) REVERT: F 50 ASP cc_start: 0.8615 (m-30) cc_final: 0.8305 (m-30) REVERT: F 61 GLN cc_start: 0.8500 (tp-100) cc_final: 0.8195 (tp-100) REVERT: F 72 GLU cc_start: 0.8619 (tt0) cc_final: 0.8392 (tt0) REVERT: F 85 GLU cc_start: 0.8785 (OUTLIER) cc_final: 0.8367 (mp0) REVERT: G 168 ARG cc_start: 0.8124 (ptm-80) cc_final: 0.7726 (ptm-80) REVERT: I 78 GLU cc_start: 0.8055 (tm-30) cc_final: 0.7776 (tp30) REVERT: J 206 MET cc_start: 0.8635 (OUTLIER) cc_final: 0.8289 (mmm) REVERT: J 332 GLN cc_start: 0.8550 (tp40) cc_final: 0.7717 (pm20) REVERT: J 351 ARG cc_start: 0.8291 (mtt180) cc_final: 0.8071 (mmt90) REVERT: J 357 ARG cc_start: 0.9036 (ttp-170) cc_final: 0.8746 (ttp80) REVERT: J 378 ASN cc_start: 0.8699 (m-40) cc_final: 0.7962 (p0) REVERT: O 74 LYS cc_start: 0.8937 (mmtt) cc_final: 0.8690 (tppt) REVERT: P 31 LYS cc_start: 0.7738 (tptt) cc_final: 0.7123 (tttp) REVERT: Q 133 GLU cc_start: 0.8132 (OUTLIER) cc_final: 0.7828 (mt-10) REVERT: S 36 LYS cc_start: 0.8758 (mmtm) cc_final: 0.8379 (mmmm) REVERT: S 71 ARG cc_start: 0.8132 (mtm110) cc_final: 0.7802 (mtt-85) REVERT: S 72 ASP cc_start: 0.8531 (m-30) cc_final: 0.8300 (m-30) REVERT: S 91 GLU cc_start: 0.7749 (OUTLIER) cc_final: 0.7544 (pp20) REVERT: T 83 ARG cc_start: 0.8741 (OUTLIER) cc_final: 0.7858 (mtt-85) REVERT: U 42 ARG cc_start: 0.7675 (mtm-85) cc_final: 0.7442 (mtm-85) REVERT: U 52 ARG cc_start: 0.8376 (mtt90) cc_final: 0.8092 (mtp180) REVERT: V 50 ILE cc_start: 0.8660 (tt) cc_final: 0.8423 (tt) outliers start: 96 outliers final: 40 residues processed: 514 average time/residue: 0.7132 time to fit residues: 436.9202 Evaluate side-chains 477 residues out of total 3044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 428 time to evaluate : 1.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 698 ASP 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 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 765 MET 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 122 ILE 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 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 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 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 286 ASP 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 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 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: 10.0000 chunk 236 optimal weight: 10.0000 chunk 233 optimal weight: 1.9990 chunk 98 optimal weight: 3.9990 chunk 254 optimal weight: 0.6980 chunk 91 optimal weight: 20.0000 chunk 245 optimal weight: 0.8980 chunk 28 optimal weight: 3.9990 chunk 141 optimal weight: 0.8980 chunk 286 optimal weight: 0.5980 chunk 115 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B1252 HIS C 235 ASN D 38 HIS ** D 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 72 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** E 220 HIS ** E 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 65 GLN ** I 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 222 HIS J 230 ASN J 331 GLN J 360 GLN K 464 GLN O 110 ASN ** Q 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4313 r_free = 0.4313 target = 0.135565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.094993 restraints weight = 90529.361| |-----------------------------------------------------------------------------| r_work (start): 0.3476 rms_B_bonded: 2.73 r_work: 0.3242 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.3419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 35557 Z= 0.166 Angle : 0.678 9.810 49302 Z= 0.364 Chirality : 0.044 0.245 5443 Planarity : 0.004 0.046 5219 Dihedral : 25.151 173.502 7155 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 12.85 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.64 % Favored : 94.33 % Rotamer: Outliers : 2.86 % Allowed : 16.75 % Favored : 80.39 % 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: -1.76 (0.14), residues: 3335 helix: -0.43 (0.11), residues: 1889 sheet: -2.38 (0.39), residues: 162 loop : -2.03 (0.16), residues: 1284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG J 293 TYR 0.027 0.002 TYR E 226 PHE 0.024 0.002 PHE B1269 TRP 0.028 0.001 TRP D 261 HIS 0.014 0.001 HIS B1293 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.17 (35556) covalent geometry : angle 0.67798 / 0.36 (49302) hydrogen bonds : bond 0.06673 / 4.29 ( 1493) hydrogen bonds : angle 4.41338 / 2.98 ( 4038) metal coordination : bond 0.00142 / 0.07 ( 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 550 residues out of total 3044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 463 time to evaluate : 1.108 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: A 811 GLU cc_start: 0.8513 (tt0) cc_final: 0.8134 (tt0) REVERT: A 940 LYS cc_start: 0.9087 (tttm) cc_final: 0.8657 (ttpt) REVERT: A 986 TYR cc_start: 0.7599 (t80) cc_final: 0.6652 (m-80) REVERT: A 1016 TYR cc_start: 0.6731 (m-10) cc_final: 0.6403 (m-10) REVERT: A 1156 GLU cc_start: 0.8281 (tp30) cc_final: 0.7870 (tp30) REVERT: A 1261 LYS cc_start: 0.7784 (mmtt) cc_final: 0.7497 (mptp) REVERT: A 1273 ARG cc_start: 0.8749 (mmm-85) cc_final: 0.7870 (tpt-90) REVERT: A 1316 TYR cc_start: 0.7648 (p90) cc_final: 0.7244 (p90) REVERT: B 881 ASP cc_start: 0.8878 (t0) cc_final: 0.8417 (p0) REVERT: B 912 TRP cc_start: 0.7926 (OUTLIER) cc_final: 0.6860 (t-100) REVERT: B 1257 MET cc_start: 0.7836 (ptp) cc_final: 0.7494 (ppp) REVERT: B 1317 ILE cc_start: 0.7843 (mm) cc_final: 0.7503 (mm) REVERT: C 100 GLU cc_start: 0.8561 (mp0) cc_final: 0.8254 (mp0) REVERT: C 153 LYS cc_start: 0.9228 (OUTLIER) cc_final: 0.8897 (mttp) REVERT: C 370 ASP cc_start: 0.8532 (t0) cc_final: 0.8279 (t0) REVERT: D 232 TYR cc_start: 0.6410 (m-10) cc_final: 0.6139 (m-10) REVERT: D 259 MET cc_start: 0.8285 (ptm) cc_final: 0.7759 (ppp) REVERT: D 288 MET cc_start: 0.8909 (ptt) cc_final: 0.8509 (mpp) REVERT: D 305 MET cc_start: 0.8432 (ttp) cc_final: 0.7998 (mtt) REVERT: D 306 MET cc_start: 0.7755 (tmm) cc_final: 0.7024 (tmm) REVERT: D 322 TRP cc_start: 0.9084 (m-10) cc_final: 0.8539 (m-10) REVERT: D 344 TYR cc_start: 0.8438 (t80) cc_final: 0.8152 (t80) REVERT: D 347 TYR cc_start: 0.9191 (m-80) cc_final: 0.8927 (m-80) REVERT: D 369 LEU cc_start: 0.9314 (mt) cc_final: 0.8910 (pp) REVERT: D 376 ILE cc_start: 0.9395 (mp) cc_final: 0.9190 (mp) REVERT: E 227 TYR cc_start: 0.9000 (m-10) cc_final: 0.8766 (m-10) REVERT: E 286 TRP cc_start: 0.7864 (OUTLIER) cc_final: 0.7042 (t60) REVERT: F 50 ASP cc_start: 0.8614 (m-30) cc_final: 0.8307 (m-30) REVERT: F 61 GLN cc_start: 0.8493 (tp-100) cc_final: 0.8263 (tp-100) REVERT: F 72 GLU cc_start: 0.8646 (tt0) cc_final: 0.8408 (tt0) REVERT: F 85 GLU cc_start: 0.8795 (OUTLIER) cc_final: 0.8383 (mp0) REVERT: G 168 ARG cc_start: 0.8162 (ptm-80) cc_final: 0.7840 (ptm-80) REVERT: G 175 ILE cc_start: 0.8101 (OUTLIER) cc_final: 0.7744 (pp) REVERT: I 43 MET cc_start: 0.8329 (ttm) cc_final: 0.8067 (mmt) REVERT: J 206 MET cc_start: 0.8597 (OUTLIER) cc_final: 0.8303 (mmm) REVERT: J 332 GLN cc_start: 0.8565 (tp40) cc_final: 0.7799 (pm20) REVERT: J 342 ARG cc_start: 0.7354 (OUTLIER) cc_final: 0.6897 (ttp-110) REVERT: J 351 ARG cc_start: 0.8257 (mtt180) cc_final: 0.8026 (mmt90) REVERT: J 357 ARG cc_start: 0.9033 (ttp-170) cc_final: 0.8697 (ttp80) REVERT: J 378 ASN cc_start: 0.8715 (m-40) cc_final: 0.8004 (p0) REVERT: O 74 LYS cc_start: 0.8913 (mmtt) cc_final: 0.8642 (tppt) REVERT: O 84 GLN cc_start: 0.9113 (OUTLIER) cc_final: 0.8411 (tm-30) REVERT: P 31 LYS cc_start: 0.7688 (tptt) cc_final: 0.7097 (tttp) REVERT: Q 133 GLU cc_start: 0.8098 (OUTLIER) cc_final: 0.7793 (mt-10) REVERT: S 36 LYS cc_start: 0.8731 (mmtm) cc_final: 0.8351 (mmmm) REVERT: S 71 ARG cc_start: 0.8104 (mtm110) cc_final: 0.7780 (mtt-85) REVERT: S 91 GLU cc_start: 0.7732 (OUTLIER) cc_final: 0.7251 (pm20) REVERT: T 83 ARG cc_start: 0.8746 (OUTLIER) cc_final: 0.7662 (mtt-85) REVERT: U 42 ARG cc_start: 0.7680 (mtm-85) cc_final: 0.7428 (mtm-85) REVERT: U 52 ARG cc_start: 0.8399 (mtt90) cc_final: 0.8101 (mtp180) REVERT: U 59 GLU cc_start: 0.8482 (OUTLIER) cc_final: 0.8226 (pt0) REVERT: V 50 ILE cc_start: 0.8551 (tt) cc_final: 0.8189 (tt) outliers start: 87 outliers final: 32 residues processed: 507 average time/residue: 0.6737 time to fit residues: 410.0334 Evaluate side-chains 466 residues out of total 3044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 422 time to evaluate : 0.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 861 THR Chi-restraints excluded: chain A residue 1144 ILE Chi-restraints excluded: chain A residue 1250 VAL 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 912 TRP Chi-restraints excluded: chain B residue 1219 LEU Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 153 LYS Chi-restraints excluded: chain D residue 61 MET Chi-restraints excluded: chain D residue 199 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 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 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 O residue 84 GLN 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 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 58 THR Chi-restraints excluded: chain U residue 59 GLU 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: 1.9990 chunk 189 optimal weight: 0.3980 chunk 116 optimal weight: 4.9990 chunk 245 optimal weight: 0.7980 chunk 250 optimal weight: 6.9990 chunk 296 optimal weight: 7.9990 chunk 47 optimal weight: 5.9990 chunk 335 optimal weight: 10.0000 chunk 74 optimal weight: 20.0000 chunk 238 optimal weight: 2.9990 chunk 206 optimal weight: 0.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 815 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1150 HIS A1206 GLN B1141 ASN ** D 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 72 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 ** G 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 360 GLN P 92 GLN ** Q 113 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 = 0.4298 r_free = 0.4298 target = 0.134648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.092612 restraints weight = 89890.438| |-----------------------------------------------------------------------------| r_work (start): 0.3449 rms_B_bonded: 2.34 r_work: 0.3260 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.3548 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= 0.218 Angle : 0.697 11.252 49302 Z= 0.370 Chirality : 0.045 0.246 5443 Planarity : 0.004 0.045 5219 Dihedral : 25.158 172.529 7155 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.09 % Favored : 93.88 % Rotamer: Outliers : 2.60 % Allowed : 17.64 % Favored : 79.76 % 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: -0.21 (0.12), residues: 1879 sheet: -2.12 (0.41), residues: 151 loop : -1.99 (0.16), residues: 1305 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG J 293 TYR 0.022 0.002 TYR E 226 PHE 0.022 0.002 PHE G 111 TRP 0.025 0.001 TRP A 912 HIS 0.013 0.001 HIS B1293 Details of bonding type rmsd/Z covalent geometry : bond 0.00472 / 0.22 (35556) covalent geometry : angle 0.69738 / 0.37 (49302) hydrogen bonds : bond 0.06483 / 4.19 ( 1493) hydrogen bonds : angle 4.38777 / 2.96 ( 4038) metal coordination : bond 0.00350 / 0.18 ( 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 535 residues out of total 3044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 456 time to evaluate : 1.320 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: 0.8467 (tt0) cc_final: 0.8100 (tt0) REVERT: A 940 LYS cc_start: 0.9090 (tttm) cc_final: 0.8671 (ttpt) REVERT: A 947 GLN cc_start: 0.8886 (tm-30) cc_final: 0.8639 (tm-30) REVERT: A 986 TYR cc_start: 0.7583 (t80) cc_final: 0.6644 (m-80) REVERT: A 1016 TYR cc_start: 0.6641 (m-10) cc_final: 0.6314 (m-10) REVERT: A 1156 GLU cc_start: 0.8218 (tp30) cc_final: 0.7793 (tp30) REVERT: A 1261 LYS cc_start: 0.7745 (mmtt) cc_final: 0.7463 (mptp) REVERT: A 1273 ARG cc_start: 0.8783 (mmm-85) cc_final: 0.7768 (tpt-90) REVERT: A 1316 TYR cc_start: 0.7634 (p90) cc_final: 0.7192 (p90) REVERT: B 881 ASP cc_start: 0.8750 (t0) cc_final: 0.8340 (p0) REVERT: B 912 TRP cc_start: 0.8003 (OUTLIER) cc_final: 0.6961 (t-100) REVERT: B 1194 MET cc_start: 0.2030 (ptt) cc_final: 0.1715 (ppp) REVERT: B 1232 TYR cc_start: 0.7624 (OUTLIER) cc_final: 0.7305 (t80) REVERT: B 1257 MET cc_start: 0.7780 (ptp) cc_final: 0.6859 (ppp) REVERT: C 100 GLU cc_start: 0.8541 (mp0) cc_final: 0.8229 (mp0) REVERT: C 153 LYS cc_start: 0.9263 (OUTLIER) cc_final: 0.8808 (mttp) REVERT: C 370 ASP cc_start: 0.8481 (t0) cc_final: 0.8255 (t0) REVERT: D 259 MET cc_start: 0.8205 (ptm) cc_final: 0.7661 (ppp) REVERT: D 305 MET cc_start: 0.8384 (ttp) cc_final: 0.8004 (mtt) REVERT: D 306 MET cc_start: 0.7649 (tmm) cc_final: 0.7203 (tmm) REVERT: D 322 TRP cc_start: 0.9161 (m-10) cc_final: 0.8619 (m-10) REVERT: D 347 TYR cc_start: 0.9209 (m-80) cc_final: 0.8897 (m-80) REVERT: D 369 LEU cc_start: 0.9291 (mt) cc_final: 0.8895 (pp) REVERT: D 376 ILE cc_start: 0.9380 (mp) cc_final: 0.9164 (mp) REVERT: E 227 TYR cc_start: 0.8999 (m-10) cc_final: 0.8756 (m-10) REVERT: E 284 GLN cc_start: 0.8494 (tm-30) cc_final: 0.8148 (tm-30) REVERT: E 286 TRP cc_start: 0.7886 (OUTLIER) cc_final: 0.7052 (t60) REVERT: E 288 ASP cc_start: 0.8162 (m-30) cc_final: 0.7881 (m-30) REVERT: F 50 ASP cc_start: 0.8593 (m-30) cc_final: 0.8295 (m-30) REVERT: F 85 GLU cc_start: 0.8757 (OUTLIER) cc_final: 0.8332 (mp0) REVERT: G 168 ARG cc_start: 0.8202 (ptm-80) cc_final: 0.7894 (ptm-80) REVERT: G 175 ILE cc_start: 0.8162 (OUTLIER) cc_final: 0.7821 (pp) REVERT: I 43 MET cc_start: 0.8266 (ttm) cc_final: 0.7916 (mmp) REVERT: I 77 GLU cc_start: 0.8402 (mm-30) cc_final: 0.8117 (mm-30) REVERT: I 79 LEU cc_start: 0.8484 (tm) cc_final: 0.7994 (tp) REVERT: J 206 MET cc_start: 0.8588 (OUTLIER) cc_final: 0.8268 (mmm) REVERT: J 332 GLN cc_start: 0.8657 (tp40) cc_final: 0.7805 (pm20) REVERT: J 357 ARG cc_start: 0.8978 (ttp-170) cc_final: 0.8446 (ttm170) REVERT: J 358 ASN cc_start: 0.8557 (m110) cc_final: 0.8230 (m110) REVERT: J 378 ASN cc_start: 0.8695 (m-40) cc_final: 0.8017 (p0) REVERT: O 74 LYS cc_start: 0.8940 (mmtt) cc_final: 0.8654 (tppt) REVERT: O 84 GLN cc_start: 0.9122 (OUTLIER) cc_final: 0.8303 (tm-30) REVERT: P 31 LYS cc_start: 0.7706 (tptt) cc_final: 0.7097 (tttp) REVERT: Q 133 GLU cc_start: 0.8084 (OUTLIER) cc_final: 0.7779 (mt-10) REVERT: S 36 LYS cc_start: 0.8748 (mmtm) cc_final: 0.8350 (mmmm) REVERT: S 71 ARG cc_start: 0.8075 (mtm110) cc_final: 0.7744 (mtt-85) REVERT: T 83 ARG cc_start: 0.8725 (OUTLIER) cc_final: 0.7809 (mtt-85) REVERT: U 42 ARG cc_start: 0.7743 (mtm-85) cc_final: 0.7463 (mtm-85) REVERT: U 52 ARG cc_start: 0.8344 (mtt90) cc_final: 0.8054 (mtp180) REVERT: U 59 GLU cc_start: 0.8547 (OUTLIER) cc_final: 0.8301 (pt0) REVERT: V 50 ILE cc_start: 0.8649 (tt) cc_final: 0.8292 (tt) REVERT: V 59 LYS cc_start: 0.8890 (OUTLIER) cc_final: 0.8626 (tttm) outliers start: 79 outliers final: 31 residues processed: 497 average time/residue: 0.7075 time to fit residues: 421.6545 Evaluate side-chains 468 residues out of total 3044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 425 time to evaluate : 1.463 ------------------------------------------------------------------------------- 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 1177 THR 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 775 TRP Chi-restraints excluded: chain B residue 912 TRP Chi-restraints excluded: chain B residue 1219 LEU Chi-restraints excluded: chain B residue 1232 TYR Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 153 LYS Chi-restraints excluded: chain D residue 61 MET 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 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 O residue 84 GLN 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 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 59 LYS 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: 0.9990 chunk 221 optimal weight: 20.0000 chunk 48 optimal weight: 0.8980 chunk 171 optimal weight: 3.9990 chunk 97 optimal weight: 5.9990 chunk 187 optimal weight: 6.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 815 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 38 HIS ** D 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 ** both conformations clash, **PLEASE CHECK MANUALLY** F 61 GLN G 91 ASN ** G 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 370 ASN ** Q 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4302 r_free = 0.4302 target = 0.134704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 84)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.092647 restraints weight = 90384.460| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 2.33 r_work: 0.3260 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.3686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 35557 Z= 0.219 Angle : 0.698 11.133 49302 Z= 0.371 Chirality : 0.045 0.248 5443 Planarity : 0.004 0.048 5219 Dihedral : 25.181 171.454 7155 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 12.81 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.09 % Favored : 93.88 % Rotamer: Outliers : 2.56 % Allowed : 18.33 % Favored : 79.11 % 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: -1.39 (0.14), residues: 3335 helix: -0.12 (0.12), residues: 1899 sheet: -2.10 (0.41), residues: 161 loop : -1.93 (0.16), residues: 1275 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG J 293 TYR 0.023 0.002 TYR D 162 PHE 0.027 0.002 PHE B1269 TRP 0.031 0.002 TRP A 912 HIS 0.011 0.001 HIS B1293 Details of bonding type rmsd/Z covalent geometry : bond 0.00476 / 0.22 (35556) covalent geometry : angle 0.69760 / 0.37 (49302) hydrogen bonds : bond 0.06399 / 4.13 ( 1493) hydrogen bonds : angle 4.34306 / 2.92 ( 4038) metal coordination : bond 0.00344 / 0.18 ( 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 534 residues out of total 3044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 456 time to evaluate : 0.934 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: A 811 GLU cc_start: 0.8462 (tt0) cc_final: 0.8083 (tt0) REVERT: A 940 LYS cc_start: 0.9094 (tttm) cc_final: 0.8677 (ttpt) REVERT: A 947 GLN cc_start: 0.8934 (tm-30) cc_final: 0.8689 (tm-30) REVERT: A 986 TYR cc_start: 0.7561 (t80) cc_final: 0.6633 (m-80) REVERT: A 1016 TYR cc_start: 0.6651 (m-10) cc_final: 0.6315 (m-10) REVERT: A 1156 GLU cc_start: 0.8188 (tp30) cc_final: 0.7775 (tp30) REVERT: A 1261 LYS cc_start: 0.7750 (mmtt) cc_final: 0.7454 (mptp) REVERT: A 1273 ARG cc_start: 0.8776 (mmm-85) cc_final: 0.7738 (tpt-90) REVERT: A 1316 TYR cc_start: 0.7633 (p90) cc_final: 0.7181 (p90) REVERT: B 834 ILE cc_start: 0.8082 (OUTLIER) cc_final: 0.7544 (tt) REVERT: B 881 ASP cc_start: 0.8746 (t0) cc_final: 0.8363 (p0) REVERT: B 912 TRP cc_start: 0.8020 (OUTLIER) cc_final: 0.6966 (t-100) REVERT: B 1257 MET cc_start: 0.7771 (ptp) cc_final: 0.6899 (ppp) REVERT: C 100 GLU cc_start: 0.8545 (mp0) cc_final: 0.8214 (mp0) REVERT: C 370 ASP cc_start: 0.8488 (t0) cc_final: 0.8283 (t0) REVERT: D 259 MET cc_start: 0.8182 (ptm) cc_final: 0.7680 (ppp) REVERT: D 288 MET cc_start: 0.8851 (ptt) cc_final: 0.8516 (mpp) REVERT: D 305 MET cc_start: 0.8390 (ttp) cc_final: 0.7969 (mtt) REVERT: D 306 MET cc_start: 0.7588 (tmm) cc_final: 0.7099 (tmm) REVERT: D 315 MET cc_start: 0.6569 (ttp) cc_final: 0.5522 (tpt) REVERT: D 316 ARG cc_start: 0.8290 (ttm-80) cc_final: 0.8074 (ttm-80) REVERT: D 322 TRP cc_start: 0.9179 (m-10) cc_final: 0.8592 (m-10) REVERT: D 344 TYR cc_start: 0.8478 (t80) cc_final: 0.8161 (t80) REVERT: E 226 TYR cc_start: 0.8250 (p90) cc_final: 0.8048 (OUTLIER) REVERT: E 227 TYR cc_start: 0.8959 (m-10) cc_final: 0.8721 (m-10) REVERT: E 284 GLN cc_start: 0.8480 (tm-30) cc_final: 0.8152 (tm-30) REVERT: E 286 TRP cc_start: 0.7907 (OUTLIER) cc_final: 0.7051 (t60) REVERT: E 288 ASP cc_start: 0.8132 (m-30) cc_final: 0.7918 (m-30) REVERT: F 50 ASP cc_start: 0.8601 (m-30) cc_final: 0.8299 (m-30) REVERT: F 85 GLU cc_start: 0.8733 (OUTLIER) cc_final: 0.8319 (mp0) REVERT: G 168 ARG cc_start: 0.8235 (ptm-80) cc_final: 0.7952 (ptm-80) REVERT: G 175 ILE cc_start: 0.8140 (OUTLIER) cc_final: 0.7770 (pp) REVERT: I 43 MET cc_start: 0.8235 (ttm) cc_final: 0.7973 (mmp) REVERT: I 79 LEU cc_start: 0.8532 (tm) cc_final: 0.7954 (tp) REVERT: J 342 ARG cc_start: 0.7414 (OUTLIER) cc_final: 0.6994 (ttm-80) REVERT: J 357 ARG cc_start: 0.8986 (ttp-170) cc_final: 0.8455 (ttm170) REVERT: J 358 ASN cc_start: 0.8597 (m110) cc_final: 0.8269 (m110) REVERT: J 378 ASN cc_start: 0.8678 (m-40) cc_final: 0.8059 (p0) REVERT: O 84 GLN cc_start: 0.9133 (OUTLIER) cc_final: 0.8290 (tm-30) REVERT: P 31 LYS cc_start: 0.7732 (tptt) cc_final: 0.7145 (tttp) REVERT: Q 133 GLU cc_start: 0.8079 (OUTLIER) cc_final: 0.7767 (mt-10) REVERT: S 36 LYS cc_start: 0.8748 (mmtm) cc_final: 0.8356 (mmmm) REVERT: S 71 ARG cc_start: 0.8086 (mtm110) cc_final: 0.7772 (mtt-85) REVERT: T 83 ARG cc_start: 0.8716 (OUTLIER) cc_final: 0.7687 (mtt-85) REVERT: U 42 ARG cc_start: 0.7733 (mtm-85) cc_final: 0.7478 (mtm-85) REVERT: U 52 ARG cc_start: 0.8379 (mtt90) cc_final: 0.8054 (mtp180) REVERT: U 94 GLU cc_start: 0.8630 (mm-30) cc_final: 0.8279 (mm-30) REVERT: U 120 MET cc_start: 0.9060 (mmm) cc_final: 0.8798 (mtm) REVERT: V 50 ILE cc_start: 0.8671 (OUTLIER) cc_final: 0.8330 (tt) REVERT: V 59 LYS cc_start: 0.8899 (OUTLIER) cc_final: 0.8637 (tttm) outliers start: 78 outliers final: 41 residues processed: 497 average time/residue: 0.6665 time to fit residues: 397.7743 Evaluate side-chains 480 residues out of total 3044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 429 time to evaluate : 1.105 ------------------------------------------------------------------------------- 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 996 ILE Chi-restraints excluded: chain A residue 1144 ILE Chi-restraints excluded: chain A residue 1146 ILE 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 834 ILE Chi-restraints excluded: chain B residue 912 TRP Chi-restraints excluded: chain B residue 1219 LEU Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain D residue 38 HIS Chi-restraints excluded: chain D residue 53 MET Chi-restraints excluded: chain D residue 61 MET 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 267 VAL 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 214 MET 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 217 VAL Chi-restraints excluded: chain J residue 342 ARG Chi-restraints excluded: chain J residue 344 LEU Chi-restraints excluded: chain O residue 84 GLN 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 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 31 LYS Chi-restraints excluded: chain V residue 50 ILE 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: 0.6980 chunk 285 optimal weight: 0.5980 chunk 262 optimal weight: 0.7980 chunk 280 optimal weight: 4.9990 chunk 81 optimal weight: 2.9990 chunk 50 optimal weight: 5.9990 chunk 150 optimal weight: 3.9990 chunk 214 optimal weight: 50.0000 chunk 273 optimal weight: 0.6980 chunk 266 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 815 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1143 ASN C 330 ASN ** D 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 72 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 82 ASN ** G 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 350 GLN J 370 ASN ** Q 113 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 = 0.4314 r_free = 0.4314 target = 0.135590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.095366 restraints weight = 90494.045| |-----------------------------------------------------------------------------| r_work (start): 0.3481 rms_B_bonded: 2.65 r_work: 0.3261 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.3846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 35557 Z= 0.158 Angle : 0.677 11.554 49302 Z= 0.360 Chirality : 0.043 0.243 5443 Planarity : 0.004 0.075 5219 Dihedral : 25.098 170.303 7155 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 12.78 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.88 % Favored : 94.09 % Rotamer: Outliers : 2.40 % Allowed : 18.89 % Favored : 78.71 % 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: -1.26 (0.14), residues: 3335 helix: -0.00 (0.12), residues: 1908 sheet: -1.80 (0.43), residues: 148 loop : -1.93 (0.16), residues: 1279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG J 293 TYR 0.026 0.002 TYR D 346 PHE 0.027 0.001 PHE G 111 TRP 0.032 0.002 TRP A 912 HIS 0.019 0.001 HIS D 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.16 (35556) covalent geometry : angle 0.67711 / 0.36 (49302) hydrogen bonds : bond 0.06356 / 4.09 ( 1493) hydrogen bonds : angle 4.26112 / 2.87 ( 4038) metal coordination : bond 0.00194 / 0.10 ( 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 540 residues out of total 3044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 467 time to evaluate : 1.178 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: 0.8511 (tt0) cc_final: 0.8192 (tt0) REVERT: A 940 LYS cc_start: 0.9066 (tttm) cc_final: 0.8624 (ttpt) REVERT: A 947 GLN cc_start: 0.8948 (tm-30) cc_final: 0.8703 (tm-30) REVERT: A 986 TYR cc_start: 0.7614 (t80) cc_final: 0.6702 (m-80) REVERT: A 1016 TYR cc_start: 0.6642 (m-10) cc_final: 0.6279 (m-10) REVERT: A 1156 GLU cc_start: 0.8195 (tp30) cc_final: 0.7783 (tp30) REVERT: A 1261 LYS cc_start: 0.7767 (mmtt) cc_final: 0.7472 (mptp) REVERT: A 1273 ARG cc_start: 0.8737 (mmm-85) cc_final: 0.8521 (tpt90) REVERT: A 1300 MET cc_start: 0.6990 (ttp) cc_final: 0.6394 (ttm) REVERT: A 1301 PHE cc_start: 0.8637 (m-80) cc_final: 0.8281 (m-80) REVERT: A 1316 TYR cc_start: 0.7744 (p90) cc_final: 0.7303 (p90) REVERT: B 821 ILE cc_start: 0.8398 (OUTLIER) cc_final: 0.7995 (tp) REVERT: B 834 ILE cc_start: 0.8203 (OUTLIER) cc_final: 0.7690 (tt) REVERT: B 881 ASP cc_start: 0.8916 (t0) cc_final: 0.8480 (p0) REVERT: B 912 TRP cc_start: 0.8047 (OUTLIER) cc_final: 0.7707 (t-100) REVERT: B 916 TRP cc_start: 0.8656 (m-10) cc_final: 0.8157 (m-10) REVERT: B 1257 MET cc_start: 0.7837 (ptp) cc_final: 0.7046 (ppp) REVERT: C 100 GLU cc_start: 0.8571 (mp0) cc_final: 0.8243 (mp0) REVERT: C 153 LYS cc_start: 0.9202 (OUTLIER) cc_final: 0.8479 (mttp) REVERT: C 370 ASP cc_start: 0.8502 (t0) cc_final: 0.8292 (t0) REVERT: D 61 MET cc_start: 0.7952 (ppp) cc_final: 0.7605 (pp-130) REVERT: D 76 GLN cc_start: 0.7408 (pm20) cc_final: 0.7027 (mp10) REVERT: D 259 MET cc_start: 0.8253 (ptm) cc_final: 0.7694 (ppp) REVERT: D 288 MET cc_start: 0.8700 (ptt) cc_final: 0.8329 (mpp) REVERT: D 315 MET cc_start: 0.6640 (ttp) cc_final: 0.5645 (tpt) REVERT: D 322 TRP cc_start: 0.9117 (m-10) cc_final: 0.8634 (m-10) REVERT: D 344 TYR cc_start: 0.8531 (t80) cc_final: 0.8237 (t80) REVERT: D 369 LEU cc_start: 0.9343 (mt) cc_final: 0.8864 (pp) REVERT: E 226 TYR cc_start: 0.8292 (OUTLIER) cc_final: 0.8064 (OUTLIER) REVERT: E 227 TYR cc_start: 0.8953 (m-10) cc_final: 0.8675 (m-10) REVERT: E 286 TRP cc_start: 0.7899 (OUTLIER) cc_final: 0.7365 (t60) REVERT: E 288 ASP cc_start: 0.8108 (m-30) cc_final: 0.7886 (m-30) REVERT: F 50 ASP cc_start: 0.8601 (m-30) cc_final: 0.8312 (m-30) REVERT: F 85 GLU cc_start: 0.8770 (OUTLIER) cc_final: 0.8347 (mp0) REVERT: G 168 ARG cc_start: 0.8202 (ptm-80) cc_final: 0.7977 (ptm-80) REVERT: G 175 ILE cc_start: 0.8142 (OUTLIER) cc_final: 0.7769 (pp) REVERT: H 244 ARG cc_start: 0.7828 (tpt170) cc_final: 0.7418 (ttm170) REVERT: I 43 MET cc_start: 0.8221 (ttm) cc_final: 0.7988 (mmp) REVERT: I 79 LEU cc_start: 0.8519 (tm) cc_final: 0.7906 (tp) REVERT: J 332 GLN cc_start: 0.8615 (tp40) cc_final: 0.7698 (pm20) REVERT: J 342 ARG cc_start: 0.7365 (OUTLIER) cc_final: 0.6956 (ttm-80) REVERT: J 350 GLN cc_start: 0.8199 (OUTLIER) cc_final: 0.7761 (mm-40) REVERT: J 357 ARG cc_start: 0.8960 (ttp-170) cc_final: 0.8689 (ttp80) REVERT: J 358 ASN cc_start: 0.8567 (m110) cc_final: 0.8216 (m110) REVERT: J 375 ARG cc_start: 0.8398 (mmm160) cc_final: 0.7588 (mtp85) REVERT: J 378 ASN cc_start: 0.8652 (m-40) cc_final: 0.8035 (p0) REVERT: O 84 GLN cc_start: 0.9105 (OUTLIER) cc_final: 0.8338 (tm-30) REVERT: P 31 LYS cc_start: 0.7726 (tptt) cc_final: 0.7133 (tttp) REVERT: Q 133 GLU cc_start: 0.8071 (OUTLIER) cc_final: 0.7856 (mt-10) REVERT: S 36 LYS cc_start: 0.8729 (mmtm) cc_final: 0.8376 (mmmm) REVERT: S 71 ARG cc_start: 0.8086 (mtm110) cc_final: 0.7784 (mtm-85) REVERT: T 48 ASP cc_start: 0.7937 (m-30) cc_final: 0.7486 (t70) REVERT: T 83 ARG cc_start: 0.8717 (OUTLIER) cc_final: 0.7656 (mtt-85) REVERT: U 52 ARG cc_start: 0.8370 (mtt90) cc_final: 0.8082 (mtp180) REVERT: U 94 GLU cc_start: 0.8633 (mm-30) cc_final: 0.8295 (mm-30) REVERT: U 120 MET cc_start: 0.9077 (mmm) cc_final: 0.8816 (mtm) REVERT: V 50 ILE cc_start: 0.8594 (OUTLIER) cc_final: 0.8237 (tt) outliers start: 73 outliers final: 36 residues processed: 503 average time/residue: 0.6858 time to fit residues: 415.2485 Evaluate side-chains 477 residues out of total 3044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 428 time to evaluate : 1.240 ------------------------------------------------------------------------------- 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 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 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 834 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 B residue 1219 LEU Chi-restraints excluded: chain C residue 122 ILE 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 226 TYR 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 117 LEU 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 30 THR Chi-restraints excluded: chain I residue 39 CYS Chi-restraints excluded: chain J residue 342 ARG Chi-restraints excluded: chain J residue 344 LEU Chi-restraints excluded: chain J residue 350 GLN Chi-restraints excluded: chain O residue 84 GLN 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 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 31 LYS Chi-restraints excluded: chain V residue 50 ILE 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: 0.0870 chunk 107 optimal weight: 0.7980 chunk 70 optimal weight: 0.7980 chunk 12 optimal weight: 0.8980 chunk 32 optimal weight: 0.7980 chunk 86 optimal weight: 0.7980 chunk 262 optimal weight: 0.3980 chunk 57 optimal weight: 6.9990 chunk 226 optimal weight: 30.0000 chunk 15 optimal weight: 0.9980 chunk 248 optimal weight: 0.8980 overall best weight: 0.5758 ------------------------------------------------------------------------------- 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** C 31 ASN D 38 HIS ** D 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 78 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** ** D 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 220 HIS G 183 GLN ** I 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 360 GLN J 370 ASN ** 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4320 r_free = 0.4320 target = 0.135992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.095904 restraints weight = 90277.225| |-----------------------------------------------------------------------------| r_work (start): 0.3496 rms_B_bonded: 2.64 r_work: 0.3276 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.3981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 35557 Z= 0.152 Angle : 0.695 13.569 49302 Z= 0.367 Chirality : 0.044 0.333 5443 Planarity : 0.004 0.097 5219 Dihedral : 25.021 169.496 7155 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 12.78 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.91 % Favored : 94.06 % Rotamer: Outliers : 2.10 % Allowed : 19.84 % Favored : 78.06 % Cbeta Deviations : 0.03 % 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: -1.19 (0.14), residues: 3335 helix: 0.07 (0.12), residues: 1896 sheet: -1.78 (0.43), residues: 149 loop : -1.92 (0.16), residues: 1290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG J 293 TYR 0.024 0.002 TYR D 347 PHE 0.029 0.001 PHE D 197 TRP 0.037 0.002 TRP A 912 HIS 0.011 0.001 HIS D 78 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.15 (35556) covalent geometry : angle 0.69477 / 0.37 (49302) hydrogen bonds : bond 0.06335 / 4.07 ( 1493) hydrogen bonds : angle 4.25836 / 2.87 ( 4038) metal coordination : bond 0.00164 / 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 519 residues out of total 3044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 455 time to evaluate : 1.254 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: 0.8516 (tt0) cc_final: 0.8248 (tt0) REVERT: A 940 LYS cc_start: 0.9057 (tttm) cc_final: 0.8614 (ttpt) REVERT: A 947 GLN cc_start: 0.8953 (tm-30) cc_final: 0.8716 (tm-30) REVERT: A 986 TYR cc_start: 0.7550 (t80) cc_final: 0.6669 (m-80) REVERT: A 1016 TYR cc_start: 0.6602 (m-10) cc_final: 0.6247 (m-10) REVERT: A 1156 GLU cc_start: 0.8175 (tp30) cc_final: 0.7772 (tp30) REVERT: A 1261 LYS cc_start: 0.7791 (mmtt) cc_final: 0.7509 (mptp) REVERT: A 1273 ARG cc_start: 0.8726 (mmm-85) cc_final: 0.8513 (tpt90) REVERT: A 1300 MET cc_start: 0.6983 (ttp) cc_final: 0.6397 (ttm) REVERT: A 1301 PHE cc_start: 0.8595 (m-80) cc_final: 0.8306 (m-80) REVERT: A 1316 TYR cc_start: 0.7704 (p90) cc_final: 0.7251 (p90) REVERT: B 773 MET cc_start: 0.4678 (mmt) cc_final: 0.4249 (mpp) REVERT: B 821 ILE cc_start: 0.8344 (OUTLIER) cc_final: 0.7904 (tp) REVERT: B 834 ILE cc_start: 0.8167 (OUTLIER) cc_final: 0.7609 (tt) REVERT: B 881 ASP cc_start: 0.8908 (t0) cc_final: 0.8503 (p0) REVERT: B 912 TRP cc_start: 0.8019 (OUTLIER) cc_final: 0.7698 (t-100) REVERT: B 916 TRP cc_start: 0.8579 (m-10) cc_final: 0.8109 (m-10) REVERT: B 1257 MET cc_start: 0.7811 (ptp) cc_final: 0.7074 (ppp) REVERT: C 73 GLU cc_start: 0.8416 (mt-10) cc_final: 0.8195 (mt-10) REVERT: C 100 GLU cc_start: 0.8584 (mp0) cc_final: 0.8245 (mp0) REVERT: C 259 MET cc_start: 0.8507 (mmm) cc_final: 0.8186 (mtm) REVERT: C 370 ASP cc_start: 0.8485 (t0) cc_final: 0.8272 (t0) REVERT: D 61 MET cc_start: 0.7962 (ppp) cc_final: 0.7750 (pp-130) REVERT: D 128 MET cc_start: 0.8675 (mmm) cc_final: 0.8333 (mpm) REVERT: D 259 MET cc_start: 0.8147 (ptm) cc_final: 0.7593 (ppp) REVERT: D 315 MET cc_start: 0.6591 (ttp) cc_final: 0.5670 (tpt) REVERT: D 316 ARG cc_start: 0.8588 (tpp80) cc_final: 0.7958 (tpp80) REVERT: D 322 TRP cc_start: 0.9139 (m-10) cc_final: 0.8661 (m-10) REVERT: D 344 TYR cc_start: 0.8510 (t80) cc_final: 0.8198 (t80) REVERT: D 369 LEU cc_start: 0.9344 (mt) cc_final: 0.8872 (pp) REVERT: E 227 TYR cc_start: 0.8879 (m-10) cc_final: 0.8613 (m-10) REVERT: E 286 TRP cc_start: 0.7765 (OUTLIER) cc_final: 0.7014 (t60) REVERT: E 288 ASP cc_start: 0.7901 (m-30) cc_final: 0.7655 (m-30) REVERT: F 50 ASP cc_start: 0.8552 (m-30) cc_final: 0.8268 (m-30) REVERT: F 61 GLN cc_start: 0.8428 (tp40) cc_final: 0.8206 (tp-100) REVERT: F 85 GLU cc_start: 0.8764 (OUTLIER) cc_final: 0.8346 (mp0) REVERT: G 168 ARG cc_start: 0.8242 (ptm-80) cc_final: 0.7989 (ptm-80) REVERT: G 175 ILE cc_start: 0.8141 (OUTLIER) cc_final: 0.7751 (pp) REVERT: H 244 ARG cc_start: 0.7741 (tpt170) cc_final: 0.7532 (ttt-90) REVERT: I 43 MET cc_start: 0.8132 (ttm) cc_final: 0.7881 (mmp) REVERT: I 79 LEU cc_start: 0.8416 (tm) cc_final: 0.7932 (tp) REVERT: J 177 ASN cc_start: 0.7627 (p0) cc_final: 0.6761 (t0) REVERT: J 206 MET cc_start: 0.8513 (OUTLIER) cc_final: 0.8155 (mmm) REVERT: J 332 GLN cc_start: 0.8598 (tp40) cc_final: 0.7690 (pm20) REVERT: J 357 ARG cc_start: 0.8972 (ttp-170) cc_final: 0.8691 (ttp80) REVERT: J 358 ASN cc_start: 0.8526 (m110) cc_final: 0.8169 (m110) REVERT: J 375 ARG cc_start: 0.8383 (mmm160) cc_final: 0.7521 (mtp85) REVERT: J 378 ASN cc_start: 0.8645 (m-40) cc_final: 0.8015 (p0) REVERT: P 31 LYS cc_start: 0.7672 (tptt) cc_final: 0.7127 (tttp) REVERT: P 53 SER cc_start: 0.9048 (p) cc_final: 0.8775 (p) REVERT: Q 133 GLU cc_start: 0.8078 (OUTLIER) cc_final: 0.7867 (mt-10) REVERT: S 36 LYS cc_start: 0.8700 (mmtm) cc_final: 0.8332 (mmmm) REVERT: S 71 ARG cc_start: 0.8093 (mtm110) cc_final: 0.7801 (mtm-85) REVERT: S 72 ASP cc_start: 0.8492 (m-30) cc_final: 0.8220 (m-30) REVERT: S 91 GLU cc_start: 0.7801 (pp20) cc_final: 0.7447 (pp20) REVERT: T 48 ASP cc_start: 0.7899 (m-30) cc_final: 0.7475 (t70) REVERT: T 83 ARG cc_start: 0.8717 (OUTLIER) cc_final: 0.7683 (mtt-85) REVERT: U 42 ARG cc_start: 0.7864 (mtm-85) cc_final: 0.7459 (mtm-85) REVERT: U 52 ARG cc_start: 0.8389 (mtt90) cc_final: 0.8103 (mtp180) REVERT: U 94 GLU cc_start: 0.8638 (mm-30) cc_final: 0.8306 (mm-30) REVERT: U 120 MET cc_start: 0.9046 (mmm) cc_final: 0.8800 (mtm) REVERT: V 50 ILE cc_start: 0.8553 (OUTLIER) cc_final: 0.8130 (tt) outliers start: 64 outliers final: 35 residues processed: 488 average time/residue: 0.6954 time to fit residues: 409.1251 Evaluate side-chains 478 residues out of total 3044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 433 time to evaluate : 1.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 698 ASP Chi-restraints excluded: chain A residue 861 THR Chi-restraints excluded: chain A residue 934 THR 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 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 B residue 1204 TYR Chi-restraints excluded: chain B residue 1219 LEU Chi-restraints excluded: chain C residue 13 VAL Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain D residue 78 HIS 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 308 VAL 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 117 LEU 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 344 LEU 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 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 31 LYS Chi-restraints excluded: chain V residue 50 ILE 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: 6.9990 chunk 100 optimal weight: 30.0000 chunk 52 optimal weight: 0.9980 chunk 284 optimal weight: 0.9980 chunk 302 optimal weight: 0.9980 chunk 252 optimal weight: 6.9990 chunk 70 optimal weight: 1.9990 chunk 348 optimal weight: 9.9990 chunk 139 optimal weight: 9.9990 chunk 261 optimal weight: 4.9990 chunk 182 optimal weight: 0.8980 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 815 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 930 HIS ** C 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 78 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** ** D 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 220 HIS ** G 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 370 ASN ** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.135487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.093270 restraints weight = 90190.794| |-----------------------------------------------------------------------------| r_work (start): 0.3465 rms_B_bonded: 2.38 r_work: 0.3281 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.4011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 35557 Z= 0.195 Angle : 0.719 12.311 49302 Z= 0.378 Chirality : 0.044 0.325 5443 Planarity : 0.004 0.073 5219 Dihedral : 24.999 168.935 7153 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 13.02 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.73 % Favored : 94.24 % Rotamer: Outliers : 1.68 % Allowed : 20.83 % Favored : 77.50 % Cbeta Deviations : 0.03 % 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: -1.13 (0.14), residues: 3335 helix: 0.10 (0.12), residues: 1901 sheet: -1.71 (0.43), residues: 148 loop : -1.87 (0.16), residues: 1286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG J 293 TYR 0.054 0.002 TYR E 226 PHE 0.031 0.002 PHE G 119 TRP 0.041 0.002 TRP A 912 HIS 0.037 0.001 HIS D 78 Details of bonding type rmsd/Z covalent geometry : bond 0.00426 / 0.19 (35556) covalent geometry : angle 0.71930 / 0.38 (49302) hydrogen bonds : bond 0.06234 / 4.02 ( 1493) hydrogen bonds : angle 4.26724 / 2.88 ( 4038) metal coordination : bond 0.00288 / 0.15 ( 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 490 residues out of total 3044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 439 time to evaluate : 1.129 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 940 LYS cc_start: 0.9056 (tttm) cc_final: 0.8614 (ttpt) REVERT: A 947 GLN cc_start: 0.8948 (tm-30) cc_final: 0.8714 (tm-30) REVERT: A 986 TYR cc_start: 0.7540 (t80) cc_final: 0.6656 (m-80) REVERT: A 1016 TYR cc_start: 0.6621 (m-10) cc_final: 0.6258 (m-10) REVERT: A 1261 LYS cc_start: 0.7760 (mmtt) cc_final: 0.7477 (mptp) REVERT: A 1273 ARG cc_start: 0.8753 (mmm-85) cc_final: 0.8517 (tpt90) REVERT: A 1300 MET cc_start: 0.7054 (ttp) cc_final: 0.6469 (ttm) REVERT: A 1301 PHE cc_start: 0.8603 (m-80) cc_final: 0.8285 (m-80) REVERT: A 1316 TYR cc_start: 0.7621 (p90) cc_final: 0.7167 (p90) REVERT: B 821 ILE cc_start: 0.8328 (OUTLIER) cc_final: 0.7887 (tp) REVERT: B 834 ILE cc_start: 0.8011 (OUTLIER) cc_final: 0.7450 (tt) REVERT: B 881 ASP cc_start: 0.8761 (t0) cc_final: 0.8420 (p0) REVERT: B 912 TRP cc_start: 0.8008 (OUTLIER) cc_final: 0.7693 (t-100) REVERT: B 916 TRP cc_start: 0.8558 (m-10) cc_final: 0.8079 (m-10) REVERT: B 1257 MET cc_start: 0.7764 (ptp) cc_final: 0.7043 (ppp) REVERT: C 100 GLU cc_start: 0.8567 (mp0) cc_final: 0.8225 (mp0) REVERT: C 259 MET cc_start: 0.8520 (mmm) cc_final: 0.8191 (mtm) REVERT: D 128 MET cc_start: 0.8653 (mmm) cc_final: 0.8329 (mpm) REVERT: D 251 PHE cc_start: 0.8377 (p90) cc_final: 0.8177 (p90) REVERT: D 259 MET cc_start: 0.8117 (ptm) cc_final: 0.7558 (ppp) REVERT: D 288 MET cc_start: 0.8993 (mpp) cc_final: 0.8703 (mpp) REVERT: D 315 MET cc_start: 0.6618 (ttp) cc_final: 0.5769 (tpt) REVERT: D 322 TRP cc_start: 0.9165 (m-10) cc_final: 0.8729 (m-10) REVERT: D 344 TYR cc_start: 0.8500 (t80) cc_final: 0.8210 (t80) REVERT: D 354 SER cc_start: 0.8354 (m) cc_final: 0.7747 (p) REVERT: D 369 LEU cc_start: 0.9299 (mt) cc_final: 0.8826 (pp) REVERT: E 286 TRP cc_start: 0.7783 (OUTLIER) cc_final: 0.7066 (t60) REVERT: F 50 ASP cc_start: 0.8513 (m-30) cc_final: 0.8240 (m-30) REVERT: F 85 GLU cc_start: 0.8749 (OUTLIER) cc_final: 0.8325 (mp0) REVERT: G 175 ILE cc_start: 0.8153 (OUTLIER) cc_final: 0.7788 (pp) REVERT: H 244 ARG cc_start: 0.7680 (tpt170) cc_final: 0.7364 (ttm170) REVERT: I 79 LEU cc_start: 0.8400 (tm) cc_final: 0.7951 (tp) REVERT: J 177 ASN cc_start: 0.7543 (p0) cc_final: 0.6620 (t0) REVERT: J 206 MET cc_start: 0.8497 (OUTLIER) cc_final: 0.8137 (mmm) REVERT: J 332 GLN cc_start: 0.8607 (tp40) cc_final: 0.7629 (pm20) REVERT: J 357 ARG cc_start: 0.8948 (ttp-170) cc_final: 0.8746 (ttp80) REVERT: J 358 ASN cc_start: 0.8565 (m110) cc_final: 0.8225 (m110) REVERT: J 375 ARG cc_start: 0.8408 (mmm160) cc_final: 0.7549 (mtp85) REVERT: J 378 ASN cc_start: 0.8635 (m-40) cc_final: 0.8001 (p0) REVERT: P 31 LYS cc_start: 0.7705 (tptt) cc_final: 0.7142 (tttp) REVERT: P 53 SER cc_start: 0.9061 (p) cc_final: 0.8793 (p) REVERT: Q 133 GLU cc_start: 0.8085 (OUTLIER) cc_final: 0.7879 (mt-10) REVERT: S 36 LYS cc_start: 0.8714 (mmtm) cc_final: 0.8345 (mmmm) REVERT: S 71 ARG cc_start: 0.8025 (mtm110) cc_final: 0.7737 (mtt-85) REVERT: S 72 ASP cc_start: 0.8507 (m-30) cc_final: 0.8244 (m-30) REVERT: S 91 GLU cc_start: 0.7755 (pp20) cc_final: 0.7374 (pp20) REVERT: T 48 ASP cc_start: 0.7881 (m-30) cc_final: 0.7485 (t70) REVERT: T 83 ARG cc_start: 0.8717 (OUTLIER) cc_final: 0.7703 (mtt-85) REVERT: U 42 ARG cc_start: 0.7845 (mtm-85) cc_final: 0.7001 (mtt-85) REVERT: U 52 ARG cc_start: 0.8332 (mtt90) cc_final: 0.8061 (mtp180) REVERT: U 94 GLU cc_start: 0.8651 (mm-30) cc_final: 0.8305 (mm-30) REVERT: U 120 MET cc_start: 0.9045 (mmm) cc_final: 0.8793 (mtm) REVERT: V 50 ILE cc_start: 0.8575 (OUTLIER) cc_final: 0.8216 (tt) outliers start: 51 outliers final: 29 residues processed: 459 average time/residue: 0.6786 time to fit residues: 374.2846 Evaluate side-chains 473 residues out of total 3044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 434 time to evaluate : 1.038 ------------------------------------------------------------------------------- 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 A residue 1180 PHE Chi-restraints excluded: chain A residue 1250 VAL 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 B residue 1204 TYR Chi-restraints excluded: chain C residue 13 VAL Chi-restraints excluded: chain C residue 122 ILE 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 233 ILE Chi-restraints excluded: chain E residue 286 TRP Chi-restraints excluded: chain F residue 85 GLU Chi-restraints excluded: chain F residue 117 LEU 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 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 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 31 LYS Chi-restraints excluded: chain V residue 50 ILE 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: 5.9990 chunk 132 optimal weight: 0.5980 chunk 332 optimal weight: 40.0000 chunk 330 optimal weight: 0.9980 chunk 251 optimal weight: 0.0970 chunk 123 optimal weight: 0.5980 chunk 199 optimal weight: 0.0010 chunk 235 optimal weight: 1.9990 chunk 247 optimal weight: 0.6980 chunk 140 optimal weight: 0.0570 chunk 56 optimal weight: 0.9980 overall best weight: 0.2702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 815 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 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 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 331 ASN E 220 HIS ** E 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 343 GLN ** J 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 370 ASN ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4335 r_free = 0.4335 target = 0.137097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.095772 restraints weight = 90470.631| |-----------------------------------------------------------------------------| r_work (start): 0.3520 rms_B_bonded: 2.43 r_work: 0.3336 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.4274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 35557 Z= 0.139 Angle : 0.713 21.194 49302 Z= 0.373 Chirality : 0.043 0.260 5443 Planarity : 0.004 0.069 5219 Dihedral : 24.850 167.189 7153 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 12.58 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.58 % Favored : 94.39 % Rotamer: Outliers : 1.31 % Allowed : 21.32 % Favored : 77.37 % 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: -0.99 (0.14), residues: 3335 helix: 0.24 (0.12), residues: 1906 sheet: -1.73 (0.43), residues: 149 loop : -1.86 (0.16), residues: 1280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG J 293 TYR 0.024 0.002 TYR E 227 PHE 0.030 0.002 PHE B1224 TRP 0.034 0.002 TRP A 912 HIS 0.011 0.001 HIS B1293 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.14 (35556) covalent geometry : angle 0.71258 / 0.37 (49302) hydrogen bonds : bond 0.06450 / 4.15 ( 1493) hydrogen bonds : angle 4.19439 / 2.84 ( 4038) metal coordination : bond 0.00052 / 0.03 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14941.25 seconds wall clock time: 254 minutes 46.93 seconds (15286.93 seconds total)