Starting phenix.real_space_refine on Sun Jun 7 05:35:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9v2v_64741/06_2026/9v2v_64741.cif Found real_map, /net/cci-nas-00/data/ceres_data/9v2v_64741/06_2026/9v2v_64741.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9v2v_64741/06_2026/9v2v_64741.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9v2v_64741/06_2026/9v2v_64741.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9v2v_64741/06_2026/9v2v_64741.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9v2v_64741/06_2026/9v2v_64741.map" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 1 6.06 5 P 308 5.49 5 S 113 5.16 5 C 20731 2.51 5 N 6095 2.21 5 O 6993 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 98 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/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: 6.95, per 1000 atoms: 0.20 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: 2.48 Conformation dependent library (CDL) restraints added in 1.0 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: 5.01 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: 8.81 Time building geometry restraints manager: 3.41 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 1.490 1.350 0.140 3.00e-02 1.11e+03 2.19e+01 bond pdb=" C1' DA Y 17 " pdb=" N9 DA Y 17 " ideal model delta sigma weight residual 1.460 1.373 0.087 2.00e-02 2.50e+03 1.90e+01 bond pdb=" C SER J 187 " pdb=" N PRO J 188 " ideal model delta sigma weight residual 1.332 1.367 -0.035 8.20e-03 1.49e+04 1.80e+01 bond pdb=" C1' DT Y 15 " pdb=" N1 DT Y 15 " ideal model delta sigma weight residual 1.490 1.369 0.121 3.00e-02 1.11e+03 1.62e+01 bond pdb=" C1' DG X -6 " pdb=" N9 DG X -6 " ideal model delta sigma weight residual 1.460 1.380 0.080 2.00e-02 2.50e+03 1.62e+01 ... (remaining 35551 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.16: 45590 2.16 - 4.31: 3198 4.31 - 6.47: 407 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: 4470 0.094 - 0.189: 884 0.189 - 0.283: 84 0.283 - 0.378: 4 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: 19.900 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.810 Check model and map are aligned: 0.100 Set scattering table: 0.090 Process input model: 38.550 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:9.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 69.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7424 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= 0.766 Angle : 1.215 10.777 49302 Z= 0.705 Chirality : 0.074 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 0.01719 / 0.76 (35556) covalent geometry : angle 1.21526 / 0.70 (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 : 1.164 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: 0.8277 time to fit residues: 688.7047 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 : 1.143 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** D 105 ASN ** D 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 189 HIS D 263 GLN E 204 GLN E 209 GLN E 253 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 J 196 GLN J 213 GLN J 232 ASN J 331 GLN K 463 ASN K 464 GLN O 104 GLN P 46 HIS P 106 HIS 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: 42 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4344 r_free = 0.4344 target = 0.136889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.096160 restraints weight = 90903.839| |-----------------------------------------------------------------------------| r_work (start): 0.3553 rms_B_bonded: 2.28 r_work: 0.3380 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work: 0.3232 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.2706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 35557 Z= 0.170 Angle : 0.685 11.897 49302 Z= 0.379 Chirality : 0.041 0.160 5443 Planarity : 0.005 0.075 5219 Dihedral : 24.891 178.435 7172 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.07 % Favored : 94.84 % Rotamer: Outliers : 2.96 % Allowed : 11.24 % Favored : 85.81 % 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: -3.28 (0.12), residues: 3335 helix: -1.90 (0.10), residues: 1860 sheet: -2.72 (0.37), residues: 166 loop : -2.32 (0.15), residues: 1309 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B1209 TYR 0.025 0.002 TYR D 117 PHE 0.024 0.002 PHE B1269 TRP 0.025 0.002 TRP A 912 HIS 0.013 0.001 HIS H 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.17 (35556) covalent geometry : angle 0.68471 / 0.38 (49302) hydrogen bonds : bond 0.07314 / 4.66 ( 1493) hydrogen bonds : angle 4.98052 / 3.36 ( 4038) metal coordination : bond 0.00752 / 0.40 ( 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 636 residues out of total 3044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 546 time to evaluate : 1.214 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: 0.8563 (tt0) cc_final: 0.8081 (tt0) REVERT: A 940 LYS cc_start: 0.9042 (tppp) cc_final: 0.8838 (tttm) REVERT: A 986 TYR cc_start: 0.7702 (t80) cc_final: 0.6937 (m-80) REVERT: A 1146 ILE cc_start: 0.8943 (pt) cc_final: 0.8651 (OUTLIER) REVERT: A 1156 GLU cc_start: 0.8389 (tp30) cc_final: 0.8021 (tp30) REVERT: A 1261 LYS cc_start: 0.7850 (mmtt) cc_final: 0.7554 (tptp) REVERT: A 1301 PHE cc_start: 0.8658 (m-80) cc_final: 0.8350 (m-80) REVERT: A 1316 TYR cc_start: 0.7744 (p90) cc_final: 0.7394 (p90) REVERT: B 821 ILE cc_start: 0.8224 (OUTLIER) cc_final: 0.7977 (tp) REVERT: B 834 ILE cc_start: 0.8225 (OUTLIER) cc_final: 0.7624 (tt) REVERT: B 881 ASP cc_start: 0.8749 (t0) cc_final: 0.8271 (p0) REVERT: B 916 TRP cc_start: 0.8187 (m-10) cc_final: 0.7171 (m-10) REVERT: B 1026 PHE cc_start: 0.7707 (p90) cc_final: 0.7451 (p90) REVERT: B 1257 MET cc_start: 0.7902 (ptp) cc_final: 0.6747 (ppp) REVERT: B 1317 ILE cc_start: 0.7830 (mm) cc_final: 0.7278 (mm) REVERT: C 94 LEU cc_start: 0.9183 (tp) cc_final: 0.8978 (tm) REVERT: C 100 GLU cc_start: 0.8604 (mp0) cc_final: 0.8330 (mp0) REVERT: C 114 ASP cc_start: 0.8538 (p0) cc_final: 0.8329 (p0) REVERT: D 232 TYR cc_start: 0.6592 (m-10) cc_final: 0.6321 (m-10) REVERT: D 247 TYR cc_start: 0.8812 (t80) cc_final: 0.8478 (t80) REVERT: D 255 ILE cc_start: 0.9425 (mm) cc_final: 0.9088 (mp) REVERT: D 297 TYR cc_start: 0.8247 (t80) cc_final: 0.7867 (t80) REVERT: D 305 MET cc_start: 0.8467 (ttp) cc_final: 0.7983 (mtt) REVERT: D 306 MET cc_start: 0.7938 (mtp) cc_final: 0.7417 (mtp) REVERT: D 322 TRP cc_start: 0.8847 (m-10) cc_final: 0.8507 (m-10) REVERT: D 344 TYR cc_start: 0.8555 (t80) cc_final: 0.7867 (t80) REVERT: D 345 GLU cc_start: 0.8245 (pm20) cc_final: 0.7915 (tm-30) REVERT: D 347 TYR cc_start: 0.9091 (m-80) cc_final: 0.8780 (m-80) REVERT: D 369 LEU cc_start: 0.9115 (mt) cc_final: 0.8783 (pp) REVERT: D 376 ILE cc_start: 0.9373 (mp) cc_final: 0.9082 (mp) REVERT: E 226 TYR cc_start: 0.8452 (p90) cc_final: 0.8032 (p90) REVERT: E 227 TYR cc_start: 0.9081 (m-10) cc_final: 0.8794 (m-10) REVERT: F 50 ASP cc_start: 0.8752 (m-30) cc_final: 0.8435 (m-30) REVERT: F 65 GLN cc_start: 0.9103 (mt0) cc_final: 0.8902 (mt0) REVERT: F 85 GLU cc_start: 0.8805 (OUTLIER) cc_final: 0.8451 (mp0) REVERT: G 168 ARG cc_start: 0.8118 (ptm-80) cc_final: 0.7613 (ptm-80) REVERT: I 78 GLU cc_start: 0.8280 (pt0) cc_final: 0.8052 (pp20) REVERT: I 84 GLU cc_start: 0.8716 (tm-30) cc_final: 0.8503 (tp30) REVERT: I 87 MET cc_start: 0.8438 (ttp) cc_final: 0.7919 (ttp) REVERT: J 298 ASN cc_start: 0.5219 (m-40) cc_final: 0.3815 (t0) REVERT: J 342 ARG cc_start: 0.7437 (ttm170) cc_final: 0.6972 (ttm-80) REVERT: J 357 ARG cc_start: 0.9097 (ttp-170) cc_final: 0.8729 (ttp80) REVERT: J 358 ASN cc_start: 0.8401 (m110) cc_final: 0.8038 (m110) REVERT: J 361 LYS cc_start: 0.9330 (mtpp) cc_final: 0.9114 (mtpt) REVERT: O 15 LYS cc_start: 0.7558 (tmtt) cc_final: 0.7303 (ttpp) REVERT: P 31 LYS cc_start: 0.7695 (tptt) cc_final: 0.7105 (tttp) REVERT: Q 133 GLU cc_start: 0.8048 (OUTLIER) cc_final: 0.7782 (mt-10) REVERT: S 36 LYS cc_start: 0.8743 (mmtm) cc_final: 0.8412 (mmmm) REVERT: S 71 ARG cc_start: 0.8244 (mtm110) cc_final: 0.7937 (mtm-85) REVERT: S 72 ASP cc_start: 0.8556 (m-30) cc_final: 0.8334 (m-30) REVERT: S 91 GLU cc_start: 0.7824 (OUTLIER) cc_final: 0.7359 (pm20) REVERT: T 83 ARG cc_start: 0.8761 (OUTLIER) cc_final: 0.7708 (mtt-85) REVERT: U 52 ARG cc_start: 0.8562 (mtt90) cc_final: 0.8202 (mtm110) REVERT: U 94 GLU cc_start: 0.8798 (mm-30) cc_final: 0.8487 (mm-30) REVERT: V 50 ILE cc_start: 0.8469 (tt) cc_final: 0.8117 (tt) outliers start: 90 outliers final: 30 residues processed: 593 average time/residue: 0.6982 time to fit residues: 490.5081 Evaluate side-chains 468 residues out of total 3044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 433 time to evaluate : 1.181 ------------------------------------------------------------------------------- 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 996 ILE 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 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 370 ASP Chi-restraints excluded: chain D residue 123 SER Chi-restraints excluded: chain D residue 167 VAL 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 326 THR Chi-restraints excluded: chain D residue 338 LEU 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 P residue 105 LYS 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 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: 0.5980 chunk 275 optimal weight: 0.3980 chunk 247 optimal weight: 4.9990 chunk 249 optimal weight: 0.0970 chunk 234 optimal weight: 0.7980 chunk 115 optimal weight: 3.9990 chunk 206 optimal weight: 0.8980 chunk 4 optimal weight: 8.9990 chunk 45 optimal weight: 0.5980 chunk 280 optimal weight: 2.9990 chunk 86 optimal weight: 9.9990 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 829 GLN A1081 ASN A1143 ASN A1222 GLN ** B 801 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1137 ASN ** B1252 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 231 ASN D 359 ASN ** E 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 92 HIS G 173 HIS ** G 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 178 HIS J 196 GLN J 331 GLN ** J 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 370 ASN ** Q 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4331 r_free = 0.4331 target = 0.136720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.095062 restraints weight = 91206.784| |-----------------------------------------------------------------------------| r_work (start): 0.3504 rms_B_bonded: 2.41 r_work: 0.3320 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.3326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 35557 Z= 0.154 Angle : 0.628 9.941 49302 Z= 0.344 Chirality : 0.040 0.239 5443 Planarity : 0.004 0.047 5219 Dihedral : 24.653 177.127 7157 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.28 % Favored : 94.69 % Rotamer: Outliers : 2.46 % Allowed : 14.52 % Favored : 83.02 % 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: -2.18 (0.13), residues: 3335 helix: -0.82 (0.11), residues: 1868 sheet: -2.48 (0.38), residues: 165 loop : -2.13 (0.16), residues: 1302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG J 293 TYR 0.018 0.002 TYR D 343 PHE 0.024 0.002 PHE B1269 TRP 0.012 0.001 TRP B1223 HIS 0.006 0.001 HIS H 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.15 (35556) covalent geometry : angle 0.62760 / 0.34 (49302) hydrogen bonds : bond 0.06406 / 4.11 ( 1493) hydrogen bonds : angle 4.39677 / 2.96 ( 4038) metal coordination : bond 0.00158 / 0.08 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6670 Ramachandran restraints generated. 3335 Oldfield, 0 Emsley, 3335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6670 Ramachandran restraints generated. 3335 Oldfield, 0 Emsley, 3335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 569 residues out of total 3044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 494 time to evaluate : 1.268 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 811 GLU cc_start: 0.8404 (tt0) cc_final: 0.8003 (tt0) REVERT: A 940 LYS cc_start: 0.9007 (tppp) cc_final: 0.8709 (tttm) REVERT: A 986 TYR cc_start: 0.7464 (t80) cc_final: 0.6654 (m-80) REVERT: A 1016 TYR cc_start: 0.6790 (m-10) cc_final: 0.6488 (m-80) REVERT: A 1156 GLU cc_start: 0.8139 (tp30) cc_final: 0.7762 (tp30) REVERT: A 1261 LYS cc_start: 0.7699 (mmtt) cc_final: 0.7420 (tptp) REVERT: A 1316 TYR cc_start: 0.7619 (p90) cc_final: 0.7206 (p90) REVERT: B 821 ILE cc_start: 0.8236 (OUTLIER) cc_final: 0.7778 (tp) REVERT: B 834 ILE cc_start: 0.8214 (OUTLIER) cc_final: 0.7690 (tt) REVERT: B 881 ASP cc_start: 0.8711 (t0) cc_final: 0.8301 (p0) REVERT: B 912 TRP cc_start: 0.7877 (OUTLIER) cc_final: 0.6811 (t-100) REVERT: B 1026 PHE cc_start: 0.7450 (p90) cc_final: 0.7217 (p90) REVERT: B 1257 MET cc_start: 0.7803 (ptp) cc_final: 0.7409 (ppp) REVERT: B 1294 MET cc_start: 0.7671 (ptp) cc_final: 0.6576 (tpp) REVERT: C 99 ARG cc_start: 0.8338 (ppt170) cc_final: 0.7952 (ppt-90) REVERT: C 100 GLU cc_start: 0.8440 (mp0) cc_final: 0.7995 (mp0) REVERT: C 114 ASP cc_start: 0.8398 (p0) cc_final: 0.8158 (p0) REVERT: D 49 HIS cc_start: 0.9246 (t-170) cc_final: 0.8905 (t-170) REVERT: D 232 TYR cc_start: 0.6346 (m-10) cc_final: 0.6066 (m-10) REVERT: D 247 TYR cc_start: 0.8978 (t80) cc_final: 0.8711 (t80) REVERT: D 251 PHE cc_start: 0.8436 (p90) cc_final: 0.8203 (p90) REVERT: D 322 TRP cc_start: 0.9057 (m-10) cc_final: 0.8529 (m-10) REVERT: D 324 PHE cc_start: 0.9044 (t80) cc_final: 0.8770 (t80) REVERT: D 344 TYR cc_start: 0.8506 (t80) cc_final: 0.8214 (t80) REVERT: D 347 TYR cc_start: 0.9137 (m-80) cc_final: 0.8873 (m-80) REVERT: D 371 LYS cc_start: 0.9089 (ptpt) cc_final: 0.8859 (ptpt) REVERT: E 226 TYR cc_start: 0.8597 (p90) cc_final: 0.8396 (p90) REVERT: E 227 TYR cc_start: 0.9049 (m-10) cc_final: 0.8794 (m-10) REVERT: E 270 LYS cc_start: 0.8799 (mttp) cc_final: 0.8488 (mtmt) REVERT: F 50 ASP cc_start: 0.8666 (m-30) cc_final: 0.8383 (m-30) REVERT: F 85 GLU cc_start: 0.8737 (OUTLIER) cc_final: 0.8352 (mp0) REVERT: F 135 MET cc_start: 0.3349 (mpm) cc_final: 0.3012 (mpm) REVERT: G 137 LYS cc_start: 0.8776 (mmtt) cc_final: 0.8504 (mmpt) REVERT: G 168 ARG cc_start: 0.8189 (ptm-80) cc_final: 0.7790 (ptm-80) REVERT: G 175 ILE cc_start: 0.8113 (OUTLIER) cc_final: 0.7833 (pp) REVERT: I 77 GLU cc_start: 0.8470 (mm-30) cc_final: 0.8206 (mm-30) REVERT: I 87 MET cc_start: 0.8348 (ttp) cc_final: 0.7821 (ttp) REVERT: J 342 ARG cc_start: 0.7456 (ttm170) cc_final: 0.7164 (ttm-80) REVERT: J 351 ARG cc_start: 0.8319 (mtt180) cc_final: 0.8079 (mtt180) REVERT: J 357 ARG cc_start: 0.9008 (ttp-170) cc_final: 0.8691 (ttp80) REVERT: J 375 ARG cc_start: 0.8360 (mmm160) cc_final: 0.7793 (mmm160) REVERT: J 378 ASN cc_start: 0.8666 (m-40) cc_final: 0.7979 (p0) REVERT: O 74 LYS cc_start: 0.8818 (mmtt) cc_final: 0.8518 (tppt) REVERT: O 91 GLU cc_start: 0.8435 (tm-30) cc_final: 0.8198 (tm-30) REVERT: P 31 LYS cc_start: 0.7590 (tptt) cc_final: 0.7032 (tttp) REVERT: Q 133 GLU cc_start: 0.8058 (OUTLIER) cc_final: 0.7757 (mt-10) REVERT: S 36 LYS cc_start: 0.8673 (mmtm) cc_final: 0.8309 (mmmm) REVERT: S 71 ARG cc_start: 0.8020 (mtm110) cc_final: 0.7754 (mtm-85) REVERT: S 72 ASP cc_start: 0.8420 (m-30) cc_final: 0.8136 (m-30) REVERT: S 91 GLU cc_start: 0.7667 (OUTLIER) cc_final: 0.7172 (pm20) REVERT: T 48 ASP cc_start: 0.8004 (m-30) cc_final: 0.7486 (t70) REVERT: T 83 ARG cc_start: 0.8682 (OUTLIER) cc_final: 0.7580 (mtt-85) REVERT: U 42 ARG cc_start: 0.8040 (mtt-85) cc_final: 0.6667 (mtm-85) REVERT: U 52 ARG cc_start: 0.8304 (mtt90) cc_final: 0.7921 (mtm110) REVERT: U 94 GLU cc_start: 0.8597 (mm-30) cc_final: 0.8270 (mm-30) REVERT: V 50 ILE cc_start: 0.8335 (tt) cc_final: 0.8003 (tt) outliers start: 75 outliers final: 25 residues processed: 532 average time/residue: 0.7535 time to fit residues: 476.7805 Evaluate side-chains 463 residues out of total 3044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 430 time to evaluate : 1.311 ------------------------------------------------------------------------------- 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 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 912 TRP Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain D residue 168 LEU Chi-restraints excluded: chain D residue 199 THR 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 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 175 ILE Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain I residue 39 CYS Chi-restraints excluded: chain P residue 110 GLU Chi-restraints excluded: chain Q residue 133 GLU Chi-restraints excluded: chain R residue 49 LEU Chi-restraints excluded: chain R residue 84 MET 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 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: 0.0270 chunk 276 optimal weight: 1.9990 chunk 246 optimal weight: 0.8980 chunk 35 optimal weight: 5.9990 chunk 3 optimal weight: 9.9990 chunk 169 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 chunk 83 optimal weight: 10.0000 chunk 281 optimal weight: 0.6980 chunk 226 optimal weight: 40.0000 chunk 164 optimal weight: 6.9990 overall best weight: 0.9242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 998 HIS ** A1150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 801 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1252 HIS ** C 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 235 ASN ** D 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 331 ASN ** E 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 61 GLN F 65 GLN ** G 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 96 ASN J 196 GLN J 222 HIS J 230 ASN J 331 GLN ** J 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 360 GLN ** Q 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4318 r_free = 0.4318 target = 0.136015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.094252 restraints weight = 90487.988| |-----------------------------------------------------------------------------| r_work (start): 0.3484 rms_B_bonded: 2.38 r_work: 0.3300 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.3586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 35557 Z= 0.182 Angle : 0.624 9.066 49302 Z= 0.340 Chirality : 0.040 0.207 5443 Planarity : 0.004 0.043 5219 Dihedral : 24.635 175.486 7155 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.28 % Favored : 94.69 % Rotamer: Outliers : 3.09 % Allowed : 15.51 % Favored : 81.41 % 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: -1.64 (0.14), residues: 3335 helix: -0.36 (0.11), residues: 1896 sheet: -2.13 (0.41), residues: 157 loop : -1.97 (0.16), residues: 1282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG J 293 TYR 0.042 0.002 TYR H 268 PHE 0.022 0.002 PHE B1269 TRP 0.014 0.001 TRP A 912 HIS 0.009 0.001 HIS D 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00407 / 0.18 (35556) covalent geometry : angle 0.62421 / 0.34 (49302) hydrogen bonds : bond 0.06056 / 3.90 ( 1493) hydrogen bonds : angle 4.18222 / 2.82 ( 4038) metal coordination : bond 0.00129 / 0.07 ( 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 564 residues out of total 3044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 470 time to evaluate : 1.455 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: 0.8416 (tt0) cc_final: 0.8047 (tt0) REVERT: A 940 LYS cc_start: 0.9004 (tppp) cc_final: 0.8748 (tttm) REVERT: A 986 TYR cc_start: 0.7480 (t80) cc_final: 0.6689 (m-80) REVERT: A 1016 TYR cc_start: 0.6708 (m-10) cc_final: 0.6386 (m-10) REVERT: A 1156 GLU cc_start: 0.8124 (tp30) cc_final: 0.7752 (tp30) REVERT: A 1301 PHE cc_start: 0.8510 (m-80) cc_final: 0.8278 (m-80) REVERT: B 821 ILE cc_start: 0.8268 (OUTLIER) cc_final: 0.7954 (tp) REVERT: B 834 ILE cc_start: 0.8213 (OUTLIER) cc_final: 0.7712 (tt) REVERT: B 881 ASP cc_start: 0.8721 (t0) cc_final: 0.8332 (p0) REVERT: B 912 TRP cc_start: 0.7884 (OUTLIER) cc_final: 0.7601 (t-100) REVERT: B 916 TRP cc_start: 0.8403 (m-10) cc_final: 0.8082 (m-10) REVERT: B 1026 PHE cc_start: 0.7474 (p90) cc_final: 0.7264 (p90) REVERT: B 1257 MET cc_start: 0.7806 (ptp) cc_final: 0.6885 (ppp) REVERT: B 1266 MET cc_start: 0.8741 (pmm) cc_final: 0.7832 (mmt) REVERT: B 1294 MET cc_start: 0.7807 (ptp) cc_final: 0.6507 (tpp) REVERT: C 99 ARG cc_start: 0.8410 (ppt170) cc_final: 0.8136 (ppt170) REVERT: C 100 GLU cc_start: 0.8482 (mp0) cc_final: 0.8217 (mp0) REVERT: C 114 ASP cc_start: 0.8398 (p0) cc_final: 0.8166 (p0) REVERT: C 153 LYS cc_start: 0.9191 (OUTLIER) cc_final: 0.8344 (mttp) REVERT: C 370 ASP cc_start: 0.8426 (t0) cc_final: 0.8188 (t0) REVERT: D 232 TYR cc_start: 0.6365 (m-10) cc_final: 0.6077 (m-10) REVERT: D 247 TYR cc_start: 0.8937 (t80) cc_final: 0.8469 (t80) REVERT: D 276 LEU cc_start: 0.8304 (OUTLIER) cc_final: 0.7939 (mm) REVERT: D 297 TYR cc_start: 0.8270 (t80) cc_final: 0.7946 (t80) REVERT: D 322 TRP cc_start: 0.9119 (m-10) cc_final: 0.8531 (m-10) REVERT: D 344 TYR cc_start: 0.8497 (t80) cc_final: 0.8246 (t80) REVERT: D 347 TYR cc_start: 0.9206 (m-80) cc_final: 0.8827 (m-80) REVERT: D 369 LEU cc_start: 0.9304 (mt) cc_final: 0.8996 (pp) REVERT: D 376 ILE cc_start: 0.9303 (mp) cc_final: 0.8976 (mp) REVERT: E 227 TYR cc_start: 0.9014 (m-10) cc_final: 0.8793 (m-10) REVERT: E 235 ASP cc_start: 0.8462 (OUTLIER) cc_final: 0.8256 (p0) REVERT: E 286 TRP cc_start: 0.7774 (OUTLIER) cc_final: 0.7141 (t60) REVERT: F 50 ASP cc_start: 0.8662 (m-30) cc_final: 0.8415 (m-30) REVERT: F 61 GLN cc_start: 0.8479 (tp40) cc_final: 0.8220 (tp-100) REVERT: F 72 GLU cc_start: 0.8571 (tt0) cc_final: 0.8343 (tt0) REVERT: F 85 GLU cc_start: 0.8745 (OUTLIER) cc_final: 0.8355 (mp0) REVERT: F 292 THR cc_start: 0.6650 (OUTLIER) cc_final: 0.6399 (m) REVERT: G 102 MET cc_start: 0.5093 (mmt) cc_final: 0.4882 (mmm) REVERT: G 168 ARG cc_start: 0.8176 (ptm-80) cc_final: 0.7768 (ptm-80) REVERT: G 175 ILE cc_start: 0.7903 (OUTLIER) cc_final: 0.7624 (pp) REVERT: I 87 MET cc_start: 0.8300 (ttp) cc_final: 0.7744 (ttp) REVERT: J 161 ASN cc_start: 0.7855 (p0) cc_final: 0.7620 (p0) REVERT: J 206 MET cc_start: 0.8498 (OUTLIER) cc_final: 0.8194 (mmm) REVERT: J 298 ASN cc_start: 0.5306 (m-40) cc_final: 0.3656 (t0) REVERT: J 332 GLN cc_start: 0.8616 (tp40) cc_final: 0.7682 (pm20) REVERT: J 342 ARG cc_start: 0.7443 (ttm170) cc_final: 0.7081 (ttm-80) REVERT: J 351 ARG cc_start: 0.8307 (mtt180) cc_final: 0.8027 (mtt180) REVERT: J 358 ASN cc_start: 0.8539 (m110) cc_final: 0.8159 (m110) REVERT: J 375 ARG cc_start: 0.8364 (mmm160) cc_final: 0.7762 (mtp180) REVERT: J 378 ASN cc_start: 0.8623 (m-40) cc_final: 0.8024 (p0) REVERT: P 31 LYS cc_start: 0.7648 (tptt) cc_final: 0.7098 (tttp) REVERT: Q 133 GLU cc_start: 0.8069 (OUTLIER) cc_final: 0.7748 (mt-10) REVERT: S 36 LYS cc_start: 0.8678 (mmtm) cc_final: 0.8314 (mmmm) REVERT: S 71 ARG cc_start: 0.8058 (mtm110) cc_final: 0.7760 (mtt-85) REVERT: S 72 ASP cc_start: 0.8444 (m-30) cc_final: 0.8209 (m-30) REVERT: T 48 ASP cc_start: 0.7975 (m-30) cc_final: 0.7498 (t70) REVERT: T 83 ARG cc_start: 0.8683 (OUTLIER) cc_final: 0.7615 (mtt-85) REVERT: U 42 ARG cc_start: 0.8081 (mtt-85) cc_final: 0.6720 (mtm-85) REVERT: U 52 ARG cc_start: 0.8324 (mtt90) cc_final: 0.8038 (mtp180) REVERT: U 94 GLU cc_start: 0.8601 (mm-30) cc_final: 0.8282 (mm-30) REVERT: V 50 ILE cc_start: 0.8465 (tt) cc_final: 0.8130 (tt) REVERT: V 59 LYS cc_start: 0.8881 (OUTLIER) cc_final: 0.8628 (tttm) outliers start: 94 outliers final: 28 residues processed: 519 average time/residue: 0.7314 time to fit residues: 452.1022 Evaluate side-chains 469 residues out of total 3044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 427 time to evaluate : 1.226 ------------------------------------------------------------------------------- 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 934 THR Chi-restraints excluded: chain A residue 1161 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 821 ILE Chi-restraints excluded: chain B residue 834 ILE Chi-restraints excluded: chain B residue 912 TRP Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 153 LYS Chi-restraints excluded: chain C residue 332 VAL 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 338 LEU Chi-restraints excluded: chain D residue 354 SER Chi-restraints excluded: chain E residue 205 LEU Chi-restraints excluded: chain E residue 235 ASP Chi-restraints excluded: chain E residue 286 TRP Chi-restraints excluded: chain F residue 85 GLU Chi-restraints excluded: chain F residue 292 THR Chi-restraints excluded: chain G residue 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 344 LEU 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 59 LYS Chi-restraints excluded: chain V residue 96 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 95 optimal weight: 20.0000 chunk 236 optimal weight: 0.0870 chunk 233 optimal weight: 0.9980 chunk 98 optimal weight: 9.9990 chunk 254 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 245 optimal weight: 4.9990 chunk 28 optimal weight: 3.9990 chunk 141 optimal weight: 9.9990 chunk 286 optimal weight: 0.5980 chunk 115 optimal weight: 0.9990 overall best weight: 0.9362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1081 ASN A1150 HIS A1206 GLN ** B 801 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 815 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1221 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** E 220 HIS ** E 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 183 GLN I 65 GLN J 331 GLN J 370 ASN O 110 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4320 r_free = 0.4320 target = 0.136082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.094145 restraints weight = 90742.520| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 2.37 r_work: 0.3297 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.3793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 35557 Z= 0.182 Angle : 0.633 11.278 49302 Z= 0.341 Chirality : 0.040 0.160 5443 Planarity : 0.004 0.059 5219 Dihedral : 24.625 174.361 7155 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.55 % Favored : 94.42 % Rotamer: Outliers : 2.79 % Allowed : 16.75 % Favored : 80.45 % 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: -1.31 (0.14), residues: 3335 helix: -0.06 (0.12), residues: 1893 sheet: -2.07 (0.40), residues: 159 loop : -1.87 (0.16), residues: 1283 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG J 293 TYR 0.024 0.001 TYR E 226 PHE 0.023 0.001 PHE B1269 TRP 0.028 0.001 TRP D 261 HIS 0.015 0.001 HIS D 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00408 / 0.18 (35556) covalent geometry : angle 0.63285 / 0.34 (49302) hydrogen bonds : bond 0.05982 / 3.85 ( 1493) hydrogen bonds : angle 4.09587 / 2.76 ( 4038) metal coordination : bond 0.00208 / 0.11 ( 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 549 residues out of total 3044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 464 time to evaluate : 1.289 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 811 GLU cc_start: 0.8461 (tt0) cc_final: 0.8080 (tt0) REVERT: A 940 LYS cc_start: 0.8994 (tppp) cc_final: 0.8716 (tttm) REVERT: A 986 TYR cc_start: 0.7471 (t80) cc_final: 0.6640 (m-80) REVERT: A 1016 TYR cc_start: 0.6575 (m-10) cc_final: 0.6227 (m-10) REVERT: A 1156 GLU cc_start: 0.8132 (tp30) cc_final: 0.7756 (tp30) REVERT: A 1261 LYS cc_start: 0.7708 (mmtt) cc_final: 0.7405 (mptp) REVERT: A 1300 MET cc_start: 0.6852 (ttp) cc_final: 0.6192 (ttm) REVERT: A 1301 PHE cc_start: 0.8528 (m-80) cc_final: 0.8239 (m-80) REVERT: A 1316 TYR cc_start: 0.7644 (p90) cc_final: 0.7187 (p90) REVERT: B 821 ILE cc_start: 0.8261 (OUTLIER) cc_final: 0.7939 (tp) REVERT: B 881 ASP cc_start: 0.8715 (t0) cc_final: 0.8350 (p0) REVERT: B 912 TRP cc_start: 0.7905 (OUTLIER) cc_final: 0.7611 (t-100) REVERT: B 916 TRP cc_start: 0.8440 (m-10) cc_final: 0.8067 (m-10) REVERT: B 1026 PHE cc_start: 0.7489 (p90) cc_final: 0.7214 (p90) REVERT: B 1257 MET cc_start: 0.7692 (ptp) cc_final: 0.6917 (ppp) REVERT: C 100 GLU cc_start: 0.8527 (mp0) cc_final: 0.8216 (mp0) REVERT: C 114 ASP cc_start: 0.8391 (p0) cc_final: 0.8165 (p0) REVERT: D 40 MET cc_start: 0.6002 (tpt) cc_final: 0.5289 (mmm) REVERT: D 41 LYS cc_start: 0.7717 (tppp) cc_final: 0.7110 (tppp) REVERT: D 76 GLN cc_start: 0.7318 (pm20) cc_final: 0.7040 (mp10) REVERT: D 247 TYR cc_start: 0.8938 (t80) cc_final: 0.8495 (t80) REVERT: D 276 LEU cc_start: 0.8256 (OUTLIER) cc_final: 0.8013 (mm) REVERT: D 297 TYR cc_start: 0.8297 (t80) cc_final: 0.8017 (t80) REVERT: D 322 TRP cc_start: 0.9147 (m-10) cc_final: 0.8589 (m-10) REVERT: D 347 TYR cc_start: 0.9157 (m-80) cc_final: 0.8734 (m-80) REVERT: D 369 LEU cc_start: 0.9318 (mt) cc_final: 0.8902 (pp) REVERT: E 227 TYR cc_start: 0.8983 (m-10) cc_final: 0.8755 (m-10) REVERT: E 235 ASP cc_start: 0.8544 (OUTLIER) cc_final: 0.8326 (p0) REVERT: F 50 ASP cc_start: 0.8639 (m-30) cc_final: 0.8390 (m-30) REVERT: F 61 GLN cc_start: 0.8462 (tp40) cc_final: 0.8205 (tp-100) REVERT: F 85 GLU cc_start: 0.8752 (OUTLIER) cc_final: 0.8363 (mp0) REVERT: F 292 THR cc_start: 0.6608 (OUTLIER) cc_final: 0.6351 (m) REVERT: G 137 LYS cc_start: 0.8737 (mmtt) cc_final: 0.8435 (mmpt) REVERT: G 168 ARG cc_start: 0.8204 (ptm-80) cc_final: 0.7887 (ptm-80) REVERT: G 175 ILE cc_start: 0.7912 (OUTLIER) cc_final: 0.7601 (pp) REVERT: H 244 ARG cc_start: 0.7497 (tpt170) cc_final: 0.7212 (ttm170) REVERT: I 43 MET cc_start: 0.8314 (ttm) cc_final: 0.8018 (mmp) REVERT: I 79 LEU cc_start: 0.8554 (tm) cc_final: 0.7929 (tp) REVERT: I 87 MET cc_start: 0.8199 (ttp) cc_final: 0.7533 (ttp) REVERT: J 206 MET cc_start: 0.8421 (OUTLIER) cc_final: 0.8155 (mmm) REVERT: J 228 GLU cc_start: 0.7778 (OUTLIER) cc_final: 0.7547 (tt0) REVERT: J 332 GLN cc_start: 0.8623 (tp40) cc_final: 0.7690 (pm20) REVERT: J 342 ARG cc_start: 0.7473 (ttm170) cc_final: 0.6876 (ttm-80) REVERT: J 350 GLN cc_start: 0.8363 (pt0) cc_final: 0.7988 (pt0) REVERT: J 351 ARG cc_start: 0.8332 (mtt180) cc_final: 0.7766 (mtt180) REVERT: J 358 ASN cc_start: 0.8591 (m110) cc_final: 0.8213 (m110) REVERT: J 375 ARG cc_start: 0.8377 (mmm160) cc_final: 0.7532 (mtt-85) REVERT: J 378 ASN cc_start: 0.8622 (m-40) cc_final: 0.7985 (p0) REVERT: P 31 LYS cc_start: 0.7630 (tptt) cc_final: 0.7070 (tttp) REVERT: P 53 SER cc_start: 0.9046 (p) cc_final: 0.8781 (p) REVERT: Q 133 GLU cc_start: 0.8071 (OUTLIER) cc_final: 0.7763 (mt-10) REVERT: S 36 LYS cc_start: 0.8705 (mmtm) cc_final: 0.8318 (mmmm) REVERT: S 71 ARG cc_start: 0.8046 (mtm110) cc_final: 0.7762 (mtt-85) REVERT: S 72 ASP cc_start: 0.8442 (m-30) cc_final: 0.8219 (m-30) REVERT: T 48 ASP cc_start: 0.7901 (m-30) cc_final: 0.7473 (t70) REVERT: T 83 ARG cc_start: 0.8674 (OUTLIER) cc_final: 0.7636 (mtt-85) REVERT: U 42 ARG cc_start: 0.8170 (mtt-85) cc_final: 0.6794 (mtm-85) REVERT: U 52 ARG cc_start: 0.8347 (mtt90) cc_final: 0.8058 (mtp180) REVERT: U 94 GLU cc_start: 0.8626 (mm-30) cc_final: 0.8297 (mm-30) REVERT: V 50 ILE cc_start: 0.8501 (tt) cc_final: 0.8145 (tt) REVERT: V 59 LYS cc_start: 0.8876 (OUTLIER) cc_final: 0.8623 (tttm) outliers start: 85 outliers final: 34 residues processed: 510 average time/residue: 0.7145 time to fit residues: 434.7548 Evaluate side-chains 476 residues out of total 3044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 430 time to evaluate : 1.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 702 LEU Chi-restraints excluded: chain A residue 773 MET Chi-restraints excluded: chain A residue 861 THR Chi-restraints excluded: chain A residue 934 THR Chi-restraints excluded: chain A residue 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 912 TRP Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain D residue 78 HIS Chi-restraints excluded: chain D residue 167 VAL 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 235 ASP 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 I residue 82 SER Chi-restraints excluded: chain J residue 200 MET Chi-restraints excluded: chain J residue 206 MET Chi-restraints excluded: chain J residue 217 VAL Chi-restraints excluded: chain J residue 228 GLU Chi-restraints excluded: chain J residue 344 LEU Chi-restraints excluded: chain 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 59 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: 5.9990 chunk 189 optimal weight: 0.9990 chunk 116 optimal weight: 0.9980 chunk 245 optimal weight: 0.8980 chunk 250 optimal weight: 0.3980 chunk 296 optimal weight: 0.7980 chunk 47 optimal weight: 2.9990 chunk 335 optimal weight: 2.9990 chunk 74 optimal weight: 8.9990 chunk 238 optimal weight: 2.9990 chunk 206 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 801 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 815 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 930 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1221 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 231 ASN D 285 ASN ** E 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 331 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4322 r_free = 0.4322 target = 0.136229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.094695 restraints weight = 89948.920| |-----------------------------------------------------------------------------| r_work (start): 0.3490 rms_B_bonded: 2.35 r_work: 0.3303 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.4022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 35557 Z= 0.170 Angle : 0.633 10.892 49302 Z= 0.339 Chirality : 0.040 0.150 5443 Planarity : 0.004 0.057 5219 Dihedral : 24.582 173.253 7155 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.55 % Favored : 94.42 % Rotamer: Outliers : 2.20 % Allowed : 18.46 % Favored : 79.34 % 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: -1.10 (0.14), residues: 3335 helix: 0.11 (0.12), residues: 1906 sheet: -1.97 (0.41), residues: 159 loop : -1.80 (0.16), residues: 1270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG J 293 TYR 0.025 0.001 TYR B1232 PHE 0.027 0.001 PHE G 111 TRP 0.024 0.001 TRP D 261 HIS 0.011 0.001 HIS D 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.17 (35556) covalent geometry : angle 0.63279 / 0.34 (49302) hydrogen bonds : bond 0.05896 / 3.80 ( 1493) hydrogen bonds : angle 3.99512 / 2.69 ( 4038) metal coordination : bond 0.00153 / 0.08 ( 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 531 residues out of total 3044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 464 time to evaluate : 1.301 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 811 GLU cc_start: 0.8447 (tt0) cc_final: 0.8150 (tt0) REVERT: A 940 LYS cc_start: 0.8963 (tppp) cc_final: 0.8676 (tttm) REVERT: A 942 LEU cc_start: 0.8445 (tt) cc_final: 0.8228 (pp) REVERT: A 986 TYR cc_start: 0.7501 (t80) cc_final: 0.6638 (m-80) REVERT: A 1016 TYR cc_start: 0.6529 (m-10) cc_final: 0.5964 (m-10) REVERT: A 1156 GLU cc_start: 0.8132 (tp30) cc_final: 0.7748 (tp30) REVERT: A 1261 LYS cc_start: 0.7735 (mmtt) cc_final: 0.7465 (mptp) REVERT: A 1300 MET cc_start: 0.6904 (OUTLIER) cc_final: 0.6269 (ttm) REVERT: A 1301 PHE cc_start: 0.8555 (m-80) cc_final: 0.8277 (m-80) REVERT: A 1316 TYR cc_start: 0.7566 (p90) cc_final: 0.7104 (p90) REVERT: B 821 ILE cc_start: 0.8304 (OUTLIER) cc_final: 0.7941 (tp) REVERT: B 860 MET cc_start: 0.2374 (ptt) cc_final: 0.2077 (ppp) REVERT: B 881 ASP cc_start: 0.8818 (t0) cc_final: 0.8446 (p0) REVERT: B 912 TRP cc_start: 0.8012 (OUTLIER) cc_final: 0.7714 (t-100) REVERT: B 916 TRP cc_start: 0.8492 (m-10) cc_final: 0.8116 (m-10) REVERT: B 1257 MET cc_start: 0.7753 (ptp) cc_final: 0.7061 (ppp) REVERT: C 100 GLU cc_start: 0.8529 (mp0) cc_final: 0.8213 (mp0) REVERT: D 40 MET cc_start: 0.5671 (tpt) cc_final: 0.4898 (mmm) REVERT: D 41 LYS cc_start: 0.7739 (tppp) cc_final: 0.6938 (tppp) REVERT: D 247 TYR cc_start: 0.8889 (t80) cc_final: 0.8434 (t80) REVERT: D 276 LEU cc_start: 0.8192 (OUTLIER) cc_final: 0.7921 (mm) REVERT: D 288 MET cc_start: 0.8686 (mpp) cc_final: 0.8283 (mpp) REVERT: D 297 TYR cc_start: 0.8348 (t80) cc_final: 0.8097 (t80) REVERT: D 316 ARG cc_start: 0.8730 (tpp80) cc_final: 0.7978 (tpp80) REVERT: D 322 TRP cc_start: 0.9169 (m-10) cc_final: 0.8582 (m-10) REVERT: D 344 TYR cc_start: 0.8518 (t80) cc_final: 0.8267 (t80) REVERT: D 369 LEU cc_start: 0.9326 (mt) cc_final: 0.8909 (pp) REVERT: E 226 TYR cc_start: 0.8415 (OUTLIER) cc_final: 0.8185 (p90) REVERT: E 227 TYR cc_start: 0.8979 (m-10) cc_final: 0.8715 (m-10) REVERT: E 291 LYS cc_start: 0.8529 (tppt) cc_final: 0.8242 (tppt) REVERT: F 50 ASP cc_start: 0.8661 (m-30) cc_final: 0.8428 (m-30) REVERT: F 65 GLN cc_start: 0.9069 (OUTLIER) cc_final: 0.8694 (mt0) REVERT: F 85 GLU cc_start: 0.8743 (OUTLIER) cc_final: 0.8351 (mp0) REVERT: F 292 THR cc_start: 0.6548 (OUTLIER) cc_final: 0.6276 (m) REVERT: G 137 LYS cc_start: 0.8743 (mmtt) cc_final: 0.8441 (mmpt) REVERT: G 168 ARG cc_start: 0.8224 (ptm-80) cc_final: 0.7938 (ptm-80) REVERT: G 175 ILE cc_start: 0.7953 (OUTLIER) cc_final: 0.7622 (pp) REVERT: H 244 ARG cc_start: 0.7530 (tpt170) cc_final: 0.7262 (ttm170) REVERT: I 43 MET cc_start: 0.8294 (ttm) cc_final: 0.7931 (mmt) REVERT: I 71 ASN cc_start: 0.9132 (t0) cc_final: 0.8665 (p0) REVERT: I 79 LEU cc_start: 0.8552 (tm) cc_final: 0.8315 (tt) REVERT: I 87 MET cc_start: 0.8231 (ttp) cc_final: 0.7618 (ttp) REVERT: J 206 MET cc_start: 0.8383 (OUTLIER) cc_final: 0.8144 (mmm) REVERT: J 332 GLN cc_start: 0.8628 (tp40) cc_final: 0.7767 (pm20) REVERT: J 342 ARG cc_start: 0.7456 (ttm170) cc_final: 0.7217 (ttm-80) REVERT: J 351 ARG cc_start: 0.8363 (mtt180) cc_final: 0.7970 (mtt180) REVERT: J 357 ARG cc_start: 0.8803 (ttp80) cc_final: 0.8513 (ttp80) REVERT: J 358 ASN cc_start: 0.8606 (m110) cc_final: 0.8249 (m110) REVERT: J 375 ARG cc_start: 0.8372 (mmm160) cc_final: 0.7397 (mtp85) REVERT: J 378 ASN cc_start: 0.8574 (m-40) cc_final: 0.8008 (p0) REVERT: P 31 LYS cc_start: 0.7604 (tptt) cc_final: 0.7056 (tttp) REVERT: P 53 SER cc_start: 0.9009 (p) cc_final: 0.8748 (p) REVERT: Q 133 GLU cc_start: 0.8077 (OUTLIER) cc_final: 0.7860 (mt-10) REVERT: S 36 LYS cc_start: 0.8700 (mmtm) cc_final: 0.8321 (mmmm) REVERT: S 71 ARG cc_start: 0.8036 (mtm110) cc_final: 0.7764 (mtm-85) REVERT: S 72 ASP cc_start: 0.8436 (m-30) cc_final: 0.8197 (m-30) REVERT: S 91 GLU cc_start: 0.7758 (pp20) cc_final: 0.7260 (pm20) REVERT: T 48 ASP cc_start: 0.7916 (m-30) cc_final: 0.7508 (t70) REVERT: T 83 ARG cc_start: 0.8690 (OUTLIER) cc_final: 0.7666 (mtt-85) REVERT: U 42 ARG cc_start: 0.8171 (mtt-85) cc_final: 0.6773 (mtm-85) REVERT: U 52 ARG cc_start: 0.8375 (mtt90) cc_final: 0.8044 (mtp180) REVERT: U 59 GLU cc_start: 0.8434 (OUTLIER) cc_final: 0.7815 (pm20) REVERT: U 94 GLU cc_start: 0.8630 (mm-30) cc_final: 0.8300 (mm-30) REVERT: V 50 ILE cc_start: 0.8503 (tt) cc_final: 0.8090 (tt) REVERT: V 59 LYS cc_start: 0.8891 (OUTLIER) cc_final: 0.8640 (tttm) outliers start: 67 outliers final: 31 residues processed: 499 average time/residue: 0.7003 time to fit residues: 419.3218 Evaluate side-chains 474 residues out of total 3044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 429 time to evaluate : 1.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 702 LEU Chi-restraints excluded: chain A residue 773 MET Chi-restraints excluded: chain A residue 1177 THR Chi-restraints excluded: chain A residue 1180 PHE Chi-restraints excluded: chain A residue 1250 VAL Chi-restraints excluded: chain A residue 1300 MET Chi-restraints excluded: chain B residue 771 ASP Chi-restraints excluded: chain B residue 775 TRP Chi-restraints excluded: chain B residue 821 ILE Chi-restraints excluded: chain B residue 912 TRP Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain D residue 78 HIS Chi-restraints excluded: chain D residue 215 PHE Chi-restraints excluded: chain D residue 249 SER Chi-restraints excluded: chain D residue 267 VAL Chi-restraints excluded: chain D residue 276 LEU Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain E residue 205 LEU Chi-restraints excluded: chain E residue 226 TYR Chi-restraints excluded: chain F residue 65 GLN Chi-restraints excluded: chain F residue 85 GLU Chi-restraints excluded: chain F residue 292 THR Chi-restraints excluded: chain G residue 106 GLU Chi-restraints excluded: chain G residue 175 ILE Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain I residue 39 CYS Chi-restraints excluded: chain J residue 200 MET Chi-restraints excluded: chain J residue 206 MET Chi-restraints excluded: chain J residue 335 ASN Chi-restraints excluded: chain J residue 344 LEU Chi-restraints excluded: chain O residue 113 SER Chi-restraints excluded: chain O residue 114 VAL 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 84 MET 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: 0.6980 chunk 360 optimal weight: 10.0000 chunk 19 optimal weight: 0.4980 chunk 342 optimal weight: 2.9990 chunk 345 optimal weight: 10.0000 chunk 294 optimal weight: 0.9990 chunk 221 optimal weight: 20.0000 chunk 48 optimal weight: 5.9990 chunk 171 optimal weight: 0.1980 chunk 97 optimal weight: 7.9990 chunk 187 optimal weight: 0.6980 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 801 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 815 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1221 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 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 220 HIS ** E 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 61 GLN ** G 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 331 GLN ** J 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 360 GLN 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4331 r_free = 0.4331 target = 0.136825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.095377 restraints weight = 90737.888| |-----------------------------------------------------------------------------| r_work (start): 0.3508 rms_B_bonded: 2.38 r_work: 0.3327 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.4242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 35557 Z= 0.153 Angle : 0.630 11.266 49302 Z= 0.338 Chirality : 0.040 0.287 5443 Planarity : 0.004 0.063 5219 Dihedral : 24.513 172.244 7155 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.28 % Favored : 94.69 % Rotamer: Outliers : 2.20 % Allowed : 19.32 % Favored : 78.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.94 (0.14), residues: 3335 helix: 0.25 (0.12), residues: 1910 sheet: -1.88 (0.42), residues: 160 loop : -1.75 (0.17), residues: 1265 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.000 ARG J 293 TYR 0.026 0.001 TYR D 346 PHE 0.021 0.001 PHE B1269 TRP 0.025 0.001 TRP D 261 HIS 0.012 0.001 HIS B1293 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.15 (35556) covalent geometry : angle 0.62982 / 0.34 (49302) hydrogen bonds : bond 0.05873 / 3.78 ( 1493) hydrogen bonds : angle 3.93016 / 2.65 ( 4038) metal coordination : bond 0.00130 / 0.07 ( 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 526 residues out of total 3044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 459 time to evaluate : 1.252 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 940 LYS cc_start: 0.8940 (tppp) cc_final: 0.8632 (tttm) REVERT: A 986 TYR cc_start: 0.7486 (t80) cc_final: 0.6638 (m-80) REVERT: A 1261 LYS cc_start: 0.7746 (mmtt) cc_final: 0.7492 (mptp) REVERT: A 1300 MET cc_start: 0.6849 (OUTLIER) cc_final: 0.6217 (ttm) REVERT: A 1301 PHE cc_start: 0.8523 (m-80) cc_final: 0.8244 (m-80) REVERT: A 1316 TYR cc_start: 0.7562 (p90) cc_final: 0.7351 (p90) REVERT: B 821 ILE cc_start: 0.8166 (OUTLIER) cc_final: 0.7806 (tp) REVERT: B 860 MET cc_start: 0.2441 (ptt) cc_final: 0.1465 (pp-130) REVERT: B 881 ASP cc_start: 0.8671 (t0) cc_final: 0.8378 (p0) REVERT: B 912 TRP cc_start: 0.7901 (OUTLIER) cc_final: 0.7608 (t-100) REVERT: B 916 TRP cc_start: 0.8401 (m-10) cc_final: 0.7989 (m-10) REVERT: B 1257 MET cc_start: 0.7620 (ptp) cc_final: 0.7146 (ppp) REVERT: B 1266 MET cc_start: 0.8510 (pmm) cc_final: 0.7897 (mmt) REVERT: C 100 GLU cc_start: 0.8523 (mp0) cc_final: 0.8252 (mp0) REVERT: C 191 ASP cc_start: 0.8629 (p0) cc_final: 0.8342 (p0) REVERT: D 40 MET cc_start: 0.5857 (tpt) cc_final: 0.5186 (mmm) REVERT: D 41 LYS cc_start: 0.7468 (tppp) cc_final: 0.7083 (tppp) REVERT: D 184 ASP cc_start: 0.7151 (t0) cc_final: 0.6912 (OUTLIER) REVERT: D 247 TYR cc_start: 0.8759 (t80) cc_final: 0.8361 (t80) REVERT: D 277 SER cc_start: 0.7754 (t) cc_final: 0.7467 (m) REVERT: D 288 MET cc_start: 0.8600 (mpp) cc_final: 0.7911 (mpp) REVERT: D 316 ARG cc_start: 0.8592 (tpp80) cc_final: 0.8107 (tpp80) REVERT: D 322 TRP cc_start: 0.9091 (m-10) cc_final: 0.8601 (m-10) REVERT: D 369 LEU cc_start: 0.9271 (mt) cc_final: 0.8872 (pp) REVERT: E 226 TYR cc_start: 0.8359 (OUTLIER) cc_final: 0.8096 (p90) REVERT: E 227 TYR cc_start: 0.8902 (m-10) cc_final: 0.8646 (m-10) REVERT: E 235 ASP cc_start: 0.8579 (OUTLIER) cc_final: 0.8291 (p0) REVERT: E 291 LYS cc_start: 0.8540 (tppt) cc_final: 0.8248 (tppt) REVERT: F 61 GLN cc_start: 0.8344 (tp40) cc_final: 0.7885 (tp-100) REVERT: F 65 GLN cc_start: 0.8974 (OUTLIER) cc_final: 0.8715 (mt0) REVERT: F 85 GLU cc_start: 0.8716 (OUTLIER) cc_final: 0.8331 (mp0) REVERT: F 292 THR cc_start: 0.6517 (OUTLIER) cc_final: 0.6243 (m) REVERT: G 137 LYS cc_start: 0.8742 (mmtt) cc_final: 0.8488 (mmpt) REVERT: G 168 ARG cc_start: 0.8239 (ptm-80) cc_final: 0.7942 (ptm-80) REVERT: G 175 ILE cc_start: 0.7964 (OUTLIER) cc_final: 0.7484 (pp) REVERT: G 177 GLU cc_start: 0.6392 (tp30) cc_final: 0.6072 (tp30) REVERT: I 43 MET cc_start: 0.8147 (ttm) cc_final: 0.7835 (mmt) REVERT: I 71 ASN cc_start: 0.9124 (t0) cc_final: 0.8754 (p0) REVERT: I 79 LEU cc_start: 0.8551 (tm) cc_final: 0.8312 (tt) REVERT: I 87 MET cc_start: 0.8196 (ttp) cc_final: 0.7642 (ttp) REVERT: I 91 SER cc_start: 0.9440 (m) cc_final: 0.9177 (p) REVERT: J 177 ASN cc_start: 0.7459 (p0) cc_final: 0.6537 (t0) REVERT: J 228 GLU cc_start: 0.7749 (OUTLIER) cc_final: 0.7542 (tt0) REVERT: J 332 GLN cc_start: 0.8647 (tp40) cc_final: 0.7783 (pm20) REVERT: J 350 GLN cc_start: 0.8368 (pt0) cc_final: 0.8111 (pt0) REVERT: J 351 ARG cc_start: 0.8417 (mtt180) cc_final: 0.7993 (mtt180) REVERT: J 357 ARG cc_start: 0.8873 (ttp80) cc_final: 0.8476 (ttp80) REVERT: J 358 ASN cc_start: 0.8566 (m110) cc_final: 0.8261 (m110) REVERT: J 375 ARG cc_start: 0.8352 (mmm160) cc_final: 0.7426 (mtp85) REVERT: J 378 ASN cc_start: 0.8528 (m-40) cc_final: 0.8023 (p0) REVERT: P 31 LYS cc_start: 0.7552 (tptt) cc_final: 0.7035 (tttp) REVERT: P 53 SER cc_start: 0.9010 (p) cc_final: 0.8743 (p) REVERT: S 36 LYS cc_start: 0.8675 (mmtm) cc_final: 0.8303 (mmmm) REVERT: S 71 ARG cc_start: 0.8044 (mtm110) cc_final: 0.7780 (mtm-85) REVERT: S 72 ASP cc_start: 0.8443 (m-30) cc_final: 0.8197 (m-30) REVERT: S 91 GLU cc_start: 0.7728 (OUTLIER) cc_final: 0.7238 (pm20) REVERT: T 48 ASP cc_start: 0.7817 (m-30) cc_final: 0.7438 (t70) REVERT: T 83 ARG cc_start: 0.8694 (OUTLIER) cc_final: 0.7693 (mtt-85) REVERT: U 42 ARG cc_start: 0.8191 (mtt-85) cc_final: 0.6917 (mtm-85) REVERT: U 52 ARG cc_start: 0.8331 (mtt90) cc_final: 0.8082 (mtp180) REVERT: U 94 GLU cc_start: 0.8620 (mm-30) cc_final: 0.8260 (mm-30) REVERT: V 50 ILE cc_start: 0.8416 (tt) cc_final: 0.8037 (tt) outliers start: 67 outliers final: 34 residues processed: 495 average time/residue: 0.7341 time to fit residues: 434.9790 Evaluate side-chains 472 residues out of total 3044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 427 time to evaluate : 0.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 698 ASP Chi-restraints excluded: chain A residue 702 LEU Chi-restraints excluded: chain A residue 773 MET Chi-restraints excluded: chain A residue 861 THR Chi-restraints excluded: chain A residue 1177 THR Chi-restraints excluded: chain A residue 1180 PHE Chi-restraints excluded: chain A residue 1300 MET Chi-restraints excluded: chain B residue 771 ASP Chi-restraints excluded: chain B residue 775 TRP Chi-restraints excluded: chain B residue 821 ILE Chi-restraints excluded: chain B residue 912 TRP Chi-restraints excluded: chain B residue 1204 TYR Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain D residue 78 HIS Chi-restraints excluded: chain D residue 215 PHE Chi-restraints excluded: chain D residue 249 SER Chi-restraints excluded: chain D residue 267 VAL 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 235 ASP Chi-restraints excluded: chain F residue 65 GLN Chi-restraints excluded: chain F residue 85 GLU Chi-restraints excluded: chain F residue 292 THR Chi-restraints excluded: chain G residue 106 GLU Chi-restraints excluded: chain G residue 175 ILE Chi-restraints excluded: chain H residue 271 VAL Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain I residue 39 CYS Chi-restraints excluded: chain J residue 228 GLU Chi-restraints excluded: chain J residue 344 LEU Chi-restraints excluded: chain O residue 114 VAL Chi-restraints excluded: chain Q residue 58 THR 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 V residue 84 MET 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: 0.7980 chunk 32 optimal weight: 0.9980 chunk 285 optimal weight: 0.0980 chunk 262 optimal weight: 0.9980 chunk 280 optimal weight: 0.7980 chunk 81 optimal weight: 9.9990 chunk 50 optimal weight: 4.9990 chunk 150 optimal weight: 10.0000 chunk 214 optimal weight: 30.0000 chunk 273 optimal weight: 0.8980 chunk 266 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1081 ASN ** B 801 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 815 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1141 ASN ** B1221 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 38 HIS ** D 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 375 ASN E 220 HIS ** E 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 331 GLN ** J 350 GLN ** 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4346 r_free = 0.4346 target = 0.137221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.099569 restraints weight = 90818.304| |-----------------------------------------------------------------------------| r_work (start): 0.3609 rms_B_bonded: 2.62 r_work: 0.3326 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.4371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 35557 Z= 0.162 Angle : 0.649 12.498 49302 Z= 0.344 Chirality : 0.040 0.279 5443 Planarity : 0.004 0.063 5219 Dihedral : 24.501 171.830 7155 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 11.99 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.55 % Favored : 94.42 % Rotamer: Outliers : 2.04 % Allowed : 20.43 % Favored : 77.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.82 (0.14), residues: 3335 helix: 0.33 (0.12), residues: 1915 sheet: -1.70 (0.43), residues: 158 loop : -1.70 (0.17), residues: 1262 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG J 293 TYR 0.027 0.001 TYR B1232 PHE 0.028 0.001 PHE G 111 TRP 0.026 0.001 TRP A 912 HIS 0.012 0.001 HIS B1293 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.16 (35556) covalent geometry : angle 0.64924 / 0.34 (49302) hydrogen bonds : bond 0.05816 / 3.75 ( 1493) hydrogen bonds : angle 3.92214 / 2.66 ( 4038) metal coordination : bond 0.00141 / 0.07 ( 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 504 residues out of total 3044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 442 time to evaluate : 1.207 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 773 MET cc_start: 0.5349 (OUTLIER) cc_final: 0.5079 (ptm) REVERT: A 940 LYS cc_start: 0.8935 (tppp) cc_final: 0.8633 (tttm) REVERT: A 986 TYR cc_start: 0.7573 (t80) cc_final: 0.6769 (m-80) REVERT: A 1261 LYS cc_start: 0.7789 (mmtt) cc_final: 0.7487 (mptp) REVERT: A 1300 MET cc_start: 0.6930 (OUTLIER) cc_final: 0.6324 (ttm) REVERT: A 1301 PHE cc_start: 0.8519 (m-80) cc_final: 0.8301 (m-80) REVERT: B 812 GLU cc_start: 0.8223 (pm20) cc_final: 0.7995 (pm20) REVERT: B 821 ILE cc_start: 0.8230 (OUTLIER) cc_final: 0.7886 (tp) REVERT: B 860 MET cc_start: 0.2844 (ptt) cc_final: 0.1799 (pp-130) REVERT: B 881 ASP cc_start: 0.8891 (t0) cc_final: 0.8505 (p0) REVERT: B 912 TRP cc_start: 0.7972 (OUTLIER) cc_final: 0.7635 (t-100) REVERT: B 916 TRP cc_start: 0.8505 (m-10) cc_final: 0.8036 (m-10) REVERT: B 1257 MET cc_start: 0.7839 (ptp) cc_final: 0.7305 (ppp) REVERT: B 1266 MET cc_start: 0.8591 (pmm) cc_final: 0.7978 (mmt) REVERT: C 100 GLU cc_start: 0.8549 (mp0) cc_final: 0.8330 (mp0) REVERT: C 112 VAL cc_start: 0.9210 (OUTLIER) cc_final: 0.8917 (m) REVERT: C 191 ASP cc_start: 0.8585 (p0) cc_final: 0.8310 (p0) REVERT: D 40 MET cc_start: 0.5824 (tpt) cc_final: 0.5185 (mmm) REVERT: D 41 LYS cc_start: 0.7705 (tppp) cc_final: 0.7258 (tppp) REVERT: D 47 MET cc_start: 0.8791 (mpt) cc_final: 0.8511 (mpp) REVERT: D 128 MET cc_start: 0.8612 (mmm) cc_final: 0.8295 (mpm) REVERT: D 184 ASP cc_start: 0.7255 (t0) cc_final: 0.6962 (OUTLIER) REVERT: D 247 TYR cc_start: 0.8797 (t80) cc_final: 0.8398 (t80) REVERT: D 277 SER cc_start: 0.7706 (t) cc_final: 0.7457 (m) REVERT: D 288 MET cc_start: 0.8572 (mpp) cc_final: 0.8053 (mpp) REVERT: D 315 MET cc_start: 0.5654 (tpt) cc_final: 0.4401 (tpt) REVERT: D 322 TRP cc_start: 0.9094 (m-10) cc_final: 0.8614 (m-10) REVERT: E 226 TYR cc_start: 0.8295 (p90) cc_final: 0.8083 (p90) REVERT: E 227 TYR cc_start: 0.8867 (m-10) cc_final: 0.8661 (m-80) REVERT: E 235 ASP cc_start: 0.8515 (OUTLIER) cc_final: 0.8237 (p0) REVERT: F 85 GLU cc_start: 0.8747 (OUTLIER) cc_final: 0.8390 (mp0) REVERT: F 292 THR cc_start: 0.6464 (OUTLIER) cc_final: 0.6182 (m) REVERT: G 137 LYS cc_start: 0.8709 (mmtt) cc_final: 0.8444 (mmpt) REVERT: G 175 ILE cc_start: 0.7987 (OUTLIER) cc_final: 0.7623 (pp) REVERT: G 181 ILE cc_start: 0.6984 (pp) cc_final: 0.6743 (pp) REVERT: H 244 ARG cc_start: 0.6891 (ttm170) cc_final: 0.6684 (ttt90) REVERT: I 43 MET cc_start: 0.8116 (ttm) cc_final: 0.7808 (mmt) REVERT: I 71 ASN cc_start: 0.9150 (t0) cc_final: 0.8763 (p0) REVERT: I 73 ASN cc_start: 0.8451 (p0) cc_final: 0.8224 (p0) REVERT: I 79 LEU cc_start: 0.8549 (tm) cc_final: 0.8257 (tt) REVERT: I 87 MET cc_start: 0.8221 (ttp) cc_final: 0.7809 (ttp) REVERT: I 91 SER cc_start: 0.9446 (m) cc_final: 0.9115 (p) REVERT: I 108 TYR cc_start: 0.7575 (t80) cc_final: 0.7273 (t80) REVERT: J 177 ASN cc_start: 0.7706 (p0) cc_final: 0.6845 (t0) REVERT: J 211 TYR cc_start: 0.8275 (m-10) cc_final: 0.8037 (m-10) REVERT: J 332 GLN cc_start: 0.8626 (tp40) cc_final: 0.7775 (pm20) REVERT: J 350 GLN cc_start: 0.8375 (pt0) cc_final: 0.7993 (pp30) REVERT: J 351 ARG cc_start: 0.8394 (mtt180) cc_final: 0.8098 (mtt180) REVERT: J 357 ARG cc_start: 0.8818 (ttp80) cc_final: 0.8482 (ttp80) REVERT: J 358 ASN cc_start: 0.8564 (m110) cc_final: 0.8361 (m110) REVERT: J 375 ARG cc_start: 0.8362 (mmm160) cc_final: 0.7472 (mtp85) REVERT: J 378 ASN cc_start: 0.8591 (m-40) cc_final: 0.8072 (p0) REVERT: P 31 LYS cc_start: 0.7542 (tptt) cc_final: 0.7042 (tttp) REVERT: P 53 SER cc_start: 0.9039 (p) cc_final: 0.8791 (p) REVERT: S 36 LYS cc_start: 0.8698 (mmtm) cc_final: 0.8361 (mmmm) REVERT: S 71 ARG cc_start: 0.8095 (mtm110) cc_final: 0.7864 (mtm-85) REVERT: S 72 ASP cc_start: 0.8498 (m-30) cc_final: 0.8275 (m-30) REVERT: S 91 GLU cc_start: 0.7797 (OUTLIER) cc_final: 0.7388 (pp20) REVERT: T 48 ASP cc_start: 0.7808 (m-30) cc_final: 0.7490 (t70) REVERT: T 83 ARG cc_start: 0.8727 (OUTLIER) cc_final: 0.7764 (mtt-85) REVERT: U 42 ARG cc_start: 0.8244 (mtt-85) cc_final: 0.6977 (mtm-85) REVERT: U 52 ARG cc_start: 0.8410 (mtt90) cc_final: 0.8185 (mtp180) REVERT: U 59 GLU cc_start: 0.8485 (OUTLIER) cc_final: 0.7899 (pm20) REVERT: U 94 GLU cc_start: 0.8644 (mm-30) cc_final: 0.8352 (mm-30) REVERT: U 120 MET cc_start: 0.9022 (mmm) cc_final: 0.8769 (mtm) REVERT: V 50 ILE cc_start: 0.8459 (tt) cc_final: 0.8061 (tt) REVERT: V 59 LYS cc_start: 0.8951 (OUTLIER) cc_final: 0.8721 (tttm) outliers start: 62 outliers final: 33 residues processed: 471 average time/residue: 0.7415 time to fit residues: 418.2868 Evaluate side-chains 474 residues out of total 3044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 429 time to evaluate : 1.209 ------------------------------------------------------------------------------- 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 1177 THR Chi-restraints excluded: chain A residue 1180 PHE Chi-restraints excluded: chain A residue 1250 VAL Chi-restraints excluded: chain A residue 1300 MET Chi-restraints excluded: chain B residue 771 ASP Chi-restraints excluded: chain B residue 775 TRP Chi-restraints excluded: chain B residue 821 ILE Chi-restraints excluded: chain B residue 912 TRP Chi-restraints excluded: chain C residue 13 VAL Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain D residue 38 HIS 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 308 VAL Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain E residue 205 LEU Chi-restraints excluded: chain E residue 235 ASP Chi-restraints excluded: chain F residue 85 GLU Chi-restraints excluded: chain F residue 292 THR Chi-restraints excluded: chain G residue 106 GLU Chi-restraints excluded: chain G residue 175 ILE Chi-restraints excluded: chain H residue 271 VAL Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain I residue 39 CYS Chi-restraints excluded: chain J residue 226 ILE Chi-restraints excluded: chain O residue 114 VAL Chi-restraints excluded: chain P residue 110 GLU Chi-restraints excluded: chain Q residue 58 THR 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 51 ILE 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 84 MET 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: 0.5980 chunk 107 optimal weight: 0.7980 chunk 70 optimal weight: 7.9990 chunk 12 optimal weight: 0.8980 chunk 32 optimal weight: 4.9990 chunk 86 optimal weight: 5.9990 chunk 262 optimal weight: 0.6980 chunk 57 optimal weight: 50.0000 chunk 226 optimal weight: 30.0000 chunk 15 optimal weight: 0.0970 chunk 248 optimal weight: 0.8980 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 801 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 815 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 220 HIS ** E 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 61 GLN ** G 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 96 ASN J 196 GLN J 331 GLN ** J 350 GLN ** 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4351 r_free = 0.4351 target = 0.137486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.099455 restraints weight = 90498.511| |-----------------------------------------------------------------------------| r_work (start): 0.3596 rms_B_bonded: 2.61 r_work: 0.3348 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.4519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 35557 Z= 0.156 Angle : 0.659 13.052 49302 Z= 0.349 Chirality : 0.040 0.267 5443 Planarity : 0.004 0.068 5219 Dihedral : 24.485 171.360 7155 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.40 % Favored : 94.57 % Rotamer: Outliers : 1.87 % Allowed : 20.80 % Favored : 77.33 % 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: -0.71 (0.14), residues: 3335 helix: 0.42 (0.12), residues: 1908 sheet: -1.65 (0.43), residues: 159 loop : -1.64 (0.17), residues: 1268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG J 293 TYR 0.027 0.001 TYR D 297 PHE 0.020 0.001 PHE B1269 TRP 0.030 0.001 TRP A 912 HIS 0.012 0.001 HIS B1293 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.16 (35556) covalent geometry : angle 0.65879 / 0.35 (49302) hydrogen bonds : bond 0.05822 / 3.76 ( 1493) hydrogen bonds : angle 3.91568 / 2.65 ( 4038) metal coordination : bond 0.00129 / 0.07 ( 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 497 residues out of total 3044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 440 time to evaluate : 1.332 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 773 MET cc_start: 0.5177 (OUTLIER) cc_final: 0.4919 (ptm) REVERT: A 940 LYS cc_start: 0.8922 (tppp) cc_final: 0.8597 (tttm) REVERT: A 986 TYR cc_start: 0.7586 (t80) cc_final: 0.6756 (m-80) REVERT: A 1261 LYS cc_start: 0.7775 (mmtt) cc_final: 0.7480 (mptp) REVERT: A 1300 MET cc_start: 0.6939 (OUTLIER) cc_final: 0.6275 (ttm) REVERT: A 1301 PHE cc_start: 0.8514 (m-80) cc_final: 0.8272 (m-80) REVERT: A 1316 TYR cc_start: 0.7614 (p90) cc_final: 0.7184 (p90) REVERT: B 821 ILE cc_start: 0.8134 (OUTLIER) cc_final: 0.7761 (tp) REVERT: B 841 MET cc_start: 0.6336 (pmt) cc_final: 0.6034 (pmm) REVERT: B 860 MET cc_start: 0.2680 (ptt) cc_final: 0.1515 (pp-130) REVERT: B 881 ASP cc_start: 0.8830 (t0) cc_final: 0.8465 (p0) REVERT: B 912 TRP cc_start: 0.7955 (OUTLIER) cc_final: 0.7639 (t-100) REVERT: B 916 TRP cc_start: 0.8439 (m-10) cc_final: 0.7451 (m-10) REVERT: B 1257 MET cc_start: 0.7698 (ptp) cc_final: 0.7217 (ppp) REVERT: C 112 VAL cc_start: 0.9165 (OUTLIER) cc_final: 0.8938 (m) REVERT: C 191 ASP cc_start: 0.8523 (p0) cc_final: 0.8322 (p0) REVERT: D 40 MET cc_start: 0.5886 (tpt) cc_final: 0.4130 (mmm) REVERT: D 41 LYS cc_start: 0.7793 (tppp) cc_final: 0.7057 (mmmm) REVERT: D 184 ASP cc_start: 0.7286 (t0) cc_final: 0.6996 (OUTLIER) REVERT: D 277 SER cc_start: 0.7607 (t) cc_final: 0.7322 (m) REVERT: D 288 MET cc_start: 0.8603 (mpp) cc_final: 0.7971 (mpp) REVERT: D 322 TRP cc_start: 0.9088 (m-10) cc_final: 0.8692 (m-10) REVERT: D 344 TYR cc_start: 0.8469 (t80) cc_final: 0.8008 (t80) REVERT: D 345 GLU cc_start: 0.8310 (pm20) cc_final: 0.7852 (tm-30) REVERT: F 61 GLN cc_start: 0.8307 (tp40) cc_final: 0.8098 (tp-100) REVERT: F 85 GLU cc_start: 0.8707 (OUTLIER) cc_final: 0.8350 (mp0) REVERT: F 292 THR cc_start: 0.6455 (OUTLIER) cc_final: 0.6153 (m) REVERT: G 175 ILE cc_start: 0.8010 (OUTLIER) cc_final: 0.7642 (pp) REVERT: I 40 VAL cc_start: 0.8377 (OUTLIER) cc_final: 0.7698 (p) REVERT: I 71 ASN cc_start: 0.9168 (t0) cc_final: 0.8786 (p0) REVERT: I 87 MET cc_start: 0.8303 (ttp) cc_final: 0.7722 (ttp) REVERT: I 91 SER cc_start: 0.9438 (m) cc_final: 0.9089 (p) REVERT: I 108 TYR cc_start: 0.7511 (t80) cc_final: 0.7294 (t80) REVERT: J 177 ASN cc_start: 0.7745 (p0) cc_final: 0.6879 (t0) REVERT: J 332 GLN cc_start: 0.8640 (tp40) cc_final: 0.7759 (pm20) REVERT: J 350 GLN cc_start: 0.8408 (pt0) cc_final: 0.8012 (pp30) REVERT: J 351 ARG cc_start: 0.8391 (mtt180) cc_final: 0.7879 (mtt180) REVERT: J 357 ARG cc_start: 0.8821 (ttp80) cc_final: 0.8492 (ttp80) REVERT: J 358 ASN cc_start: 0.8613 (m110) cc_final: 0.8339 (m110) REVERT: J 375 ARG cc_start: 0.8403 (mmm160) cc_final: 0.7566 (mtp85) REVERT: J 378 ASN cc_start: 0.8633 (m-40) cc_final: 0.8079 (p0) REVERT: P 31 LYS cc_start: 0.7498 (tptt) cc_final: 0.7013 (tttp) REVERT: P 53 SER cc_start: 0.9017 (p) cc_final: 0.8759 (p) REVERT: S 36 LYS cc_start: 0.8668 (mmtm) cc_final: 0.8338 (mmmm) REVERT: S 71 ARG cc_start: 0.8073 (mtm110) cc_final: 0.7835 (mtt-85) REVERT: S 72 ASP cc_start: 0.8492 (m-30) cc_final: 0.8254 (m-30) REVERT: S 91 GLU cc_start: 0.7764 (OUTLIER) cc_final: 0.7352 (pp20) REVERT: T 48 ASP cc_start: 0.7706 (m-30) cc_final: 0.7398 (t70) REVERT: T 83 ARG cc_start: 0.8731 (OUTLIER) cc_final: 0.7739 (mtt-85) REVERT: T 102 GLU cc_start: 0.7849 (OUTLIER) cc_final: 0.7260 (mm-30) REVERT: U 42 ARG cc_start: 0.8232 (mtt-85) cc_final: 0.6957 (mtm-85) REVERT: U 52 ARG cc_start: 0.8407 (mtt90) cc_final: 0.8167 (mtp180) REVERT: U 94 GLU cc_start: 0.8627 (mm-30) cc_final: 0.8301 (mm-30) REVERT: U 120 MET cc_start: 0.8970 (mmm) cc_final: 0.8741 (mtm) REVERT: V 50 ILE cc_start: 0.8426 (tt) cc_final: 0.8039 (tt) outliers start: 57 outliers final: 35 residues processed: 466 average time/residue: 0.6956 time to fit residues: 389.5562 Evaluate side-chains 470 residues out of total 3044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 424 time to evaluate : 1.338 ------------------------------------------------------------------------------- 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 1177 THR Chi-restraints excluded: chain A residue 1180 PHE Chi-restraints excluded: chain A residue 1300 MET Chi-restraints excluded: chain B residue 771 ASP Chi-restraints excluded: chain B residue 775 TRP Chi-restraints excluded: chain B residue 821 ILE Chi-restraints excluded: chain B residue 912 TRP Chi-restraints excluded: chain B residue 1204 TYR Chi-restraints excluded: chain C residue 13 VAL Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain D residue 38 HIS Chi-restraints excluded: chain D residue 78 HIS Chi-restraints excluded: chain D residue 215 PHE Chi-restraints excluded: chain D residue 249 SER Chi-restraints excluded: chain D residue 267 VAL 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 223 LEU Chi-restraints excluded: chain F residue 85 GLU Chi-restraints excluded: chain F residue 292 THR Chi-restraints excluded: chain G residue 106 GLU Chi-restraints excluded: chain G residue 175 ILE Chi-restraints excluded: chain H residue 271 VAL Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain I residue 39 CYS Chi-restraints excluded: chain I residue 40 VAL Chi-restraints excluded: chain J residue 226 ILE Chi-restraints excluded: chain J residue 335 ASN Chi-restraints excluded: chain O residue 114 VAL Chi-restraints excluded: chain P residue 110 GLU Chi-restraints excluded: chain Q residue 58 THR 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 51 ILE 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 84 MET 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: 7.9990 chunk 100 optimal weight: 0.8980 chunk 52 optimal weight: 4.9990 chunk 284 optimal weight: 1.9990 chunk 302 optimal weight: 0.7980 chunk 252 optimal weight: 2.9990 chunk 70 optimal weight: 10.0000 chunk 348 optimal weight: 4.9990 chunk 139 optimal weight: 8.9990 chunk 261 optimal weight: 4.9990 chunk 182 optimal weight: 0.7980 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 815 HIS ** B 801 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 815 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1221 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 38 HIS ** D 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 220 HIS F 59 ASN ** G 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 196 GLN J 213 GLN J 331 GLN ** J 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 370 ASN P 92 GLN ** Q 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 27 GLN S 104 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4316 r_free = 0.4316 target = 0.135331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.096520 restraints weight = 89275.762| |-----------------------------------------------------------------------------| r_work (start): 0.3540 rms_B_bonded: 2.46 r_work: 0.3293 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.4472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.132 35557 Z= 0.241 Angle : 0.704 12.947 49302 Z= 0.371 Chirality : 0.043 0.283 5443 Planarity : 0.004 0.075 5219 Dihedral : 24.623 171.906 7155 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 13.13 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.67 % Favored : 94.30 % Rotamer: Outliers : 1.77 % Allowed : 21.32 % Favored : 76.91 % 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: -0.78 (0.14), residues: 3335 helix: 0.28 (0.12), residues: 1927 sheet: -1.48 (0.44), residues: 150 loop : -1.57 (0.17), residues: 1258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG J 293 TYR 0.029 0.002 TYR B1232 PHE 0.028 0.002 PHE H 245 TRP 0.041 0.002 TRP A 912 HIS 0.013 0.001 HIS B1293 Details of bonding type rmsd/Z covalent geometry : bond 0.00555 / 0.24 (35556) covalent geometry : angle 0.70384 / 0.37 (49302) hydrogen bonds : bond 0.05808 / 3.76 ( 1493) hydrogen bonds : angle 4.07579 / 2.76 ( 4038) metal coordination : bond 0.00366 / 0.19 ( 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 473 residues out of total 3044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 419 time to evaluate : 1.278 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 773 MET cc_start: 0.5141 (OUTLIER) cc_final: 0.4789 (ptm) REVERT: A 940 LYS cc_start: 0.8891 (tppp) cc_final: 0.8653 (tttm) REVERT: A 986 TYR cc_start: 0.7595 (t80) cc_final: 0.6737 (m-80) REVERT: A 1261 LYS cc_start: 0.7810 (mmtt) cc_final: 0.7495 (mptp) REVERT: A 1300 MET cc_start: 0.7152 (OUTLIER) cc_final: 0.6581 (ttm) REVERT: A 1301 PHE cc_start: 0.8630 (m-80) cc_final: 0.8327 (m-80) REVERT: B 821 ILE cc_start: 0.8139 (OUTLIER) cc_final: 0.7767 (tp) REVERT: B 841 MET cc_start: 0.6491 (pmt) cc_final: 0.6183 (pmm) REVERT: B 860 MET cc_start: 0.2331 (ptt) cc_final: 0.1219 (pp-130) REVERT: B 881 ASP cc_start: 0.8858 (t0) cc_final: 0.8480 (p0) REVERT: B 912 TRP cc_start: 0.8071 (OUTLIER) cc_final: 0.7004 (t-100) REVERT: B 1257 MET cc_start: 0.7755 (ptp) cc_final: 0.7180 (ppp) REVERT: C 191 ASP cc_start: 0.8629 (p0) cc_final: 0.8379 (p0) REVERT: D 40 MET cc_start: 0.6056 (tpt) cc_final: 0.5547 (mmm) REVERT: D 41 LYS cc_start: 0.7791 (tppp) cc_final: 0.7352 (tppp) REVERT: D 47 MET cc_start: 0.8813 (mpt) cc_final: 0.8548 (mpp) REVERT: D 128 MET cc_start: 0.8609 (mmm) cc_final: 0.8322 (mpm) REVERT: D 151 HIS cc_start: 0.6382 (p90) cc_final: 0.5955 (p90) REVERT: D 165 ASP cc_start: 0.8244 (p0) cc_final: 0.8010 (p0) REVERT: D 184 ASP cc_start: 0.7511 (t0) cc_final: 0.7227 (OUTLIER) REVERT: D 277 SER cc_start: 0.7617 (t) cc_final: 0.7325 (m) REVERT: D 288 MET cc_start: 0.8700 (mpp) cc_final: 0.8136 (mpp) REVERT: D 315 MET cc_start: 0.5948 (tpt) cc_final: 0.5564 (tpt) REVERT: D 322 TRP cc_start: 0.9189 (m-10) cc_final: 0.8635 (m-10) REVERT: D 345 GLU cc_start: 0.8305 (pm20) cc_final: 0.7899 (tm-30) REVERT: E 227 TYR cc_start: 0.8561 (m-80) cc_final: 0.8267 (m-80) REVERT: F 85 GLU cc_start: 0.8701 (OUTLIER) cc_final: 0.8338 (mp0) REVERT: F 135 MET cc_start: 0.2817 (mmt) cc_final: 0.1709 (ptp) REVERT: G 175 ILE cc_start: 0.8039 (OUTLIER) cc_final: 0.7651 (pp) REVERT: I 71 ASN cc_start: 0.9181 (t0) cc_final: 0.8790 (p0) REVERT: I 87 MET cc_start: 0.8403 (ttp) cc_final: 0.7856 (ttp) REVERT: I 108 TYR cc_start: 0.7577 (t80) cc_final: 0.7359 (t80) REVERT: J 177 ASN cc_start: 0.7784 (p0) cc_final: 0.6912 (t0) REVERT: J 332 GLN cc_start: 0.8631 (tp40) cc_final: 0.7747 (pm20) REVERT: J 350 GLN cc_start: 0.8421 (pt0) cc_final: 0.8027 (pp30) REVERT: J 351 ARG cc_start: 0.8421 (mtt180) cc_final: 0.8112 (mtt180) REVERT: J 358 ASN cc_start: 0.8740 (m110) cc_final: 0.8477 (m110) REVERT: J 375 ARG cc_start: 0.8359 (mmm160) cc_final: 0.7578 (mtp85) REVERT: J 378 ASN cc_start: 0.8672 (m-40) cc_final: 0.8150 (p0) REVERT: P 31 LYS cc_start: 0.7640 (tptt) cc_final: 0.7119 (tttp) REVERT: P 53 SER cc_start: 0.9083 (p) cc_final: 0.8828 (p) REVERT: S 36 LYS cc_start: 0.8750 (mmtm) cc_final: 0.8389 (mmmm) REVERT: S 71 ARG cc_start: 0.8139 (mtm110) cc_final: 0.7914 (mtm-85) REVERT: S 91 GLU cc_start: 0.7792 (OUTLIER) cc_final: 0.7385 (pp20) REVERT: T 48 ASP cc_start: 0.7904 (m-30) cc_final: 0.7563 (t70) REVERT: T 83 ARG cc_start: 0.8784 (OUTLIER) cc_final: 0.7921 (mtt-85) REVERT: U 42 ARG cc_start: 0.8229 (mtt-85) cc_final: 0.6967 (mtm-85) REVERT: U 52 ARG cc_start: 0.8441 (mtt90) cc_final: 0.8146 (mtp180) REVERT: U 59 GLU cc_start: 0.8472 (pm20) cc_final: 0.8057 (pm20) REVERT: V 50 ILE cc_start: 0.8620 (tt) cc_final: 0.8265 (tt) outliers start: 54 outliers final: 35 residues processed: 444 average time/residue: 0.7367 time to fit residues: 392.2769 Evaluate side-chains 453 residues out of total 3044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 411 time to evaluate : 1.278 ------------------------------------------------------------------------------- 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 1016 TYR Chi-restraints excluded: chain A residue 1177 THR Chi-restraints excluded: chain A residue 1180 PHE Chi-restraints excluded: chain A residue 1300 MET Chi-restraints excluded: chain B residue 771 ASP Chi-restraints excluded: chain B residue 775 TRP Chi-restraints excluded: chain B residue 821 ILE Chi-restraints excluded: chain B residue 912 TRP Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain D residue 38 HIS Chi-restraints excluded: chain D residue 78 HIS Chi-restraints excluded: chain D residue 215 PHE Chi-restraints excluded: chain D residue 249 SER Chi-restraints excluded: chain D residue 267 VAL 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 223 LEU Chi-restraints excluded: chain F residue 85 GLU Chi-restraints excluded: chain F residue 292 THR Chi-restraints excluded: chain G residue 106 GLU Chi-restraints excluded: chain G residue 175 ILE Chi-restraints excluded: chain H residue 271 VAL Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain J residue 226 ILE Chi-restraints excluded: chain J residue 335 ASN Chi-restraints excluded: chain O residue 113 SER Chi-restraints excluded: chain O residue 114 VAL Chi-restraints excluded: chain Q residue 58 THR 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 51 ILE Chi-restraints excluded: chain T residue 81 ASN Chi-restraints excluded: chain T residue 83 ARG Chi-restraints excluded: chain T residue 87 THR Chi-restraints excluded: chain T residue 102 GLU Chi-restraints excluded: chain V residue 96 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 353 optimal weight: 0.9990 chunk 132 optimal weight: 0.6980 chunk 332 optimal weight: 10.0000 chunk 330 optimal weight: 0.9990 chunk 251 optimal weight: 0.0370 chunk 123 optimal weight: 0.6980 chunk 199 optimal weight: 0.7980 chunk 235 optimal weight: 7.9990 chunk 247 optimal weight: 0.9990 chunk 140 optimal weight: 0.9980 chunk 56 optimal weight: 7.9990 overall best weight: 0.6458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 801 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 815 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 886 HIS ** B1221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 220 HIS ** E 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 173 HIS J 196 GLN J 331 GLN ** J 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 370 ASN K 465 HIS ** Q 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 104 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4340 r_free = 0.4340 target = 0.136919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.098521 restraints weight = 90428.151| |-----------------------------------------------------------------------------| r_work (start): 0.3572 rms_B_bonded: 2.58 r_work: 0.3336 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.4632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 35557 Z= 0.165 Angle : 0.691 14.415 49302 Z= 0.364 Chirality : 0.040 0.246 5443 Planarity : 0.004 0.085 5219 Dihedral : 24.598 171.717 7155 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 12.55 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.46 % Favored : 94.51 % Rotamer: Outliers : 1.71 % Allowed : 21.58 % Favored : 76.71 % 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: -0.69 (0.14), residues: 3335 helix: 0.39 (0.12), residues: 1921 sheet: -1.38 (0.44), residues: 150 loop : -1.61 (0.17), residues: 1264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG J 293 TYR 0.060 0.002 TYR A1016 PHE 0.019 0.001 PHE U 67 TRP 0.046 0.002 TRP A 912 HIS 0.013 0.001 HIS B1293 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.17 (35556) covalent geometry : angle 0.69101 / 0.36 (49302) hydrogen bonds : bond 0.05842 / 3.76 ( 1493) hydrogen bonds : angle 4.03397 / 2.73 ( 4038) metal coordination : bond 0.00183 / 0.10 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16176.17 seconds wall clock time: 275 minutes 26.11 seconds (16526.11 seconds total)