Starting phenix.real_space_refine on Mon Aug 10 01:43:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9v2w_64742/08_2026/9v2w_64742.cif Found real_map, /net/cci-nas-00/data/ceres_data/9v2w_64742/08_2026/9v2w_64742.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9v2w_64742/08_2026/9v2w_64742.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9v2w_64742/08_2026/9v2w_64742.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9v2w_64742/08_2026/9v2w_64742.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9v2w_64742/08_2026/9v2w_64742.map" } resolution = 3.4 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 656 5.49 5 S 82 5.16 5 C 23160 2.51 5 N 7275 2.21 5 O 8764 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 67 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 39938 Number of models: 1 Model: "" Number of chains: 27 Chain: "A" Number of atoms: 5799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 694, 5799 Classifications: {'peptide': 694} Link IDs: {'PTRANS': 24, 'TRANS': 669} Chain breaks: 8 Chain: "B" 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: "C" Number of atoms: 2999 Number of conformers: 1 Conformer: "" Number of residues, atoms: 378, 2999 Classifications: {'peptide': 378} Link IDs: {'PTRANS': 17, 'TRANS': 360} Chain: "D" 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: "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: 1328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1328 Classifications: {'peptide': 158} Link IDs: {'PTRANS': 6, 'TRANS': 151} Chain breaks: 1 Chain: "G" Number of atoms: 1002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 1002 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 5, 'TRANS': 113} Chain: "H" 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: "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: 1167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1167 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 6, 'TRANS': 134} 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: "L" Number of atoms: 618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 618 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 1, 'TRANS': 75} Chain: "M" 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: "N" 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: "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: "W" 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: "Z" Number of atoms: 629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 629 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "X" Number of atoms: 6786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 329, 6786 Classifications: {'DNA': 329} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 328} Chain: "Y" Number of atoms: 6697 Number of conformers: 1 Conformer: "" Number of residues, atoms: 329, 6697 Classifications: {'DNA': 329} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 328} 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: 8.18, per 1000 atoms: 0.20 Number of scatterers: 39938 At special positions: 0 Unit cell: (134.9, 185.31, 229.33, 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 82 16.00 P 656 15.00 O 8764 8.00 N 7275 7.00 C 23160 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: 3.32 Conformation dependent library (CDL) restraints added in 1.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN C 501 " pdb="ZN ZN C 501 " - pdb=" ND1 HIS C 188 " 6362 Ramachandran restraints generated. 3181 Oldfield, 0 Emsley, 3181 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6194 Finding SS restraints... Secondary structure from input PDB file: 144 helices and 22 sheets defined 66.9% alpha, 2.6% beta 280 base pairs and 504 stacking pairs defined. Time for finding SS restraints: 5.39 Creating SS restraints... Processing helix chain 'A' and resid 240 through 251 removed outlier: 4.152A pdb=" N LEU A 244 " --> pdb=" O ASP A 240 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ASP A 247 " --> pdb=" O ASN A 243 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ILE A 248 " --> pdb=" O LEU A 244 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ASP A 251 " --> pdb=" O ASP A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 268 removed outlier: 3.570A pdb=" N VAL A 262 " --> pdb=" O ASP A 258 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ARG A 265 " --> pdb=" O GLY A 261 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N THR A 268 " --> pdb=" O GLU A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 283 removed outlier: 4.020A pdb=" N GLN A 278 " --> pdb=" O PRO A 274 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N GLY A 279 " --> pdb=" O ILE A 275 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N PHE A 280 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ASN A 281 " --> pdb=" O ILE A 277 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N THR A 282 " --> pdb=" O GLN A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 310 removed outlier: 3.674A pdb=" N MET A 306 " --> pdb=" O THR A 303 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N THR A 308 " --> pdb=" O PRO A 305 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N THR A 309 " --> pdb=" O MET A 306 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N THR A 310 " --> pdb=" O GLY A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 331 removed outlier: 3.727A pdb=" N ALA A 325 " --> pdb=" O GLY A 321 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N PHE A 331 " --> pdb=" O GLU A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 415 removed outlier: 3.685A pdb=" N GLN A 410 " --> pdb=" O VAL A 406 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N VAL A 415 " --> pdb=" O ALA A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 422 Processing helix chain 'A' and resid 426 through 440 removed outlier: 4.094A pdb=" N LYS A 430 " --> pdb=" O PRO A 426 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N GLU A 434 " --> pdb=" O LYS A 430 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N GLN A 437 " --> pdb=" O LEU A 433 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N THR A 438 " --> pdb=" O GLU A 434 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N GLN A 440 " --> pdb=" O LEU A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 455 removed outlier: 3.717A pdb=" N THR A 454 " --> pdb=" O TYR A 450 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N HIS A 455 " --> pdb=" O ALA A 451 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 450 through 455' Processing helix chain 'A' and resid 456 through 458 No H-bonds generated for 'chain 'A' and resid 456 through 458' Processing helix chain 'A' and resid 460 through 469 removed outlier: 3.878A pdb=" N LEU A 464 " --> pdb=" O ALA A 460 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LYS A 469 " --> pdb=" O GLU A 465 " (cutoff:3.500A) Processing helix chain 'A' and resid 663 through 673 Processing helix chain 'A' and resid 678 through 694 removed outlier: 3.580A pdb=" N ILE A 688 " --> pdb=" O GLU A 684 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU A 689 " --> pdb=" O PHE A 685 " (cutoff:3.500A) Processing helix chain 'A' and resid 698 through 705 Processing helix chain 'A' and resid 706 through 711 removed outlier: 3.535A pdb=" N GLY A 711 " --> pdb=" O ASP A 707 " (cutoff:3.500A) Processing helix chain 'A' and resid 801 through 840 removed outlier: 3.529A pdb=" N PHE A 808 " --> pdb=" O GLU A 804 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N TYR A 817 " --> pdb=" O GLU A 813 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N TYR A 820 " --> pdb=" O GLU A 816 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N ILE A 821 " --> pdb=" O TYR A 817 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASN A 824 " --> pdb=" O TYR A 820 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N THR A 833 " --> pdb=" O GLN A 829 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ILE A 834 " --> pdb=" O CYS A 830 " (cutoff:3.500A) Processing helix chain 'A' and resid 842 through 848 removed outlier: 3.671A pdb=" N ASN A 848 " --> pdb=" O ASN A 844 " (cutoff:3.500A) Processing helix chain 'A' and resid 862 through 871 Processing helix chain 'A' and resid 872 through 886 removed outlier: 4.237A pdb=" N PHE A 877 " --> pdb=" O LYS A 873 " (cutoff:3.500A) removed outlier: 5.046A pdb=" N GLU A 878 " --> pdb=" O GLU A 874 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ILE A 879 " --> pdb=" O ARG A 875 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 922 removed outlier: 3.728A pdb=" N ALA A 891 " --> pdb=" O PRO A 887 " (cutoff:3.500A) Proline residue: A 892 - end of helix removed outlier: 4.159A pdb=" N ARG A 897 " --> pdb=" O VAL A 893 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ALA A 908 " --> pdb=" O GLU A 904 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLU A 911 " --> pdb=" O ARG A 907 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N LYS A 914 " --> pdb=" O ARG A 910 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N VAL A 915 " --> pdb=" O GLU A 911 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N TRP A 916 " --> pdb=" O TRP A 912 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLN A 921 " --> pdb=" O ARG A 917 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LYS A 922 " --> pdb=" O GLU A 918 " (cutoff:3.500A) Processing helix chain 'A' and resid 923 through 929 Processing helix chain 'A' and resid 929 through 939 removed outlier: 3.784A pdb=" N THR A 934 " --> pdb=" O HIS A 930 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LYS A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N GLN A 937 " --> pdb=" O LEU A 933 " (cutoff:3.500A) Processing helix chain 'A' and resid 940 through 949 removed outlier: 4.063A pdb=" N THR A 944 " --> pdb=" O LYS A 941 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N THR A 945 " --> pdb=" O LEU A 942 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N LYS A 946 " --> pdb=" O LEU A 943 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLN A 947 " --> pdb=" O THR A 944 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU A 948 " --> pdb=" O THR A 945 " (cutoff:3.500A) Processing helix chain 'A' and resid 983 through 999 removed outlier: 3.552A pdb=" N ASP A 987 " --> pdb=" O ASN A 983 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N LEU A 989 " --> pdb=" O PHE A 985 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N THR A 994 " --> pdb=" O CYS A 990 " (cutoff:3.500A) Processing helix chain 'A' and resid 1003 through 1022 removed outlier: 4.099A pdb=" N LEU A1013 " --> pdb=" O ARG A1009 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU A1014 " --> pdb=" O LEU A1010 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ILE A1018 " --> pdb=" O LEU A1014 " (cutoff:3.500A) Processing helix chain 'A' and resid 1075 through 1080 removed outlier: 3.805A pdb=" N ARG A1079 " --> pdb=" O GLN A1075 " (cutoff:3.500A) Processing helix chain 'A' and resid 1143 through 1164 removed outlier: 3.647A pdb=" N ILE A1154 " --> pdb=" O HIS A1150 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ILE A1161 " --> pdb=" O ARG A1157 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LYS A1162 " --> pdb=" O LEU A1158 " (cutoff:3.500A) Processing helix chain 'A' and resid 1164 through 1174 removed outlier: 4.153A pdb=" N LYS A1170 " --> pdb=" O GLU A1166 " (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 1216 removed outlier: 3.609A pdb=" N LEU A1208 " --> pdb=" O TYR A1204 " (cutoff:3.500A) Processing helix chain 'A' and resid 1220 through 1232 removed outlier: 3.526A pdb=" N GLU A1226 " --> pdb=" O GLN A1222 " (cutoff:3.500A) Processing helix chain 'A' and resid 1241 through 1259 Processing helix chain 'A' and resid 1259 through 1274 removed outlier: 3.638A pdb=" N ALA A1267 " --> pdb=" O ALA A1263 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU A1268 " --> pdb=" O GLU A1264 " (cutoff:3.500A) Processing helix chain 'A' and resid 1279 through 1294 removed outlier: 4.064A pdb=" N GLN A1283 " --> pdb=" O SER A1279 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLN A1289 " --> pdb=" O ILE A1285 " (cutoff:3.500A) Processing helix chain 'B' and resid 16 through 21 Processing helix chain 'B' and resid 26 through 36 removed outlier: 3.791A pdb=" N VAL B 30 " --> pdb=" O PRO B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 73 removed outlier: 4.202A pdb=" N VAL B 49 " --> pdb=" O ALA B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 90 removed outlier: 3.558A pdb=" N ASN B 89 " --> pdb=" O LEU B 85 " (cutoff:3.500A) Processing helix chain 'B' and resid 90 through 97 Processing helix chain 'C' and resid 42 through 55 removed outlier: 3.822A pdb=" N ARG C 46 " --> pdb=" O PRO C 42 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ASN C 54 " --> pdb=" O SER C 50 " (cutoff:3.500A) Processing helix chain 'C' and resid 56 through 61 Processing helix chain 'C' and resid 70 through 75 Processing helix chain 'C' and resid 79 through 87 removed outlier: 3.897A pdb=" N PHE C 85 " --> pdb=" O GLU C 81 " (cutoff:3.500A) Processing helix chain 'C' and resid 100 through 105 Processing helix chain 'C' and resid 115 through 136 removed outlier: 3.805A pdb=" N ILE C 122 " --> pdb=" O GLU C 118 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N SER C 127 " --> pdb=" O SER C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 164 through 175 removed outlier: 3.963A pdb=" N GLU C 172 " --> pdb=" O LEU C 168 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU C 173 " --> pdb=" O GLY C 169 " (cutoff:3.500A) Processing helix chain 'C' and resid 190 through 195 removed outlier: 3.690A pdb=" N GLU C 195 " --> pdb=" O ASP C 191 " (cutoff:3.500A) Processing helix chain 'C' and resid 196 through 198 No H-bonds generated for 'chain 'C' and resid 196 through 198' Processing helix chain 'C' and resid 243 through 262 Proline residue: C 253 - end of helix Processing helix chain 'C' and resid 287 through 292 Processing helix chain 'C' and resid 292 through 300 removed outlier: 3.692A pdb=" N VAL C 298 " --> pdb=" O CYS C 294 " (cutoff:3.500A) Processing helix chain 'C' and resid 314 through 330 removed outlier: 3.998A pdb=" N ARG C 320 " --> pdb=" O ARG C 316 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 381 removed outlier: 3.669A pdb=" N ASN C 379 " --> pdb=" O ASN C 375 " (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 34 through 46 Processing helix chain 'D' and resid 52 through 81 removed outlier: 3.817A pdb=" N ASN D 81 " --> pdb=" O LEU D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 98 Processing helix chain 'D' and resid 100 through 119 removed outlier: 3.658A pdb=" N LYS D 105 " --> pdb=" O GLY D 101 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LYS D 117 " --> pdb=" O LYS D 113 " (cutoff:3.500A) Processing helix chain 'E' and resid 181 through 191 removed outlier: 4.182A pdb=" N GLU E 185 " --> pdb=" O THR E 181 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE E 189 " --> pdb=" O GLU E 185 " (cutoff:3.500A) Processing helix chain 'E' and resid 195 through 210 removed outlier: 4.040A pdb=" N GLN E 204 " --> pdb=" O LEU E 200 " (cutoff:3.500A) Processing helix chain 'E' and resid 222 through 292 removed outlier: 3.639A pdb=" N SER E 228 " --> pdb=" O GLN E 224 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE E 257 " --> pdb=" O ASN E 253 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N HIS E 264 " --> pdb=" O ARG E 260 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N THR E 272 " --> pdb=" O HIS E 268 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N THR E 282 " --> pdb=" O LEU E 278 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N TRP E 286 " --> pdb=" O THR E 282 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N ASN E 290 " --> pdb=" O TRP E 286 " (cutoff:3.500A) Processing helix chain 'E' and resid 293 through 295 No H-bonds generated for 'chain 'E' and resid 293 through 295' Processing helix chain 'F' and resid 15 through 35 removed outlier: 3.637A pdb=" N PHE F 19 " --> pdb=" O ASP F 15 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N GLU F 22 " --> pdb=" O ARG F 18 " (cutoff:3.500A) Processing helix chain 'F' and resid 35 through 54 removed outlier: 3.772A pdb=" N ARG F 43 " --> pdb=" O GLN F 39 " (cutoff:3.500A) Processing helix chain 'F' and resid 64 through 132 removed outlier: 4.070A pdb=" N GLN F 129 " --> pdb=" O ILE F 125 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N GLU F 130 " --> pdb=" O LYS F 126 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N GLU F 131 " --> pdb=" O LYS F 127 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ARG F 132 " --> pdb=" O LEU F 128 " (cutoff:3.500A) Processing helix chain 'F' and resid 300 through 314 Processing helix chain 'G' and resid 74 through 88 removed outlier: 3.628A pdb=" N GLU G 85 " --> pdb=" O LYS G 81 " (cutoff:3.500A) Processing helix chain 'G' and resid 109 through 119 removed outlier: 3.755A pdb=" N ARG G 113 " --> pdb=" O ASP G 109 " (cutoff:3.500A) Processing helix chain 'G' and resid 128 through 133 Processing helix chain 'G' and resid 134 through 136 No H-bonds generated for 'chain 'G' and resid 134 through 136' Processing helix chain 'G' and resid 137 through 141 Processing helix chain 'G' and resid 142 through 151 removed outlier: 3.753A pdb=" N LYS G 146 " --> pdb=" O THR G 142 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASN G 148 " --> pdb=" O SER G 144 " (cutoff:3.500A) Processing helix chain 'G' and resid 158 through 173 removed outlier: 3.527A pdb=" N ASP G 171 " --> pdb=" O ARG G 167 " (cutoff:3.500A) Processing helix chain 'G' and resid 183 through 188 removed outlier: 3.744A pdb=" N VAL G 188 " --> pdb=" O PHE G 184 " (cutoff:3.500A) Processing helix chain 'H' and resid 44 through 57 removed outlier: 4.050A pdb=" N LYS H 56 " --> pdb=" O ARG H 52 " (cutoff:3.500A) Processing helix chain 'H' and resid 63 through 76 removed outlier: 3.561A pdb=" N GLN H 76 " --> pdb=" O ARG H 72 " (cutoff:3.500A) Processing helix chain 'H' and resid 85 through 114 removed outlier: 3.553A pdb=" N MET H 90 " --> pdb=" O SER H 86 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VAL H 101 " --> pdb=" O GLU H 97 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ASP H 106 " --> pdb=" O ALA H 102 " (cutoff:3.500A) Processing helix chain 'H' and resid 120 through 132 Processing helix chain 'I' and resid 14 through 36 removed outlier: 3.587A pdb=" N LEU I 18 " --> pdb=" O ILE I 14 " (cutoff:3.500A) Proline residue: I 22 - end of helix removed outlier: 4.364A pdb=" N THR I 30 " --> pdb=" O SER I 26 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N LEU I 31 " --> pdb=" O ARG I 27 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ILE I 35 " --> pdb=" O LEU I 31 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ASP I 36 " --> pdb=" O LEU I 32 " (cutoff:3.500A) Processing helix chain 'I' and resid 42 through 55 removed outlier: 3.699A pdb=" N ILE I 50 " --> pdb=" O LEU I 46 " (cutoff:3.500A) Processing helix chain 'I' and resid 62 through 78 removed outlier: 3.802A pdb=" N ASN I 71 " --> pdb=" O ARG I 67 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ASN I 73 " --> pdb=" O LEU I 69 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LYS I 74 " --> pdb=" O ASN I 70 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ILE I 75 " --> pdb=" O ASN I 71 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N GLU I 77 " --> pdb=" O ASN I 73 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N GLU I 78 " --> pdb=" O LYS I 74 " (cutoff:3.500A) Processing helix chain 'I' and resid 79 through 112 removed outlier: 4.510A pdb=" N ARG I 99 " --> pdb=" O ASP I 95 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA I 107 " --> pdb=" O ARG I 103 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N VAL I 110 " --> pdb=" O LEU I 106 " (cutoff:3.500A) Processing helix chain 'J' and resid 173 through 178 removed outlier: 3.561A pdb=" N ASN J 177 " --> pdb=" O GLY J 173 " (cutoff:3.500A) Processing helix chain 'J' and resid 186 through 217 removed outlier: 3.588A pdb=" N LYS J 191 " --> pdb=" O SER J 187 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ILE J 198 " --> pdb=" O ALA J 194 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N SER J 207 " --> pdb=" O LYS J 203 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ARG J 210 " --> pdb=" O MET J 206 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N VAL J 217 " --> pdb=" O GLN J 213 " (cutoff:3.500A) Processing helix chain 'J' and resid 227 through 232 removed outlier: 3.729A pdb=" N LEU J 231 " --> pdb=" O TYR J 227 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ASN J 232 " --> pdb=" O GLU J 228 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 227 through 232' Processing helix chain 'J' and resid 286 through 290 Processing helix chain 'J' and resid 337 through 384 removed outlier: 3.901A pdb=" N GLU J 354 " --> pdb=" O GLN J 350 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ASN J 378 " --> pdb=" O GLY J 374 " (cutoff:3.500A) Processing helix chain 'K' and resid 247 through 252 removed outlier: 4.085A pdb=" N TYR K 252 " --> pdb=" O GLU K 248 " (cutoff:3.500A) Processing helix chain 'K' and resid 463 through 483 removed outlier: 3.685A pdb=" N VAL K 467 " --> pdb=" O ASN K 463 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ASN K 475 " --> pdb=" O ASP K 471 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N SER K 480 " --> pdb=" O GLY K 476 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N LEU K 481 " --> pdb=" O TYR K 477 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N MET K 483 " --> pdb=" O GLU K 479 " (cutoff:3.500A) Processing helix chain 'L' and resid 25 through 29 Processing helix chain 'L' and resid 30 through 41 Processing helix chain 'L' and resid 49 through 76 removed outlier: 3.871A pdb=" N GLU L 53 " --> pdb=" O LEU L 49 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ARG L 67 " --> pdb=" O GLU L 63 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N THR L 71 " --> pdb=" O ARG L 67 " (cutoff:3.500A) Processing helix chain 'L' and resid 82 through 94 removed outlier: 3.779A pdb=" N ARG L 92 " --> pdb=" O TYR L 88 " (cutoff:3.500A) Processing helix chain 'M' and resid 16 through 21 Processing helix chain 'M' and resid 26 through 36 removed outlier: 3.790A pdb=" N VAL M 30 " --> pdb=" O PRO M 26 " (cutoff:3.500A) Processing helix chain 'M' and resid 45 through 73 removed outlier: 4.203A pdb=" N VAL M 49 " --> pdb=" O ALA M 45 " (cutoff:3.500A) Processing helix chain 'M' and resid 79 through 90 removed outlier: 3.558A pdb=" N ASN M 89 " --> pdb=" O LEU M 85 " (cutoff:3.500A) Processing helix chain 'M' and resid 90 through 97 Processing helix chain 'N' and resid 34 through 46 Processing helix chain 'N' and resid 52 through 81 removed outlier: 3.621A pdb=" N ARG N 76 " --> pdb=" O GLY N 72 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ALA N 78 " --> pdb=" O ALA N 74 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ASN N 81 " --> pdb=" O LEU N 77 " (cutoff:3.500A) Processing helix chain 'N' and resid 87 through 98 removed outlier: 3.650A pdb=" N ILE N 91 " --> pdb=" O THR N 87 " (cutoff:3.500A) Processing helix chain 'N' and resid 100 through 117 removed outlier: 3.517A pdb=" N ALA N 104 " --> pdb=" O PRO N 100 " (cutoff:3.500A) Processing helix chain 'O' and resid 16 through 21 Processing helix chain 'O' and resid 26 through 36 removed outlier: 3.791A pdb=" N VAL O 30 " --> pdb=" O PRO O 26 " (cutoff:3.500A) Processing helix chain 'O' and resid 45 through 73 removed outlier: 4.202A pdb=" N VAL O 49 " --> pdb=" O ALA O 45 " (cutoff:3.500A) Processing helix chain 'O' and resid 79 through 90 removed outlier: 3.558A pdb=" N ASN O 89 " --> pdb=" O LEU O 85 " (cutoff:3.500A) Processing helix chain 'O' and resid 90 through 97 Processing helix chain 'P' and resid 34 through 46 Processing helix chain 'P' and resid 52 through 81 Processing helix chain 'P' and resid 87 through 98 Processing helix chain 'P' and resid 100 through 119 Processing helix chain 'Q' and resid 44 through 55 Processing helix chain 'Q' and resid 63 through 76 Processing helix chain 'Q' and resid 85 through 114 Processing helix chain 'Q' and resid 120 through 131 removed outlier: 3.622A 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: 3.904A 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 21 Processing helix chain 'S' and resid 26 through 36 removed outlier: 3.790A pdb=" N VAL S 30 " --> pdb=" O PRO S 26 " (cutoff:3.500A) Processing helix chain 'S' and resid 45 through 73 removed outlier: 4.203A pdb=" N VAL S 49 " --> pdb=" O ALA S 45 " (cutoff:3.500A) Processing helix chain 'S' and resid 79 through 90 removed outlier: 3.557A pdb=" N ASN S 89 " --> pdb=" O LEU S 85 " (cutoff:3.500A) Processing helix chain 'S' and resid 90 through 97 Processing helix chain 'T' and resid 34 through 46 Processing helix chain 'T' and resid 52 through 81 Processing helix chain 'T' and resid 87 through 99 Processing helix chain 'T' and resid 100 through 119 removed outlier: 3.502A pdb=" N LYS T 113 " --> pdb=" O SER T 109 " (cutoff:3.500A) Processing helix chain 'U' and resid 44 through 56 removed outlier: 3.662A 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 Processing helix chain 'U' and resid 120 through 131 removed outlier: 3.628A pdb=" N ILE U 124 " --> pdb=" O MET U 120 " (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: 3.663A pdb=" N ASN V 64 " --> pdb=" O VAL V 60 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ARG V 67 " --> pdb=" O GLU V 63 " (cutoff:3.500A) Processing helix chain 'V' and resid 82 through 92 Processing helix chain 'W' and resid 44 through 57 removed outlier: 3.679A pdb=" N LYS W 56 " --> pdb=" O ARG W 52 " (cutoff:3.500A) Processing helix chain 'W' and resid 63 through 76 removed outlier: 3.535A pdb=" N ARG W 69 " --> pdb=" O LEU W 65 " (cutoff:3.500A) Processing helix chain 'W' and resid 85 through 114 removed outlier: 3.543A pdb=" N MET W 90 " --> pdb=" O SER W 86 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ALA W 98 " --> pdb=" O GLU W 94 " (cutoff:3.500A) Processing helix chain 'W' and resid 120 through 131 removed outlier: 3.625A pdb=" N ILE W 124 " --> pdb=" O MET W 120 " (cutoff:3.500A) Processing helix chain 'Z' and resid 30 through 41 Processing helix chain 'Z' and resid 49 through 76 removed outlier: 3.572A pdb=" N GLU Z 53 " --> pdb=" O LEU Z 49 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ASN Z 64 " --> pdb=" O VAL Z 60 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ARG Z 67 " --> pdb=" O GLU Z 63 " (cutoff:3.500A) Processing helix chain 'Z' and resid 82 through 93 removed outlier: 3.891A pdb=" N ARG Z 92 " --> pdb=" O TYR Z 88 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N GLN Z 93 " --> pdb=" O ALA Z 89 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 755 through 757 removed outlier: 3.563A pdb=" N LYS A 756 " --> pdb=" O VAL A 783 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 976 through 977 removed outlier: 4.047A pdb=" N SER A1313 " --> pdb=" O GLU A1304 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 42 through 43 removed outlier: 7.100A pdb=" N ARG B 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'B' and resid 77 through 78 Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 101 Processing sheet with id=AA6, first strand: chain 'C' and resid 62 through 64 removed outlier: 5.852A pdb=" N VAL C 21 " --> pdb=" O GLU C 62 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N TYR C 64 " --> pdb=" O VAL C 21 " (cutoff:3.500A) removed outlier: 5.804A pdb=" N TYR C 23 " --> pdb=" O TYR C 64 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 203 through 207 removed outlier: 5.971A pdb=" N LEU C 181 " --> pdb=" O VAL C 268 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N GLN C 270 " --> pdb=" O LEU C 181 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N ILE C 183 " --> pdb=" O GLN C 270 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N VAL C 267 " --> pdb=" O MET C 306 " (cutoff:3.500A) removed outlier: 7.703A pdb=" N VAL C 308 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N LEU C 269 " --> pdb=" O VAL C 308 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 83 through 84 removed outlier: 7.646A pdb=" N ARG H 83 " --> pdb=" O VAL L 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'L' and resid 96 through 98 Processing sheet with id=AB1, first strand: chain 'M' and resid 42 through 43 removed outlier: 6.928A pdb=" N ARG M 42 " --> pdb=" O ILE N 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'M' and resid 77 through 78 Processing sheet with id=AB3, first strand: chain 'O' and resid 42 through 43 removed outlier: 7.042A pdb=" N ARG O 42 " --> pdb=" O ILE P 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'O' and resid 77 through 78 Processing sheet with id=AB5, first strand: chain 'O' and resid 100 through 102 removed outlier: 6.916A pdb=" N THR O 101 " --> pdb=" O TYR V 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'Q' and resid 83 through 84 removed outlier: 6.889A pdb=" N ARG Q 83 " --> pdb=" O VAL R 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'Q' and resid 118 through 119 Processing sheet with id=AB8, first strand: chain 'R' and resid 96 through 98 Processing sheet with id=AB9, first strand: chain 'S' and resid 42 through 43 removed outlier: 6.929A pdb=" N ARG S 42 " --> pdb=" O ILE T 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'S' and resid 77 through 78 Processing sheet with id=AC2, first strand: chain 'U' and resid 83 through 84 removed outlier: 7.107A pdb=" N ARG U 83 " --> pdb=" O VAL V 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'U' and resid 118 through 119 Processing sheet with id=AC4, first strand: chain 'W' and resid 83 through 84 removed outlier: 7.037A pdb=" N ARG W 83 " --> pdb=" O VAL Z 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 1447 hydrogen bonds defined for protein. 4287 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 696 hydrogen bonds 1292 hydrogen bond angles 0 basepair planarities 280 basepair parallelities 504 stacking parallelities Total time for adding SS restraints: 11.87 Time building geometry restraints manager: 4.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 7899 1.33 - 1.45: 12697 1.45 - 1.57: 19990 1.57 - 1.69: 1312 1.69 - 1.81: 141 Bond restraints: 42039 Sorted by residual: bond pdb=" N9 DA X 175 " pdb=" C4 DA X 175 " ideal model delta sigma weight residual 1.374 1.403 -0.029 6.00e-03 2.78e+04 2.35e+01 bond pdb=" C3' DT Y 178 " pdb=" O3' DT Y 178 " ideal model delta sigma weight residual 1.435 1.488 -0.053 1.30e-02 5.92e+03 1.65e+01 bond pdb=" C1' DT X 164 " pdb=" N1 DT X 164 " ideal model delta sigma weight residual 1.468 1.525 -0.057 1.40e-02 5.10e+03 1.64e+01 bond pdb=" C1' DC X 154 " pdb=" N1 DC X 154 " ideal model delta sigma weight residual 1.468 1.520 -0.052 1.40e-02 5.10e+03 1.38e+01 bond pdb=" CB GLU Q 94 " pdb=" CG GLU Q 94 " ideal model delta sigma weight residual 1.520 1.410 0.110 3.00e-02 1.11e+03 1.34e+01 ... (remaining 42034 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.73: 58269 2.73 - 5.47: 1177 5.47 - 8.20: 115 8.20 - 10.94: 16 10.94 - 13.67: 1 Bond angle restraints: 59578 Sorted by residual: angle pdb=" C3' DG X 173 " pdb=" O3' DG X 173 " pdb=" P DA X 174 " ideal model delta sigma weight residual 119.70 106.03 13.67 1.20e+00 6.94e-01 1.30e+02 angle pdb=" C3' DG Y 153 " pdb=" O3' DG Y 153 " pdb=" P DC Y 154 " ideal model delta sigma weight residual 119.70 109.51 10.19 1.20e+00 6.94e-01 7.21e+01 angle pdb=" C3' DT Y 156 " pdb=" O3' DT Y 156 " pdb=" P DC Y 157 " ideal model delta sigma weight residual 119.70 110.01 9.69 1.20e+00 6.94e-01 6.52e+01 angle pdb=" C3' DG X 172 " pdb=" O3' DG X 172 " pdb=" P DG X 173 " ideal model delta sigma weight residual 119.70 110.13 9.57 1.20e+00 6.94e-01 6.37e+01 angle pdb=" N ILE A 676 " pdb=" CA ILE A 676 " pdb=" C ILE A 676 " ideal model delta sigma weight residual 113.71 108.15 5.56 9.50e-01 1.11e+00 3.43e+01 ... (remaining 59573 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.60: 20542 35.60 - 71.20: 3038 71.20 - 106.81: 93 106.81 - 142.41: 7 142.41 - 178.01: 4 Dihedral angle restraints: 23684 sinusoidal: 14124 harmonic: 9560 Sorted by residual: dihedral pdb=" CD ARG R 23 " pdb=" NE ARG R 23 " pdb=" CZ ARG R 23 " pdb=" NH1 ARG R 23 " ideal model delta sinusoidal sigma weight residual 0.00 71.41 -71.41 1 1.00e+01 1.00e-02 6.54e+01 dihedral pdb=" CA PHE G 104 " pdb=" C PHE G 104 " pdb=" N GLU G 105 " pdb=" CA GLU G 105 " ideal model delta harmonic sigma weight residual -180.00 -141.88 -38.12 0 5.00e+00 4.00e-02 5.81e+01 dihedral pdb=" CA SER E 219 " pdb=" C SER E 219 " pdb=" N HIS E 220 " pdb=" CA HIS E 220 " ideal model delta harmonic sigma weight residual 180.00 146.99 33.01 0 5.00e+00 4.00e-02 4.36e+01 ... (remaining 23681 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.110: 6369 0.110 - 0.220: 284 0.220 - 0.331: 12 0.331 - 0.441: 0 0.441 - 0.551: 7 Chirality restraints: 6672 Sorted by residual: chirality pdb=" P DC Y 154 " pdb=" OP1 DC Y 154 " pdb=" OP2 DC Y 154 " pdb=" O5' DC Y 154 " both_signs ideal model delta sigma weight residual True 2.34 -2.89 -0.55 2.00e-01 2.50e+01 7.59e+00 chirality pdb=" P DG X 172 " pdb=" OP1 DG X 172 " pdb=" OP2 DG X 172 " pdb=" O5' DG X 172 " both_signs ideal model delta sigma weight residual True 2.34 -2.88 -0.55 2.00e-01 2.50e+01 7.47e+00 chirality pdb=" P DT Y 155 " pdb=" OP1 DT Y 155 " pdb=" OP2 DT Y 155 " pdb=" O5' DT Y 155 " both_signs ideal model delta sigma weight residual True 2.34 -2.87 -0.54 2.00e-01 2.50e+01 7.21e+00 ... (remaining 6669 not shown) Planarity restraints: 5302 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG R 23 " -1.042 9.50e-02 1.11e+02 4.67e-01 1.32e+02 pdb=" NE ARG R 23 " 0.062 2.00e-02 2.50e+03 pdb=" CZ ARG R 23 " 0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG R 23 " -0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG R 23 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG Z 23 " 0.593 9.50e-02 1.11e+02 2.66e-01 4.31e+01 pdb=" NE ARG Z 23 " -0.036 2.00e-02 2.50e+03 pdb=" CZ ARG Z 23 " -0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG Z 23 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG Z 23 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS S 36 " 0.016 2.00e-02 2.50e+03 3.31e-02 1.09e+01 pdb=" C LYS S 36 " -0.057 2.00e-02 2.50e+03 pdb=" O LYS S 36 " 0.022 2.00e-02 2.50e+03 pdb=" N GLY S 37 " 0.019 2.00e-02 2.50e+03 ... (remaining 5299 not shown) Histogram of nonbonded interaction distances: 1.47 - 2.15: 14 2.15 - 2.84: 12138 2.84 - 3.53: 58804 3.53 - 4.21: 114503 4.21 - 4.90: 168221 Nonbonded interactions: 353680 Sorted by model distance: nonbonded pdb=" N LEU A 225 " pdb=" OP2 DC X 182 " model vdw 1.468 3.120 nonbonded pdb=" OD2 ASP C 274 " pdb="ZN ZN C 501 " model vdw 1.667 2.230 nonbonded pdb=" NH1 ARG Z 35 " pdb=" OP2 DG X 262 " model vdw 1.772 3.120 nonbonded pdb=" NH2 ARG M 11 " pdb=" O2 DT X 298 " model vdw 1.793 3.120 nonbonded pdb=" OD1 ASP C 186 " pdb="ZN ZN C 501 " model vdw 1.806 2.230 ... (remaining 353675 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 'B' selection = chain 'M' selection = chain 'O' selection = chain 'S' } ncs_group { reference = chain 'D' selection = (chain 'N' and resid 29 through 119) selection = (chain 'P' and resid 29 through 119) selection = chain 'T' } ncs_group { reference = chain 'H' selection = (chain 'Q' and resid 37 through 133) selection = chain 'U' selection = (chain 'W' and resid 37 through 133) } ncs_group { reference = chain 'L' selection = (chain 'R' and resid 24 through 100) selection = (chain 'V' and resid 24 through 100) selection = (chain 'Z' and resid 24 through 100) } 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: 21.870 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 1.020 Check model and map are aligned: 0.120 Set scattering table: 0.100 Process input model: 47.340 Find NCS groups from input model: 0.460 Set up NCS constraints: 0.100 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:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 72.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7415 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 : 0.011 0.670 42040 Z= 0.609 Angle : 1.029 13.669 59578 Z= 0.749 Chirality : 0.057 0.551 6672 Planarity : 0.010 0.467 5302 Dihedral : 24.379 178.010 17490 Min Nonbonded Distance : 1.468 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.81 % Favored : 95.03 % Rotamer: Outliers : 0.84 % Allowed : 3.29 % Favored : 95.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.88 (0.11), residues: 3181 helix: -3.46 (0.07), residues: 2044 sheet: -2.23 (0.55), residues: 76 loop : -2.34 (0.17), residues: 1061 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG Q 116 TYR 0.050 0.004 TYR C 313 PHE 0.041 0.004 PHE B 25 TRP 0.040 0.003 TRP A 916 HIS 0.018 0.003 HIS I 33 Details of bonding type rmsd/Z covalent geometry : bond 0.01031 / 0.60 (42039) covalent geometry : angle 1.02923 / 0.75 (59578) hydrogen bonds : bond 0.22639 / 14.60 ( 2143) hydrogen bonds : angle 8.58278 / 5.94 ( 5579) metal coordination : bond 0.67045 / 35.29 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6362 Ramachandran restraints generated. 3181 Oldfield, 0 Emsley, 3181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6362 Ramachandran restraints generated. 3181 Oldfield, 0 Emsley, 3181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 944 residues out of total 2860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 920 time to evaluate : 1.246 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 841 MET cc_start: 0.7255 (ttp) cc_final: 0.5772 (ttp) REVERT: A 872 ASP cc_start: 0.7334 (m-30) cc_final: 0.6415 (m-30) REVERT: A 895 LEU cc_start: 0.8749 (tp) cc_final: 0.8129 (tp) REVERT: A 1294 MET cc_start: 0.6165 (ptp) cc_final: 0.5930 (ptp) REVERT: B 79 ILE cc_start: 0.9053 (mt) cc_final: 0.8563 (mt) REVERT: G 102 MET cc_start: 0.6509 (tmt) cc_final: 0.6146 (tmm) REVERT: G 115 TYR cc_start: 0.7237 (t80) cc_final: 0.6994 (t80) REVERT: G 129 LEU cc_start: 0.9328 (tp) cc_final: 0.9100 (tp) REVERT: H 51 ILE cc_start: 0.8808 (mt) cc_final: 0.8518 (mt) REVERT: I 87 MET cc_start: 0.7426 (tmm) cc_final: 0.6707 (tmm) REVERT: J 203 LYS cc_start: 0.8189 (ttpt) cc_final: 0.7950 (tttm) REVERT: J 343 GLN cc_start: 0.8735 (mm110) cc_final: 0.8453 (mm-40) REVERT: J 355 PHE cc_start: 0.8573 (t80) cc_final: 0.8210 (t80) REVERT: J 359 LEU cc_start: 0.8656 (mp) cc_final: 0.8414 (mt) REVERT: K 483 MET cc_start: -0.2504 (tmm) cc_final: -0.2749 (tpp) REVERT: L 53 GLU cc_start: 0.8402 (tp30) cc_final: 0.8201 (tp30) REVERT: L 79 LYS cc_start: 0.8136 (mtpt) cc_final: 0.7861 (mmtp) REVERT: L 98 TYR cc_start: 0.8788 (m-10) cc_final: 0.8175 (m-10) REVERT: M 57 TYR cc_start: 0.8272 (t80) cc_final: 0.7783 (t80) REVERT: M 61 GLU cc_start: 0.8630 (tp30) cc_final: 0.8284 (tp30) REVERT: N 54 LYS cc_start: 0.8774 (mmmt) cc_final: 0.8486 (tptp) REVERT: Q 48 LEU cc_start: 0.9314 (mt) cc_final: 0.9101 (mp) REVERT: Q 59 GLU cc_start: 0.7391 (pt0) cc_final: 0.7123 (pt0) REVERT: R 82 THR cc_start: 0.9056 (p) cc_final: 0.8726 (m) REVERT: S 104 GLN cc_start: 0.7960 (mm-40) cc_final: 0.7717 (mm-40) REVERT: W 60 LEU cc_start: 0.8375 (mt) cc_final: 0.8135 (mp) REVERT: W 105 GLU cc_start: 0.7605 (mm-30) cc_final: 0.7358 (mm-30) outliers start: 24 outliers final: 5 residues processed: 940 average time/residue: 0.3226 time to fit residues: 459.2411 Evaluate side-chains 571 residues out of total 2860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 566 time to evaluate : 1.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 443 GLN Chi-restraints excluded: chain A residue 763 THR Chi-restraints excluded: chain F residue 14 LYS Chi-restraints excluded: chain F residue 18 ARG Chi-restraints excluded: chain G residue 155 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 197 optimal weight: 9.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 0.8980 chunk 261 optimal weight: 0.5980 chunk 248 optimal weight: 0.8980 chunk 207 optimal weight: 0.9980 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 0.8980 chunk 183 optimal weight: 7.9990 chunk 298 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 431 HIS A 663 ASN ** A 779 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 798 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 974 GLN A1070 HIS A1075 GLN A1143 ASN A1252 HIS A1293 HIS ** B 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 89 ASN C 31 ASN C 54 ASN ** C 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 60 ASN D 64 ASN E 198 GLN E 213 GLN E 265 GLN F 59 ASN ** F 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 100 HIS ** G 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 190 ASN H 85 GLN ** I 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 45 ASN I 71 ASN I 88 HIS ** J 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 352 ASN J 378 ASN L 25 ASN ** L 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 38 ASN M 110 ASN N 60 ASN O 73 ASN P 46 HIS Q 68 GLN Q 76 GLN ** Q 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 108 ASN Q 125 GLN R 25 ASN R 27 GLN S 73 ASN T 46 HIS T 64 ASN ** T 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 85 GLN U 108 ASN V 25 ASN ** Z 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 93 GLN Total number of N/Q/H flips: 44 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.099098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.076541 restraints weight = 152619.842| |-----------------------------------------------------------------------------| r_work (start): 0.3524 rms_B_bonded: 2.96 r_work: 0.3104 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.2324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.093 42040 Z= 0.193 Angle : 0.756 10.188 59578 Z= 0.422 Chirality : 0.048 0.472 6672 Planarity : 0.007 0.081 5302 Dihedral : 29.444 177.843 10813 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 13.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 2.62 % Allowed : 10.94 % Favored : 86.43 % 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: -2.67 (0.13), residues: 3181 helix: -1.51 (0.10), residues: 2112 sheet: -1.41 (0.64), residues: 59 loop : -2.01 (0.19), residues: 1010 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 757 TYR 0.042 0.002 TYR D 80 PHE 0.034 0.002 PHE K 244 TRP 0.026 0.003 TRP A 912 HIS 0.011 0.001 HIS A 785 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.19 (42039) covalent geometry : angle 0.75563 / 0.42 (59578) hydrogen bonds : bond 0.08109 / 5.55 ( 2143) hydrogen bonds : angle 4.53460 / 3.16 ( 5579) metal coordination : bond 0.01855 / 0.98 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6362 Ramachandran restraints generated. 3181 Oldfield, 0 Emsley, 3181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6362 Ramachandran restraints generated. 3181 Oldfield, 0 Emsley, 3181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 715 residues out of total 2860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 640 time to evaluate : 1.264 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: A 280 PHE cc_start: 0.7719 (m-10) cc_final: 0.7433 (m-10) REVERT: A 695 ASP cc_start: 0.8640 (m-30) cc_final: 0.8362 (m-30) REVERT: A 765 MET cc_start: 0.2197 (tmm) cc_final: 0.1589 (tmm) REVERT: A 872 ASP cc_start: 0.8031 (m-30) cc_final: 0.7802 (m-30) REVERT: B 75 LYS cc_start: 0.8578 (mmmt) cc_final: 0.7983 (mmtt) REVERT: C 29 VAL cc_start: 0.9053 (p) cc_final: 0.8845 (p) REVERT: C 121 SER cc_start: 0.8963 (t) cc_final: 0.8515 (p) REVERT: C 164 ASN cc_start: 0.7628 (t0) cc_final: 0.7315 (t0) REVERT: C 261 TRP cc_start: 0.7689 (m-10) cc_final: 0.7192 (m-90) REVERT: D 39 TYR cc_start: 0.8465 (t80) cc_final: 0.7991 (t80) REVERT: D 76 ARG cc_start: 0.8743 (mtm-85) cc_final: 0.8310 (mtm-85) REVERT: E 246 LYS cc_start: 0.9282 (tppt) cc_final: 0.9067 (tppt) REVERT: E 273 ASP cc_start: 0.8774 (t0) cc_final: 0.8555 (t0) REVERT: E 287 TYR cc_start: 0.9028 (m-80) cc_final: 0.8474 (m-80) REVERT: F 65 GLN cc_start: 0.8979 (mt0) cc_final: 0.8720 (mt0) REVERT: F 118 TYR cc_start: 0.9046 (m-10) cc_final: 0.8625 (m-10) REVERT: F 299 LEU cc_start: 0.8347 (OUTLIER) cc_final: 0.8066 (mt) REVERT: G 76 GLN cc_start: 0.8698 (pt0) cc_final: 0.8476 (mt0) REVERT: G 77 GLN cc_start: 0.9199 (mm110) cc_final: 0.8129 (mp10) REVERT: G 102 MET cc_start: 0.6806 (tmt) cc_final: 0.6363 (tmm) REVERT: G 109 ASP cc_start: 0.8443 (t0) cc_final: 0.7737 (t0) REVERT: G 111 PHE cc_start: 0.8093 (t80) cc_final: 0.7787 (t80) REVERT: G 129 LEU cc_start: 0.9476 (tp) cc_final: 0.9255 (tp) REVERT: G 152 GLN cc_start: 0.8881 (pp30) cc_final: 0.8551 (pp30) REVERT: G 155 LYS cc_start: 0.7359 (OUTLIER) cc_final: 0.6809 (mmtt) REVERT: G 157 ILE cc_start: 0.9053 (pt) cc_final: 0.8833 (pt) REVERT: H 94 GLU cc_start: 0.8617 (mm-30) cc_final: 0.8393 (mm-30) REVERT: H 120 MET cc_start: 0.8568 (mmm) cc_final: 0.8137 (mmm) REVERT: H 125 GLN cc_start: 0.8808 (mt0) cc_final: 0.8470 (mp10) REVERT: I 23 LEU cc_start: 0.9015 (tp) cc_final: 0.8638 (pp) REVERT: I 105 GLU cc_start: 0.8616 (tp30) cc_final: 0.7462 (tp30) REVERT: I 108 TYR cc_start: 0.7833 (t80) cc_final: 0.7588 (t80) REVERT: J 203 LYS cc_start: 0.8730 (ttpt) cc_final: 0.8496 (tttm) REVERT: J 339 GLU cc_start: 0.9466 (tt0) cc_final: 0.8764 (tm-30) REVERT: J 342 ARG cc_start: 0.9142 (tmm-80) cc_final: 0.8515 (tmm-80) REVERT: J 343 GLN cc_start: 0.9309 (mm110) cc_final: 0.8653 (mm-40) REVERT: J 351 ARG cc_start: 0.8763 (mtt180) cc_final: 0.8242 (mtp85) REVERT: J 355 PHE cc_start: 0.9275 (t80) cc_final: 0.8936 (t80) REVERT: J 363 ARG cc_start: 0.8920 (tpt-90) cc_final: 0.8385 (tpt-90) REVERT: K 484 MET cc_start: 0.3960 (mpp) cc_final: 0.3449 (mpp) REVERT: L 35 ARG cc_start: 0.8908 (OUTLIER) cc_final: 0.8631 (ttm170) REVERT: L 53 GLU cc_start: 0.9122 (tp30) cc_final: 0.8821 (tp30) REVERT: L 54 THR cc_start: 0.9193 (m) cc_final: 0.8973 (p) REVERT: L 79 LYS cc_start: 0.8444 (mtpt) cc_final: 0.8214 (mmtp) REVERT: L 91 LYS cc_start: 0.9115 (tmtt) cc_final: 0.8577 (tmtt) REVERT: L 98 TYR cc_start: 0.8684 (m-10) cc_final: 0.8353 (m-10) REVERT: M 36 LYS cc_start: 0.8617 (pptt) cc_final: 0.8367 (pptt) REVERT: M 38 ASN cc_start: 0.7446 (t0) cc_final: 0.7221 (t0) REVERT: M 57 TYR cc_start: 0.8562 (t80) cc_final: 0.7873 (t80) REVERT: M 61 GLU cc_start: 0.9016 (tp30) cc_final: 0.8402 (tp30) REVERT: N 54 LYS cc_start: 0.8873 (mmmt) cc_final: 0.8620 (tptp) REVERT: N 56 MET cc_start: 0.9074 (OUTLIER) cc_final: 0.8737 (tpt) REVERT: T 61 SER cc_start: 0.9216 (t) cc_final: 0.8945 (m) REVERT: T 102 GLU cc_start: 0.8140 (OUTLIER) cc_final: 0.7830 (tp30) REVERT: W 50 GLU cc_start: 0.8906 (mt-10) cc_final: 0.8358 (mm-30) REVERT: W 52 ARG cc_start: 0.8076 (mtt-85) cc_final: 0.7621 (mtt90) REVERT: W 105 GLU cc_start: 0.8577 (mm-30) cc_final: 0.7927 (mm-30) REVERT: Z 88 TYR cc_start: 0.8663 (m-10) cc_final: 0.8421 (m-80) outliers start: 75 outliers final: 36 residues processed: 678 average time/residue: 0.2820 time to fit residues: 301.0730 Evaluate side-chains 607 residues out of total 2860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 566 time to evaluate : 1.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 414 TYR Chi-restraints excluded: chain A residue 443 GLN Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 763 THR Chi-restraints excluded: chain A residue 844 ASN Chi-restraints excluded: chain A residue 912 TRP Chi-restraints excluded: chain A residue 1138 LEU Chi-restraints excluded: chain A residue 1158 LEU Chi-restraints excluded: chain A residue 1178 VAL Chi-restraints excluded: chain A residue 1257 MET Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain E residue 235 ASP Chi-restraints excluded: chain F residue 18 ARG Chi-restraints excluded: chain F residue 110 ILE Chi-restraints excluded: chain F residue 299 LEU Chi-restraints excluded: chain G residue 84 ILE Chi-restraints excluded: chain G residue 113 ARG Chi-restraints excluded: chain G residue 155 LYS Chi-restraints excluded: chain G residue 174 SER Chi-restraints excluded: chain H residue 73 GLU Chi-restraints excluded: chain I residue 88 HIS Chi-restraints excluded: chain J residue 208 VAL Chi-restraints excluded: chain J residue 217 VAL Chi-restraints excluded: chain J residue 291 LEU Chi-restraints excluded: chain J residue 366 VAL Chi-restraints excluded: chain L residue 35 ARG Chi-restraints excluded: chain L residue 66 ILE Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain N residue 56 MET Chi-restraints excluded: chain N residue 84 SER Chi-restraints excluded: chain O residue 110 ASN Chi-restraints excluded: chain Q residue 76 GLN Chi-restraints excluded: chain R residue 96 THR Chi-restraints excluded: chain T residue 102 GLU Chi-restraints excluded: chain U residue 87 SER Chi-restraints excluded: chain V residue 96 THR Chi-restraints excluded: chain W residue 120 MET Chi-restraints excluded: chain W residue 130 ILE Chi-restraints excluded: chain Z residue 60 VAL Chi-restraints excluded: chain Z residue 96 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 95 optimal weight: 1.9990 chunk 191 optimal weight: 6.9990 chunk 345 optimal weight: 30.0000 chunk 249 optimal weight: 0.8980 chunk 199 optimal weight: 4.9990 chunk 114 optimal weight: 4.9990 chunk 284 optimal weight: 0.9980 chunk 118 optimal weight: 2.9990 chunk 18 optimal weight: 0.6980 chunk 152 optimal weight: 0.3980 chunk 227 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 798 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1221 HIS ** B 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 135 ASN C 151 HIS C 177 HIS ** C 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 60 ASN G 126 ASN ** G 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 68 GLN I 33 HIS ** I 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 110 ASN M 112 GLN N 60 ASN Q 76 GLN Q 125 GLN S 38 ASN ** T 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 39 HIS ** W 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 25 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.098697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.076082 restraints weight = 152128.440| |-----------------------------------------------------------------------------| r_work (start): 0.3515 rms_B_bonded: 3.16 r_work: 0.3080 rms_B_bonded: 4.54 restraints_weight: 0.5000 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.2818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 42040 Z= 0.171 Angle : 0.681 10.109 59578 Z= 0.383 Chirality : 0.045 0.439 6672 Planarity : 0.005 0.074 5302 Dihedral : 29.618 174.252 10809 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 13.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 2.48 % Allowed : 12.69 % Favored : 84.83 % 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: -1.65 (0.14), residues: 3181 helix: -0.64 (0.10), residues: 2113 sheet: -1.88 (0.56), residues: 83 loop : -1.76 (0.19), residues: 985 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 757 TYR 0.034 0.002 TYR A 755 PHE 0.021 0.002 PHE E 262 TRP 0.029 0.002 TRP A 782 HIS 0.011 0.001 HIS I 88 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.17 (42039) covalent geometry : angle 0.68105 / 0.38 (59578) hydrogen bonds : bond 0.07188 / 4.95 ( 2143) hydrogen bonds : angle 4.12598 / 2.87 ( 5579) metal coordination : bond 0.01150 / 0.61 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6362 Ramachandran restraints generated. 3181 Oldfield, 0 Emsley, 3181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6362 Ramachandran restraints generated. 3181 Oldfield, 0 Emsley, 3181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 692 residues out of total 2860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 621 time to evaluate : 1.089 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: A 280 PHE cc_start: 0.7888 (m-10) cc_final: 0.7559 (m-10) REVERT: A 826 ARG cc_start: 0.7827 (ppp-140) cc_final: 0.7347 (ttt90) REVERT: A 912 TRP cc_start: 0.7866 (OUTLIER) cc_final: 0.6606 (t60) REVERT: B 73 ASN cc_start: 0.8491 (m-40) cc_final: 0.8241 (m-40) REVERT: B 75 LYS cc_start: 0.8639 (mmmt) cc_final: 0.8077 (mmtt) REVERT: C 29 VAL cc_start: 0.9035 (p) cc_final: 0.8833 (p) REVERT: C 121 SER cc_start: 0.8928 (t) cc_final: 0.8531 (p) REVERT: C 164 ASN cc_start: 0.7732 (t0) cc_final: 0.7341 (t0) REVERT: C 261 TRP cc_start: 0.7607 (m-10) cc_final: 0.7384 (m-10) REVERT: D 70 ILE cc_start: 0.9359 (mm) cc_final: 0.9044 (tp) REVERT: D 96 ARG cc_start: 0.8759 (mmm-85) cc_final: 0.8543 (mtm180) REVERT: E 201 TYR cc_start: 0.8561 (t80) cc_final: 0.8299 (t80) REVERT: E 235 ASP cc_start: 0.8813 (OUTLIER) cc_final: 0.8495 (m-30) REVERT: E 246 LYS cc_start: 0.9160 (tppt) cc_final: 0.8840 (tppt) REVERT: E 273 ASP cc_start: 0.8869 (t0) cc_final: 0.8661 (t0) REVERT: E 287 TYR cc_start: 0.9126 (m-80) cc_final: 0.8666 (m-80) REVERT: F 65 GLN cc_start: 0.8944 (mt0) cc_final: 0.8703 (mt0) REVERT: F 118 TYR cc_start: 0.9119 (m-80) cc_final: 0.8627 (m-10) REVERT: G 77 GLN cc_start: 0.9171 (mm110) cc_final: 0.8116 (mp10) REVERT: G 102 MET cc_start: 0.6589 (tmt) cc_final: 0.6134 (tmm) REVERT: H 68 GLN cc_start: 0.8776 (OUTLIER) cc_final: 0.8222 (pt0) REVERT: H 70 LEU cc_start: 0.8293 (tp) cc_final: 0.8041 (tp) REVERT: H 122 LYS cc_start: 0.8459 (ptmt) cc_final: 0.7662 (ptmt) REVERT: H 125 GLN cc_start: 0.8759 (mt0) cc_final: 0.8526 (mp10) REVERT: H 126 LEU cc_start: 0.9124 (tp) cc_final: 0.8888 (tp) REVERT: I 23 LEU cc_start: 0.8939 (tp) cc_final: 0.8577 (pp) REVERT: I 84 GLU cc_start: 0.9281 (tp30) cc_final: 0.8936 (tp30) REVERT: I 88 HIS cc_start: 0.8838 (OUTLIER) cc_final: 0.8385 (p90) REVERT: J 203 LYS cc_start: 0.8824 (ttpt) cc_final: 0.8609 (tttm) REVERT: J 342 ARG cc_start: 0.9152 (tmm-80) cc_final: 0.8587 (tmm-80) REVERT: J 343 GLN cc_start: 0.9343 (mm110) cc_final: 0.8875 (mm-40) REVERT: J 351 ARG cc_start: 0.8822 (mtt180) cc_final: 0.8405 (mtp85) REVERT: J 363 ARG cc_start: 0.8979 (tpt-90) cc_final: 0.8426 (tmt-80) REVERT: J 370 ASN cc_start: 0.8959 (m-40) cc_final: 0.8065 (m110) REVERT: L 25 ASN cc_start: 0.7478 (t0) cc_final: 0.7084 (t0) REVERT: L 53 GLU cc_start: 0.9067 (tp30) cc_final: 0.8827 (tp30) REVERT: L 77 LYS cc_start: 0.9189 (mmmt) cc_final: 0.8814 (mmtm) REVERT: M 38 ASN cc_start: 0.7197 (t0) cc_final: 0.6841 (t0) REVERT: M 57 TYR cc_start: 0.8453 (t80) cc_final: 0.8023 (t80) REVERT: M 61 GLU cc_start: 0.8850 (tp30) cc_final: 0.8561 (tp30) REVERT: N 54 LYS cc_start: 0.8885 (mmmt) cc_final: 0.8547 (tptp) REVERT: N 90 GLU cc_start: 0.8360 (mp0) cc_final: 0.8135 (mp0) REVERT: T 61 SER cc_start: 0.9215 (t) cc_final: 0.8976 (m) REVERT: T 102 GLU cc_start: 0.8138 (OUTLIER) cc_final: 0.7908 (tp30) REVERT: U 129 ARG cc_start: 0.8120 (tpt90) cc_final: 0.7906 (tpt90) REVERT: W 50 GLU cc_start: 0.8839 (mt-10) cc_final: 0.8350 (mm-30) REVERT: W 52 ARG cc_start: 0.8018 (mtt-85) cc_final: 0.7665 (mtt90) REVERT: W 60 LEU cc_start: 0.8126 (OUTLIER) cc_final: 0.7861 (mp) REVERT: W 105 GLU cc_start: 0.8506 (mm-30) cc_final: 0.8192 (mm-30) outliers start: 71 outliers final: 41 residues processed: 653 average time/residue: 0.2580 time to fit residues: 268.2687 Evaluate side-chains 626 residues out of total 2860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 579 time to evaluate : 1.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 TYR Chi-restraints excluded: chain A residue 428 ILE Chi-restraints excluded: chain A residue 443 GLN Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 763 THR Chi-restraints excluded: chain A residue 773 MET Chi-restraints excluded: chain A residue 833 THR Chi-restraints excluded: chain A residue 912 TRP Chi-restraints excluded: chain A residue 945 THR Chi-restraints excluded: chain A residue 1178 VAL Chi-restraints excluded: chain A residue 1257 MET Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain E residue 235 ASP Chi-restraints excluded: chain F residue 91 SER Chi-restraints excluded: chain F residue 299 LEU Chi-restraints excluded: chain G residue 84 ILE Chi-restraints excluded: chain G residue 104 PHE Chi-restraints excluded: chain G residue 113 ARG Chi-restraints excluded: chain G residue 126 ASN Chi-restraints excluded: chain G residue 174 SER Chi-restraints excluded: chain H residue 68 GLN Chi-restraints excluded: chain H residue 73 GLU Chi-restraints excluded: chain H residue 117 VAL Chi-restraints excluded: chain I residue 88 HIS Chi-restraints excluded: chain J residue 217 VAL Chi-restraints excluded: chain J residue 291 LEU Chi-restraints excluded: chain J residue 366 VAL Chi-restraints excluded: chain L residue 66 ILE Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain M residue 62 ILE Chi-restraints excluded: chain M residue 110 ASN Chi-restraints excluded: chain O residue 38 ASN Chi-restraints excluded: chain O residue 101 THR Chi-restraints excluded: chain O residue 110 ASN Chi-restraints excluded: chain R residue 96 THR Chi-restraints excluded: chain S residue 95 LYS Chi-restraints excluded: chain S residue 101 THR Chi-restraints excluded: chain T residue 43 LYS Chi-restraints excluded: chain T residue 102 GLU Chi-restraints excluded: chain U residue 87 SER Chi-restraints excluded: chain V residue 96 THR Chi-restraints excluded: chain W residue 60 LEU Chi-restraints excluded: chain W residue 130 ILE Chi-restraints excluded: chain Z residue 60 VAL Chi-restraints excluded: chain Z residue 96 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 220 optimal weight: 1.9990 chunk 248 optimal weight: 0.8980 chunk 45 optimal weight: 7.9990 chunk 62 optimal weight: 2.9990 chunk 105 optimal weight: 0.6980 chunk 69 optimal weight: 0.0370 chunk 9 optimal weight: 20.0000 chunk 316 optimal weight: 9.9990 chunk 244 optimal weight: 6.9990 chunk 325 optimal weight: 10.0000 chunk 104 optimal weight: 1.9990 overall best weight: 1.1262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 313 ASN ** A 798 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 265 GLN F 48 GLN G 126 ASN ** G 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 47 ASN I 71 ASN J 196 GLN ** J 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 38 ASN ** M 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 60 ASN P 106 HIS R 27 GLN ** T 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.097920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.075131 restraints weight = 150942.505| |-----------------------------------------------------------------------------| r_work (start): 0.3492 rms_B_bonded: 2.97 r_work: 0.3066 rms_B_bonded: 4.50 restraints_weight: 0.5000 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.3100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 42040 Z= 0.175 Angle : 0.669 11.973 59578 Z= 0.372 Chirality : 0.045 0.420 6672 Planarity : 0.005 0.074 5302 Dihedral : 29.730 173.933 10801 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 13.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 2.41 % Allowed : 14.13 % Favored : 83.46 % 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: -1.09 (0.14), residues: 3181 helix: -0.17 (0.11), residues: 2114 sheet: -2.01 (0.57), residues: 83 loop : -1.61 (0.19), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.001 ARG K 247 TYR 0.039 0.002 TYR D 80 PHE 0.062 0.002 PHE E 262 TRP 0.030 0.002 TRP A 782 HIS 0.008 0.001 HIS I 33 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.18 (42039) covalent geometry : angle 0.66856 / 0.37 (59578) hydrogen bonds : bond 0.06821 / 4.69 ( 2143) hydrogen bonds : angle 3.94296 / 2.74 ( 5579) metal coordination : bond 0.00587 / 0.31 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6362 Ramachandran restraints generated. 3181 Oldfield, 0 Emsley, 3181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6362 Ramachandran restraints generated. 3181 Oldfield, 0 Emsley, 3181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 670 residues out of total 2860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 601 time to evaluate : 1.188 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: A 280 PHE cc_start: 0.7942 (m-10) cc_final: 0.7598 (m-10) REVERT: A 912 TRP cc_start: 0.7760 (OUTLIER) cc_final: 0.6711 (t60) REVERT: A 945 THR cc_start: 0.8477 (OUTLIER) cc_final: 0.8050 (t) REVERT: A 1138 LEU cc_start: 0.9500 (mt) cc_final: 0.9282 (mt) REVERT: C 121 SER cc_start: 0.8883 (t) cc_final: 0.8535 (p) REVERT: C 164 ASN cc_start: 0.7674 (t0) cc_final: 0.7332 (t0) REVERT: C 176 TYR cc_start: 0.8656 (m-10) cc_final: 0.8303 (m-10) REVERT: C 261 TRP cc_start: 0.7636 (m-10) cc_final: 0.7371 (m-10) REVERT: D 52 SER cc_start: 0.8931 (t) cc_final: 0.8711 (p) REVERT: D 73 GLU cc_start: 0.8643 (mm-30) cc_final: 0.8125 (mm-30) REVERT: D 96 ARG cc_start: 0.8686 (mmm-85) cc_final: 0.8476 (mtm180) REVERT: E 201 TYR cc_start: 0.8490 (t80) cc_final: 0.8206 (t80) REVERT: E 214 MET cc_start: 0.6237 (mpp) cc_final: 0.5264 (mpp) REVERT: E 226 TYR cc_start: 0.8283 (m-80) cc_final: 0.8029 (m-10) REVERT: E 227 TYR cc_start: 0.8757 (m-80) cc_final: 0.8477 (m-80) REVERT: E 235 ASP cc_start: 0.8832 (OUTLIER) cc_final: 0.8517 (m-30) REVERT: E 273 ASP cc_start: 0.8897 (t0) cc_final: 0.8678 (t0) REVERT: E 287 TYR cc_start: 0.9004 (m-80) cc_final: 0.8635 (m-80) REVERT: F 48 GLN cc_start: 0.8466 (mp-120) cc_final: 0.8251 (mp10) REVERT: F 65 GLN cc_start: 0.9025 (mt0) cc_final: 0.8737 (mt0) REVERT: F 118 TYR cc_start: 0.9099 (m-80) cc_final: 0.8784 (m-10) REVERT: G 76 GLN cc_start: 0.8519 (mt0) cc_final: 0.8283 (pt0) REVERT: G 77 GLN cc_start: 0.8899 (mm110) cc_final: 0.8308 (mp10) REVERT: G 161 ASP cc_start: 0.9228 (t0) cc_final: 0.8546 (t0) REVERT: H 55 GLN cc_start: 0.8555 (mt0) cc_final: 0.8338 (mt0) REVERT: H 68 GLN cc_start: 0.8794 (mt0) cc_final: 0.8325 (pt0) REVERT: H 70 LEU cc_start: 0.8185 (tp) cc_final: 0.7863 (tp) REVERT: H 90 MET cc_start: 0.9033 (mmt) cc_final: 0.8639 (mmp) REVERT: H 122 LYS cc_start: 0.8351 (ptmt) cc_final: 0.7449 (ptmt) REVERT: H 125 GLN cc_start: 0.8687 (mt0) cc_final: 0.8457 (mp10) REVERT: I 23 LEU cc_start: 0.8961 (tp) cc_final: 0.8580 (pp) REVERT: J 342 ARG cc_start: 0.9173 (tmm-80) cc_final: 0.8593 (tmm-80) REVERT: J 343 GLN cc_start: 0.9324 (mm110) cc_final: 0.8832 (mm-40) REVERT: J 351 ARG cc_start: 0.9084 (mtt180) cc_final: 0.8696 (mtp85) REVERT: J 368 LYS cc_start: 0.8727 (pttt) cc_final: 0.8483 (pttp) REVERT: J 370 ASN cc_start: 0.8893 (m-40) cc_final: 0.8144 (m-40) REVERT: L 25 ASN cc_start: 0.7549 (t0) cc_final: 0.7153 (t0) REVERT: L 35 ARG cc_start: 0.8850 (mtm110) cc_final: 0.8572 (ttm170) REVERT: L 78 ARG cc_start: 0.8548 (mtm-85) cc_final: 0.8286 (mtp85) REVERT: L 91 LYS cc_start: 0.9081 (tmtt) cc_final: 0.8664 (tmtt) REVERT: M 24 GLN cc_start: 0.8934 (mm-40) cc_final: 0.8389 (mm-40) REVERT: M 38 ASN cc_start: 0.7270 (t0) cc_final: 0.6869 (t0) REVERT: M 57 TYR cc_start: 0.8512 (t80) cc_final: 0.8038 (t80) REVERT: N 54 LYS cc_start: 0.8921 (mmmt) cc_final: 0.8515 (tptp) REVERT: N 56 MET cc_start: 0.8779 (tpt) cc_final: 0.8475 (tpt) REVERT: N 58 ILE cc_start: 0.9095 (mt) cc_final: 0.8874 (mt) REVERT: U 41 TYR cc_start: 0.9308 (m-80) cc_final: 0.9014 (m-80) REVERT: U 129 ARG cc_start: 0.8087 (tpt90) cc_final: 0.7867 (tpt90) REVERT: W 50 GLU cc_start: 0.8761 (mt-10) cc_final: 0.8315 (mm-30) REVERT: W 52 ARG cc_start: 0.8031 (mtt-85) cc_final: 0.7684 (mtt90) REVERT: W 81 ASP cc_start: 0.8027 (t0) cc_final: 0.7755 (t0) REVERT: W 105 GLU cc_start: 0.8419 (mm-30) cc_final: 0.8146 (mm-30) REVERT: Z 88 TYR cc_start: 0.8405 (m-80) cc_final: 0.8197 (m-80) outliers start: 69 outliers final: 51 residues processed: 629 average time/residue: 0.2606 time to fit residues: 262.4924 Evaluate side-chains 625 residues out of total 2860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 571 time to evaluate : 1.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 TYR Chi-restraints excluded: chain A residue 428 ILE Chi-restraints excluded: chain A residue 443 GLN Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 763 THR Chi-restraints excluded: chain A residue 844 ASN Chi-restraints excluded: chain A residue 912 TRP Chi-restraints excluded: chain A residue 945 THR Chi-restraints excluded: chain A residue 989 LEU Chi-restraints excluded: chain A residue 1178 VAL Chi-restraints excluded: chain A residue 1257 MET Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 79 ILE Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 198 TYR Chi-restraints excluded: chain C residue 323 CYS Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain E residue 235 ASP Chi-restraints excluded: chain F residue 91 SER Chi-restraints excluded: chain F residue 299 LEU Chi-restraints excluded: chain G residue 84 ILE Chi-restraints excluded: chain G residue 113 ARG Chi-restraints excluded: chain G residue 125 ASP Chi-restraints excluded: chain G residue 174 SER Chi-restraints excluded: chain H residue 117 VAL Chi-restraints excluded: chain I residue 47 ASN Chi-restraints excluded: chain I residue 88 HIS Chi-restraints excluded: chain I residue 105 GLU Chi-restraints excluded: chain J residue 291 LEU Chi-restraints excluded: chain J residue 366 VAL Chi-restraints excluded: chain L residue 66 ILE Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain M residue 62 ILE Chi-restraints excluded: chain N residue 84 SER Chi-restraints excluded: chain O residue 101 THR Chi-restraints excluded: chain O residue 110 ASN Chi-restraints excluded: chain O residue 113 SER Chi-restraints excluded: chain O residue 114 VAL Chi-restraints excluded: chain Q residue 73 GLU Chi-restraints excluded: chain Q residue 77 ASP Chi-restraints excluded: chain Q residue 122 LYS Chi-restraints excluded: chain R residue 96 THR Chi-restraints excluded: chain S residue 95 LYS Chi-restraints excluded: chain S residue 101 THR Chi-restraints excluded: chain S residue 114 VAL Chi-restraints excluded: chain T residue 43 LYS Chi-restraints excluded: chain T residue 45 VAL Chi-restraints excluded: chain U residue 87 SER Chi-restraints excluded: chain V residue 96 THR Chi-restraints excluded: chain W residue 130 ILE Chi-restraints excluded: chain Z residue 49 LEU Chi-restraints excluded: chain Z residue 60 VAL Chi-restraints excluded: chain Z residue 96 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 209 optimal weight: 8.9990 chunk 61 optimal weight: 0.9990 chunk 189 optimal weight: 0.9980 chunk 101 optimal weight: 0.0010 chunk 157 optimal weight: 3.9990 chunk 219 optimal weight: 0.6980 chunk 352 optimal weight: 20.0000 chunk 356 optimal weight: 30.0000 chunk 368 optimal weight: 7.9990 chunk 159 optimal weight: 0.9980 chunk 131 optimal weight: 0.9980 overall best weight: 0.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 798 HIS A1274 ASN ** B 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 94 ASN ** C 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 47 ASN I 88 HIS ** J 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 60 ASN ** T 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 108 ASN ** 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 = 0.4115 r_free = 0.4115 target = 0.098227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.075553 restraints weight = 151457.159| |-----------------------------------------------------------------------------| r_work (start): 0.3504 rms_B_bonded: 3.02 r_work: 0.3076 rms_B_bonded: 4.56 restraints_weight: 0.5000 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.3319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 42040 Z= 0.152 Angle : 0.655 10.543 59578 Z= 0.364 Chirality : 0.044 0.402 6672 Planarity : 0.004 0.067 5302 Dihedral : 29.770 173.392 10801 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 13.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 2.41 % Allowed : 15.35 % Favored : 82.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.70 (0.14), residues: 3181 helix: 0.16 (0.11), residues: 2104 sheet: -2.01 (0.54), residues: 83 loop : -1.50 (0.20), residues: 994 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 76 TYR 0.025 0.002 TYR B 57 PHE 0.059 0.002 PHE E 262 TRP 0.030 0.002 TRP A 782 HIS 0.004 0.001 HIS P 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.15 (42039) covalent geometry : angle 0.65537 / 0.36 (59578) hydrogen bonds : bond 0.06613 / 4.57 ( 2143) hydrogen bonds : angle 3.85132 / 2.67 ( 5579) metal coordination : bond 0.00442 / 0.23 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6362 Ramachandran restraints generated. 3181 Oldfield, 0 Emsley, 3181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6362 Ramachandran restraints generated. 3181 Oldfield, 0 Emsley, 3181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 670 residues out of total 2860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 601 time to evaluate : 1.157 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: A 280 PHE cc_start: 0.7996 (m-10) cc_final: 0.7632 (m-10) REVERT: A 945 THR cc_start: 0.8529 (OUTLIER) cc_final: 0.8110 (t) REVERT: C 121 SER cc_start: 0.8908 (t) cc_final: 0.8500 (p) REVERT: C 164 ASN cc_start: 0.7681 (t0) cc_final: 0.7325 (t0) REVERT: C 176 TYR cc_start: 0.8743 (m-10) cc_final: 0.8468 (m-10) REVERT: C 214 PHE cc_start: 0.8381 (OUTLIER) cc_final: 0.7885 (m-10) REVERT: D 52 SER cc_start: 0.8954 (t) cc_final: 0.8728 (p) REVERT: D 70 ILE cc_start: 0.9342 (mm) cc_final: 0.9027 (tp) REVERT: D 73 GLU cc_start: 0.8645 (mm-30) cc_final: 0.8141 (mm-30) REVERT: E 195 GLN cc_start: 0.5439 (OUTLIER) cc_final: 0.4285 (pm20) REVERT: E 201 TYR cc_start: 0.8476 (t80) cc_final: 0.8195 (t80) REVERT: E 214 MET cc_start: 0.6234 (mpp) cc_final: 0.5165 (mpp) REVERT: E 227 TYR cc_start: 0.8753 (m-10) cc_final: 0.8455 (m-10) REVERT: E 235 ASP cc_start: 0.8857 (OUTLIER) cc_final: 0.8281 (m-30) REVERT: E 270 LYS cc_start: 0.8954 (mmtm) cc_final: 0.8647 (mttp) REVERT: E 273 ASP cc_start: 0.8953 (t0) cc_final: 0.8739 (t0) REVERT: E 287 TYR cc_start: 0.8978 (m-80) cc_final: 0.8645 (m-80) REVERT: F 118 TYR cc_start: 0.9078 (m-80) cc_final: 0.8748 (m-10) REVERT: F 299 LEU cc_start: 0.8132 (OUTLIER) cc_final: 0.7847 (mt) REVERT: G 76 GLN cc_start: 0.8531 (mt0) cc_final: 0.8253 (pt0) REVERT: G 77 GLN cc_start: 0.8908 (mm110) cc_final: 0.8352 (mp10) REVERT: G 115 TYR cc_start: 0.8370 (t80) cc_final: 0.7934 (t80) REVERT: G 157 ILE cc_start: 0.8764 (tp) cc_final: 0.8522 (tt) REVERT: G 169 HIS cc_start: 0.8902 (t-90) cc_final: 0.8440 (t-90) REVERT: H 65 LEU cc_start: 0.7465 (tt) cc_final: 0.7114 (tt) REVERT: H 68 GLN cc_start: 0.8833 (mt0) cc_final: 0.8389 (pt0) REVERT: H 70 LEU cc_start: 0.8139 (tp) cc_final: 0.7819 (tp) REVERT: H 122 LYS cc_start: 0.8361 (ptmt) cc_final: 0.7414 (ptmt) REVERT: H 125 GLN cc_start: 0.8739 (mt0) cc_final: 0.8468 (mp10) REVERT: I 23 LEU cc_start: 0.8954 (tp) cc_final: 0.8601 (pp) REVERT: J 200 MET cc_start: 0.9074 (tpp) cc_final: 0.8559 (tpp) REVERT: J 339 GLU cc_start: 0.9501 (tt0) cc_final: 0.8792 (tm-30) REVERT: J 342 ARG cc_start: 0.9181 (tmm-80) cc_final: 0.8569 (tmm-80) REVERT: J 343 GLN cc_start: 0.9331 (mm110) cc_final: 0.8596 (mm-40) REVERT: J 351 ARG cc_start: 0.9101 (mtt180) cc_final: 0.8835 (mtt-85) REVERT: J 363 ARG cc_start: 0.8959 (tmt-80) cc_final: 0.8362 (tpm170) REVERT: J 370 ASN cc_start: 0.8830 (m-40) cc_final: 0.7916 (m-40) REVERT: L 25 ASN cc_start: 0.7534 (t0) cc_final: 0.7181 (t0) REVERT: L 35 ARG cc_start: 0.8855 (mtm110) cc_final: 0.8539 (ttm170) REVERT: L 78 ARG cc_start: 0.8617 (mtm-85) cc_final: 0.8283 (mtp85) REVERT: L 91 LYS cc_start: 0.9195 (tmtt) cc_final: 0.8771 (tmtt) REVERT: M 24 GLN cc_start: 0.8993 (mm-40) cc_final: 0.8487 (mm-40) REVERT: M 38 ASN cc_start: 0.7341 (t0) cc_final: 0.6930 (t0) REVERT: M 57 TYR cc_start: 0.8577 (t80) cc_final: 0.8167 (t80) REVERT: N 54 LYS cc_start: 0.8949 (mmmt) cc_final: 0.8429 (tptp) REVERT: N 58 ILE cc_start: 0.9047 (mt) cc_final: 0.8793 (mt) REVERT: N 70 ILE cc_start: 0.9452 (mt) cc_final: 0.9214 (tp) REVERT: P 48 ASP cc_start: 0.8097 (p0) cc_final: 0.7887 (p0) REVERT: U 129 ARG cc_start: 0.8077 (tpt90) cc_final: 0.7844 (tpt90) REVERT: W 50 GLU cc_start: 0.8812 (mt-10) cc_final: 0.8327 (mm-30) REVERT: W 81 ASP cc_start: 0.8002 (t0) cc_final: 0.7764 (t0) REVERT: W 105 GLU cc_start: 0.8415 (mm-30) cc_final: 0.8135 (mm-30) outliers start: 69 outliers final: 42 residues processed: 635 average time/residue: 0.2655 time to fit residues: 270.1772 Evaluate side-chains 606 residues out of total 2860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 559 time to evaluate : 1.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 TYR Chi-restraints excluded: chain A residue 428 ILE Chi-restraints excluded: chain A residue 443 GLN Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 763 THR Chi-restraints excluded: chain A residue 826 ARG Chi-restraints excluded: chain A residue 945 THR Chi-restraints excluded: chain A residue 1178 VAL Chi-restraints excluded: chain A residue 1257 MET Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 79 ILE Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain C residue 198 TYR Chi-restraints excluded: chain C residue 214 PHE Chi-restraints excluded: chain C residue 323 CYS Chi-restraints excluded: chain D residue 58 ILE Chi-restraints excluded: chain E residue 195 GLN Chi-restraints excluded: chain E residue 225 VAL Chi-restraints excluded: chain E residue 235 ASP Chi-restraints excluded: chain F residue 299 LEU Chi-restraints excluded: chain G residue 84 ILE Chi-restraints excluded: chain G residue 104 PHE Chi-restraints excluded: chain G residue 113 ARG Chi-restraints excluded: chain G residue 174 SER Chi-restraints excluded: chain H residue 73 GLU Chi-restraints excluded: chain I residue 88 HIS Chi-restraints excluded: chain J residue 213 GLN Chi-restraints excluded: chain J residue 291 LEU Chi-restraints excluded: chain L residue 62 LEU Chi-restraints excluded: chain L residue 66 ILE Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain N residue 84 SER Chi-restraints excluded: chain O residue 101 THR Chi-restraints excluded: chain O residue 110 ASN Chi-restraints excluded: chain O residue 113 SER Chi-restraints excluded: chain Q residue 77 ASP Chi-restraints excluded: chain R residue 96 THR Chi-restraints excluded: chain S residue 95 LYS Chi-restraints excluded: chain S residue 101 THR Chi-restraints excluded: chain S residue 114 VAL Chi-restraints excluded: chain T residue 45 VAL Chi-restraints excluded: chain V residue 96 THR Chi-restraints excluded: chain W residue 60 LEU Chi-restraints excluded: chain W residue 130 ILE Chi-restraints excluded: chain Z residue 49 LEU Chi-restraints excluded: chain Z residue 60 VAL Chi-restraints excluded: chain Z residue 96 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 364 optimal weight: 9.9990 chunk 0 optimal weight: 20.0000 chunk 245 optimal weight: 0.5980 chunk 288 optimal weight: 1.9990 chunk 350 optimal weight: 20.0000 chunk 248 optimal weight: 0.6980 chunk 212 optimal weight: 8.9990 chunk 267 optimal weight: 1.9990 chunk 260 optimal weight: 6.9990 chunk 209 optimal weight: 5.9990 chunk 69 optimal weight: 2.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 89 ASN ** C 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 47 ASN ** J 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 60 ASN ** T 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.097000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.071354 restraints weight = 151728.197| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 1.95 r_work: 0.3103 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.3516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 42040 Z= 0.202 Angle : 0.683 10.078 59578 Z= 0.374 Chirality : 0.046 0.398 6672 Planarity : 0.005 0.076 5302 Dihedral : 29.864 173.247 10801 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 13.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 2.55 % Allowed : 15.77 % Favored : 81.68 % 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: -0.50 (0.15), residues: 3181 helix: 0.33 (0.11), residues: 2107 sheet: -2.02 (0.54), residues: 83 loop : -1.46 (0.20), residues: 991 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 168 TYR 0.030 0.002 TYR Z 88 PHE 0.062 0.002 PHE E 262 TRP 0.037 0.002 TRP A 912 HIS 0.008 0.001 HIS T 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00411 / 0.20 (42039) covalent geometry : angle 0.68335 / 0.37 (59578) hydrogen bonds : bond 0.06620 / 4.50 ( 2143) hydrogen bonds : angle 3.82802 / 2.66 ( 5579) metal coordination : bond 0.00711 / 0.37 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6362 Ramachandran restraints generated. 3181 Oldfield, 0 Emsley, 3181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6362 Ramachandran restraints generated. 3181 Oldfield, 0 Emsley, 3181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 655 residues out of total 2860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 582 time to evaluate : 0.987 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 280 PHE cc_start: 0.8039 (m-10) cc_final: 0.7679 (m-10) REVERT: A 443 GLN cc_start: 0.6136 (OUTLIER) cc_final: 0.5910 (tp-100) REVERT: A 822 GLU cc_start: 0.8222 (mp0) cc_final: 0.7837 (mp0) REVERT: A 945 THR cc_start: 0.8592 (OUTLIER) cc_final: 0.8180 (t) REVERT: B 104 GLN cc_start: 0.8347 (mp10) cc_final: 0.7889 (mp10) REVERT: C 121 SER cc_start: 0.8967 (t) cc_final: 0.8446 (p) REVERT: C 164 ASN cc_start: 0.7725 (t0) cc_final: 0.7273 (t0) REVERT: C 176 TYR cc_start: 0.8724 (m-10) cc_final: 0.8461 (m-10) REVERT: C 214 PHE cc_start: 0.8342 (OUTLIER) cc_final: 0.7962 (m-10) REVERT: D 52 SER cc_start: 0.8925 (t) cc_final: 0.8341 (p) REVERT: D 73 GLU cc_start: 0.8512 (mm-30) cc_final: 0.7934 (mm-30) REVERT: E 201 TYR cc_start: 0.8516 (t80) cc_final: 0.8235 (t80) REVERT: E 214 MET cc_start: 0.6160 (mpp) cc_final: 0.5116 (mpp) REVERT: E 227 TYR cc_start: 0.8801 (m-10) cc_final: 0.8498 (m-10) REVERT: E 235 ASP cc_start: 0.8802 (OUTLIER) cc_final: 0.8487 (m-30) REVERT: E 273 ASP cc_start: 0.8917 (t0) cc_final: 0.8703 (t0) REVERT: E 287 TYR cc_start: 0.8936 (m-80) cc_final: 0.8630 (m-80) REVERT: F 118 TYR cc_start: 0.9088 (m-80) cc_final: 0.8763 (m-10) REVERT: F 290 THR cc_start: 0.2123 (OUTLIER) cc_final: 0.1737 (p) REVERT: G 76 GLN cc_start: 0.8537 (mt0) cc_final: 0.8281 (pt0) REVERT: G 77 GLN cc_start: 0.8946 (mm110) cc_final: 0.8368 (mp10) REVERT: G 141 LYS cc_start: 0.8561 (mptt) cc_final: 0.8156 (mptt) REVERT: H 65 LEU cc_start: 0.7460 (tt) cc_final: 0.7112 (tt) REVERT: H 68 GLN cc_start: 0.8804 (mt0) cc_final: 0.8350 (pt0) REVERT: H 70 LEU cc_start: 0.8149 (tp) cc_final: 0.7820 (tp) REVERT: H 122 LYS cc_start: 0.8362 (ptmt) cc_final: 0.7398 (ptmt) REVERT: H 125 GLN cc_start: 0.8695 (mt0) cc_final: 0.8403 (mp10) REVERT: I 23 LEU cc_start: 0.8948 (tp) cc_final: 0.8592 (pp) REVERT: I 84 GLU cc_start: 0.9237 (tp30) cc_final: 0.9011 (tp30) REVERT: I 88 HIS cc_start: 0.8761 (OUTLIER) cc_final: 0.8361 (p90) REVERT: J 203 LYS cc_start: 0.8740 (ptmt) cc_final: 0.8431 (ptmt) REVERT: J 210 ARG cc_start: 0.9290 (mmt90) cc_final: 0.8946 (ptp-170) REVERT: J 228 GLU cc_start: 0.7009 (pt0) cc_final: 0.6471 (mt-10) REVERT: J 339 GLU cc_start: 0.9499 (tt0) cc_final: 0.8778 (tm-30) REVERT: J 342 ARG cc_start: 0.9160 (tmm-80) cc_final: 0.8565 (tmm-80) REVERT: J 343 GLN cc_start: 0.9341 (mm110) cc_final: 0.8611 (mm-40) REVERT: J 351 ARG cc_start: 0.9120 (mtt180) cc_final: 0.8455 (mtp85) REVERT: J 363 ARG cc_start: 0.8986 (tmt-80) cc_final: 0.8352 (tpm170) REVERT: J 370 ASN cc_start: 0.8789 (m-40) cc_final: 0.7878 (m-40) REVERT: L 25 ASN cc_start: 0.7485 (t0) cc_final: 0.7190 (t0) REVERT: L 35 ARG cc_start: 0.8855 (mtm110) cc_final: 0.8538 (ttm170) REVERT: L 54 THR cc_start: 0.8767 (p) cc_final: 0.8490 (t) REVERT: L 78 ARG cc_start: 0.8545 (mtm-85) cc_final: 0.8100 (mtp85) REVERT: L 84 MET cc_start: 0.8540 (tpp) cc_final: 0.8304 (tpp) REVERT: L 91 LYS cc_start: 0.9275 (tmtt) cc_final: 0.8794 (tmtt) REVERT: M 24 GLN cc_start: 0.9031 (mm-40) cc_final: 0.8482 (mm-40) REVERT: M 38 ASN cc_start: 0.7393 (t0) cc_final: 0.6977 (t0) REVERT: N 54 LYS cc_start: 0.8974 (mmmt) cc_final: 0.8422 (tptp) REVERT: N 58 ILE cc_start: 0.9026 (mt) cc_final: 0.8757 (mt) REVERT: R 50 ILE cc_start: 0.8568 (OUTLIER) cc_final: 0.8312 (tt) REVERT: U 129 ARG cc_start: 0.7967 (tpt90) cc_final: 0.7717 (tpt90) REVERT: W 50 GLU cc_start: 0.8777 (mt-10) cc_final: 0.8310 (mm-30) REVERT: W 81 ASP cc_start: 0.7968 (t0) cc_final: 0.7738 (t0) REVERT: Z 88 TYR cc_start: 0.8359 (m-80) cc_final: 0.8105 (m-80) outliers start: 73 outliers final: 52 residues processed: 613 average time/residue: 0.2499 time to fit residues: 245.5589 Evaluate side-chains 620 residues out of total 2860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 561 time to evaluate : 1.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 TYR Chi-restraints excluded: chain A residue 428 ILE Chi-restraints excluded: chain A residue 443 GLN Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 763 THR Chi-restraints excluded: chain A residue 844 ASN Chi-restraints excluded: chain A residue 945 THR Chi-restraints excluded: chain A residue 1178 VAL Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 79 ILE Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 96 MET Chi-restraints excluded: chain C residue 170 ILE Chi-restraints excluded: chain C residue 198 TYR Chi-restraints excluded: chain C residue 214 PHE Chi-restraints excluded: chain C residue 323 CYS Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain E residue 225 VAL Chi-restraints excluded: chain E residue 235 ASP Chi-restraints excluded: chain E residue 268 HIS Chi-restraints excluded: chain F residue 290 THR Chi-restraints excluded: chain F residue 299 LEU Chi-restraints excluded: chain G residue 84 ILE Chi-restraints excluded: chain G residue 104 PHE Chi-restraints excluded: chain G residue 108 THR Chi-restraints excluded: chain G residue 113 ARG Chi-restraints excluded: chain G residue 184 PHE Chi-restraints excluded: chain H residue 73 GLU Chi-restraints excluded: chain H residue 117 VAL Chi-restraints excluded: chain I residue 88 HIS Chi-restraints excluded: chain J residue 213 GLN Chi-restraints excluded: chain J residue 217 VAL Chi-restraints excluded: chain J residue 291 LEU Chi-restraints excluded: chain J residue 362 ILE Chi-restraints excluded: chain L residue 66 ILE Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain M residue 79 ILE Chi-restraints excluded: chain O residue 101 THR Chi-restraints excluded: chain O residue 110 ASN Chi-restraints excluded: chain O residue 113 SER Chi-restraints excluded: chain O residue 114 VAL Chi-restraints excluded: chain Q residue 73 GLU Chi-restraints excluded: chain Q residue 77 ASP Chi-restraints excluded: chain Q residue 87 SER Chi-restraints excluded: chain R residue 50 ILE Chi-restraints excluded: chain R residue 96 THR Chi-restraints excluded: chain S residue 95 LYS Chi-restraints excluded: chain S residue 101 THR Chi-restraints excluded: chain S residue 110 ASN Chi-restraints excluded: chain S residue 114 VAL Chi-restraints excluded: chain T residue 45 VAL Chi-restraints excluded: chain U residue 87 SER Chi-restraints excluded: chain V residue 96 THR Chi-restraints excluded: chain W residue 60 LEU Chi-restraints excluded: chain W residue 130 ILE Chi-restraints excluded: chain Z residue 49 LEU Chi-restraints excluded: chain Z residue 60 VAL Chi-restraints excluded: chain Z residue 96 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 359 optimal weight: 50.0000 chunk 207 optimal weight: 0.9990 chunk 278 optimal weight: 0.6980 chunk 325 optimal weight: 10.0000 chunk 100 optimal weight: 0.0570 chunk 337 optimal weight: 20.0000 chunk 140 optimal weight: 9.9990 chunk 369 optimal weight: 5.9990 chunk 251 optimal weight: 0.5980 chunk 75 optimal weight: 2.9990 chunk 117 optimal weight: 0.2980 overall best weight: 0.5300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1254 HIS ** B 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 49 HIS ** C 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 68 GLN I 47 ASN J 196 GLN ** J 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 60 ASN O 73 ASN ** T 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 39 HIS ** Z 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 = 0.4112 r_free = 0.4112 target = 0.097997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.075276 restraints weight = 151479.664| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 3.16 r_work: 0.3081 rms_B_bonded: 4.58 restraints_weight: 0.5000 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.3683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 42040 Z= 0.144 Angle : 0.656 12.692 59578 Z= 0.362 Chirality : 0.045 0.389 6672 Planarity : 0.004 0.074 5302 Dihedral : 29.862 173.066 10801 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 13.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 2.38 % Allowed : 16.64 % Favored : 80.98 % 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: -0.32 (0.15), residues: 3181 helix: 0.48 (0.11), residues: 2103 sheet: -2.10 (0.54), residues: 83 loop : -1.39 (0.20), residues: 995 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 76 TYR 0.028 0.002 TYR D 80 PHE 0.058 0.002 PHE E 262 TRP 0.063 0.002 TRP A 912 HIS 0.005 0.001 HIS M 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.14 (42039) covalent geometry : angle 0.65626 / 0.36 (59578) hydrogen bonds : bond 0.06505 / 4.48 ( 2143) hydrogen bonds : angle 3.76952 / 2.62 ( 5579) metal coordination : bond 0.00248 / 0.13 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6362 Ramachandran restraints generated. 3181 Oldfield, 0 Emsley, 3181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6362 Ramachandran restraints generated. 3181 Oldfield, 0 Emsley, 3181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 643 residues out of total 2860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 575 time to evaluate : 1.238 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: A 280 PHE cc_start: 0.8087 (m-10) cc_final: 0.7744 (m-10) REVERT: A 945 THR cc_start: 0.8528 (OUTLIER) cc_final: 0.8125 (t) REVERT: B 104 GLN cc_start: 0.8358 (mp10) cc_final: 0.7942 (mp10) REVERT: C 51 LEU cc_start: 0.8937 (tp) cc_final: 0.8718 (tp) REVERT: C 121 SER cc_start: 0.8901 (t) cc_final: 0.8422 (p) REVERT: C 128 MET cc_start: 0.7929 (OUTLIER) cc_final: 0.7729 (mpp) REVERT: C 164 ASN cc_start: 0.7678 (t0) cc_final: 0.7252 (t0) REVERT: C 214 PHE cc_start: 0.8233 (OUTLIER) cc_final: 0.7832 (m-10) REVERT: D 68 GLU cc_start: 0.8561 (tp30) cc_final: 0.8356 (tm-30) REVERT: D 70 ILE cc_start: 0.9336 (mm) cc_final: 0.9073 (tp) REVERT: D 73 GLU cc_start: 0.8409 (mm-30) cc_final: 0.8054 (mm-30) REVERT: D 96 ARG cc_start: 0.8506 (mtm180) cc_final: 0.8296 (mtp180) REVERT: E 195 GLN cc_start: 0.5516 (OUTLIER) cc_final: 0.5124 (pp30) REVERT: E 201 TYR cc_start: 0.8543 (t80) cc_final: 0.8250 (t80) REVERT: E 214 MET cc_start: 0.6209 (mpp) cc_final: 0.5158 (mpp) REVERT: E 227 TYR cc_start: 0.8749 (m-10) cc_final: 0.8473 (m-10) REVERT: E 235 ASP cc_start: 0.8688 (OUTLIER) cc_final: 0.8374 (m-30) REVERT: E 246 LYS cc_start: 0.9042 (tppt) cc_final: 0.8811 (tppt) REVERT: E 270 LYS cc_start: 0.8922 (mmtm) cc_final: 0.8475 (mttp) REVERT: E 273 ASP cc_start: 0.8862 (t0) cc_final: 0.8649 (t0) REVERT: E 287 TYR cc_start: 0.8902 (m-80) cc_final: 0.8639 (m-80) REVERT: F 48 GLN cc_start: 0.8800 (mm110) cc_final: 0.8568 (mm110) REVERT: F 65 GLN cc_start: 0.9202 (mt0) cc_final: 0.8838 (mp10) REVERT: F 118 TYR cc_start: 0.9057 (m-80) cc_final: 0.8521 (m-10) REVERT: F 299 LEU cc_start: 0.8011 (OUTLIER) cc_final: 0.7718 (mt) REVERT: G 76 GLN cc_start: 0.8548 (mt0) cc_final: 0.7766 (pt0) REVERT: G 77 GLN cc_start: 0.8959 (mm110) cc_final: 0.8275 (mp10) REVERT: H 65 LEU cc_start: 0.7524 (tt) cc_final: 0.7171 (tt) REVERT: H 68 GLN cc_start: 0.8735 (OUTLIER) cc_final: 0.8185 (pt0) REVERT: H 70 LEU cc_start: 0.8166 (tp) cc_final: 0.7787 (tp) REVERT: H 90 MET cc_start: 0.8967 (mmt) cc_final: 0.8695 (mmm) REVERT: H 122 LYS cc_start: 0.8327 (ptmt) cc_final: 0.7545 (ptmt) REVERT: H 125 GLN cc_start: 0.8667 (mt0) cc_final: 0.8440 (mp10) REVERT: I 23 LEU cc_start: 0.8900 (tp) cc_final: 0.8553 (pp) REVERT: J 203 LYS cc_start: 0.8752 (ptmt) cc_final: 0.8457 (ptmt) REVERT: J 210 ARG cc_start: 0.9317 (mmt90) cc_final: 0.9087 (mmt90) REVERT: J 339 GLU cc_start: 0.9501 (tt0) cc_final: 0.8814 (tm-30) REVERT: J 342 ARG cc_start: 0.9161 (tmm-80) cc_final: 0.8581 (tmm-80) REVERT: J 343 GLN cc_start: 0.9337 (mm110) cc_final: 0.8608 (mm-40) REVERT: J 351 ARG cc_start: 0.9123 (mtt180) cc_final: 0.8744 (mtp85) REVERT: J 363 ARG cc_start: 0.8914 (tmt-80) cc_final: 0.8313 (tpm170) REVERT: J 370 ASN cc_start: 0.8805 (m-40) cc_final: 0.7897 (m-40) REVERT: L 25 ASN cc_start: 0.7342 (t0) cc_final: 0.7133 (t0) REVERT: L 35 ARG cc_start: 0.8853 (mtm110) cc_final: 0.8571 (ttm170) REVERT: L 78 ARG cc_start: 0.8518 (mtm-85) cc_final: 0.8118 (mtp85) REVERT: L 91 LYS cc_start: 0.9274 (tmtt) cc_final: 0.8784 (tmtt) REVERT: M 24 GLN cc_start: 0.8935 (mm-40) cc_final: 0.8464 (mm-40) REVERT: M 38 ASN cc_start: 0.7518 (t0) cc_final: 0.7093 (t0) REVERT: N 54 LYS cc_start: 0.8984 (mmmt) cc_final: 0.8504 (tptp) REVERT: N 56 MET cc_start: 0.8807 (tpt) cc_final: 0.8589 (tpt) REVERT: N 58 ILE cc_start: 0.9005 (mt) cc_final: 0.8735 (mt) REVERT: T 84 SER cc_start: 0.8488 (m) cc_final: 0.7660 (p) REVERT: W 50 GLU cc_start: 0.8762 (mt-10) cc_final: 0.8295 (mm-30) REVERT: W 81 ASP cc_start: 0.7928 (t0) cc_final: 0.7658 (t0) REVERT: W 105 GLU cc_start: 0.8249 (mm-30) cc_final: 0.8035 (mm-30) REVERT: Z 88 TYR cc_start: 0.8399 (m-80) cc_final: 0.8189 (m-80) outliers start: 68 outliers final: 50 residues processed: 603 average time/residue: 0.2566 time to fit residues: 248.2866 Evaluate side-chains 597 residues out of total 2860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 540 time to evaluate : 1.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 TYR Chi-restraints excluded: chain A residue 428 ILE Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 763 THR Chi-restraints excluded: chain A residue 902 ASP Chi-restraints excluded: chain A residue 945 THR Chi-restraints excluded: chain A residue 1178 VAL Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 79 ILE Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 96 MET Chi-restraints excluded: chain C residue 128 MET Chi-restraints excluded: chain C residue 198 TYR Chi-restraints excluded: chain C residue 214 PHE Chi-restraints excluded: chain E residue 195 GLN Chi-restraints excluded: chain E residue 225 VAL Chi-restraints excluded: chain E residue 235 ASP Chi-restraints excluded: chain E residue 268 HIS Chi-restraints excluded: chain F residue 61 GLN Chi-restraints excluded: chain F residue 299 LEU Chi-restraints excluded: chain G residue 84 ILE Chi-restraints excluded: chain G residue 104 PHE Chi-restraints excluded: chain G residue 113 ARG Chi-restraints excluded: chain G residue 174 SER Chi-restraints excluded: chain G residue 184 PHE Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 68 GLN Chi-restraints excluded: chain I residue 47 ASN Chi-restraints excluded: chain I residue 88 HIS Chi-restraints excluded: chain J residue 213 GLN Chi-restraints excluded: chain J residue 217 VAL Chi-restraints excluded: chain J residue 291 LEU Chi-restraints excluded: chain J residue 362 ILE Chi-restraints excluded: chain L residue 30 THR Chi-restraints excluded: chain L residue 62 LEU Chi-restraints excluded: chain L residue 66 ILE Chi-restraints excluded: chain L residue 87 VAL Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain M residue 30 VAL Chi-restraints excluded: chain M residue 34 LEU Chi-restraints excluded: chain M residue 79 ILE Chi-restraints excluded: chain O residue 110 ASN Chi-restraints excluded: chain O residue 113 SER Chi-restraints excluded: chain Q residue 77 ASP Chi-restraints excluded: chain Q residue 87 SER Chi-restraints excluded: chain R residue 96 THR Chi-restraints excluded: chain S residue 95 LYS Chi-restraints excluded: chain S residue 114 VAL Chi-restraints excluded: chain T residue 45 VAL Chi-restraints excluded: chain V residue 96 THR Chi-restraints excluded: chain W residue 60 LEU Chi-restraints excluded: chain W residue 130 ILE Chi-restraints excluded: chain Z residue 49 LEU Chi-restraints excluded: chain Z residue 60 VAL Chi-restraints excluded: chain Z residue 85 ASP Chi-restraints excluded: chain Z residue 96 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 111 optimal weight: 1.9990 chunk 124 optimal weight: 3.9990 chunk 92 optimal weight: 0.7980 chunk 175 optimal weight: 1.9990 chunk 133 optimal weight: 0.9990 chunk 42 optimal weight: 3.9990 chunk 66 optimal weight: 8.9990 chunk 167 optimal weight: 1.9990 chunk 225 optimal weight: 0.8980 chunk 98 optimal weight: 2.9990 chunk 183 optimal weight: 0.8980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1234 ASN ** B 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 87 HIS ** J 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 60 ASN Q 125 GLN ** Z 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 = 0.4101 r_free = 0.4101 target = 0.097416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.073035 restraints weight = 150693.368| |-----------------------------------------------------------------------------| r_work (start): 0.3449 rms_B_bonded: 2.22 r_work: 0.3070 rms_B_bonded: 4.40 restraints_weight: 0.5000 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.3797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 42040 Z= 0.167 Angle : 0.671 13.062 59578 Z= 0.368 Chirality : 0.045 0.389 6672 Planarity : 0.004 0.074 5302 Dihedral : 29.853 172.881 10798 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 13.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 2.34 % Allowed : 17.34 % Favored : 80.31 % 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: -0.25 (0.15), residues: 3181 helix: 0.52 (0.11), residues: 2107 sheet: -2.09 (0.54), residues: 83 loop : -1.35 (0.20), residues: 991 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG G 168 TYR 0.047 0.002 TYR N 37 PHE 0.037 0.002 PHE A 669 TRP 0.036 0.002 TRP A 912 HIS 0.006 0.001 HIS L 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.17 (42039) covalent geometry : angle 0.67098 / 0.37 (59578) hydrogen bonds : bond 0.06467 / 4.42 ( 2143) hydrogen bonds : angle 3.77960 / 2.62 ( 5579) metal coordination : bond 0.00415 / 0.22 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6362 Ramachandran restraints generated. 3181 Oldfield, 0 Emsley, 3181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6362 Ramachandran restraints generated. 3181 Oldfield, 0 Emsley, 3181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 632 residues out of total 2860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 565 time to evaluate : 1.200 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: A 280 PHE cc_start: 0.8112 (m-10) cc_final: 0.7762 (m-10) REVERT: A 306 MET cc_start: 0.8437 (ppp) cc_final: 0.8103 (ppp) REVERT: A 945 THR cc_start: 0.8588 (OUTLIER) cc_final: 0.8188 (t) REVERT: B 104 GLN cc_start: 0.8397 (mp10) cc_final: 0.7954 (mp10) REVERT: C 116 LEU cc_start: 0.9322 (OUTLIER) cc_final: 0.9013 (tm) REVERT: C 121 SER cc_start: 0.8960 (t) cc_final: 0.8440 (p) REVERT: C 164 ASN cc_start: 0.7825 (t0) cc_final: 0.7477 (t0) REVERT: C 214 PHE cc_start: 0.8276 (OUTLIER) cc_final: 0.7930 (m-10) REVERT: D 52 SER cc_start: 0.8916 (t) cc_final: 0.8386 (p) REVERT: D 70 ILE cc_start: 0.9358 (mm) cc_final: 0.9089 (tp) REVERT: D 73 GLU cc_start: 0.8376 (mm-30) cc_final: 0.8009 (mm-30) REVERT: D 118 TYR cc_start: 0.7917 (t80) cc_final: 0.7615 (t80) REVERT: E 195 GLN cc_start: 0.5464 (OUTLIER) cc_final: 0.5069 (pp30) REVERT: E 201 TYR cc_start: 0.8458 (t80) cc_final: 0.8167 (t80) REVERT: E 214 MET cc_start: 0.6172 (mpp) cc_final: 0.5131 (mpp) REVERT: E 270 LYS cc_start: 0.8910 (mmtm) cc_final: 0.8598 (mttp) REVERT: E 273 ASP cc_start: 0.8883 (t0) cc_final: 0.8672 (t0) REVERT: E 287 TYR cc_start: 0.8878 (m-80) cc_final: 0.8510 (m-80) REVERT: F 48 GLN cc_start: 0.8881 (mm110) cc_final: 0.8672 (mm110) REVERT: F 65 GLN cc_start: 0.9268 (mt0) cc_final: 0.8883 (mp10) REVERT: F 118 TYR cc_start: 0.9071 (m-80) cc_final: 0.8740 (m-10) REVERT: G 76 GLN cc_start: 0.8599 (mt0) cc_final: 0.7828 (pt0) REVERT: G 77 GLN cc_start: 0.8948 (mm110) cc_final: 0.8244 (mp10) REVERT: G 141 LYS cc_start: 0.8480 (mptt) cc_final: 0.8052 (mptt) REVERT: H 68 GLN cc_start: 0.8770 (mt0) cc_final: 0.8509 (mm-40) REVERT: H 122 LYS cc_start: 0.8348 (ptmt) cc_final: 0.7385 (ptmt) REVERT: H 125 GLN cc_start: 0.8693 (mt0) cc_final: 0.8426 (mp10) REVERT: I 23 LEU cc_start: 0.8885 (tp) cc_final: 0.8534 (pp) REVERT: I 84 GLU cc_start: 0.9231 (tp30) cc_final: 0.8989 (tp30) REVERT: J 203 LYS cc_start: 0.8761 (ptmt) cc_final: 0.8473 (ptmt) REVERT: J 206 MET cc_start: 0.8668 (ptp) cc_final: 0.8141 (ptp) REVERT: J 228 GLU cc_start: 0.7020 (pt0) cc_final: 0.6705 (mt-10) REVERT: J 339 GLU cc_start: 0.9490 (tt0) cc_final: 0.8805 (tm-30) REVERT: J 342 ARG cc_start: 0.9151 (tmm-80) cc_final: 0.8576 (tmm-80) REVERT: J 343 GLN cc_start: 0.9321 (mm110) cc_final: 0.8588 (mm-40) REVERT: J 351 ARG cc_start: 0.9133 (mtt180) cc_final: 0.8564 (mtp85) REVERT: J 363 ARG cc_start: 0.8937 (tmt-80) cc_final: 0.8338 (tpm170) REVERT: J 370 ASN cc_start: 0.8789 (m-40) cc_final: 0.7891 (m-40) REVERT: L 78 ARG cc_start: 0.8587 (mtm-85) cc_final: 0.8156 (mtp85) REVERT: M 38 ASN cc_start: 0.7601 (t0) cc_final: 0.7181 (t0) REVERT: N 54 LYS cc_start: 0.9049 (mmmt) cc_final: 0.8686 (mmmt) REVERT: N 58 ILE cc_start: 0.8993 (mt) cc_final: 0.8717 (mt) REVERT: Q 42 ARG cc_start: 0.8628 (mtt-85) cc_final: 0.8423 (mmt-90) REVERT: R 84 MET cc_start: 0.8720 (mmm) cc_final: 0.8473 (tmm) REVERT: W 50 GLU cc_start: 0.8830 (mt-10) cc_final: 0.8304 (mm-30) REVERT: W 81 ASP cc_start: 0.7999 (t0) cc_final: 0.7780 (t0) REVERT: Z 88 TYR cc_start: 0.8438 (m-80) cc_final: 0.8237 (m-80) outliers start: 67 outliers final: 53 residues processed: 592 average time/residue: 0.2512 time to fit residues: 237.8754 Evaluate side-chains 606 residues out of total 2860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 549 time to evaluate : 1.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 TYR Chi-restraints excluded: chain A residue 428 ILE Chi-restraints excluded: chain A residue 763 THR Chi-restraints excluded: chain A residue 902 ASP Chi-restraints excluded: chain A residue 945 THR Chi-restraints excluded: chain A residue 1178 VAL Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 79 ILE Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 111 ILE Chi-restraints excluded: chain C residue 96 MET Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 198 TYR Chi-restraints excluded: chain C residue 204 MET Chi-restraints excluded: chain C residue 214 PHE Chi-restraints excluded: chain D residue 58 ILE Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain E residue 195 GLN Chi-restraints excluded: chain E residue 225 VAL Chi-restraints excluded: chain E residue 268 HIS Chi-restraints excluded: chain F residue 299 LEU Chi-restraints excluded: chain G residue 84 ILE Chi-restraints excluded: chain G residue 104 PHE Chi-restraints excluded: chain G residue 113 ARG Chi-restraints excluded: chain G residue 184 PHE Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 73 GLU Chi-restraints excluded: chain I residue 17 VAL Chi-restraints excluded: chain I residue 88 HIS Chi-restraints excluded: chain J residue 213 GLN Chi-restraints excluded: chain J residue 217 VAL Chi-restraints excluded: chain J residue 291 LEU Chi-restraints excluded: chain J residue 362 ILE Chi-restraints excluded: chain L residue 66 ILE Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain M residue 30 VAL Chi-restraints excluded: chain M residue 34 LEU Chi-restraints excluded: chain M residue 79 ILE Chi-restraints excluded: chain N residue 42 LEU Chi-restraints excluded: chain O residue 101 THR Chi-restraints excluded: chain O residue 110 ASN Chi-restraints excluded: chain O residue 113 SER Chi-restraints excluded: chain O residue 114 VAL Chi-restraints excluded: chain Q residue 77 ASP Chi-restraints excluded: chain Q residue 87 SER Chi-restraints excluded: chain R residue 96 THR Chi-restraints excluded: chain S residue 95 LYS Chi-restraints excluded: chain S residue 101 THR Chi-restraints excluded: chain S residue 113 SER Chi-restraints excluded: chain S residue 114 VAL Chi-restraints excluded: chain T residue 45 VAL Chi-restraints excluded: chain V residue 96 THR Chi-restraints excluded: chain W residue 60 LEU Chi-restraints excluded: chain W residue 130 ILE Chi-restraints excluded: chain Z residue 49 LEU Chi-restraints excluded: chain Z residue 60 VAL Chi-restraints excluded: chain Z residue 96 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 225 optimal weight: 0.5980 chunk 242 optimal weight: 0.8980 chunk 324 optimal weight: 10.0000 chunk 188 optimal weight: 6.9990 chunk 274 optimal weight: 0.9990 chunk 263 optimal weight: 0.6980 chunk 311 optimal weight: 20.0000 chunk 207 optimal weight: 0.8980 chunk 19 optimal weight: 6.9990 chunk 221 optimal weight: 0.3980 chunk 270 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 89 ASN ** C 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 375 ASN ** E 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 290 ASN ** H 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 108 ASN ** J 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 60 ASN ** T 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.097857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.075257 restraints weight = 151974.790| |-----------------------------------------------------------------------------| r_work (start): 0.3500 rms_B_bonded: 3.26 r_work: 0.3062 rms_B_bonded: 4.68 restraints_weight: 0.5000 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.3910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 42040 Z= 0.149 Angle : 0.670 12.038 59578 Z= 0.369 Chirality : 0.045 0.381 6672 Planarity : 0.004 0.074 5302 Dihedral : 29.849 173.035 10798 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 13.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 2.03 % Allowed : 18.22 % Favored : 79.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.20 (0.15), residues: 3181 helix: 0.55 (0.11), residues: 2110 sheet: -2.07 (0.55), residues: 83 loop : -1.32 (0.20), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG G 168 TYR 0.041 0.002 TYR N 37 PHE 0.037 0.002 PHE N 67 TRP 0.038 0.002 TRP A 912 HIS 0.007 0.001 HIS L 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.15 (42039) covalent geometry : angle 0.67025 / 0.37 (59578) hydrogen bonds : bond 0.06441 / 4.40 ( 2143) hydrogen bonds : angle 3.77815 / 2.63 ( 5579) metal coordination : bond 0.00254 / 0.13 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6362 Ramachandran restraints generated. 3181 Oldfield, 0 Emsley, 3181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6362 Ramachandran restraints generated. 3181 Oldfield, 0 Emsley, 3181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 624 residues out of total 2860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 566 time to evaluate : 0.880 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: A 280 PHE cc_start: 0.8151 (m-10) cc_final: 0.7782 (m-10) REVERT: A 704 GLU cc_start: 0.9288 (tt0) cc_final: 0.8570 (tm-30) REVERT: A 945 THR cc_start: 0.8597 (OUTLIER) cc_final: 0.8195 (t) REVERT: A 1294 MET cc_start: 0.7845 (ptp) cc_final: 0.7526 (ptp) REVERT: B 75 LYS cc_start: 0.8699 (mmmt) cc_final: 0.8324 (mmtt) REVERT: B 104 GLN cc_start: 0.8416 (mp10) cc_final: 0.7994 (mp10) REVERT: C 116 LEU cc_start: 0.9304 (OUTLIER) cc_final: 0.9007 (tm) REVERT: C 121 SER cc_start: 0.8982 (t) cc_final: 0.8482 (p) REVERT: C 164 ASN cc_start: 0.7734 (t0) cc_final: 0.7424 (t0) REVERT: C 214 PHE cc_start: 0.8200 (OUTLIER) cc_final: 0.7797 (m-10) REVERT: D 52 SER cc_start: 0.8907 (t) cc_final: 0.8394 (p) REVERT: D 70 ILE cc_start: 0.9368 (mm) cc_final: 0.9153 (tp) REVERT: D 73 GLU cc_start: 0.8366 (mm-30) cc_final: 0.7992 (mm-30) REVERT: D 89 ARG cc_start: 0.8289 (ttm-80) cc_final: 0.8053 (ttm-80) REVERT: D 106 HIS cc_start: 0.7164 (OUTLIER) cc_final: 0.6955 (m170) REVERT: D 118 TYR cc_start: 0.7869 (t80) cc_final: 0.7594 (t80) REVERT: E 195 GLN cc_start: 0.5490 (OUTLIER) cc_final: 0.5128 (pp30) REVERT: E 201 TYR cc_start: 0.8599 (t80) cc_final: 0.8322 (t80) REVERT: E 214 MET cc_start: 0.6162 (mpp) cc_final: 0.5174 (mpp) REVERT: E 227 TYR cc_start: 0.8848 (m-80) cc_final: 0.8612 (m-80) REVERT: E 270 LYS cc_start: 0.8950 (mmtm) cc_final: 0.8642 (mttp) REVERT: E 273 ASP cc_start: 0.8880 (t0) cc_final: 0.8677 (t0) REVERT: F 48 GLN cc_start: 0.8934 (mm110) cc_final: 0.8695 (mm110) REVERT: F 65 GLN cc_start: 0.9267 (mt0) cc_final: 0.8878 (mp10) REVERT: F 118 TYR cc_start: 0.9098 (m-80) cc_final: 0.8768 (m-10) REVERT: G 76 GLN cc_start: 0.8614 (mt0) cc_final: 0.8115 (pt0) REVERT: G 77 GLN cc_start: 0.8944 (mm110) cc_final: 0.8354 (mp10) REVERT: G 109 ASP cc_start: 0.8224 (t0) cc_final: 0.7714 (t0) REVERT: H 68 GLN cc_start: 0.8747 (mt0) cc_final: 0.8370 (mm-40) REVERT: H 122 LYS cc_start: 0.8323 (ptmt) cc_final: 0.7488 (ptmt) REVERT: H 125 GLN cc_start: 0.8712 (mt0) cc_final: 0.8429 (mp10) REVERT: I 23 LEU cc_start: 0.8857 (tp) cc_final: 0.8518 (pp) REVERT: J 203 LYS cc_start: 0.8807 (ptmt) cc_final: 0.8530 (ptmt) REVERT: J 339 GLU cc_start: 0.9504 (tt0) cc_final: 0.8814 (tm-30) REVERT: J 342 ARG cc_start: 0.9129 (tmm-80) cc_final: 0.8558 (tmm-80) REVERT: J 343 GLN cc_start: 0.9338 (mm110) cc_final: 0.8615 (mm-40) REVERT: J 351 ARG cc_start: 0.9123 (mtt180) cc_final: 0.8418 (mtp85) REVERT: J 363 ARG cc_start: 0.8950 (tmt-80) cc_final: 0.8318 (tpm170) REVERT: J 370 ASN cc_start: 0.8784 (m-40) cc_final: 0.7835 (m-40) REVERT: L 78 ARG cc_start: 0.8602 (mtm-85) cc_final: 0.8103 (mtp85) REVERT: M 24 GLN cc_start: 0.8972 (mm-40) cc_final: 0.8449 (mm-40) REVERT: M 38 ASN cc_start: 0.7682 (t0) cc_final: 0.7282 (t0) REVERT: N 54 LYS cc_start: 0.9103 (mmmt) cc_final: 0.8838 (mmmt) REVERT: P 48 ASP cc_start: 0.8055 (p0) cc_final: 0.7803 (p0) REVERT: Q 42 ARG cc_start: 0.8611 (mtt-85) cc_final: 0.8408 (mmt-90) REVERT: U 41 TYR cc_start: 0.9257 (m-80) cc_final: 0.8950 (m-80) REVERT: V 22 LEU cc_start: 0.6289 (mt) cc_final: 0.6047 (tp) REVERT: W 50 GLU cc_start: 0.8784 (mt-10) cc_final: 0.8295 (mm-30) REVERT: W 81 ASP cc_start: 0.7905 (t0) cc_final: 0.7688 (t0) REVERT: Z 88 TYR cc_start: 0.8480 (m-80) cc_final: 0.8252 (m-80) outliers start: 58 outliers final: 49 residues processed: 592 average time/residue: 0.2496 time to fit residues: 236.5661 Evaluate side-chains 596 residues out of total 2860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 542 time to evaluate : 1.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 TYR Chi-restraints excluded: chain A residue 428 ILE Chi-restraints excluded: chain A residue 763 THR Chi-restraints excluded: chain A residue 902 ASP Chi-restraints excluded: chain A residue 945 THR Chi-restraints excluded: chain A residue 1178 VAL Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 79 ILE Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 111 ILE Chi-restraints excluded: chain C residue 96 MET Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 198 TYR Chi-restraints excluded: chain C residue 204 MET Chi-restraints excluded: chain C residue 214 PHE Chi-restraints excluded: chain D residue 58 ILE Chi-restraints excluded: chain D residue 80 TYR Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 106 HIS Chi-restraints excluded: chain E residue 195 GLN Chi-restraints excluded: chain E residue 225 VAL Chi-restraints excluded: chain E residue 268 HIS Chi-restraints excluded: chain F residue 61 GLN Chi-restraints excluded: chain F residue 290 THR Chi-restraints excluded: chain F residue 299 LEU Chi-restraints excluded: chain G residue 104 PHE Chi-restraints excluded: chain G residue 174 SER Chi-restraints excluded: chain G residue 184 PHE Chi-restraints excluded: chain H residue 73 GLU Chi-restraints excluded: chain I residue 17 VAL Chi-restraints excluded: chain I residue 88 HIS Chi-restraints excluded: chain J residue 213 GLN Chi-restraints excluded: chain J residue 217 VAL Chi-restraints excluded: chain J residue 291 LEU Chi-restraints excluded: chain L residue 66 ILE Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain M residue 30 VAL Chi-restraints excluded: chain M residue 79 ILE Chi-restraints excluded: chain O residue 101 THR Chi-restraints excluded: chain O residue 113 SER Chi-restraints excluded: chain O residue 114 VAL Chi-restraints excluded: chain Q residue 77 ASP Chi-restraints excluded: chain Q residue 87 SER Chi-restraints excluded: chain R residue 96 THR Chi-restraints excluded: chain S residue 113 SER Chi-restraints excluded: chain S residue 114 VAL Chi-restraints excluded: chain T residue 45 VAL Chi-restraints excluded: chain U residue 87 SER Chi-restraints excluded: chain V residue 96 THR Chi-restraints excluded: chain W residue 60 LEU Chi-restraints excluded: chain W residue 130 ILE Chi-restraints excluded: chain Z residue 49 LEU Chi-restraints excluded: chain Z residue 60 VAL Chi-restraints excluded: chain Z residue 96 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 227 optimal weight: 0.6980 chunk 17 optimal weight: 8.9990 chunk 117 optimal weight: 0.9980 chunk 332 optimal weight: 30.0000 chunk 228 optimal weight: 0.5980 chunk 88 optimal weight: 1.9990 chunk 36 optimal weight: 0.7980 chunk 156 optimal weight: 1.9990 chunk 18 optimal weight: 4.9990 chunk 216 optimal weight: 10.0000 chunk 272 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 89 ASN ** C 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 60 ASN Q 39 HIS ** T 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.097772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.073046 restraints weight = 151081.249| |-----------------------------------------------------------------------------| r_work (start): 0.3441 rms_B_bonded: 1.95 r_work: 0.3103 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.3998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 42040 Z= 0.153 Angle : 0.685 12.871 59578 Z= 0.374 Chirality : 0.045 0.370 6672 Planarity : 0.004 0.075 5302 Dihedral : 29.835 172.941 10798 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 14.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 1.96 % Allowed : 18.74 % Favored : 79.30 % 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: -0.15 (0.15), residues: 3181 helix: 0.58 (0.11), residues: 2111 sheet: -2.01 (0.55), residues: 83 loop : -1.27 (0.20), residues: 987 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 168 TYR 0.030 0.002 TYR N 37 PHE 0.076 0.002 PHE E 262 TRP 0.034 0.002 TRP A 912 HIS 0.007 0.001 HIS L 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.15 (42039) covalent geometry : angle 0.68505 / 0.37 (59578) hydrogen bonds : bond 0.06463 / 4.39 ( 2143) hydrogen bonds : angle 3.77917 / 2.62 ( 5579) metal coordination : bond 0.00275 / 0.14 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6362 Ramachandran restraints generated. 3181 Oldfield, 0 Emsley, 3181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6362 Ramachandran restraints generated. 3181 Oldfield, 0 Emsley, 3181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 612 residues out of total 2860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 556 time to evaluate : 1.237 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 280 PHE cc_start: 0.7993 (m-10) cc_final: 0.7662 (m-10) REVERT: A 306 MET cc_start: 0.8049 (ppp) cc_final: 0.7795 (ppp) REVERT: A 704 GLU cc_start: 0.9239 (tt0) cc_final: 0.8542 (tm-30) REVERT: A 945 THR cc_start: 0.8517 (OUTLIER) cc_final: 0.8246 (t) REVERT: A 996 ILE cc_start: 0.8570 (mm) cc_final: 0.8330 (pt) REVERT: A 1177 THR cc_start: 0.7292 (m) cc_final: 0.6982 (t) REVERT: A 1294 MET cc_start: 0.7761 (ptp) cc_final: 0.7451 (ptp) REVERT: B 75 LYS cc_start: 0.8643 (mmmt) cc_final: 0.8299 (mmtt) REVERT: B 104 GLN cc_start: 0.8398 (mp10) cc_final: 0.7999 (mp10) REVERT: C 116 LEU cc_start: 0.9281 (OUTLIER) cc_final: 0.8983 (tm) REVERT: C 121 SER cc_start: 0.8953 (t) cc_final: 0.8441 (p) REVERT: C 164 ASN cc_start: 0.7655 (t0) cc_final: 0.7350 (t0) REVERT: C 214 PHE cc_start: 0.8143 (OUTLIER) cc_final: 0.7826 (m-10) REVERT: D 52 SER cc_start: 0.8868 (t) cc_final: 0.8380 (p) REVERT: D 70 ILE cc_start: 0.9351 (mm) cc_final: 0.9149 (tp) REVERT: D 73 GLU cc_start: 0.8256 (mm-30) cc_final: 0.7896 (mm-30) REVERT: D 89 ARG cc_start: 0.8260 (ttm-80) cc_final: 0.8029 (ttm-80) REVERT: D 118 TYR cc_start: 0.7711 (t80) cc_final: 0.7475 (t80) REVERT: E 195 GLN cc_start: 0.5416 (OUTLIER) cc_final: 0.5021 (pp30) REVERT: E 201 TYR cc_start: 0.8473 (t80) cc_final: 0.8191 (t80) REVERT: E 214 MET cc_start: 0.6170 (mpp) cc_final: 0.5180 (mpp) REVERT: E 227 TYR cc_start: 0.8755 (m-80) cc_final: 0.8545 (m-80) REVERT: E 270 LYS cc_start: 0.8903 (mmtm) cc_final: 0.8562 (mttp) REVERT: F 48 GLN cc_start: 0.8987 (mm110) cc_final: 0.8723 (mm110) REVERT: F 65 GLN cc_start: 0.9221 (mt0) cc_final: 0.8905 (mp10) REVERT: F 118 TYR cc_start: 0.9018 (m-80) cc_final: 0.8666 (m-10) REVERT: G 76 GLN cc_start: 0.8495 (mt0) cc_final: 0.7697 (pt0) REVERT: G 77 GLN cc_start: 0.8969 (mm110) cc_final: 0.8283 (mp10) REVERT: H 68 GLN cc_start: 0.8651 (mt0) cc_final: 0.8257 (pt0) REVERT: H 122 LYS cc_start: 0.8315 (ptmt) cc_final: 0.7331 (ptmt) REVERT: H 125 GLN cc_start: 0.8632 (mt0) cc_final: 0.8386 (mp10) REVERT: I 23 LEU cc_start: 0.8863 (tp) cc_final: 0.8506 (pp) REVERT: J 203 LYS cc_start: 0.8766 (ptmt) cc_final: 0.8556 (ptmt) REVERT: J 339 GLU cc_start: 0.9473 (tt0) cc_final: 0.8789 (tm-30) REVERT: J 342 ARG cc_start: 0.9143 (tmm-80) cc_final: 0.8546 (tmm-80) REVERT: J 343 GLN cc_start: 0.9308 (mm110) cc_final: 0.8560 (mm-40) REVERT: J 351 ARG cc_start: 0.9087 (mtt180) cc_final: 0.8446 (mtp85) REVERT: J 363 ARG cc_start: 0.8842 (tmt-80) cc_final: 0.8532 (tmt-80) REVERT: J 370 ASN cc_start: 0.8786 (m-40) cc_final: 0.7995 (m-40) REVERT: L 78 ARG cc_start: 0.8525 (mtm-85) cc_final: 0.8100 (mtp85) REVERT: M 24 GLN cc_start: 0.8924 (mm-40) cc_final: 0.8425 (mm-40) REVERT: M 38 ASN cc_start: 0.7693 (t0) cc_final: 0.7282 (t0) REVERT: M 84 GLN cc_start: 0.8402 (tp-100) cc_final: 0.8139 (tp-100) REVERT: P 48 ASP cc_start: 0.7950 (p0) cc_final: 0.7709 (p0) REVERT: U 41 TYR cc_start: 0.9233 (m-80) cc_final: 0.8932 (m-80) REVERT: V 22 LEU cc_start: 0.6396 (mt) cc_final: 0.6171 (tp) REVERT: W 50 GLU cc_start: 0.8729 (mt-10) cc_final: 0.8261 (mm-30) REVERT: W 81 ASP cc_start: 0.7811 (t0) cc_final: 0.7606 (t0) outliers start: 56 outliers final: 51 residues processed: 579 average time/residue: 0.2611 time to fit residues: 242.4335 Evaluate side-chains 599 residues out of total 2860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 544 time to evaluate : 1.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 TYR Chi-restraints excluded: chain A residue 428 ILE Chi-restraints excluded: chain A residue 763 THR Chi-restraints excluded: chain A residue 902 ASP Chi-restraints excluded: chain A residue 945 THR Chi-restraints excluded: chain A residue 1178 VAL Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 79 ILE Chi-restraints excluded: chain B residue 95 LYS Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 111 ILE Chi-restraints excluded: chain C residue 96 MET Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 198 TYR Chi-restraints excluded: chain C residue 204 MET Chi-restraints excluded: chain C residue 214 PHE Chi-restraints excluded: chain D residue 58 ILE Chi-restraints excluded: chain D residue 80 TYR Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain E residue 195 GLN Chi-restraints excluded: chain E residue 225 VAL Chi-restraints excluded: chain E residue 268 HIS Chi-restraints excluded: chain F residue 61 GLN Chi-restraints excluded: chain F residue 290 THR Chi-restraints excluded: chain F residue 299 LEU Chi-restraints excluded: chain G residue 104 PHE Chi-restraints excluded: chain G residue 113 ARG Chi-restraints excluded: chain G residue 174 SER Chi-restraints excluded: chain H residue 73 GLU Chi-restraints excluded: chain I residue 17 VAL Chi-restraints excluded: chain I residue 88 HIS Chi-restraints excluded: chain J residue 213 GLN Chi-restraints excluded: chain J residue 217 VAL Chi-restraints excluded: chain J residue 291 LEU Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain M residue 30 VAL Chi-restraints excluded: chain M residue 79 ILE Chi-restraints excluded: chain O residue 101 THR Chi-restraints excluded: chain O residue 113 SER Chi-restraints excluded: chain O residue 114 VAL Chi-restraints excluded: chain Q residue 77 ASP Chi-restraints excluded: chain Q residue 87 SER Chi-restraints excluded: chain R residue 96 THR Chi-restraints excluded: chain S residue 101 THR Chi-restraints excluded: chain S residue 113 SER Chi-restraints excluded: chain S residue 114 VAL Chi-restraints excluded: chain T residue 45 VAL Chi-restraints excluded: chain U residue 87 SER Chi-restraints excluded: chain V residue 96 THR Chi-restraints excluded: chain W residue 60 LEU Chi-restraints excluded: chain W residue 130 ILE Chi-restraints excluded: chain Z residue 49 LEU Chi-restraints excluded: chain Z residue 60 VAL Chi-restraints excluded: chain Z residue 85 ASP Chi-restraints excluded: chain Z residue 96 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 101 optimal weight: 0.9980 chunk 142 optimal weight: 1.9990 chunk 140 optimal weight: 9.9990 chunk 326 optimal weight: 50.0000 chunk 259 optimal weight: 0.9980 chunk 163 optimal weight: 6.9990 chunk 166 optimal weight: 0.4980 chunk 25 optimal weight: 1.9990 chunk 195 optimal weight: 9.9990 chunk 42 optimal weight: 4.9990 chunk 340 optimal weight: 20.0000 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 106 HIS ** E 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 68 GLN ** J 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 60 ASN O 104 GLN Q 125 GLN ** T 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.097411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.071571 restraints weight = 150310.879| |-----------------------------------------------------------------------------| r_work (start): 0.3391 rms_B_bonded: 1.80 r_work: 0.3116 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.4101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 42040 Z= 0.178 Angle : 0.707 14.095 59578 Z= 0.384 Chirality : 0.046 0.377 6672 Planarity : 0.004 0.074 5302 Dihedral : 29.881 173.033 10798 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 14.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 1.99 % Allowed : 19.16 % Favored : 78.85 % 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: -0.17 (0.15), residues: 3181 helix: 0.57 (0.11), residues: 2109 sheet: -1.95 (0.55), residues: 83 loop : -1.29 (0.20), residues: 989 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 96 TYR 0.061 0.002 TYR Z 88 PHE 0.053 0.002 PHE E 262 TRP 0.036 0.002 TRP A 912 HIS 0.009 0.001 HIS G 169 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.18 (42039) covalent geometry : angle 0.70652 / 0.38 (59578) hydrogen bonds : bond 0.06520 / 4.38 ( 2143) hydrogen bonds : angle 3.84193 / 2.67 ( 5579) metal coordination : bond 0.00389 / 0.20 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11643.45 seconds wall clock time: 199 minutes 34.66 seconds (11974.66 seconds total)