Starting phenix.real_space_refine on Sat Aug 8 12:17:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8r2m_18851/08_2026/8r2m_18851.cif Found real_map, /net/cci-nas-00/data/ceres_data/8r2m_18851/08_2026/8r2m_18851.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.44 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8r2m_18851/08_2026/8r2m_18851.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8r2m_18851/08_2026/8r2m_18851.map" model { file = "/net/cci-nas-00/data/ceres_data/8r2m_18851/08_2026/8r2m_18851.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8r2m_18851/08_2026/8r2m_18851.cif" } resolution = 3.44 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= 0.025 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: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 53 5.49 5 Mg 1 5.21 5 S 94 5.16 5 C 17539 2.51 5 N 5036 2.21 5 O 5551 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 45 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: 28276 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 1716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1716 Classifications: {'peptide': 226} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 211} Chain: "B" Number of atoms: 1808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1808 Classifications: {'peptide': 239} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 222} Chain: "C" Number of atoms: 8602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1110, 8602 Classifications: {'peptide': 1110} Link IDs: {'PCIS': 1, 'PTRANS': 58, 'TRANS': 1050} Chain: "D" Number of atoms: 10010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1281, 10010 Classifications: {'peptide': 1281} Link IDs: {'PCIS': 2, 'PTRANS': 55, 'TRANS': 1223} Chain: "F" Number of atoms: 2432 Number of conformers: 1 Conformer: "" Number of residues, atoms: 303, 2432 Classifications: {'peptide': 303} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 294} Chain: "H" Number of atoms: 1163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1163 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 4, 'TRANS': 138} Chain: "J" Number of atoms: 842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 842 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 7, 'TRANS': 96} Chain: "O" Number of atoms: 638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 638 Classifications: {'DNA': 31} Link IDs: {'rna3p': 30} Chain: "P" Number of atoms: 446 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 446 Classifications: {'DNA': 22} Link IDs: {'rna3p': 21} Chain: "E" Number of atoms: 616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 616 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 71} Chain breaks: 1 Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 19173 SG CYS D 890 33.275 59.709 67.770 1.00 32.01 S ATOM 19735 SG CYS D 967 36.335 61.791 68.674 1.00 29.59 S ATOM 19777 SG CYS D 974 33.828 60.833 71.242 1.00 24.73 S ATOM 19796 SG CYS D 977 35.997 58.220 69.894 1.00 26.92 S ATOM 12600 SG CYS D 60 37.887 124.394 82.559 1.00 48.71 S ATOM 12618 SG CYS D 62 38.767 128.015 83.308 1.00 49.53 S ATOM 12727 SG CYS D 75 36.145 127.075 80.767 1.00 50.37 S ATOM 12753 SG CYS D 78 39.765 126.193 80.023 1.00 46.26 S Time building chain proxies: 5.81, per 1000 atoms: 0.21 Number of scatterers: 28276 At special positions: 0 Unit cell: (127.541, 168.387, 161.718, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 94 16.00 P 53 15.00 Mg 1 11.99 O 5551 8.00 N 5036 7.00 C 17539 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.31 Conformation dependent library (CDL) restraints added in 997.3 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D2001 " pdb="ZN ZN D2001 " - pdb=" SG CYS D 974 " pdb="ZN ZN D2001 " - pdb=" SG CYS D 977 " pdb="ZN ZN D2001 " - pdb=" SG CYS D 890 " pdb="ZN ZN D2001 " - pdb=" SG CYS D 967 " pdb=" ZN D2002 " pdb="ZN ZN D2002 " - pdb=" SG CYS D 60 " pdb="ZN ZN D2002 " - pdb=" SG CYS D 75 " pdb="ZN ZN D2002 " - pdb=" SG CYS D 78 " pdb="ZN ZN D2002 " - pdb=" SG CYS D 62 " Number of angles added : 12 6932 Ramachandran restraints generated. 3466 Oldfield, 0 Emsley, 3466 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6420 Finding SS restraints... Secondary structure from input PDB file: 128 helices and 46 sheets defined 43.4% alpha, 17.0% beta 22 base pairs and 43 stacking pairs defined. Time for finding SS restraints: 3.32 Creating SS restraints... Processing helix chain 'A' and resid 30 through 45 Processing helix chain 'A' and resid 72 through 81 Processing helix chain 'A' and resid 108 through 110 No H-bonds generated for 'chain 'A' and resid 108 through 110' Processing helix chain 'A' and resid 151 through 156 removed outlier: 3.716A pdb=" N SER A 155 " --> pdb=" O GLN A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 224 removed outlier: 4.696A pdb=" N LEU A 221 " --> pdb=" O GLU A 217 " (cutoff:3.500A) removed outlier: 5.056A pdb=" N ALA A 222 " --> pdb=" O LEU A 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 46 removed outlier: 3.729A pdb=" N THR B 33 " --> pdb=" O GLY B 29 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ASN B 36 " --> pdb=" O TYR B 32 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N SER B 37 " --> pdb=" O THR B 33 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N ILE B 46 " --> pdb=" O LEU B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 81 Processing helix chain 'B' and resid 108 through 110 No H-bonds generated for 'chain 'B' and resid 108 through 110' Processing helix chain 'B' and resid 203 through 224 removed outlier: 3.777A pdb=" N LEU B 221 " --> pdb=" O GLU B 217 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N ALA B 222 " --> pdb=" O LEU B 218 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 57 removed outlier: 3.966A pdb=" N SER C 51 " --> pdb=" O VAL C 47 " (cutoff:3.500A) Processing helix chain 'C' and resid 58 through 68 Processing helix chain 'C' and resid 75 through 85 Processing helix chain 'C' and resid 109 through 117 Processing helix chain 'C' and resid 225 through 232 Processing helix chain 'C' and resid 235 through 244 Processing helix chain 'C' and resid 246 through 256 removed outlier: 3.733A pdb=" N MET C 250 " --> pdb=" O SER C 246 " (cutoff:3.500A) Processing helix chain 'C' and resid 260 through 273 removed outlier: 3.777A pdb=" N ALA C 264 " --> pdb=" O GLY C 260 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU C 265 " --> pdb=" O THR C 261 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N ARG C 270 " --> pdb=" O LEU C 266 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N LYS C 271 " --> pdb=" O ASP C 267 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N LEU C 272 " --> pdb=" O ILE C 268 " (cutoff:3.500A) Processing helix chain 'C' and resid 279 through 291 removed outlier: 4.045A pdb=" N LEU C 287 " --> pdb=" O ALA C 283 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N GLU C 288 " --> pdb=" O GLN C 284 " (cutoff:3.500A) Processing helix chain 'C' and resid 302 through 312 Processing helix chain 'C' and resid 325 through 342 Processing helix chain 'C' and resid 371 through 395 removed outlier: 3.666A pdb=" N GLN C 379 " --> pdb=" O LEU C 375 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 409 removed outlier: 3.632A pdb=" N LEU C 408 " --> pdb=" O THR C 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 411 through 425 Processing helix chain 'C' and resid 435 through 444 removed outlier: 3.668A pdb=" N ARG C 444 " --> pdb=" O LEU C 440 " (cutoff:3.500A) Processing helix chain 'C' and resid 461 through 465 removed outlier: 3.553A pdb=" N ASP C 465 " --> pdb=" O GLU C 462 " (cutoff:3.500A) Processing helix chain 'C' and resid 467 through 471 removed outlier: 3.566A pdb=" N TYR C 471 " --> pdb=" O PRO C 468 " (cutoff:3.500A) Processing helix chain 'C' and resid 524 through 528 removed outlier: 3.917A pdb=" N ASP C 528 " --> pdb=" O ALA C 524 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 524 through 528' Processing helix chain 'C' and resid 565 through 567 No H-bonds generated for 'chain 'C' and resid 565 through 567' Processing helix chain 'C' and resid 573 through 578 removed outlier: 4.254A pdb=" N MET C 577 " --> pdb=" O PRO C 574 " (cutoff:3.500A) Processing helix chain 'C' and resid 581 through 585 Processing helix chain 'C' and resid 587 through 591 Processing helix chain 'C' and resid 592 through 604 removed outlier: 3.629A pdb=" N MET C 598 " --> pdb=" O ASN C 594 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ARG C 604 " --> pdb=" O ALA C 600 " (cutoff:3.500A) Processing helix chain 'C' and resid 620 through 629 removed outlier: 4.325A pdb=" N ARG C 624 " --> pdb=" O GLY C 620 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ALA C 626 " --> pdb=" O GLU C 622 " (cutoff:3.500A) Processing helix chain 'C' and resid 730 through 735 Processing helix chain 'C' and resid 770 through 775 removed outlier: 4.334A pdb=" N ASP C 774 " --> pdb=" O VAL C 771 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LEU C 775 " --> pdb=" O LEU C 772 " (cutoff:3.500A) Processing helix chain 'C' and resid 806 through 817 Processing helix chain 'C' and resid 847 through 849 No H-bonds generated for 'chain 'C' and resid 847 through 849' Processing helix chain 'C' and resid 891 through 895 Processing helix chain 'C' and resid 911 through 916 removed outlier: 4.501A pdb=" N ARG C 915 " --> pdb=" O HIS C 911 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ARG C 916 " --> pdb=" O GLY C 912 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 911 through 916' Processing helix chain 'C' and resid 919 through 933 Processing helix chain 'C' and resid 944 through 948 Processing helix chain 'C' and resid 951 through 954 Processing helix chain 'C' and resid 972 through 982 removed outlier: 3.875A pdb=" N ALA C 977 " --> pdb=" O GLU C 973 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLY C 978 " --> pdb=" O GLY C 974 " (cutoff:3.500A) Processing helix chain 'C' and resid 1027 through 1031 removed outlier: 4.093A pdb=" N ASP C1030 " --> pdb=" O LEU C1027 " (cutoff:3.500A) Processing helix chain 'C' and resid 1060 through 1070 Processing helix chain 'C' and resid 1073 through 1081 Processing helix chain 'C' and resid 1086 through 1100 removed outlier: 4.252A pdb=" N VAL C1091 " --> pdb=" O THR C1087 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LYS C1092 " --> pdb=" O VAL C1088 " (cutoff:3.500A) Processing helix chain 'C' and resid 1109 through 1121 removed outlier: 3.630A pdb=" N LYS C1113 " --> pdb=" O PRO C1109 " (cutoff:3.500A) Processing helix chain 'D' and resid 16 through 23 Processing helix chain 'D' and resid 48 through 53 Processing helix chain 'D' and resid 67 through 71 Processing helix chain 'D' and resid 84 through 90 Processing helix chain 'D' and resid 103 through 108 removed outlier: 3.631A pdb=" N PHE D 107 " --> pdb=" O HIS D 103 " (cutoff:3.500A) Processing helix chain 'D' and resid 112 through 119 Processing helix chain 'D' and resid 124 through 130 Processing helix chain 'D' and resid 140 through 146 Processing helix chain 'D' and resid 147 through 186 removed outlier: 3.636A pdb=" N VAL D 162 " --> pdb=" O GLU D 158 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLN D 165 " --> pdb=" O ALA D 161 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ALA D 186 " --> pdb=" O ALA D 182 " (cutoff:3.500A) Processing helix chain 'D' and resid 190 through 228 removed outlier: 3.567A pdb=" N ARG D 194 " --> pdb=" O LYS D 190 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N VAL D 197 " --> pdb=" O VAL D 193 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ARG D 198 " --> pdb=" O ARG D 194 " (cutoff:3.500A) Processing helix chain 'D' and resid 237 through 249 removed outlier: 3.653A pdb=" N TYR D 241 " --> pdb=" O ASP D 237 " (cutoff:3.500A) Processing helix chain 'D' and resid 257 through 267 removed outlier: 4.212A pdb=" N ASN D 267 " --> pdb=" O LYS D 263 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 283 removed outlier: 3.999A pdb=" N GLU D 273 " --> pdb=" O ASP D 269 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 304 removed outlier: 3.550A pdb=" N LYS D 297 " --> pdb=" O LEU D 293 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N VAL D 298 " --> pdb=" O LYS D 294 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 311 removed outlier: 4.178A pdb=" N GLY D 311 " --> pdb=" O SER D 308 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 308 through 311' Processing helix chain 'D' and resid 321 through 325 Processing helix chain 'D' and resid 339 through 358 removed outlier: 3.830A pdb=" N ARG D 345 " --> pdb=" O ASN D 341 " (cutoff:3.500A) Processing helix chain 'D' and resid 363 through 383 removed outlier: 3.959A pdb=" N ASN D 369 " --> pdb=" O ILE D 365 " (cutoff:3.500A) Processing helix chain 'D' and resid 403 through 408 removed outlier: 4.096A pdb=" N GLY D 408 " --> pdb=" O ASP D 404 " (cutoff:3.500A) Processing helix chain 'D' and resid 445 through 463 Proline residue: D 454 - end of helix Processing helix chain 'D' and resid 468 through 478 Processing helix chain 'D' and resid 482 through 491 removed outlier: 3.774A pdb=" N VAL D 486 " --> pdb=" O GLN D 482 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLU D 489 " --> pdb=" O ASP D 485 " (cutoff:3.500A) Processing helix chain 'D' and resid 505 through 507 No H-bonds generated for 'chain 'D' and resid 505 through 507' Processing helix chain 'D' and resid 528 through 533 Processing helix chain 'D' and resid 548 through 558 Processing helix chain 'D' and resid 560 through 564 Processing helix chain 'D' and resid 579 through 590 Processing helix chain 'D' and resid 614 through 624 Processing helix chain 'D' and resid 643 through 651 removed outlier: 3.581A pdb=" N GLN D 649 " --> pdb=" O ASP D 645 " (cutoff:3.500A) Processing helix chain 'D' and resid 667 through 674 Processing helix chain 'D' and resid 688 through 703 Processing helix chain 'D' and resid 704 through 725 removed outlier: 3.714A pdb=" N ARG D 725 " --> pdb=" O TYR D 721 " (cutoff:3.500A) Processing helix chain 'D' and resid 740 through 761 Processing helix chain 'D' and resid 765 through 792 Processing helix chain 'D' and resid 796 through 804 removed outlier: 3.598A pdb=" N VAL D 802 " --> pdb=" O ILE D 798 " (cutoff:3.500A) Processing helix chain 'D' and resid 809 through 818 Processing helix chain 'D' and resid 844 through 880 removed outlier: 4.044A pdb=" N HIS D 853 " --> pdb=" O PHE D 849 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N GLY D 854 " --> pdb=" O ILE D 850 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N ALA D 863 " --> pdb=" O LEU D 859 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N LEU D 864 " --> pdb=" O ALA D 860 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ALA D 867 " --> pdb=" O ALA D 863 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ASP D 868 " --> pdb=" O LEU D 864 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N SER D 869 " --> pdb=" O ARG D 865 " (cutoff:3.500A) Processing helix chain 'D' and resid 944 through 954 Processing helix chain 'D' and resid 963 through 967 Processing helix chain 'D' and resid 975 through 979 Processing helix chain 'D' and resid 993 through 1004 Processing helix chain 'D' and resid 1005 through 1009 Processing helix chain 'D' and resid 1028 through 1038 Processing helix chain 'D' and resid 1118 through 1126 Processing helix chain 'D' and resid 1127 through 1146 removed outlier: 4.209A pdb=" N ILE D1133 " --> pdb=" O ARG D1129 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N GLN D1146 " --> pdb=" O VAL D1142 " (cutoff:3.500A) Processing helix chain 'D' and resid 1151 through 1163 removed outlier: 3.837A pdb=" N ILE D1155 " --> pdb=" O HIS D1151 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ILE D1158 " --> pdb=" O HIS D1154 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N GLN D1161 " --> pdb=" O VAL D1157 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N MET D1162 " --> pdb=" O ILE D1158 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LEU D1163 " --> pdb=" O VAL D1159 " (cutoff:3.500A) Processing helix chain 'D' and resid 1184 through 1194 Processing helix chain 'D' and resid 1210 through 1217 Processing helix chain 'D' and resid 1220 through 1228 removed outlier: 3.558A pdb=" N PHE D1227 " --> pdb=" O SER D1223 " (cutoff:3.500A) Processing helix chain 'D' and resid 1229 through 1241 Processing helix chain 'D' and resid 1248 through 1256 removed outlier: 3.577A pdb=" N VAL D1253 " --> pdb=" O LEU D1249 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ILE D1254 " --> pdb=" O LYS D1250 " (cutoff:3.500A) Processing helix chain 'D' and resid 1261 through 1264 Processing helix chain 'D' and resid 1265 through 1270 Processing helix chain 'D' and resid 1276 through 1283 Processing helix chain 'F' and resid 166 through 174 Processing helix chain 'F' and resid 180 through 205 removed outlier: 3.539A pdb=" N GLU F 184 " --> pdb=" O ASN F 180 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N VAL F 185 " --> pdb=" O ALA F 181 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLU F 186 " --> pdb=" O GLU F 182 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ALA F 205 " --> pdb=" O LEU F 201 " (cutoff:3.500A) Processing helix chain 'F' and resid 206 through 208 No H-bonds generated for 'chain 'F' and resid 206 through 208' Processing helix chain 'F' and resid 212 through 249 removed outlier: 4.638A pdb=" N ARG F 239 " --> pdb=" O GLU F 235 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N LEU F 240 " --> pdb=" O ALA F 236 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N VAL F 241 " --> pdb=" O ASN F 237 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N VAL F 242 " --> pdb=" O LEU F 238 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N SER F 243 " --> pdb=" O ARG F 239 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU F 244 " --> pdb=" O LEU F 240 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N ARG F 247 " --> pdb=" O SER F 243 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N TYR F 248 " --> pdb=" O LEU F 244 " (cutoff:3.500A) Processing helix chain 'F' and resid 254 through 273 removed outlier: 3.636A pdb=" N LEU F 264 " --> pdb=" O GLN F 260 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLY F 265 " --> pdb=" O GLU F 261 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ARG F 268 " --> pdb=" O LEU F 264 " (cutoff:3.500A) Processing helix chain 'F' and resid 280 through 301 removed outlier: 3.747A pdb=" N TYR F 284 " --> pdb=" O LYS F 280 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N TRP F 287 " --> pdb=" O THR F 283 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N TRP F 288 " --> pdb=" O TYR F 284 " (cutoff:3.500A) Processing helix chain 'F' and resid 307 through 329 Processing helix chain 'F' and resid 333 through 342 removed outlier: 3.827A pdb=" N GLU F 340 " --> pdb=" O GLU F 336 " (cutoff:3.500A) Processing helix chain 'F' and resid 344 through 356 Processing helix chain 'F' and resid 384 through 405 removed outlier: 3.727A pdb=" N THR F 392 " --> pdb=" O ALA F 388 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N GLN F 399 " --> pdb=" O GLN F 395 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU F 405 " --> pdb=" O VAL F 401 " (cutoff:3.500A) Processing helix chain 'F' and resid 406 through 417 removed outlier: 4.221A pdb=" N VAL F 412 " --> pdb=" O ARG F 408 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N VAL F 413 " --> pdb=" O GLU F 409 " (cutoff:3.500A) Processing helix chain 'F' and resid 426 through 435 removed outlier: 3.959A pdb=" N GLY F 431 " --> pdb=" O LEU F 427 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N GLN F 432 " --> pdb=" O ASP F 428 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N VAL F 433 " --> pdb=" O GLU F 429 " (cutoff:3.500A) Processing helix chain 'F' and resid 437 through 454 Processing helix chain 'F' and resid 454 through 462 removed outlier: 3.566A pdb=" N GLN F 459 " --> pdb=" O PRO F 455 " (cutoff:3.500A) removed outlier: 5.493A pdb=" N VAL F 460 " --> pdb=" O SER F 456 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N LEU F 461 " --> pdb=" O ARG F 457 " (cutoff:3.500A) Processing helix chain 'F' and resid 463 through 465 No H-bonds generated for 'chain 'F' and resid 463 through 465' Processing helix chain 'H' and resid 5 through 41 Processing helix chain 'H' and resid 45 through 67 removed outlier: 3.895A pdb=" N GLU H 52 " --> pdb=" O GLU H 48 " (cutoff:3.500A) Processing helix chain 'H' and resid 93 through 96 removed outlier: 4.226A pdb=" N ASP H 96 " --> pdb=" O ARG H 93 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 93 through 96' Processing helix chain 'H' and resid 106 through 109 Processing helix chain 'H' and resid 110 through 115 Processing helix chain 'J' and resid 80 through 86 Processing helix chain 'J' and resid 90 through 106 removed outlier: 3.800A pdb=" N LEU J 104 " --> pdb=" O GLU J 100 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE J 105 " --> pdb=" O ARG J 101 " (cutoff:3.500A) Processing helix chain 'E' and resid 30 through 34 removed outlier: 4.183A pdb=" N THR E 33 " --> pdb=" O LEU E 30 " (cutoff:3.500A) Processing helix chain 'E' and resid 36 through 42 removed outlier: 3.602A pdb=" N SER E 42 " --> pdb=" O ASP E 38 " (cutoff:3.500A) Processing helix chain 'E' and resid 46 through 67 Processing helix chain 'E' and resid 87 through 98 Processing sheet with id=AA1, first strand: chain 'A' and resid 8 through 15 removed outlier: 6.296A pdb=" N ARG A 18 " --> pdb=" O VAL A 14 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N ASP A 190 " --> pdb=" O PRO A 25 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 93 through 100 removed outlier: 7.164A pdb=" N GLU A 135 " --> pdb=" O ILE A 56 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N ILE A 56 " --> pdb=" O GLU A 135 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N GLU A 137 " --> pdb=" O ILE A 54 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N ILE A 54 " --> pdb=" O GLU A 137 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N VAL A 139 " --> pdb=" O THR A 52 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLU A 141 " --> pdb=" O ALA A 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 85 through 87 Processing sheet with id=AA4, first strand: chain 'A' and resid 103 through 106 Processing sheet with id=AA5, first strand: chain 'A' and resid 146 through 147 Processing sheet with id=AA6, first strand: chain 'B' and resid 8 through 15 removed outlier: 6.382A pdb=" N ARG B 18 " --> pdb=" O VAL B 14 " (cutoff:3.500A) removed outlier: 5.703A pdb=" N ARG B 18 " --> pdb=" O THR B 198 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N THR B 198 " --> pdb=" O ARG B 18 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N ARG B 20 " --> pdb=" O VAL B 196 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N VAL B 196 " --> pdb=" O ARG B 20 " (cutoff:3.500A) removed outlier: 5.411A pdb=" N VAL B 22 " --> pdb=" O ILE B 194 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N ILE B 194 " --> pdb=" O VAL B 22 " (cutoff:3.500A) removed outlier: 5.505A pdb=" N GLU B 24 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 7.648A pdb=" N LEU B 192 " --> pdb=" O GLU B 24 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 93 through 100 removed outlier: 7.464A pdb=" N GLU B 135 " --> pdb=" O ILE B 56 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N ILE B 56 " --> pdb=" O GLU B 135 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N GLU B 137 " --> pdb=" O ILE B 54 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N ILE B 54 " --> pdb=" O GLU B 137 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N VAL B 139 " --> pdb=" O THR B 52 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 85 through 86 Processing sheet with id=AA9, first strand: chain 'B' and resid 103 through 106 removed outlier: 3.996A pdb=" N GLY B 103 " --> pdb=" O LEU B 128 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 146 through 147 Processing sheet with id=AB2, first strand: chain 'C' and resid 30 through 31 removed outlier: 6.617A pdb=" N VAL C 30 " --> pdb=" O ALA C 964 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 87 through 88 removed outlier: 5.331A pdb=" N LEU C 96 " --> pdb=" O ILE C 131 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N ILE C 131 " --> pdb=" O LEU C 96 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N PHE C 98 " --> pdb=" O GLU C 129 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N GLU C 129 " --> pdb=" O PHE C 98 " (cutoff:3.500A) removed outlier: 5.135A pdb=" N ASP C 100 " --> pdb=" O THR C 127 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N THR C 127 " --> pdb=" O ASP C 100 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 87 through 88 removed outlier: 5.331A pdb=" N LEU C 96 " --> pdb=" O ILE C 131 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N ILE C 131 " --> pdb=" O LEU C 96 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N PHE C 98 " --> pdb=" O GLU C 129 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N GLU C 129 " --> pdb=" O PHE C 98 " (cutoff:3.500A) removed outlier: 5.135A pdb=" N ASP C 100 " --> pdb=" O THR C 127 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N THR C 127 " --> pdb=" O ASP C 100 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N GLY C 146 " --> pdb=" O LEU C 124 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N VAL C 126 " --> pdb=" O PHE C 144 " (cutoff:3.500A) removed outlier: 5.558A pdb=" N PHE C 144 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N ALA C 128 " --> pdb=" O THR C 142 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N THR C 142 " --> pdb=" O ALA C 128 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 157 through 159 Processing sheet with id=AB6, first strand: chain 'C' and resid 367 through 370 removed outlier: 3.572A pdb=" N SER C 168 " --> pdb=" O ARG C 445 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 175 through 182 removed outlier: 4.272A pdb=" N HIS C 191 " --> pdb=" O VAL C 207 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU C 203 " --> pdb=" O VAL C 195 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N THR C 212 " --> pdb=" O ASP C 208 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 345 through 346 Processing sheet with id=AB9, first strand: chain 'C' and resid 496 through 497 removed outlier: 5.220A pdb=" N GLN C 518 " --> pdb=" O LYS C 509 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N GLU C 511 " --> pdb=" O THR C 516 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N THR C 516 " --> pdb=" O GLU C 511 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 496 through 497 removed outlier: 3.621A pdb=" N VAL C 532 " --> pdb=" O ARG C 553 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 633 through 634 removed outlier: 6.519A pdb=" N VAL C 633 " --> pdb=" O ILE C 693 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 658 through 662 removed outlier: 6.094A pdb=" N MET C 652 " --> pdb=" O ILE C 641 " (cutoff:3.500A) removed outlier: 5.486A pdb=" N ILE C 641 " --> pdb=" O MET C 652 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 699 through 700 Processing sheet with id=AC5, first strand: chain 'C' and resid 998 through 999 removed outlier: 6.693A pdb=" N ILE C 726 " --> pdb=" O LYS C 888 " (cutoff:3.500A) removed outlier: 7.910A pdb=" N LEU C 890 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N LEU C 728 " --> pdb=" O LEU C 890 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ILE C 727 " --> pdb=" O ILE C 907 " (cutoff:3.500A) removed outlier: 9.089A pdb=" N ILE C 906 " --> pdb=" O ASN C 709 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N LEU C 711 " --> pdb=" O ILE C 906 " (cutoff:3.500A) removed outlier: 7.658A pdb=" N LEU C 908 " --> pdb=" O LEU C 711 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N ALA C 713 " --> pdb=" O LEU C 908 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N THR C1015 " --> pdb=" O ILE C 714 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 756 through 757 removed outlier: 6.670A pdb=" N ASP C 752 " --> pdb=" O VAL C 856 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N VAL C 856 " --> pdb=" O ASP C 752 " (cutoff:3.500A) removed outlier: 8.063A pdb=" N ASN C 857 " --> pdb=" O SER C 845 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N SER C 845 " --> pdb=" O ASN C 857 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N LEU C 859 " --> pdb=" O VAL C 843 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N VAL C 843 " --> pdb=" O LEU C 859 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N ARG C 861 " --> pdb=" O ILE C 841 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N ILE C 841 " --> pdb=" O ARG C 861 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N TYR C 863 " --> pdb=" O ILE C 839 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N LYS C 867 " --> pdb=" O SER C 835 " (cutoff:3.500A) removed outlier: 10.300A pdb=" N SER C 835 " --> pdb=" O LYS C 867 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 759 through 760 Processing sheet with id=AC8, first strand: chain 'C' and resid 792 through 794 removed outlier: 6.748A pdb=" N LEU C 828 " --> pdb=" O LEU C 793 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 935 through 936 Processing sheet with id=AD1, first strand: chain 'C' and resid 1033 through 1035 removed outlier: 7.683A pdb=" N ILE D 522 " --> pdb=" O ARG D 427 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N VAL D 429 " --> pdb=" O ILE D 522 " (cutoff:3.500A) removed outlier: 7.360A pdb=" N LEU D 524 " --> pdb=" O VAL D 429 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N VAL D 431 " --> pdb=" O LEU D 524 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 1057 through 1058 removed outlier: 3.775A pdb=" N GLN C1057 " --> pdb=" O VAL D 422 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 1124 through 1129 Processing sheet with id=AD4, first strand: chain 'D' and resid 24 through 27 removed outlier: 7.726A pdb=" N HIS D 94 " --> pdb=" O TYR D 25 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N GLU D 27 " --> pdb=" O HIS D 94 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N GLU D 96 " --> pdb=" O GLU D 27 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LEU D 97 " --> pdb=" O ASP D 315 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N ASP D 315 " --> pdb=" O LEU D 97 " (cutoff:3.500A) removed outlier: 10.808A pdb=" N ALA D 99 " --> pdb=" O VAL D 313 " (cutoff:3.500A) removed outlier: 9.953A pdb=" N VAL D 313 " --> pdb=" O ALA D 99 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 234 through 235 removed outlier: 5.086A pdb=" N ILE D 136 " --> pdb=" O ALA D 255 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N ALA D 255 " --> pdb=" O ILE D 136 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'F' and resid 359 through 360 removed outlier: 6.724A pdb=" N PHE D 335 " --> pdb=" O ILE F 359 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N GLN D 329 " --> pdb=" O SER J 9 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N SER J 9 " --> pdb=" O GLN D 329 " (cutoff:3.500A) removed outlier: 5.700A pdb=" N GLU F 378 " --> pdb=" O GLY J 8 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 611 through 612 Processing sheet with id=AD8, first strand: chain 'D' and resid 885 through 887 Processing sheet with id=AD9, first strand: chain 'D' and resid 896 through 899 removed outlier: 4.688A pdb=" N THR D 923 " --> pdb=" O ARG D 962 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 901 through 902 Processing sheet with id=AE2, first strand: chain 'D' and resid 928 through 929 removed outlier: 6.705A pdb=" N ALA D 928 " --> pdb=" O ILE D 936 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 1044 through 1045 Processing sheet with id=AE4, first strand: chain 'D' and resid 1076 through 1082 removed outlier: 3.852A pdb=" N LYS D1080 " --> pdb=" O PHE D1063 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N PHE D1063 " --> pdb=" O LYS D1080 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 1181 through 1183 removed outlier: 6.921A pdb=" N ALA D1203 " --> pdb=" O ILE D1169 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 1272 through 1275 Processing sheet with id=AE7, first strand: chain 'F' and resid 364 through 365 removed outlier: 4.195A pdb=" N SER F 371 " --> pdb=" O ILE F 365 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'H' and resid 71 through 76 removed outlier: 3.635A pdb=" N GLY H 73 " --> pdb=" O ILE H 85 " (cutoff:3.500A) removed outlier: 9.255A pdb=" N ARG H 82 " --> pdb=" O LEU H 100 " (cutoff:3.500A) removed outlier: 8.598A pdb=" N LEU H 102 " --> pdb=" O ARG H 82 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N TYR H 84 " --> pdb=" O LEU H 102 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'H' and resid 125 through 132 removed outlier: 6.779A pdb=" N ARG H 126 " --> pdb=" O ASP H 141 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N ASP H 141 " --> pdb=" O ARG H 126 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N GLN H 128 " --> pdb=" O PHE H 139 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N PHE H 139 " --> pdb=" O GLN H 128 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N HIS H 130 " --> pdb=" O VAL H 137 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LYS H 135 " --> pdb=" O LEU H 132 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'J' and resid 39 through 45 1214 hydrogen bonds defined for protein. 3420 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 51 hydrogen bonds 102 hydrogen bond angles 0 basepair planarities 22 basepair parallelities 43 stacking parallelities Total time for adding SS restraints: 6.96 Time building geometry restraints manager: 3.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9225 1.34 - 1.45: 3391 1.45 - 1.57: 15964 1.57 - 1.69: 104 1.69 - 1.81: 167 Bond restraints: 28851 Sorted by residual: bond pdb=" C3' DC P 22 " pdb=" C2' DC P 22 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.58e+00 bond pdb=" C3' DT P 13 " pdb=" C2' DT P 13 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 8.66e+00 bond pdb=" C3' DA O 6 " pdb=" C2' DA O 6 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.40e+00 bond pdb=" C3' DC P 1 " pdb=" C2' DC P 1 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 7.95e+00 bond pdb=" C3' DT O 23 " pdb=" C2' DT O 23 " ideal model delta sigma weight residual 1.516 1.537 -0.021 8.00e-03 1.56e+04 7.08e+00 ... (remaining 28846 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.32: 38110 1.32 - 2.65: 874 2.65 - 3.97: 270 3.97 - 5.29: 20 5.29 - 6.61: 3 Bond angle restraints: 39277 Sorted by residual: angle pdb=" O4' DG P 21 " pdb=" C1' DG P 21 " pdb=" N9 DG P 21 " ideal model delta sigma weight residual 108.00 112.35 -4.35 7.00e-01 2.04e+00 3.86e+01 angle pdb=" C ALA J 48 " pdb=" CA ALA J 48 " pdb=" CB ALA J 48 " ideal model delta sigma weight residual 117.23 110.62 6.61 1.36e+00 5.41e-01 2.37e+01 angle pdb=" N3 DT O 15 " pdb=" C4 DT O 15 " pdb=" O4 DT O 15 " ideal model delta sigma weight residual 119.90 122.52 -2.62 6.00e-01 2.78e+00 1.91e+01 angle pdb=" O4' DT O 16 " pdb=" C1' DT O 16 " pdb=" N1 DT O 16 " ideal model delta sigma weight residual 108.00 111.03 -3.03 7.00e-01 2.04e+00 1.87e+01 angle pdb=" N3 DT O 4 " pdb=" C4 DT O 4 " pdb=" O4 DT O 4 " ideal model delta sigma weight residual 119.90 122.45 -2.55 6.00e-01 2.78e+00 1.81e+01 ... (remaining 39272 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.43: 16928 32.43 - 64.86: 581 64.86 - 97.29: 57 97.29 - 129.72: 0 129.72 - 162.14: 1 Dihedral angle restraints: 17567 sinusoidal: 7588 harmonic: 9979 Sorted by residual: dihedral pdb=" CA LYS C 154 " pdb=" C LYS C 154 " pdb=" N GLY C 155 " pdb=" CA GLY C 155 " ideal model delta harmonic sigma weight residual 180.00 160.14 19.86 0 5.00e+00 4.00e-02 1.58e+01 dihedral pdb=" C4' DA P 7 " pdb=" C3' DA P 7 " pdb=" O3' DA P 7 " pdb=" P DA P 8 " ideal model delta sinusoidal sigma weight residual 220.00 57.86 162.14 1 3.50e+01 8.16e-04 1.53e+01 dihedral pdb=" CA LEU B 34 " pdb=" C LEU B 34 " pdb=" N GLY B 35 " pdb=" CA GLY B 35 " ideal model delta harmonic sigma weight residual -180.00 -160.91 -19.09 0 5.00e+00 4.00e-02 1.46e+01 ... (remaining 17564 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 3124 0.034 - 0.067: 840 0.067 - 0.101: 269 0.101 - 0.135: 182 0.135 - 0.168: 38 Chirality restraints: 4453 Sorted by residual: chirality pdb=" C3' DG O 5 " pdb=" C4' DG O 5 " pdb=" O3' DG O 5 " pdb=" C2' DG O 5 " both_signs ideal model delta sigma weight residual False -2.73 -2.56 -0.17 2.00e-01 2.50e+01 7.10e-01 chirality pdb=" C3' DA P 20 " pdb=" C4' DA P 20 " pdb=" O3' DA P 20 " pdb=" C2' DA P 20 " both_signs ideal model delta sigma weight residual False -2.73 -2.56 -0.17 2.00e-01 2.50e+01 6.86e-01 chirality pdb=" C3' DA P 7 " pdb=" C4' DA P 7 " pdb=" O3' DA P 7 " pdb=" C2' DA P 7 " both_signs ideal model delta sigma weight residual False -2.73 -2.58 -0.16 2.00e-01 2.50e+01 6.05e-01 ... (remaining 4450 not shown) Planarity restraints: 5001 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP J 82 " 0.021 2.00e-02 2.50e+03 1.49e-02 5.51e+00 pdb=" CG TRP J 82 " -0.040 2.00e-02 2.50e+03 pdb=" CD1 TRP J 82 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 TRP J 82 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP J 82 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP J 82 " 0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP J 82 " 0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP J 82 " 0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP J 82 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP J 82 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 60 " 0.157 9.50e-02 1.11e+02 7.07e-02 3.30e+00 pdb=" NE ARG C 60 " -0.012 2.00e-02 2.50e+03 pdb=" CZ ARG C 60 " 0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG C 60 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG C 60 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D1232 " 0.156 9.50e-02 1.11e+02 7.01e-02 3.21e+00 pdb=" NE ARG D1232 " -0.012 2.00e-02 2.50e+03 pdb=" CZ ARG D1232 " 0.006 2.00e-02 2.50e+03 pdb=" NH1 ARG D1232 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG D1232 " 0.003 2.00e-02 2.50e+03 ... (remaining 4998 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 165 2.57 - 3.15: 23318 3.15 - 3.73: 41895 3.73 - 4.32: 58153 4.32 - 4.90: 98405 Nonbonded interactions: 221936 Sorted by model distance: nonbonded pdb=" OG1 THR B 74 " pdb=" OE2 GLU D 608 " model vdw 1.987 3.040 nonbonded pdb=" OD1 ASP D1049 " pdb=" OH TYR D1078 " model vdw 2.022 3.040 nonbonded pdb=" OD2 ASP D 989 " pdb=" OG SER E 46 " model vdw 2.081 3.040 nonbonded pdb=" OG SER C 845 " pdb=" OD2 ASP C 848 " model vdw 2.106 3.040 nonbonded pdb=" OD2 ASP C 432 " pdb=" OG SER C 438 " model vdw 2.113 3.040 ... (remaining 221931 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and resid 1 through 226) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.590 Check model and map are aligned: 0.080 Set scattering table: 0.050 Process input model: 31.830 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.060 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:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.088 28859 Z= 0.181 Angle : 0.537 6.615 39289 Z= 0.341 Chirality : 0.042 0.168 4453 Planarity : 0.004 0.071 5001 Dihedral : 15.398 162.144 11147 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 0.03 % Allowed : 0.03 % Favored : 99.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % 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: 0.87 (0.15), residues: 3466 helix: 1.28 (0.15), residues: 1295 sheet: 0.03 (0.26), residues: 392 loop : 0.32 (0.15), residues: 1779 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG D 875 TYR 0.018 0.001 TYR H 6 PHE 0.030 0.001 PHE C 816 TRP 0.040 0.001 TRP J 82 HIS 0.009 0.001 HIS J 81 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.18 (28851) covalent geometry : angle 0.53572 / 0.34 (39277) hydrogen bonds : bond 0.15476 / 10.78 ( 1259) hydrogen bonds : angle 5.95193 / 4.15 ( 3522) metal coordination : bond 0.04830 / 2.29 ( 8) metal coordination : angle 1.97881 / 1.20 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6932 Ramachandran restraints generated. 3466 Oldfield, 0 Emsley, 3466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6932 Ramachandran restraints generated. 3466 Oldfield, 0 Emsley, 3466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 2931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 327 time to evaluate : 1.094 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 outliers start: 1 outliers final: 0 residues processed: 327 average time/residue: 0.2073 time to fit residues: 101.9396 Evaluate side-chains 206 residues out of total 2931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 206 time to evaluate : 1.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 197 optimal weight: 10.0000 chunk 215 optimal weight: 8.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 9.9990 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 4.9990 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 0.8980 chunk 183 optimal weight: 9.9990 chunk 298 optimal weight: 4.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 119 HIS A 152 ASN B 185 GLN ** C 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 534 GLN C 742 HIS F 199 GLN ** J 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.089215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.061925 restraints weight = 89603.895| |-----------------------------------------------------------------------------| r_work (start): 0.2851 rms_B_bonded: 3.31 r_work: 0.2690 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.2690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8908 moved from start: 0.1619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.093 28859 Z= 0.234 Angle : 0.667 11.284 39289 Z= 0.348 Chirality : 0.045 0.229 4453 Planarity : 0.005 0.049 5001 Dihedral : 12.607 163.410 4426 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.02 % Allowed : 6.35 % Favored : 92.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.78 (0.14), residues: 3466 helix: 1.27 (0.15), residues: 1307 sheet: -0.02 (0.26), residues: 380 loop : 0.19 (0.15), residues: 1779 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 278 TYR 0.018 0.002 TYR C 722 PHE 0.018 0.002 PHE C 364 TRP 0.055 0.002 TRP J 82 HIS 0.008 0.001 HIS J 81 Details of bonding type rmsd/Z covalent geometry : bond 0.00544 / 0.23 (28851) covalent geometry : angle 0.66393 / 0.35 (39277) hydrogen bonds : bond 0.05209 / 3.60 ( 1259) hydrogen bonds : angle 4.86990 / 3.40 ( 3522) metal coordination : bond 0.01325 / 0.67 ( 8) metal coordination : angle 3.42180 / 1.99 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6932 Ramachandran restraints generated. 3466 Oldfield, 0 Emsley, 3466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6932 Ramachandran restraints generated. 3466 Oldfield, 0 Emsley, 3466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 2931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 224 time to evaluate : 1.026 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: C 202 TRP cc_start: 0.8231 (m100) cc_final: 0.7839 (m100) REVERT: C 250 MET cc_start: 0.8362 (mmm) cc_final: 0.8080 (mmm) REVERT: C 652 MET cc_start: 0.8557 (OUTLIER) cc_final: 0.8239 (tpp) REVERT: C 772 LEU cc_start: 0.9090 (pt) cc_final: 0.8841 (pp) REVERT: D 120 LEU cc_start: 0.8939 (mt) cc_final: 0.8700 (mt) REVERT: D 155 MET cc_start: 0.5488 (tpt) cc_final: 0.5262 (tpt) REVERT: D 214 ARG cc_start: 0.9080 (tpp-160) cc_final: 0.8535 (mmm160) REVERT: D 242 ARG cc_start: 0.9014 (mmt-90) cc_final: 0.8579 (mmt-90) REVERT: H 113 TYR cc_start: 0.9252 (m-80) cc_final: 0.8778 (m-10) REVERT: J 32 TYR cc_start: 0.7920 (m-80) cc_final: 0.6994 (m-80) REVERT: J 47 ASP cc_start: 0.8861 (t0) cc_final: 0.8634 (m-30) outliers start: 30 outliers final: 16 residues processed: 239 average time/residue: 0.1869 time to fit residues: 70.6612 Evaluate side-chains 209 residues out of total 2931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 192 time to evaluate : 0.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 390 VAL Chi-restraints excluded: chain C residue 511 GLU Chi-restraints excluded: chain C residue 652 MET Chi-restraints excluded: chain C residue 943 VAL Chi-restraints excluded: chain C residue 1116 LEU Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 365 ILE Chi-restraints excluded: chain D residue 914 HIS Chi-restraints excluded: chain D residue 1234 LEU Chi-restraints excluded: chain F residue 420 THR Chi-restraints excluded: chain H residue 12 SER Chi-restraints excluded: chain H residue 130 HIS Chi-restraints excluded: chain H residue 132 LEU Chi-restraints excluded: chain H residue 137 VAL Chi-restraints excluded: chain J residue 84 MET Chi-restraints excluded: chain J residue 97 LEU Chi-restraints excluded: chain E residue 42 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 169 optimal weight: 9.9990 chunk 233 optimal weight: 0.8980 chunk 303 optimal weight: 6.9990 chunk 8 optimal weight: 8.9990 chunk 276 optimal weight: 1.9990 chunk 37 optimal weight: 10.0000 chunk 64 optimal weight: 30.0000 chunk 209 optimal weight: 0.9990 chunk 269 optimal weight: 4.9990 chunk 101 optimal weight: 3.9990 chunk 174 optimal weight: 40.0000 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 191 HIS ** C 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 926 HIS D 686 GLN ** J 81 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 = 0.3587 r_free = 0.3587 target = 0.088347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.061620 restraints weight = 89408.656| |-----------------------------------------------------------------------------| r_work (start): 0.2873 rms_B_bonded: 3.07 r_work: 0.2720 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.2720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8918 moved from start: 0.1933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 28859 Z= 0.177 Angle : 0.595 13.461 39289 Z= 0.310 Chirality : 0.043 0.220 4453 Planarity : 0.004 0.053 5001 Dihedral : 12.712 162.175 4426 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.19 % Allowed : 8.50 % Favored : 90.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % 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: 0.90 (0.14), residues: 3466 helix: 1.44 (0.15), residues: 1308 sheet: 0.13 (0.27), residues: 356 loop : 0.17 (0.15), residues: 1802 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 334 TYR 0.012 0.001 TYR E 75 PHE 0.020 0.002 PHE D 107 TRP 0.056 0.002 TRP J 82 HIS 0.008 0.001 HIS J 81 Details of bonding type rmsd/Z covalent geometry : bond 0.00408 / 0.18 (28851) covalent geometry : angle 0.59199 / 0.31 (39277) hydrogen bonds : bond 0.04611 / 3.22 ( 1259) hydrogen bonds : angle 4.60661 / 3.21 ( 3522) metal coordination : bond 0.01043 / 0.53 ( 8) metal coordination : angle 3.21086 / 1.88 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6932 Ramachandran restraints generated. 3466 Oldfield, 0 Emsley, 3466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6932 Ramachandran restraints generated. 3466 Oldfield, 0 Emsley, 3466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 2931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 204 time to evaluate : 0.932 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 72 ASN cc_start: 0.8811 (p0) cc_final: 0.8491 (p0) REVERT: C 94 MET cc_start: 0.8012 (pmm) cc_final: 0.7512 (pmm) REVERT: C 150 MET cc_start: 0.8975 (mmm) cc_final: 0.8749 (mmm) REVERT: C 202 TRP cc_start: 0.8099 (m100) cc_final: 0.7875 (t60) REVERT: C 250 MET cc_start: 0.8483 (mmm) cc_final: 0.8198 (mmm) REVERT: C 652 MET cc_start: 0.8516 (tpp) cc_final: 0.8294 (tpp) REVERT: C 772 LEU cc_start: 0.9092 (pt) cc_final: 0.8829 (pp) REVERT: D 120 LEU cc_start: 0.8919 (mt) cc_final: 0.8658 (mt) REVERT: D 214 ARG cc_start: 0.9122 (tpp-160) cc_final: 0.8683 (mmm160) REVERT: D 242 ARG cc_start: 0.8957 (mmt-90) cc_final: 0.8466 (mmt-90) REVERT: D 387 ARG cc_start: 0.7738 (tpt90) cc_final: 0.7534 (tpt90) REVERT: D 1113 MET cc_start: 0.8754 (mmm) cc_final: 0.7982 (tpp) REVERT: F 341 MET cc_start: 0.8814 (mmt) cc_final: 0.8567 (tpp) REVERT: H 113 TYR cc_start: 0.9165 (m-80) cc_final: 0.8772 (m-10) REVERT: J 32 TYR cc_start: 0.8231 (m-80) cc_final: 0.7734 (m-80) outliers start: 35 outliers final: 19 residues processed: 228 average time/residue: 0.1801 time to fit residues: 66.2530 Evaluate side-chains 204 residues out of total 2931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 185 time to evaluate : 1.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 390 VAL Chi-restraints excluded: chain C residue 511 GLU Chi-restraints excluded: chain C residue 943 VAL Chi-restraints excluded: chain C residue 1116 LEU Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 328 VAL Chi-restraints excluded: chain D residue 365 ILE Chi-restraints excluded: chain D residue 914 HIS Chi-restraints excluded: chain D residue 1042 ARG Chi-restraints excluded: chain D residue 1234 LEU Chi-restraints excluded: chain F residue 164 ASP Chi-restraints excluded: chain F residue 420 THR Chi-restraints excluded: chain H residue 12 SER Chi-restraints excluded: chain H residue 132 LEU Chi-restraints excluded: chain H residue 137 VAL Chi-restraints excluded: chain J residue 14 VAL Chi-restraints excluded: chain J residue 22 HIS Chi-restraints excluded: chain J residue 24 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 140 optimal weight: 6.9990 chunk 261 optimal weight: 9.9990 chunk 179 optimal weight: 7.9990 chunk 53 optimal weight: 5.9990 chunk 284 optimal weight: 2.9990 chunk 77 optimal weight: 7.9990 chunk 75 optimal weight: 20.0000 chunk 256 optimal weight: 0.9990 chunk 101 optimal weight: 4.9990 chunk 279 optimal weight: 3.9990 chunk 199 optimal weight: 0.0980 overall best weight: 2.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 200 ASN ** C 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.087950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.061053 restraints weight = 89089.010| |-----------------------------------------------------------------------------| r_work (start): 0.2861 rms_B_bonded: 3.09 r_work: 0.2702 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.2702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8937 moved from start: 0.2151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 28859 Z= 0.178 Angle : 0.587 10.126 39289 Z= 0.304 Chirality : 0.043 0.227 4453 Planarity : 0.004 0.056 5001 Dihedral : 12.697 161.973 4426 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.71 % Allowed : 9.28 % Favored : 89.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % 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: 0.91 (0.14), residues: 3466 helix: 1.50 (0.15), residues: 1311 sheet: 0.00 (0.26), residues: 369 loop : 0.16 (0.15), residues: 1786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 821 TYR 0.014 0.001 TYR H 21 PHE 0.019 0.001 PHE D 107 TRP 0.054 0.002 TRP J 82 HIS 0.007 0.001 HIS J 81 Details of bonding type rmsd/Z covalent geometry : bond 0.00418 / 0.18 (28851) covalent geometry : angle 0.58417 / 0.30 (39277) hydrogen bonds : bond 0.04399 / 3.07 ( 1259) hydrogen bonds : angle 4.50563 / 3.14 ( 3522) metal coordination : bond 0.01029 / 0.52 ( 8) metal coordination : angle 3.18208 / 1.86 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6932 Ramachandran restraints generated. 3466 Oldfield, 0 Emsley, 3466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6932 Ramachandran restraints generated. 3466 Oldfield, 0 Emsley, 3466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 2931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 197 time to evaluate : 1.535 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 72 ASN cc_start: 0.8845 (p0) cc_final: 0.8473 (p0) REVERT: C 150 MET cc_start: 0.8990 (mmm) cc_final: 0.8764 (mmm) REVERT: C 652 MET cc_start: 0.8518 (tpp) cc_final: 0.8217 (tpp) REVERT: C 772 LEU cc_start: 0.9087 (pt) cc_final: 0.8815 (pp) REVERT: D 120 LEU cc_start: 0.8963 (mt) cc_final: 0.8684 (mt) REVERT: D 214 ARG cc_start: 0.9065 (tpp-160) cc_final: 0.8594 (mmm160) REVERT: D 242 ARG cc_start: 0.9004 (mmt-90) cc_final: 0.8657 (mmt-90) REVERT: D 387 ARG cc_start: 0.7780 (tpt90) cc_final: 0.7480 (tpt90) REVERT: D 1113 MET cc_start: 0.8828 (mmm) cc_final: 0.7972 (tpp) REVERT: F 201 LEU cc_start: 0.9431 (OUTLIER) cc_final: 0.8966 (mp) REVERT: H 113 TYR cc_start: 0.9180 (m-80) cc_final: 0.8729 (m-10) REVERT: J 32 TYR cc_start: 0.8357 (m-80) cc_final: 0.7385 (m-80) outliers start: 50 outliers final: 24 residues processed: 235 average time/residue: 0.1809 time to fit residues: 69.0296 Evaluate side-chains 209 residues out of total 2931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 184 time to evaluate : 1.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain C residue 390 VAL Chi-restraints excluded: chain C residue 511 GLU Chi-restraints excluded: chain C residue 559 VAL Chi-restraints excluded: chain C residue 943 VAL Chi-restraints excluded: chain C residue 965 THR Chi-restraints excluded: chain C residue 976 LEU Chi-restraints excluded: chain C residue 1116 LEU Chi-restraints excluded: chain D residue 12 ILE Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 365 ILE Chi-restraints excluded: chain D residue 914 HIS Chi-restraints excluded: chain D residue 1042 ARG Chi-restraints excluded: chain D residue 1234 LEU Chi-restraints excluded: chain F residue 185 VAL Chi-restraints excluded: chain F residue 201 LEU Chi-restraints excluded: chain F residue 420 THR Chi-restraints excluded: chain H residue 12 SER Chi-restraints excluded: chain H residue 132 LEU Chi-restraints excluded: chain H residue 137 VAL Chi-restraints excluded: chain J residue 14 VAL Chi-restraints excluded: chain J residue 22 HIS Chi-restraints excluded: chain J residue 84 MET Chi-restraints excluded: chain E residue 42 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 22 optimal weight: 5.9990 chunk 285 optimal weight: 10.0000 chunk 41 optimal weight: 9.9990 chunk 270 optimal weight: 7.9990 chunk 280 optimal weight: 0.6980 chunk 43 optimal weight: 0.9990 chunk 33 optimal weight: 0.0970 chunk 345 optimal weight: 1.9990 chunk 29 optimal weight: 7.9990 chunk 284 optimal weight: 4.9990 chunk 196 optimal weight: 7.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 200 ASN ** C 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.089351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.062942 restraints weight = 88737.428| |-----------------------------------------------------------------------------| r_work (start): 0.2904 rms_B_bonded: 3.10 r_work: 0.2742 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.2742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8924 moved from start: 0.2288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 28859 Z= 0.140 Angle : 0.568 11.602 39289 Z= 0.294 Chirality : 0.042 0.219 4453 Planarity : 0.004 0.058 5001 Dihedral : 12.681 160.371 4426 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.50 % Allowed : 10.75 % Favored : 87.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % 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: 0.98 (0.14), residues: 3466 helix: 1.60 (0.15), residues: 1315 sheet: 0.06 (0.27), residues: 360 loop : 0.16 (0.15), residues: 1791 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG F 167 TYR 0.011 0.001 TYR H 21 PHE 0.020 0.001 PHE F 376 TRP 0.052 0.001 TRP J 82 HIS 0.010 0.001 HIS F 454 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.14 (28851) covalent geometry : angle 0.56519 / 0.29 (39277) hydrogen bonds : bond 0.04105 / 2.87 ( 1259) hydrogen bonds : angle 4.41147 / 3.06 ( 3522) metal coordination : bond 0.00781 / 0.39 ( 8) metal coordination : angle 3.12169 / 1.82 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6932 Ramachandran restraints generated. 3466 Oldfield, 0 Emsley, 3466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6932 Ramachandran restraints generated. 3466 Oldfield, 0 Emsley, 3466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 2931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 193 time to evaluate : 1.011 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 100 GLN cc_start: 0.8313 (mm-40) cc_final: 0.7666 (mm-40) REVERT: C 72 ASN cc_start: 0.8852 (p0) cc_final: 0.8445 (p0) REVERT: C 150 MET cc_start: 0.9021 (mmm) cc_final: 0.8797 (mmm) REVERT: C 652 MET cc_start: 0.8482 (tpp) cc_final: 0.8186 (tpp) REVERT: C 772 LEU cc_start: 0.9083 (pt) cc_final: 0.8826 (pp) REVERT: D 120 LEU cc_start: 0.8962 (mt) cc_final: 0.8663 (mt) REVERT: D 214 ARG cc_start: 0.9068 (tpp-160) cc_final: 0.8563 (mmm160) REVERT: D 242 ARG cc_start: 0.9046 (mmt-90) cc_final: 0.8685 (mmt-90) REVERT: D 248 TYR cc_start: 0.8719 (OUTLIER) cc_final: 0.8374 (m-80) REVERT: D 373 MET cc_start: 0.8538 (mtm) cc_final: 0.8269 (mtm) REVERT: D 387 ARG cc_start: 0.7715 (tpt90) cc_final: 0.7496 (tpt90) REVERT: D 1113 MET cc_start: 0.8834 (mmm) cc_final: 0.7930 (tpp) REVERT: F 201 LEU cc_start: 0.9375 (mp) cc_final: 0.9087 (mt) REVERT: H 113 TYR cc_start: 0.9197 (m-80) cc_final: 0.8701 (m-10) REVERT: J 32 TYR cc_start: 0.8403 (m-80) cc_final: 0.7474 (m-80) outliers start: 44 outliers final: 26 residues processed: 228 average time/residue: 0.1695 time to fit residues: 62.8469 Evaluate side-chains 207 residues out of total 2931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 180 time to evaluate : 0.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain C residue 390 VAL Chi-restraints excluded: chain C residue 559 VAL Chi-restraints excluded: chain C residue 657 THR Chi-restraints excluded: chain C residue 943 VAL Chi-restraints excluded: chain C residue 965 THR Chi-restraints excluded: chain C residue 976 LEU Chi-restraints excluded: chain C residue 1082 ILE Chi-restraints excluded: chain C residue 1116 LEU Chi-restraints excluded: chain D residue 12 ILE Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 248 TYR Chi-restraints excluded: chain D residue 328 VAL Chi-restraints excluded: chain D residue 365 ILE Chi-restraints excluded: chain D residue 914 HIS Chi-restraints excluded: chain D residue 1042 ARG Chi-restraints excluded: chain F residue 164 ASP Chi-restraints excluded: chain F residue 185 VAL Chi-restraints excluded: chain F residue 373 LEU Chi-restraints excluded: chain F residue 420 THR Chi-restraints excluded: chain H residue 12 SER Chi-restraints excluded: chain H residue 67 ASP Chi-restraints excluded: chain H residue 132 LEU Chi-restraints excluded: chain H residue 137 VAL Chi-restraints excluded: chain J residue 22 HIS Chi-restraints excluded: chain E residue 42 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 117 optimal weight: 0.0980 chunk 197 optimal weight: 0.5980 chunk 311 optimal weight: 10.0000 chunk 55 optimal weight: 3.9990 chunk 65 optimal weight: 5.9990 chunk 124 optimal weight: 6.9990 chunk 341 optimal weight: 30.0000 chunk 141 optimal weight: 0.8980 chunk 150 optimal weight: 4.9990 chunk 63 optimal weight: 0.0050 chunk 195 optimal weight: 8.9990 overall best weight: 1.1196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 200 ASN ** C 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.089942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.063720 restraints weight = 87995.368| |-----------------------------------------------------------------------------| r_work (start): 0.2925 rms_B_bonded: 3.11 r_work: 0.2758 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.2758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8907 moved from start: 0.2418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 28859 Z= 0.113 Angle : 0.558 15.977 39289 Z= 0.286 Chirality : 0.042 0.211 4453 Planarity : 0.004 0.058 5001 Dihedral : 12.662 159.379 4426 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.64 % Allowed : 11.16 % Favored : 87.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % 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: 1.03 (0.14), residues: 3466 helix: 1.68 (0.15), residues: 1310 sheet: 0.10 (0.27), residues: 351 loop : 0.15 (0.15), residues: 1805 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D1053 TYR 0.013 0.001 TYR A 176 PHE 0.015 0.001 PHE D 107 TRP 0.076 0.002 TRP J 82 HIS 0.008 0.001 HIS F 454 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.11 (28851) covalent geometry : angle 0.55624 / 0.29 (39277) hydrogen bonds : bond 0.03789 / 2.65 ( 1259) hydrogen bonds : angle 4.30108 / 2.98 ( 3522) metal coordination : bond 0.00589 / 0.29 ( 8) metal coordination : angle 2.87417 / 1.68 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6932 Ramachandran restraints generated. 3466 Oldfield, 0 Emsley, 3466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6932 Ramachandran restraints generated. 3466 Oldfield, 0 Emsley, 3466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 2931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 198 time to evaluate : 1.113 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 LYS cc_start: 0.9102 (ttpt) cc_final: 0.8788 (ptmt) REVERT: B 5 GLN cc_start: 0.8264 (pm20) cc_final: 0.8057 (pm20) REVERT: C 150 MET cc_start: 0.8983 (mmm) cc_final: 0.8767 (mmm) REVERT: C 652 MET cc_start: 0.8441 (tpp) cc_final: 0.8140 (tpp) REVERT: C 772 LEU cc_start: 0.9073 (pt) cc_final: 0.8824 (pp) REVERT: D 120 LEU cc_start: 0.8958 (mt) cc_final: 0.8688 (mt) REVERT: D 214 ARG cc_start: 0.9082 (tpp-160) cc_final: 0.8717 (mmm160) REVERT: D 242 ARG cc_start: 0.9042 (mmt-90) cc_final: 0.8674 (mmt-90) REVERT: D 248 TYR cc_start: 0.8747 (OUTLIER) cc_final: 0.8467 (m-80) REVERT: D 373 MET cc_start: 0.8514 (mtm) cc_final: 0.8287 (mtm) REVERT: D 941 HIS cc_start: 0.7539 (t-170) cc_final: 0.7274 (t-170) REVERT: D 1113 MET cc_start: 0.8811 (mmm) cc_final: 0.8012 (tpp) REVERT: F 201 LEU cc_start: 0.9366 (OUTLIER) cc_final: 0.9059 (mm) REVERT: H 142 GLU cc_start: 0.8052 (tm-30) cc_final: 0.7584 (tm-30) REVERT: J 24 LEU cc_start: 0.8754 (mp) cc_final: 0.8307 (tp) REVERT: J 32 TYR cc_start: 0.8475 (m-80) cc_final: 0.7536 (m-80) outliers start: 48 outliers final: 26 residues processed: 235 average time/residue: 0.1709 time to fit residues: 64.1031 Evaluate side-chains 211 residues out of total 2931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 183 time to evaluate : 1.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 133 LYS Chi-restraints excluded: chain C residue 390 VAL Chi-restraints excluded: chain C residue 395 MET Chi-restraints excluded: chain C residue 559 VAL Chi-restraints excluded: chain C residue 657 THR Chi-restraints excluded: chain C residue 819 LYS Chi-restraints excluded: chain C residue 943 VAL Chi-restraints excluded: chain C residue 965 THR Chi-restraints excluded: chain C residue 976 LEU Chi-restraints excluded: chain C residue 1082 ILE Chi-restraints excluded: chain C residue 1116 LEU Chi-restraints excluded: chain D residue 12 ILE Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 248 TYR Chi-restraints excluded: chain D residue 328 VAL Chi-restraints excluded: chain D residue 1042 ARG Chi-restraints excluded: chain F residue 164 ASP Chi-restraints excluded: chain F residue 185 VAL Chi-restraints excluded: chain F residue 201 LEU Chi-restraints excluded: chain F residue 356 ARG Chi-restraints excluded: chain F residue 420 THR Chi-restraints excluded: chain H residue 12 SER Chi-restraints excluded: chain H residue 67 ASP Chi-restraints excluded: chain H residue 137 VAL Chi-restraints excluded: chain J residue 22 HIS Chi-restraints excluded: chain J residue 84 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 120 optimal weight: 3.9990 chunk 15 optimal weight: 10.0000 chunk 340 optimal weight: 30.0000 chunk 133 optimal weight: 6.9990 chunk 344 optimal weight: 6.9990 chunk 294 optimal weight: 2.9990 chunk 248 optimal weight: 4.9990 chunk 60 optimal weight: 8.9990 chunk 319 optimal weight: 4.9990 chunk 176 optimal weight: 9.9990 chunk 99 optimal weight: 8.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 200 ASN ** C 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 470 HIS D 914 HIS ** J 81 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 = 0.3562 r_free = 0.3562 target = 0.087074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.059993 restraints weight = 90532.244| |-----------------------------------------------------------------------------| r_work (start): 0.2827 rms_B_bonded: 3.14 r_work: 0.2669 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.2669 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8987 moved from start: 0.2667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.061 28859 Z= 0.295 Angle : 0.679 13.008 39289 Z= 0.347 Chirality : 0.045 0.208 4453 Planarity : 0.005 0.062 5001 Dihedral : 12.834 159.964 4426 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 1.91 % Allowed : 11.80 % Favored : 86.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.78 (0.14), residues: 3466 helix: 1.53 (0.15), residues: 1305 sheet: -0.31 (0.25), residues: 393 loop : 0.04 (0.15), residues: 1768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG H 14 TYR 0.019 0.002 TYR D 130 PHE 0.032 0.002 PHE H 97 TRP 0.100 0.003 TRP J 82 HIS 0.006 0.001 HIS F 454 Details of bonding type rmsd/Z covalent geometry : bond 0.00690 / 0.29 (28851) covalent geometry : angle 0.67660 / 0.35 (39277) hydrogen bonds : bond 0.04873 / 3.40 ( 1259) hydrogen bonds : angle 4.57182 / 3.18 ( 3522) metal coordination : bond 0.01701 / 0.88 ( 8) metal coordination : angle 3.38803 / 2.03 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6932 Ramachandran restraints generated. 3466 Oldfield, 0 Emsley, 3466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6932 Ramachandran restraints generated. 3466 Oldfield, 0 Emsley, 3466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 2931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 187 time to evaluate : 1.161 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 LYS cc_start: 0.9112 (ttpt) cc_final: 0.8813 (ptmt) REVERT: B 5 GLN cc_start: 0.8272 (pm20) cc_final: 0.8033 (pm20) REVERT: C 150 MET cc_start: 0.9071 (mmm) cc_final: 0.8855 (mmm) REVERT: C 652 MET cc_start: 0.8467 (OUTLIER) cc_final: 0.8124 (tpp) REVERT: C 772 LEU cc_start: 0.9160 (pt) cc_final: 0.8908 (pp) REVERT: D 214 ARG cc_start: 0.9163 (tpp-160) cc_final: 0.8654 (mmm160) REVERT: D 242 ARG cc_start: 0.9067 (mmt-90) cc_final: 0.8705 (mmt-90) REVERT: D 248 TYR cc_start: 0.8705 (OUTLIER) cc_final: 0.8458 (m-80) REVERT: D 941 HIS cc_start: 0.7730 (t-170) cc_final: 0.7368 (t-170) REVERT: D 1113 MET cc_start: 0.8954 (mmm) cc_final: 0.8422 (mmm) REVERT: F 201 LEU cc_start: 0.9380 (OUTLIER) cc_final: 0.9102 (mm) REVERT: H 113 TYR cc_start: 0.9244 (m-80) cc_final: 0.8731 (m-10) REVERT: H 142 GLU cc_start: 0.8074 (tm-30) cc_final: 0.7625 (tm-30) REVERT: J 24 LEU cc_start: 0.8838 (mp) cc_final: 0.8395 (tp) REVERT: J 32 TYR cc_start: 0.8594 (m-80) cc_final: 0.7764 (m-80) outliers start: 56 outliers final: 39 residues processed: 227 average time/residue: 0.1799 time to fit residues: 66.3781 Evaluate side-chains 218 residues out of total 2931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 176 time to evaluate : 1.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 364 PHE Chi-restraints excluded: chain C residue 388 GLU Chi-restraints excluded: chain C residue 390 VAL Chi-restraints excluded: chain C residue 511 GLU Chi-restraints excluded: chain C residue 559 VAL Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain C residue 640 VAL Chi-restraints excluded: chain C residue 652 MET Chi-restraints excluded: chain C residue 657 THR Chi-restraints excluded: chain C residue 819 LYS Chi-restraints excluded: chain C residue 943 VAL Chi-restraints excluded: chain C residue 965 THR Chi-restraints excluded: chain C residue 976 LEU Chi-restraints excluded: chain C residue 1082 ILE Chi-restraints excluded: chain C residue 1098 VAL Chi-restraints excluded: chain C residue 1116 LEU Chi-restraints excluded: chain D residue 12 ILE Chi-restraints excluded: chain D residue 129 ILE Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 248 TYR Chi-restraints excluded: chain D residue 1042 ARG Chi-restraints excluded: chain F residue 185 VAL Chi-restraints excluded: chain F residue 201 LEU Chi-restraints excluded: chain F residue 373 LEU Chi-restraints excluded: chain F residue 420 THR Chi-restraints excluded: chain H residue 12 SER Chi-restraints excluded: chain H residue 47 VAL Chi-restraints excluded: chain H residue 67 ASP Chi-restraints excluded: chain H residue 130 HIS Chi-restraints excluded: chain H residue 132 LEU Chi-restraints excluded: chain H residue 137 VAL Chi-restraints excluded: chain J residue 14 VAL Chi-restraints excluded: chain J residue 22 HIS Chi-restraints excluded: chain J residue 84 MET Chi-restraints excluded: chain E residue 42 SER Chi-restraints excluded: chain E residue 80 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 219 optimal weight: 3.9990 chunk 49 optimal weight: 6.9990 chunk 285 optimal weight: 2.9990 chunk 61 optimal weight: 0.7980 chunk 163 optimal weight: 0.9990 chunk 334 optimal weight: 7.9990 chunk 48 optimal weight: 0.9980 chunk 41 optimal weight: 3.9990 chunk 146 optimal weight: 5.9990 chunk 10 optimal weight: 0.9990 chunk 171 optimal weight: 6.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 534 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 914 HIS F 353 GLN ** J 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 66 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.088539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.061555 restraints weight = 90207.130| |-----------------------------------------------------------------------------| r_work (start): 0.2879 rms_B_bonded: 3.17 r_work: 0.2722 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.2722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8941 moved from start: 0.2710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 28859 Z= 0.127 Angle : 0.591 14.139 39289 Z= 0.301 Chirality : 0.042 0.208 4453 Planarity : 0.004 0.112 5001 Dihedral : 12.692 158.884 4426 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.33 % Allowed : 13.10 % Favored : 85.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % 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: 0.96 (0.14), residues: 3466 helix: 1.67 (0.15), residues: 1305 sheet: -0.15 (0.25), residues: 389 loop : 0.13 (0.15), residues: 1772 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D1053 TYR 0.014 0.001 TYR A 176 PHE 0.019 0.001 PHE H 97 TRP 0.122 0.002 TRP J 82 HIS 0.006 0.001 HIS F 454 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.13 (28851) covalent geometry : angle 0.58799 / 0.30 (39277) hydrogen bonds : bond 0.03994 / 2.77 ( 1259) hydrogen bonds : angle 4.37772 / 3.04 ( 3522) metal coordination : bond 0.00693 / 0.35 ( 8) metal coordination : angle 3.48005 / 2.03 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6932 Ramachandran restraints generated. 3466 Oldfield, 0 Emsley, 3466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6932 Ramachandran restraints generated. 3466 Oldfield, 0 Emsley, 3466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 2931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 182 time to evaluate : 0.866 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 153 LYS cc_start: 0.9098 (ttpt) cc_final: 0.8812 (ptmt) REVERT: C 145 MET cc_start: 0.8441 (OUTLIER) cc_final: 0.7746 (mpp) REVERT: C 150 MET cc_start: 0.9041 (mmm) cc_final: 0.8831 (mmm) REVERT: C 395 MET cc_start: 0.8174 (OUTLIER) cc_final: 0.7867 (ptm) REVERT: C 652 MET cc_start: 0.8407 (tpp) cc_final: 0.8092 (tpp) REVERT: C 772 LEU cc_start: 0.9100 (pt) cc_final: 0.8855 (pp) REVERT: D 214 ARG cc_start: 0.9154 (tpp-160) cc_final: 0.8678 (mmm160) REVERT: D 242 ARG cc_start: 0.9019 (mmt-90) cc_final: 0.8643 (mmt-90) REVERT: D 248 TYR cc_start: 0.8704 (OUTLIER) cc_final: 0.8419 (m-80) REVERT: D 373 MET cc_start: 0.8524 (mtm) cc_final: 0.8309 (mtm) REVERT: D 941 HIS cc_start: 0.7560 (t-170) cc_final: 0.7284 (t-170) REVERT: D 1113 MET cc_start: 0.8852 (OUTLIER) cc_final: 0.7883 (tpp) REVERT: F 201 LEU cc_start: 0.9358 (OUTLIER) cc_final: 0.9105 (mm) REVERT: H 142 GLU cc_start: 0.8083 (tm-30) cc_final: 0.7670 (tm-30) REVERT: J 24 LEU cc_start: 0.8767 (mp) cc_final: 0.8348 (tp) REVERT: J 32 TYR cc_start: 0.8593 (m-80) cc_final: 0.7767 (m-80) outliers start: 39 outliers final: 22 residues processed: 212 average time/residue: 0.1748 time to fit residues: 60.3667 Evaluate side-chains 202 residues out of total 2931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 175 time to evaluate : 0.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain C residue 145 MET Chi-restraints excluded: chain C residue 390 VAL Chi-restraints excluded: chain C residue 395 MET Chi-restraints excluded: chain C residue 559 VAL Chi-restraints excluded: chain C residue 657 THR Chi-restraints excluded: chain C residue 819 LYS Chi-restraints excluded: chain C residue 943 VAL Chi-restraints excluded: chain C residue 965 THR Chi-restraints excluded: chain C residue 976 LEU Chi-restraints excluded: chain C residue 1082 ILE Chi-restraints excluded: chain C residue 1116 LEU Chi-restraints excluded: chain D residue 12 ILE Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 248 TYR Chi-restraints excluded: chain D residue 1113 MET Chi-restraints excluded: chain F residue 185 VAL Chi-restraints excluded: chain F residue 201 LEU Chi-restraints excluded: chain F residue 420 THR Chi-restraints excluded: chain H residue 67 ASP Chi-restraints excluded: chain H residue 130 HIS Chi-restraints excluded: chain H residue 137 VAL Chi-restraints excluded: chain J residue 22 HIS Chi-restraints excluded: chain J residue 84 MET Chi-restraints excluded: chain E residue 42 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 144 optimal weight: 0.9980 chunk 146 optimal weight: 9.9990 chunk 166 optimal weight: 4.9990 chunk 132 optimal weight: 2.9990 chunk 248 optimal weight: 5.9990 chunk 177 optimal weight: 4.9990 chunk 311 optimal weight: 9.9990 chunk 292 optimal weight: 8.9990 chunk 107 optimal weight: 4.9990 chunk 188 optimal weight: 10.0000 chunk 210 optimal weight: 4.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 200 ASN ** C 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 534 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 233 GLN D 369 ASN D 914 HIS F 260 GLN ** J 81 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 = 0.3567 r_free = 0.3567 target = 0.086896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.060354 restraints weight = 89115.909| |-----------------------------------------------------------------------------| r_work (start): 0.2849 rms_B_bonded: 3.09 r_work: 0.2685 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.2685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8972 moved from start: 0.2836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 28859 Z= 0.238 Angle : 0.648 14.166 39289 Z= 0.329 Chirality : 0.044 0.207 4453 Planarity : 0.004 0.062 5001 Dihedral : 12.750 158.374 4426 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 1.57 % Allowed : 13.37 % Favored : 85.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % 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: 0.81 (0.14), residues: 3466 helix: 1.59 (0.15), residues: 1306 sheet: -0.24 (0.25), residues: 398 loop : 0.01 (0.15), residues: 1762 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 296 TYR 0.012 0.001 TYR C 722 PHE 0.023 0.002 PHE H 97 TRP 0.094 0.002 TRP J 82 HIS 0.006 0.001 HIS F 454 Details of bonding type rmsd/Z covalent geometry : bond 0.00561 / 0.24 (28851) covalent geometry : angle 0.64487 / 0.33 (39277) hydrogen bonds : bond 0.04420 / 3.07 ( 1259) hydrogen bonds : angle 4.46684 / 3.10 ( 3522) metal coordination : bond 0.01410 / 0.73 ( 8) metal coordination : angle 3.47381 / 2.07 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6932 Ramachandran restraints generated. 3466 Oldfield, 0 Emsley, 3466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6932 Ramachandran restraints generated. 3466 Oldfield, 0 Emsley, 3466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 2931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 176 time to evaluate : 1.110 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 153 LYS cc_start: 0.9141 (ttpt) cc_final: 0.8892 (ptmt) REVERT: C 145 MET cc_start: 0.8583 (OUTLIER) cc_final: 0.7510 (mtp) REVERT: C 150 MET cc_start: 0.9056 (mmm) cc_final: 0.8839 (mmm) REVERT: C 652 MET cc_start: 0.8395 (tpp) cc_final: 0.8104 (tpp) REVERT: C 772 LEU cc_start: 0.9145 (pt) cc_final: 0.8893 (pp) REVERT: D 214 ARG cc_start: 0.9218 (tpp-160) cc_final: 0.8743 (mmm160) REVERT: D 242 ARG cc_start: 0.9042 (mmt-90) cc_final: 0.8674 (mmt-90) REVERT: D 248 TYR cc_start: 0.8708 (OUTLIER) cc_final: 0.8423 (m-80) REVERT: D 941 HIS cc_start: 0.7655 (t-170) cc_final: 0.7313 (t-170) REVERT: D 1113 MET cc_start: 0.8923 (OUTLIER) cc_final: 0.8418 (mmm) REVERT: F 201 LEU cc_start: 0.9353 (OUTLIER) cc_final: 0.9061 (mt) REVERT: F 287 TRP cc_start: 0.8036 (m-10) cc_final: 0.7834 (m-10) REVERT: H 142 GLU cc_start: 0.8118 (tm-30) cc_final: 0.7693 (tm-30) REVERT: J 24 LEU cc_start: 0.8777 (mp) cc_final: 0.8444 (tp) REVERT: J 32 TYR cc_start: 0.8652 (m-80) cc_final: 0.7844 (m-80) outliers start: 46 outliers final: 31 residues processed: 211 average time/residue: 0.1798 time to fit residues: 61.7848 Evaluate side-chains 209 residues out of total 2931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 174 time to evaluate : 0.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain C residue 145 MET Chi-restraints excluded: chain C residue 364 PHE Chi-restraints excluded: chain C residue 390 VAL Chi-restraints excluded: chain C residue 559 VAL Chi-restraints excluded: chain C residue 657 THR Chi-restraints excluded: chain C residue 819 LYS Chi-restraints excluded: chain C residue 943 VAL Chi-restraints excluded: chain C residue 965 THR Chi-restraints excluded: chain C residue 976 LEU Chi-restraints excluded: chain C residue 1082 ILE Chi-restraints excluded: chain C residue 1098 VAL Chi-restraints excluded: chain C residue 1116 LEU Chi-restraints excluded: chain D residue 12 ILE Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 141 ASP Chi-restraints excluded: chain D residue 248 TYR Chi-restraints excluded: chain D residue 914 HIS Chi-restraints excluded: chain D residue 1113 MET Chi-restraints excluded: chain F residue 185 VAL Chi-restraints excluded: chain F residue 201 LEU Chi-restraints excluded: chain F residue 373 LEU Chi-restraints excluded: chain F residue 420 THR Chi-restraints excluded: chain H residue 67 ASP Chi-restraints excluded: chain H residue 123 MET Chi-restraints excluded: chain H residue 130 HIS Chi-restraints excluded: chain H residue 137 VAL Chi-restraints excluded: chain J residue 14 VAL Chi-restraints excluded: chain J residue 22 HIS Chi-restraints excluded: chain J residue 84 MET Chi-restraints excluded: chain E residue 42 SER Chi-restraints excluded: chain E residue 80 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 109 optimal weight: 2.9990 chunk 197 optimal weight: 4.9990 chunk 205 optimal weight: 3.9990 chunk 302 optimal weight: 6.9990 chunk 268 optimal weight: 6.9990 chunk 239 optimal weight: 5.9990 chunk 103 optimal weight: 0.8980 chunk 187 optimal weight: 0.9990 chunk 249 optimal weight: 4.9990 chunk 73 optimal weight: 7.9990 chunk 246 optimal weight: 2.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 534 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.087987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.061545 restraints weight = 88845.202| |-----------------------------------------------------------------------------| r_work (start): 0.2865 rms_B_bonded: 3.08 r_work: 0.2704 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.2704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8958 moved from start: 0.2884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 28859 Z= 0.167 Angle : 0.618 14.876 39289 Z= 0.314 Chirality : 0.043 0.202 4453 Planarity : 0.004 0.063 5001 Dihedral : 12.724 157.867 4426 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.33 % Allowed : 13.51 % Favored : 85.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % 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: 0.84 (0.14), residues: 3466 helix: 1.64 (0.15), residues: 1303 sheet: -0.17 (0.25), residues: 392 loop : -0.01 (0.15), residues: 1771 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D1053 TYR 0.011 0.001 TYR D 586 PHE 0.032 0.001 PHE H 97 TRP 0.086 0.002 TRP J 82 HIS 0.045 0.001 HIS D 914 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.17 (28851) covalent geometry : angle 0.61459 / 0.31 (39277) hydrogen bonds : bond 0.04113 / 2.86 ( 1259) hydrogen bonds : angle 4.39655 / 3.04 ( 3522) metal coordination : bond 0.01004 / 0.52 ( 8) metal coordination : angle 3.60635 / 2.12 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6932 Ramachandran restraints generated. 3466 Oldfield, 0 Emsley, 3466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6932 Ramachandran restraints generated. 3466 Oldfield, 0 Emsley, 3466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 2931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 181 time to evaluate : 0.995 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 145 MET cc_start: 0.8621 (OUTLIER) cc_final: 0.7664 (mtp) REVERT: C 150 MET cc_start: 0.9063 (mmm) cc_final: 0.8850 (mmm) REVERT: C 216 ARG cc_start: 0.8179 (ttm110) cc_final: 0.7968 (ttm110) REVERT: C 652 MET cc_start: 0.8392 (tpp) cc_final: 0.8100 (tpp) REVERT: C 772 LEU cc_start: 0.9139 (pt) cc_final: 0.8891 (pp) REVERT: D 214 ARG cc_start: 0.9220 (tpp-160) cc_final: 0.8731 (mmm160) REVERT: D 242 ARG cc_start: 0.9040 (mmt-90) cc_final: 0.8666 (mmt-90) REVERT: D 248 TYR cc_start: 0.8683 (OUTLIER) cc_final: 0.8405 (m-80) REVERT: D 941 HIS cc_start: 0.7591 (t-170) cc_final: 0.7250 (t-170) REVERT: D 1113 MET cc_start: 0.8883 (OUTLIER) cc_final: 0.8105 (tpp) REVERT: F 201 LEU cc_start: 0.9350 (OUTLIER) cc_final: 0.9061 (mt) REVERT: H 142 GLU cc_start: 0.8131 (tm-30) cc_final: 0.7718 (tm-30) REVERT: J 24 LEU cc_start: 0.8802 (mp) cc_final: 0.8446 (tp) REVERT: J 32 TYR cc_start: 0.8653 (m-80) cc_final: 0.7844 (m-80) outliers start: 39 outliers final: 30 residues processed: 210 average time/residue: 0.1615 time to fit residues: 54.7850 Evaluate side-chains 208 residues out of total 2931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 174 time to evaluate : 1.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain C residue 145 MET Chi-restraints excluded: chain C residue 364 PHE Chi-restraints excluded: chain C residue 390 VAL Chi-restraints excluded: chain C residue 511 GLU Chi-restraints excluded: chain C residue 559 VAL Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain C residue 657 THR Chi-restraints excluded: chain C residue 819 LYS Chi-restraints excluded: chain C residue 943 VAL Chi-restraints excluded: chain C residue 965 THR Chi-restraints excluded: chain C residue 976 LEU Chi-restraints excluded: chain C residue 1082 ILE Chi-restraints excluded: chain C residue 1098 VAL Chi-restraints excluded: chain C residue 1116 LEU Chi-restraints excluded: chain D residue 12 ILE Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 141 ASP Chi-restraints excluded: chain D residue 248 TYR Chi-restraints excluded: chain D residue 1113 MET Chi-restraints excluded: chain F residue 185 VAL Chi-restraints excluded: chain F residue 201 LEU Chi-restraints excluded: chain F residue 420 THR Chi-restraints excluded: chain H residue 67 ASP Chi-restraints excluded: chain H residue 123 MET Chi-restraints excluded: chain H residue 130 HIS Chi-restraints excluded: chain H residue 137 VAL Chi-restraints excluded: chain J residue 14 VAL Chi-restraints excluded: chain J residue 22 HIS Chi-restraints excluded: chain J residue 84 MET Chi-restraints excluded: chain E residue 42 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 314 optimal weight: 8.9990 chunk 221 optimal weight: 4.9990 chunk 48 optimal weight: 7.9990 chunk 25 optimal weight: 0.9980 chunk 131 optimal weight: 0.7980 chunk 259 optimal weight: 1.9990 chunk 12 optimal weight: 4.9990 chunk 220 optimal weight: 0.5980 chunk 309 optimal weight: 8.9990 chunk 133 optimal weight: 2.9990 chunk 210 optimal weight: 3.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 534 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 914 HIS ** J 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.088843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.061997 restraints weight = 90407.901| |-----------------------------------------------------------------------------| r_work (start): 0.2881 rms_B_bonded: 3.16 r_work: 0.2724 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.2724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8940 moved from start: 0.2932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 28859 Z= 0.130 Angle : 0.600 14.823 39289 Z= 0.303 Chirality : 0.042 0.198 4453 Planarity : 0.004 0.062 5001 Dihedral : 12.706 157.271 4426 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.30 % Allowed : 13.61 % Favored : 85.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % 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: 0.91 (0.14), residues: 3466 helix: 1.68 (0.15), residues: 1306 sheet: -0.12 (0.26), residues: 379 loop : 0.04 (0.15), residues: 1781 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D1053 TYR 0.012 0.001 TYR C 335 PHE 0.018 0.001 PHE D1063 TRP 0.077 0.002 TRP J 82 HIS 0.008 0.001 HIS J 81 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.13 (28851) covalent geometry : angle 0.59717 / 0.30 (39277) hydrogen bonds : bond 0.03817 / 2.65 ( 1259) hydrogen bonds : angle 4.30889 / 2.98 ( 3522) metal coordination : bond 0.00737 / 0.38 ( 8) metal coordination : angle 3.36397 / 1.97 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5589.85 seconds wall clock time: 96 minutes 33.28 seconds (5793.28 seconds total)