Starting phenix.real_space_refine on Mon Jul 6 08:19:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7bef_12156/07_2026/7bef_12156.cif Found real_map, /net/cci-nas-00/data/ceres_data/7bef_12156/07_2026/7bef_12156.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7bef_12156/07_2026/7bef_12156.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7bef_12156/07_2026/7bef_12156.map" model { file = "/net/cci-nas-00/data/ceres_data/7bef_12156/07_2026/7bef_12156.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7bef_12156/07_2026/7bef_12156.cif" } resolution = 4.5 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= 0.001 sd= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 146 5.49 5 S 132 5.16 5 C 20770 2.51 5 N 6015 2.21 5 O 6804 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 33867 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 2376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2376 Classifications: {'peptide': 305} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 290} Chain breaks: 1 Chain: "B" Number of atoms: 1767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1767 Classifications: {'peptide': 228} Link IDs: {'PTRANS': 9, 'TRANS': 218} Chain: "C" Number of atoms: 10556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1340, 10556 Classifications: {'peptide': 1340} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 55, 'TRANS': 1283} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'TRP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "D" Number of atoms: 10568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1362, 10568 Classifications: {'peptide': 1362} Link IDs: {'PCIS': 2, 'PTRANS': 53, 'TRANS': 1306} Chain: "E" Number of atoms: 708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 708 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 2, 'TRANS': 87} Chain: "F" Number of atoms: 4014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 496, 4014 Classifications: {'peptide': 496} Link IDs: {'PTRANS': 15, 'TRANS': 480} Chain breaks: 1 Chain: "G" Number of atoms: 881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 881 Classifications: {'peptide': 106} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 3, 'TRANS': 102} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "T" Number of atoms: 1501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1501 Classifications: {'DNA': 73} Link IDs: {'rna3p': 72} Chain: "N" Number of atoms: 1496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1496 Classifications: {'DNA': 73} Link IDs: {'rna3p': 72} Time building chain proxies: 6.86, per 1000 atoms: 0.20 Number of scatterers: 33867 At special positions: 0 Unit cell: (161.516, 200.54, 191.868, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 132 16.00 P 146 15.00 O 6804 8.00 N 6015 7.00 C 20770 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.11 Conformation dependent library (CDL) restraints added in 1.5 seconds 7818 Ramachandran restraints generated. 3909 Oldfield, 0 Emsley, 3909 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7292 Finding SS restraints... Secondary structure from input PDB file: 137 helices and 45 sheets defined 44.5% alpha, 11.4% beta 44 base pairs and 85 stacking pairs defined. Time for finding SS restraints: 3.89 Creating SS restraints... Processing helix chain 'A' and resid 35 through 50 Processing helix chain 'A' and resid 77 through 87 removed outlier: 3.991A pdb=" N GLY A 87 " --> pdb=" O LEU A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 115 No H-bonds generated for 'chain 'A' and resid 113 through 115' Processing helix chain 'A' and resid 154 through 162 removed outlier: 3.970A pdb=" N HIS A 160 " --> pdb=" O SER A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 233 removed outlier: 4.595A pdb=" N ALA A 230 " --> pdb=" O GLU A 226 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N PHE A 231 " --> pdb=" O GLN A 227 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N VAL A 232 " --> pdb=" O LEU A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 269 removed outlier: 3.709A pdb=" N CYS A 269 " --> pdb=" O ARG A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 273 removed outlier: 3.669A pdb=" N GLU A 273 " --> pdb=" O LEU A 270 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 270 through 273' Processing helix chain 'A' and resid 277 through 284 removed outlier: 3.580A pdb=" N LEU A 281 " --> pdb=" O TYR A 277 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ARG A 284 " --> pdb=" O ASP A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 290 Processing helix chain 'A' and resid 298 through 308 removed outlier: 4.004A pdb=" N GLU A 302 " --> pdb=" O LYS A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 311 No H-bonds generated for 'chain 'A' and resid 309 through 311' Processing helix chain 'B' and resid 35 through 50 removed outlier: 3.653A pdb=" N SER B 50 " --> pdb=" O ILE B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 88 Processing helix chain 'B' and resid 154 through 161 removed outlier: 3.654A pdb=" N ARG B 158 " --> pdb=" O PRO B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 233 removed outlier: 4.738A pdb=" N ALA B 230 " --> pdb=" O GLU B 226 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N PHE B 231 " --> pdb=" O GLN B 227 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ASP B 233 " --> pdb=" O GLU B 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 4 through 10 removed outlier: 4.015A pdb=" N ARG C 10 " --> pdb=" O THR C 6 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 40 removed outlier: 3.916A pdb=" N LEU C 32 " --> pdb=" O LEU C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 57 Processing helix chain 'C' and resid 81 through 89 Processing helix chain 'C' and resid 207 through 213 removed outlier: 3.515A pdb=" N LEU C 213 " --> pdb=" O ILE C 209 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 225 Processing helix chain 'C' and resid 270 through 280 Processing helix chain 'C' and resid 288 through 293 removed outlier: 4.009A pdb=" N ILE C 292 " --> pdb=" O PRO C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 329 Processing helix chain 'C' and resid 345 through 354 Processing helix chain 'C' and resid 358 through 371 Processing helix chain 'C' and resid 377 through 389 removed outlier: 3.964A pdb=" N PHE C 389 " --> pdb=" O PHE C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 398 through 409 Processing helix chain 'C' and resid 423 through 438 Processing helix chain 'C' and resid 455 through 480 removed outlier: 3.665A pdb=" N SER C 480 " --> pdb=" O LYS C 476 " (cutoff:3.500A) Processing helix chain 'C' and resid 495 through 509 removed outlier: 3.617A pdb=" N SER C 509 " --> pdb=" O PHE C 505 " (cutoff:3.500A) Processing helix chain 'C' and resid 519 through 528 Processing helix chain 'C' and resid 551 through 555 removed outlier: 3.661A pdb=" N TYR C 555 " --> pdb=" O PRO C 552 " (cutoff:3.500A) Processing helix chain 'C' and resid 565 through 569 removed outlier: 3.934A pdb=" N ASN C 568 " --> pdb=" O GLU C 565 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ILE C 569 " --> pdb=" O GLY C 566 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 565 through 569' Processing helix chain 'C' and resid 607 through 612 Processing helix chain 'C' and resid 662 through 667 Processing helix chain 'C' and resid 675 through 688 Processing helix chain 'C' and resid 704 through 712 Processing helix chain 'C' and resid 820 through 825 Processing helix chain 'C' and resid 858 through 863 removed outlier: 3.544A pdb=" N LEU C 862 " --> pdb=" O GLY C 858 " (cutoff:3.500A) Processing helix chain 'C' and resid 896 through 907 Processing helix chain 'C' and resid 944 through 956 removed outlier: 4.070A pdb=" N ILE C 948 " --> pdb=" O ARG C 944 " (cutoff:3.500A) Processing helix chain 'C' and resid 958 through 983 Processing helix chain 'C' and resid 993 through 997 removed outlier: 3.679A pdb=" N TRP C 997 " --> pdb=" O ARG C 994 " (cutoff:3.500A) Processing helix chain 'C' and resid 1005 through 1039 removed outlier: 3.716A pdb=" N ASN C1009 " --> pdb=" O GLU C1005 " (cutoff:3.500A) Processing helix chain 'C' and resid 1103 through 1107 removed outlier: 3.566A pdb=" N ARG C1106 " --> pdb=" O VAL C1103 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N MET C1107 " --> pdb=" O PRO C1104 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1103 through 1107' Processing helix chain 'C' and resid 1110 through 1133 Processing helix chain 'C' and resid 1137 through 1150 removed outlier: 3.510A pdb=" N LEU C1141 " --> pdb=" O GLU C1137 " (cutoff:3.500A) Processing helix chain 'C' and resid 1165 through 1177 Processing helix chain 'C' and resid 1191 through 1202 Processing helix chain 'C' and resid 1238 through 1243 Processing helix chain 'C' and resid 1271 through 1281 removed outlier: 3.592A pdb=" N VAL C1275 " --> pdb=" O GLY C1271 " (cutoff:3.500A) Processing helix chain 'C' and resid 1284 through 1292 removed outlier: 3.527A pdb=" N GLN C1288 " --> pdb=" O ALA C1284 " (cutoff:3.500A) Processing helix chain 'C' and resid 1297 through 1310 Processing helix chain 'C' and resid 1320 through 1333 removed outlier: 3.714A pdb=" N LEU C1333 " --> pdb=" O GLU C1329 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 34 Processing helix chain 'D' and resid 58 through 63 Processing helix chain 'D' and resid 94 through 101 removed outlier: 3.604A pdb=" N VAL D 97 " --> pdb=" O GLN D 94 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ARG D 101 " --> pdb=" O ARG D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 113 through 118 removed outlier: 3.886A pdb=" N LEU D 117 " --> pdb=" O HIS D 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 129 Processing helix chain 'D' and resid 131 through 140 removed outlier: 3.503A pdb=" N ILE D 135 " --> pdb=" O PRO D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 161 through 170 Processing helix chain 'D' and resid 181 through 192 Processing helix chain 'D' and resid 193 through 208 removed outlier: 3.602A pdb=" N GLU D 197 " --> pdb=" O ASP D 193 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ASN D 206 " --> pdb=" O ARG D 202 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLU D 207 " --> pdb=" O GLU D 203 " (cutoff:3.500A) Processing helix chain 'D' and resid 210 through 231 removed outlier: 3.543A pdb=" N GLY D 231 " --> pdb=" O PHE D 227 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 236 Processing helix chain 'D' and resid 263 through 285 Processing helix chain 'D' and resid 288 through 308 Processing helix chain 'D' and resid 326 through 333 Processing helix chain 'D' and resid 337 through 342 Processing helix chain 'D' and resid 370 through 377 Processing helix chain 'D' and resid 377 through 389 Processing helix chain 'D' and resid 393 through 403 removed outlier: 3.566A pdb=" N LYS D 399 " --> pdb=" O LYS D 395 " (cutoff:3.500A) Processing helix chain 'D' and resid 405 through 416 removed outlier: 3.718A pdb=" N GLU D 414 " --> pdb=" O ASP D 410 " (cutoff:3.500A) Processing helix chain 'D' and resid 430 through 432 No H-bonds generated for 'chain 'D' and resid 430 through 432' Processing helix chain 'D' and resid 450 through 452 No H-bonds generated for 'chain 'D' and resid 450 through 452' Processing helix chain 'D' and resid 453 through 458 Processing helix chain 'D' and resid 473 through 483 Processing helix chain 'D' and resid 504 through 514 Processing helix chain 'D' and resid 529 through 539 removed outlier: 3.741A pdb=" N ALA D 533 " --> pdb=" O GLY D 529 " (cutoff:3.500A) Processing helix chain 'D' and resid 573 through 583 Processing helix chain 'D' and resid 597 through 612 Processing helix chain 'D' and resid 614 through 636 removed outlier: 3.937A pdb=" N VAL D 618 " --> pdb=" O LEU D 614 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ILE D 619 " --> pdb=" O LYS D 615 " (cutoff:3.500A) Processing helix chain 'D' and resid 648 through 671 removed outlier: 4.230A pdb=" N GLU D 652 " --> pdb=" O GLU D 648 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLY D 671 " --> pdb=" O GLN D 667 " (cutoff:3.500A) Processing helix chain 'D' and resid 674 through 703 removed outlier: 4.469A pdb=" N THR D 703 " --> pdb=" O ASP D 699 " (cutoff:3.500A) Processing helix chain 'D' and resid 720 through 729 Processing helix chain 'D' and resid 733 through 741 removed outlier: 4.114A pdb=" N ILE D 737 " --> pdb=" O SER D 733 " (cutoff:3.500A) Processing helix chain 'D' and resid 768 through 804 removed outlier: 3.758A pdb=" N HIS D 777 " --> pdb=" O PHE D 773 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N GLY D 778 " --> pdb=" O ILE D 774 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N ALA D 791 " --> pdb=" O ALA D 787 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ASN D 792 " --> pdb=" O LEU D 788 " (cutoff:3.500A) Processing helix chain 'D' and resid 865 through 876 Processing helix chain 'D' and resid 915 through 938 removed outlier: 3.589A pdb=" N ALA D 919 " --> pdb=" O ILE D 915 " (cutoff:3.500A) Proline residue: D 926 - end of helix removed outlier: 4.175A pdb=" N PHE D 935 " --> pdb=" O THR D 931 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N HIS D 936 " --> pdb=" O MET D 932 " (cutoff:3.500A) Processing helix chain 'D' and resid 1133 through 1136 Processing helix chain 'D' and resid 1137 through 1146 removed outlier: 3.535A pdb=" N VAL D1141 " --> pdb=" O GLY D1137 " (cutoff:3.500A) Processing helix chain 'D' and resid 1216 through 1224 removed outlier: 3.514A pdb=" N ILE D1220 " --> pdb=" O ALA D1216 " (cutoff:3.500A) Processing helix chain 'D' and resid 1225 through 1245 removed outlier: 3.591A pdb=" N VAL D1229 " --> pdb=" O GLY D1225 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N VAL D1240 " --> pdb=" O GLU D1236 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N TYR D1241 " --> pdb=" O VAL D1237 " (cutoff:3.500A) Processing helix chain 'D' and resid 1249 through 1261 removed outlier: 4.276A pdb=" N ILE D1253 " --> pdb=" O ASN D1249 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ILE D1256 " --> pdb=" O HIS D1252 " (cutoff:3.500A) Processing helix chain 'D' and resid 1282 through 1296 Processing helix chain 'D' and resid 1308 through 1315 Processing helix chain 'D' and resid 1318 through 1326 removed outlier: 3.523A pdb=" N GLN D1326 " --> pdb=" O ALA D1322 " (cutoff:3.500A) Processing helix chain 'D' and resid 1327 through 1339 Processing helix chain 'D' and resid 1346 through 1354 removed outlier: 3.825A pdb=" N ASN D1350 " --> pdb=" O GLY D1346 " (cutoff:3.500A) Processing helix chain 'D' and resid 1359 through 1361 No H-bonds generated for 'chain 'D' and resid 1359 through 1361' Processing helix chain 'D' and resid 1362 through 1376 Processing helix chain 'E' and resid 6 through 14 Processing helix chain 'E' and resid 15 through 33 Processing helix chain 'E' and resid 45 through 57 Processing helix chain 'E' and resid 60 through 91 Processing helix chain 'F' and resid 80 through 91 Processing helix chain 'F' and resid 96 through 107 removed outlier: 3.874A pdb=" N THR F 107 " --> pdb=" O ARG F 103 " (cutoff:3.500A) Processing helix chain 'F' and resid 114 through 136 removed outlier: 3.843A pdb=" N ASP F 118 " --> pdb=" O GLU F 114 " (cutoff:3.500A) Processing helix chain 'F' and resid 137 through 153 removed outlier: 4.147A pdb=" N ILE F 141 " --> pdb=" O TYR F 137 " (cutoff:3.500A) Processing helix chain 'F' and resid 213 through 233 removed outlier: 4.670A pdb=" N GLU F 223 " --> pdb=" O GLU F 219 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N LEU F 224 " --> pdb=" O LYS F 220 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ASP F 233 " --> pdb=" O VAL F 229 " (cutoff:3.500A) Processing helix chain 'F' and resid 242 through 258 removed outlier: 3.910A pdb=" N GLN F 258 " --> pdb=" O GLU F 254 " (cutoff:3.500A) Processing helix chain 'F' and resid 262 through 296 removed outlier: 4.114A pdb=" N TYR F 268 " --> pdb=" O LYS F 264 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N GLN F 294 " --> pdb=" O LEU F 290 " (cutoff:3.500A) Processing helix chain 'F' and resid 299 through 310 removed outlier: 3.667A pdb=" N THR F 304 " --> pdb=" O LYS F 300 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N LEU F 305 " --> pdb=" O ASN F 301 " (cutoff:3.500A) Processing helix chain 'F' and resid 313 through 322 Processing helix chain 'F' and resid 324 through 328 removed outlier: 3.833A pdb=" N GLU F 328 " --> pdb=" O PRO F 325 " (cutoff:3.500A) Processing helix chain 'F' and resid 330 through 352 removed outlier: 4.350A pdb=" N GLU F 335 " --> pdb=" O HIS F 331 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N GLU F 336 " --> pdb=" O ASP F 332 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N HIS F 338 " --> pdb=" O SER F 334 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ARG F 339 " --> pdb=" O GLU F 335 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LYS F 343 " --> pdb=" O ARG F 339 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LEU F 344 " --> pdb=" O ALA F 340 " (cutoff:3.500A) Processing helix chain 'F' and resid 354 through 394 removed outlier: 4.938A pdb=" N ARG F 385 " --> pdb=" O GLU F 381 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N LEU F 386 " --> pdb=" O ALA F 382 " (cutoff:3.500A) Processing helix chain 'F' and resid 400 through 417 Processing helix chain 'F' and resid 426 through 446 removed outlier: 4.108A pdb=" N TYR F 430 " --> pdb=" O LYS F 426 " (cutoff:3.500A) Processing helix chain 'F' and resid 453 through 475 removed outlier: 3.512A pdb=" N GLN F 469 " --> pdb=" O ARG F 465 " (cutoff:3.500A) Processing helix chain 'F' and resid 479 through 488 Processing helix chain 'F' and resid 490 through 501 removed outlier: 3.721A pdb=" N ILE F 494 " --> pdb=" O PRO F 490 " (cutoff:3.500A) Processing helix chain 'F' and resid 530 through 551 Processing helix chain 'F' and resid 552 through 564 Processing helix chain 'F' and resid 572 through 581 Processing helix chain 'F' and resid 583 through 599 removed outlier: 3.734A pdb=" N ILE F 587 " --> pdb=" O THR F 583 " (cutoff:3.500A) Processing helix chain 'F' and resid 600 through 605 Processing helix chain 'F' and resid 607 through 611 Processing helix chain 'G' and resid 7 through 18 removed outlier: 3.632A pdb=" N VAL G 12 " --> pdb=" O ILE G 8 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N GLU G 13 " --> pdb=" O ASP G 9 " (cutoff:3.500A) Processing helix chain 'G' and resid 24 through 30 removed outlier: 3.943A pdb=" N ARG G 30 " --> pdb=" O ASP G 26 " (cutoff:3.500A) Processing helix chain 'G' and resid 31 through 33 No H-bonds generated for 'chain 'G' and resid 31 through 33' Processing helix chain 'G' and resid 35 through 46 removed outlier: 3.689A pdb=" N ARG G 41 " --> pdb=" O TRP G 37 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N LEU G 42 " --> pdb=" O HIS G 38 " (cutoff:3.500A) Processing helix chain 'G' and resid 50 through 67 removed outlier: 3.519A pdb=" N ARG G 56 " --> pdb=" O GLY G 52 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N ARG G 65 " --> pdb=" O LEU G 61 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ASP G 66 " --> pdb=" O LEU G 62 " (cutoff:3.500A) Processing helix chain 'G' and resid 73 through 78 removed outlier: 3.551A pdb=" N ILE G 77 " --> pdb=" O ARG G 73 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N CYS G 78 " --> pdb=" O VAL G 74 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 73 through 78' Processing helix chain 'G' and resid 85 through 97 removed outlier: 3.566A pdb=" N PHE G 89 " --> pdb=" O SER G 85 " (cutoff:3.500A) Processing helix chain 'G' and resid 100 through 107 removed outlier: 3.971A pdb=" N GLU G 107 " --> pdb=" O ALA G 103 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 23 through 31 removed outlier: 3.611A pdb=" N ALA A 24 " --> pdb=" O MET A 205 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N MET A 205 " --> pdb=" O ALA A 24 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N ASP A 199 " --> pdb=" O PRO A 30 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N ARG A 182 " --> pdb=" O GLU A 206 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 97 through 101 removed outlier: 7.075A pdb=" N GLN A 147 " --> pdb=" O VAL A 56 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N VAL A 56 " --> pdb=" O GLN A 147 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N VAL A 59 " --> pdb=" O LEU A 171 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 90 through 92 Processing sheet with id=AA4, first strand: chain 'A' and resid 108 through 111 Processing sheet with id=AA5, first strand: chain 'A' and resid 151 through 153 removed outlier: 4.225A pdb=" N GLY A 151 " --> pdb=" O TYR A 177 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N TYR A 177 " --> pdb=" O GLY A 151 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N VAL A 153 " --> pdb=" O ALA A 175 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N ALA A 175 " --> pdb=" O VAL A 153 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 13 through 20 removed outlier: 7.407A pdb=" N LEU B 13 " --> pdb=" O GLU B 29 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N GLU B 29 " --> pdb=" O LEU B 13 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ASP B 15 " --> pdb=" O THR B 27 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N VAL B 19 " --> pdb=" O HIS B 23 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N HIS B 23 " --> pdb=" O VAL B 19 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N ASP B 199 " --> pdb=" O PRO B 30 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 13 through 20 removed outlier: 7.407A pdb=" N LEU B 13 " --> pdb=" O GLU B 29 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N GLU B 29 " --> pdb=" O LEU B 13 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ASP B 15 " --> pdb=" O THR B 27 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N VAL B 19 " --> pdb=" O HIS B 23 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N HIS B 23 " --> pdb=" O VAL B 19 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N ASP B 199 " --> pdb=" O PRO B 30 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 98 through 99 removed outlier: 3.726A pdb=" N VAL B 98 " --> pdb=" O VAL B 146 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N VAL B 146 " --> pdb=" O VAL B 98 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 98 through 99 removed outlier: 3.726A pdb=" N VAL B 98 " --> pdb=" O VAL B 146 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N VAL B 146 " --> pdb=" O VAL B 98 " (cutoff:3.500A) removed outlier: 8.480A pdb=" N SER B 141 " --> pdb=" O ILE B 61 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N ILE B 61 " --> pdb=" O SER B 141 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N ARG B 143 " --> pdb=" O VAL B 59 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N VAL B 59 " --> pdb=" O ARG B 143 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N LYS B 145 " --> pdb=" O THR B 57 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 90 through 92 Processing sheet with id=AB2, first strand: chain 'B' and resid 108 through 110 removed outlier: 3.953A pdb=" N CYS B 131 " --> pdb=" O VAL B 110 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 152 through 153 Processing sheet with id=AB4, first strand: chain 'C' and resid 13 through 14 removed outlier: 5.670A pdb=" N LYS C 13 " --> pdb=" O ALA C1183 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 66 through 75 removed outlier: 5.448A pdb=" N LEU C 68 " --> pdb=" O VAL C 103 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N VAL C 103 " --> pdb=" O LEU C 68 " (cutoff:3.500A) removed outlier: 5.600A pdb=" N TYR C 70 " --> pdb=" O ARG C 101 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N ARG C 101 " --> pdb=" O TYR C 70 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N SER C 72 " --> pdb=" O LYS C 99 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N ALA C 94 " --> pdb=" O GLU C 126 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N GLU C 126 " --> pdb=" O ALA C 94 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N LEU C 96 " --> pdb=" O MET C 124 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N MET C 124 " --> pdb=" O LEU C 96 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ASP C 116 " --> pdb=" O ILE C 104 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 136 through 138 Processing sheet with id=AB7, first strand: chain 'C' and resid 148 through 151 Processing sheet with id=AB8, first strand: chain 'C' and resid 154 through 159 removed outlier: 4.927A pdb=" N TYR C 172 " --> pdb=" O PHE C 188 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU C 184 " --> pdb=" O ILE C 176 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ASN C 193 " --> pdb=" O ASP C 189 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 285 through 286 Processing sheet with id=AC1, first strand: chain 'C' and resid 301 through 302 removed outlier: 4.116A pdb=" N TYR C 301 " --> pdb=" O CYS C 311 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N CYS C 311 " --> pdb=" O TYR C 301 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'C' and resid 529 through 531 removed outlier: 4.358A pdb=" N SER C 574 " --> pdb=" O CYS C 559 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 580 through 581 removed outlier: 3.854A pdb=" N THR C 589 " --> pdb=" O LEU C 606 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N LEU C 606 " --> pdb=" O THR C 589 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 598 through 599 Processing sheet with id=AC5, first strand: chain 'C' and resid 722 through 727 removed outlier: 6.856A pdb=" N VAL C 733 " --> pdb=" O GLN C 725 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N VAL C 727 " --> pdb=" O ARG C 731 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N ARG C 731 " --> pdb=" O VAL C 727 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 1066 through 1067 removed outlier: 4.219A pdb=" N THR C1226 " --> pdb=" O PHE C 804 " (cutoff:3.500A) removed outlier: 9.252A pdb=" N ILE C1096 " --> pdb=" O ASN C 799 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N ARG C 801 " --> pdb=" O ILE C1096 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N LEU C1098 " --> pdb=" O ARG C 801 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N ALA C 803 " --> pdb=" O LEU C1098 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 816 through 819 removed outlier: 7.970A pdb=" N ILE C 816 " --> pdb=" O SER C1077 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N ILE C1079 " --> pdb=" O ILE C 816 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N VAL C 818 " --> pdb=" O ILE C1079 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'C' and resid 832 through 834 Processing sheet with id=AC9, first strand: chain 'C' and resid 837 through 840 removed outlier: 3.805A pdb=" N LYS C1048 " --> pdb=" O SER C 840 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 882 through 884 removed outlier: 6.817A pdb=" N LEU C 918 " --> pdb=" O LEU C 883 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 887 through 889 removed outlier: 3.792A pdb=" N THR C 888 " --> pdb=" O LYS C 914 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 1244 through 1246 Processing sheet with id=AD4, first strand: chain 'C' and resid 1268 through 1270 removed outlier: 3.659A pdb=" N GLN C1268 " --> pdb=" O VAL D 347 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 1335 through 1336 removed outlier: 3.534A pdb=" N ALA D 23 " --> pdb=" O ASN C1336 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 20 through 21 removed outlier: 3.832A pdb=" N ASP D1342 " --> pdb=" O ILE D 20 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 103 through 112 removed outlier: 10.255A pdb=" N LEU D 107 " --> pdb=" O PRO D 243 " (cutoff:3.500A) removed outlier: 11.326A pdb=" N SER D 109 " --> pdb=" O VAL D 241 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N VAL D 241 " --> pdb=" O SER D 109 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 158 through 160 removed outlier: 4.268A pdb=" N GLN D 158 " --> pdb=" O VAL D 146 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N VAL D 145 " --> pdb=" O LYS D 179 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N LYS D 179 " --> pdb=" O VAL D 145 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N ASP D 177 " --> pdb=" O ILE D 147 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 253 through 254 removed outlier: 3.946A pdb=" N VAL D 253 " --> pdb=" O ALA D 261 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 366 through 369 Processing sheet with id=AE2, first strand: chain 'D' and resid 526 through 527 removed outlier: 3.543A pdb=" N THR D 572 " --> pdb=" O VAL D 548 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 820 through 822 removed outlier: 3.725A pdb=" N ILE D 820 " --> pdb=" O VAL D 882 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N VAL D 882 " --> pdb=" O ILE D 820 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N VAL D 880 " --> pdb=" O MET D 822 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 957 through 959 removed outlier: 3.656A pdb=" N LYS D 959 " --> pdb=" O LYS D 983 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LYS D 983 " --> pdb=" O LYS D 959 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N GLU D 993 " --> pdb=" O LEU D 984 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 966 through 967 removed outlier: 3.942A pdb=" N VAL D 966 " --> pdb=" O VAL D 974 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N VAL D 974 " --> pdb=" O VAL D 966 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE5 Processing sheet with id=AE6, first strand: chain 'D' and resid 1034 through 1038 removed outlier: 3.839A pdb=" N THR D1038 " --> pdb=" O ALA D1077 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N TYR D1099 " --> pdb=" O LEU D1078 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 1046 through 1049 removed outlier: 3.581A pdb=" N THR D1047 " --> pdb=" O VAL D1060 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N VAL D1060 " --> pdb=" O THR D1047 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLN D1049 " --> pdb=" O SER D1058 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N SER D1058 " --> pdb=" O GLN D1049 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 1162 through 1165 Processing sheet with id=AE9, first strand: chain 'D' and resid 1278 through 1281 removed outlier: 4.495A pdb=" N GLU D1278 " --> pdb=" O ILE D1266 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ILE D1266 " --> pdb=" O GLU D1278 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL D1280 " --> pdb=" O ALA D1264 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ALA D1264 " --> pdb=" O VAL D1280 " (cutoff:3.500A) 1340 hydrogen bonds defined for protein. 3879 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 107 hydrogen bonds 214 hydrogen bond angles 0 basepair planarities 44 basepair parallelities 85 stacking parallelities Total time for adding SS restraints: 9.85 Time building geometry restraints manager: 4.19 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: 10597 1.34 - 1.45: 4745 1.45 - 1.57: 18823 1.57 - 1.69: 291 1.69 - 1.81: 231 Bond restraints: 34687 Sorted by residual: bond pdb=" CA ASP A 197 " pdb=" C ASP A 197 " ideal model delta sigma weight residual 1.524 1.576 -0.052 1.29e-02 6.01e+03 1.65e+01 bond pdb=" CA ASP A 199 " pdb=" C ASP A 199 " ideal model delta sigma weight residual 1.522 1.571 -0.049 1.24e-02 6.50e+03 1.56e+01 bond pdb=" C1' DT T -9 " pdb=" N1 DT T -9 " ideal model delta sigma weight residual 1.468 1.523 -0.055 1.40e-02 5.10e+03 1.54e+01 bond pdb=" C1' DT T -3 " pdb=" N1 DT T -3 " ideal model delta sigma weight residual 1.468 1.523 -0.055 1.40e-02 5.10e+03 1.53e+01 bond pdb=" C1' DA N -41 " pdb=" N9 DA N -41 " ideal model delta sigma weight residual 1.468 1.523 -0.055 1.40e-02 5.10e+03 1.53e+01 ... (remaining 34682 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.83: 47247 2.83 - 5.67: 210 5.67 - 8.50: 7 8.50 - 11.34: 3 11.34 - 14.17: 2 Bond angle restraints: 47469 Sorted by residual: angle pdb=" N LEU A 198 " pdb=" CA LEU A 198 " pdb=" C LEU A 198 " ideal model delta sigma weight residual 110.53 124.06 -13.53 1.32e+00 5.74e-01 1.05e+02 angle pdb=" N ASP A 199 " pdb=" CA ASP A 199 " pdb=" C ASP A 199 " ideal model delta sigma weight residual 108.96 123.13 -14.17 1.49e+00 4.50e-01 9.05e+01 angle pdb=" N ILE G 28 " pdb=" CA ILE G 28 " pdb=" C ILE G 28 " ideal model delta sigma weight residual 110.72 120.28 -9.56 1.01e+00 9.80e-01 8.96e+01 angle pdb=" C LEU D 368 " pdb=" N PRO D 369 " pdb=" CA PRO D 369 " ideal model delta sigma weight residual 120.03 128.34 -8.31 9.90e-01 1.02e+00 7.05e+01 angle pdb=" C2' DG T 47 " pdb=" C1' DG T 47 " pdb=" N9 DG T 47 " ideal model delta sigma weight residual 114.30 103.54 10.76 1.40e+00 5.10e-01 5.90e+01 ... (remaining 47464 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.82: 20382 35.82 - 71.64: 606 71.64 - 107.46: 3 107.46 - 143.28: 0 143.28 - 179.09: 2 Dihedral angle restraints: 20993 sinusoidal: 9681 harmonic: 11312 Sorted by residual: dihedral pdb=" CA VAL C 146 " pdb=" C VAL C 146 " pdb=" N SER C 147 " pdb=" CA SER C 147 " ideal model delta harmonic sigma weight residual 180.00 155.31 24.69 0 5.00e+00 4.00e-02 2.44e+01 dihedral pdb=" CA VAL D 501 " pdb=" C VAL D 501 " pdb=" N PRO D 502 " pdb=" CA PRO D 502 " ideal model delta harmonic sigma weight residual -180.00 -155.61 -24.39 0 5.00e+00 4.00e-02 2.38e+01 dihedral pdb=" CA GLN D 504 " pdb=" C GLN D 504 " pdb=" N ASP D 505 " pdb=" CA ASP D 505 " ideal model delta harmonic sigma weight residual 180.00 157.98 22.02 0 5.00e+00 4.00e-02 1.94e+01 ... (remaining 20990 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 4932 0.071 - 0.143: 452 0.143 - 0.214: 12 0.214 - 0.285: 1 0.285 - 0.357: 2 Chirality restraints: 5399 Sorted by residual: chirality pdb=" CA LEU A 198 " pdb=" N LEU A 198 " pdb=" C LEU A 198 " pdb=" CB LEU A 198 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.18e+00 chirality pdb=" CA ASP A 199 " pdb=" N ASP A 199 " pdb=" C ASP A 199 " pdb=" CB ASP A 199 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.62e+00 chirality pdb=" C1' DG T 47 " pdb=" O4' DG T 47 " pdb=" C2' DG T 47 " pdb=" N9 DG T 47 " both_signs ideal model delta sigma weight residual False 2.43 2.71 -0.28 2.00e-01 2.50e+01 2.00e+00 ... (remaining 5396 not shown) Planarity restraints: 5694 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR A 196 " 0.029 2.00e-02 2.50e+03 5.77e-02 3.33e+01 pdb=" C THR A 196 " -0.100 2.00e-02 2.50e+03 pdb=" O THR A 196 " 0.037 2.00e-02 2.50e+03 pdb=" N ASP A 197 " 0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU D 368 " 0.013 2.00e-02 2.50e+03 2.56e-02 6.58e+00 pdb=" C LEU D 368 " -0.044 2.00e-02 2.50e+03 pdb=" O LEU D 368 " 0.017 2.00e-02 2.50e+03 pdb=" N PRO D 369 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP G 27 " -0.012 2.00e-02 2.50e+03 2.51e-02 6.31e+00 pdb=" C ASP G 27 " 0.043 2.00e-02 2.50e+03 pdb=" O ASP G 27 " -0.017 2.00e-02 2.50e+03 pdb=" N ILE G 28 " -0.015 2.00e-02 2.50e+03 ... (remaining 5691 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 242 2.58 - 3.16: 26621 3.16 - 3.74: 51440 3.74 - 4.32: 67793 4.32 - 4.90: 111431 Nonbonded interactions: 257527 Sorted by model distance: nonbonded pdb=" C7 DT T 6 " pdb=" C5 DT T 7 " model vdw 2.003 3.680 nonbonded pdb=" O ARG B 45 " pdb=" OG SER B 49 " model vdw 2.228 3.040 nonbonded pdb=" NE1 TRP G 37 " pdb=" N7 DG N -48 " model vdw 2.249 3.200 nonbonded pdb=" C7 DT T 6 " pdb=" C6 DT T 7 " model vdw 2.256 3.760 nonbonded pdb=" OG1 THR C 657 " pdb=" O VAL C1186 " model vdw 2.264 3.040 ... (remaining 257522 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=0.30 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 2.550 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.630 Check model and map are aligned: 0.120 Set scattering table: 0.090 Process input model: 36.340 Find NCS groups from input model: 0.220 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: 0.010 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6948 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 0.055 34687 Z= 0.237 Angle : 0.553 14.173 47469 Z= 0.392 Chirality : 0.040 0.357 5399 Planarity : 0.003 0.058 5694 Dihedral : 13.208 179.095 13701 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.76 % Favored : 96.14 % Rotamer: Outliers : 1.70 % Allowed : 4.62 % Favored : 93.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.16 (0.12), residues: 3909 helix: -0.01 (0.12), residues: 1582 sheet: -1.55 (0.25), residues: 337 loop : -2.71 (0.11), residues: 1990 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 311 TYR 0.008 0.001 TYR D 679 PHE 0.008 0.001 PHE F 522 TRP 0.006 0.001 TRP A 321 HIS 0.002 0.000 HIS D 777 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.24 (34687) covalent geometry : angle 0.55294 / 0.39 (47469) hydrogen bonds : bond 0.12109 / 8.27 ( 1438) hydrogen bonds : angle 5.42221 / 3.86 ( 4093) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7818 Ramachandran restraints generated. 3909 Oldfield, 0 Emsley, 3909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7818 Ramachandran restraints generated. 3909 Oldfield, 0 Emsley, 3909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 459 residues out of total 3358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 402 time to evaluate : 1.190 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 LEU cc_start: 0.8790 (OUTLIER) cc_final: 0.8332 (tm) REVERT: A 47 LEU cc_start: 0.9631 (mt) cc_final: 0.9396 (mt) REVERT: A 316 MET cc_start: -0.0735 (pp-130) cc_final: -0.2112 (ptm) REVERT: C 545 PHE cc_start: 0.7273 (m-10) cc_final: 0.7009 (m-10) REVERT: C 704 MET cc_start: 0.8320 (OUTLIER) cc_final: 0.7904 (ppp) REVERT: C 764 CYS cc_start: 0.6849 (t) cc_final: 0.6055 (p) REVERT: C 1053 TYR cc_start: 0.8033 (m-10) cc_final: 0.7763 (m-10) REVERT: C 1131 MET cc_start: 0.9115 (mtp) cc_final: 0.8763 (mtt) REVERT: C 1166 ASP cc_start: 0.9177 (m-30) cc_final: 0.8698 (p0) REVERT: C 1315 MET cc_start: 0.7031 (ttt) cc_final: 0.6573 (tmm) REVERT: D 17 PHE cc_start: 0.7148 (p90) cc_final: 0.6771 (p90) REVERT: D 114 ILE cc_start: 0.9013 (OUTLIER) cc_final: 0.8803 (tp) REVERT: D 130 MET cc_start: 0.8968 (ttm) cc_final: 0.8547 (mmm) REVERT: D 245 LEU cc_start: 0.9193 (tp) cc_final: 0.8930 (tp) REVERT: D 304 ASP cc_start: 0.9003 (m-30) cc_final: 0.8707 (t0) REVERT: D 932 MET cc_start: 0.2291 (mtm) cc_final: 0.1858 (tpp) REVERT: D 1257 VAL cc_start: 0.9565 (t) cc_final: 0.9365 (p) REVERT: E 5 THR cc_start: 0.8488 (m) cc_final: 0.7977 (p) REVERT: E 6 VAL cc_start: 0.8354 (OUTLIER) cc_final: 0.7909 (p) REVERT: E 35 LYS cc_start: 0.9149 (mmmm) cc_final: 0.8445 (tmtt) REVERT: E 49 ILE cc_start: 0.8575 (mt) cc_final: 0.8183 (pt) REVERT: E 52 ARG cc_start: 0.8245 (ptp90) cc_final: 0.7813 (ptt180) REVERT: E 58 LEU cc_start: 0.9246 (mt) cc_final: 0.9029 (tt) REVERT: E 66 VAL cc_start: 0.9652 (t) cc_final: 0.9383 (m) REVERT: F 273 MET cc_start: 0.8582 (mtm) cc_final: 0.8374 (ptp) REVERT: F 379 MET cc_start: 0.9307 (tpp) cc_final: 0.9048 (tpt) REVERT: F 413 MET cc_start: 0.8933 (ttm) cc_final: 0.8628 (tmm) REVERT: F 487 MET cc_start: 0.8239 (tpt) cc_final: 0.8008 (tpp) REVERT: F 552 THR cc_start: 0.6666 (OUTLIER) cc_final: 0.6403 (m) outliers start: 57 outliers final: 10 residues processed: 451 average time/residue: 0.2165 time to fit residues: 154.9958 Evaluate side-chains 239 residues out of total 3358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 224 time to evaluate : 1.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 197 optimal weight: 9.9990 chunk 388 optimal weight: 10.0000 chunk 215 optimal weight: 20.0000 chunk 20 optimal weight: 20.0000 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 10.0000 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 5.9990 chunk 401 optimal weight: 40.0000 chunk 155 optimal weight: 20.0000 chunk 244 optimal weight: 10.0000 overall best weight: 7.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 137 ASN A 147 GLN B 128 HIS B 186 ASN C 406 ASN C 568 ASN C 760 ASN C 767 GLN C1080 ASN C1256 GLN ** D 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 232 ASN ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 489 ASN D 690 ASN D 700 ASN E 60 ASN ** G 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.057950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.042446 restraints weight = 353059.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.042695 restraints weight = 278697.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.042977 restraints weight = 224663.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.043470 restraints weight = 196665.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.043624 restraints weight = 180647.013| |-----------------------------------------------------------------------------| r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3169 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3169 r_free = 0.3169 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3169 r_free = 0.3169 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (8 function evaluations) r_final: 0.3169 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.2404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.120 34687 Z= 0.279 Angle : 0.732 12.385 47469 Z= 0.380 Chirality : 0.044 0.318 5399 Planarity : 0.006 0.077 5694 Dihedral : 17.309 175.173 5939 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.04 % Favored : 94.88 % Rotamer: Outliers : 0.06 % Allowed : 2.54 % Favored : 97.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.09 (0.13), residues: 3909 helix: 1.04 (0.13), residues: 1623 sheet: -1.12 (0.26), residues: 354 loop : -2.31 (0.12), residues: 1932 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 547 TYR 0.022 0.002 TYR C1229 PHE 0.032 0.002 PHE C 186 TRP 0.030 0.003 TRP D 115 HIS 0.018 0.002 HIS C 150 Details of bonding type rmsd/Z covalent geometry : bond 0.00576 / 0.28 (34687) covalent geometry : angle 0.73151 / 0.38 (47469) hydrogen bonds : bond 0.05716 / 3.85 ( 1438) hydrogen bonds : angle 4.46656 / 3.17 ( 4093) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7818 Ramachandran restraints generated. 3909 Oldfield, 0 Emsley, 3909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7818 Ramachandran restraints generated. 3909 Oldfield, 0 Emsley, 3909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 3358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 225 time to evaluate : 1.322 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 156 SER cc_start: 0.8675 (p) cc_final: 0.8449 (t) REVERT: C 674 ASP cc_start: 0.8050 (m-30) cc_final: 0.7694 (m-30) REVERT: C 681 MET cc_start: 0.8813 (mmm) cc_final: 0.8473 (mmp) REVERT: C 1107 MET cc_start: 0.8600 (ptm) cc_final: 0.8217 (pmm) REVERT: C 1131 MET cc_start: 0.9306 (mtp) cc_final: 0.8891 (mtt) REVERT: C 1170 MET cc_start: 0.9210 (mmp) cc_final: 0.8962 (mmm) REVERT: C 1180 MET cc_start: 0.7643 (ppp) cc_final: 0.7323 (ppp) REVERT: C 1290 MET cc_start: 0.7654 (mmt) cc_final: 0.7089 (mmt) REVERT: D 130 MET cc_start: 0.9145 (ttm) cc_final: 0.8606 (mmm) REVERT: D 151 MET cc_start: 0.3778 (pmm) cc_final: 0.3140 (pmm) REVERT: D 245 LEU cc_start: 0.9333 (tp) cc_final: 0.9069 (tp) REVERT: D 332 LYS cc_start: 0.7679 (tptt) cc_final: 0.7268 (tptp) REVERT: D 485 MET cc_start: 0.8833 (tpt) cc_final: 0.8433 (tpt) REVERT: D 581 MET cc_start: 0.9047 (tmm) cc_final: 0.8780 (tmm) REVERT: D 724 MET cc_start: 0.9201 (ptp) cc_final: 0.8537 (mmt) REVERT: E 5 THR cc_start: 0.8840 (m) cc_final: 0.8468 (p) REVERT: E 25 ARG cc_start: 0.8796 (tpt90) cc_final: 0.8575 (tpm170) REVERT: E 30 MET cc_start: 0.8806 (tpp) cc_final: 0.8292 (tpt) REVERT: E 49 ILE cc_start: 0.8711 (mt) cc_final: 0.8391 (pt) REVERT: F 102 MET cc_start: 0.7347 (tpp) cc_final: 0.6749 (tpp) REVERT: F 105 MET cc_start: 0.8200 (ppp) cc_final: 0.7803 (ppp) REVERT: F 379 MET cc_start: 0.9511 (tpp) cc_final: 0.9243 (tpp) REVERT: F 413 MET cc_start: 0.9049 (ttm) cc_final: 0.8644 (tpp) REVERT: F 487 MET cc_start: 0.8746 (tpt) cc_final: 0.8159 (tpp) outliers start: 2 outliers final: 0 residues processed: 226 average time/residue: 0.2285 time to fit residues: 83.2941 Evaluate side-chains 173 residues out of total 3358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 173 time to evaluate : 1.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 310 optimal weight: 4.9990 chunk 262 optimal weight: 10.0000 chunk 193 optimal weight: 0.0270 chunk 241 optimal weight: 20.0000 chunk 99 optimal weight: 5.9990 chunk 180 optimal weight: 0.8980 chunk 80 optimal weight: 30.0000 chunk 70 optimal weight: 9.9990 chunk 17 optimal weight: 4.9990 chunk 380 optimal weight: 9.9990 chunk 326 optimal weight: 0.8980 overall best weight: 2.3642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 147 GLN ** C 832 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 955 GLN ** D 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 936 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 951 GLN G 45 GLN ** G 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.058822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.043040 restraints weight = 350274.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.043280 restraints weight = 267455.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.043520 restraints weight = 218307.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.043916 restraints weight = 195348.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.044297 restraints weight = 179217.611| |-----------------------------------------------------------------------------| r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.2563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 34687 Z= 0.127 Angle : 0.529 8.968 47469 Z= 0.283 Chirality : 0.041 0.276 5399 Planarity : 0.004 0.106 5694 Dihedral : 17.355 173.784 5939 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.32 % Favored : 95.60 % Rotamer: Outliers : 0.06 % Allowed : 1.94 % Favored : 98.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % 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: -0.63 (0.13), residues: 3909 helix: 1.43 (0.13), residues: 1624 sheet: -0.84 (0.26), residues: 358 loop : -2.07 (0.13), residues: 1927 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 996 TYR 0.020 0.001 TYR C1229 PHE 0.021 0.001 PHE F 302 TRP 0.023 0.002 TRP D 115 HIS 0.011 0.001 HIS C 150 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.13 (34687) covalent geometry : angle 0.52859 / 0.28 (47469) hydrogen bonds : bond 0.03405 / 2.35 ( 1438) hydrogen bonds : angle 4.13130 / 2.92 ( 4093) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7818 Ramachandran restraints generated. 3909 Oldfield, 0 Emsley, 3909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7818 Ramachandran restraints generated. 3909 Oldfield, 0 Emsley, 3909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 3358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 210 time to evaluate : 1.249 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 LEU cc_start: 0.9687 (mt) cc_final: 0.9438 (mt) REVERT: A 316 MET cc_start: 0.1216 (ptt) cc_final: 0.1002 (ptt) REVERT: C 545 PHE cc_start: 0.8133 (m-80) cc_final: 0.7648 (m-10) REVERT: C 587 LEU cc_start: 0.9057 (pt) cc_final: 0.8817 (pt) REVERT: C 681 MET cc_start: 0.8772 (mmm) cc_final: 0.8261 (ptp) REVERT: C 1107 MET cc_start: 0.8423 (ptm) cc_final: 0.8142 (pmm) REVERT: C 1131 MET cc_start: 0.9202 (mtp) cc_final: 0.8823 (mtt) REVERT: C 1180 MET cc_start: 0.7783 (ppp) cc_final: 0.7490 (ppp) REVERT: C 1290 MET cc_start: 0.7698 (mmt) cc_final: 0.7208 (mmt) REVERT: D 130 MET cc_start: 0.9174 (ttm) cc_final: 0.8587 (mmm) REVERT: D 151 MET cc_start: 0.3658 (pmm) cc_final: 0.3079 (pmm) REVERT: D 245 LEU cc_start: 0.9350 (tp) cc_final: 0.9104 (tp) REVERT: D 332 LYS cc_start: 0.7670 (tptt) cc_final: 0.7232 (tptp) REVERT: D 604 MET cc_start: 0.9358 (mmt) cc_final: 0.8674 (mmm) REVERT: D 1040 MET cc_start: 0.0444 (ttt) cc_final: 0.0223 (ttp) REVERT: E 5 THR cc_start: 0.8771 (m) cc_final: 0.8470 (p) REVERT: E 30 MET cc_start: 0.8901 (tpp) cc_final: 0.8691 (tpp) REVERT: E 59 ILE cc_start: 0.6164 (mm) cc_final: 0.5718 (mm) REVERT: E 64 LEU cc_start: 0.9441 (mm) cc_final: 0.9180 (mm) REVERT: F 100 MET cc_start: 0.8557 (mtp) cc_final: 0.8333 (mtp) REVERT: F 102 MET cc_start: 0.7497 (tpp) cc_final: 0.6869 (tpp) REVERT: F 105 MET cc_start: 0.8321 (ppp) cc_final: 0.7925 (ppp) REVERT: F 379 MET cc_start: 0.9496 (tpp) cc_final: 0.9236 (tpt) REVERT: F 413 MET cc_start: 0.9021 (ttm) cc_final: 0.8701 (tpp) REVERT: F 487 MET cc_start: 0.8636 (tpt) cc_final: 0.8074 (tpp) outliers start: 2 outliers final: 1 residues processed: 211 average time/residue: 0.2087 time to fit residues: 71.8360 Evaluate side-chains 177 residues out of total 3358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 176 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 133 optimal weight: 0.9990 chunk 22 optimal weight: 20.0000 chunk 355 optimal weight: 50.0000 chunk 392 optimal weight: 50.0000 chunk 393 optimal weight: 30.0000 chunk 224 optimal weight: 4.9990 chunk 1 optimal weight: 0.0670 chunk 285 optimal weight: 0.0970 chunk 381 optimal weight: 0.5980 chunk 198 optimal weight: 9.9990 chunk 257 optimal weight: 10.0000 overall best weight: 1.3520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 688 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 955 GLN C1080 ASN ** C1268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 936 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.058952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.042240 restraints weight = 348791.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.042874 restraints weight = 264503.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.043331 restraints weight = 218779.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 18)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.043513 restraints weight = 194749.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.043522 restraints weight = 179040.077| |-----------------------------------------------------------------------------| r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.2718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 34687 Z= 0.108 Angle : 0.498 7.919 47469 Z= 0.269 Chirality : 0.041 0.240 5399 Planarity : 0.004 0.102 5694 Dihedral : 17.330 173.405 5939 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.66 % Favored : 95.29 % Rotamer: Outliers : 0.03 % Allowed : 2.24 % Favored : 97.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % 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: -0.43 (0.13), residues: 3909 helix: 1.58 (0.13), residues: 1625 sheet: -0.81 (0.26), residues: 347 loop : -1.91 (0.13), residues: 1937 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 28 TYR 0.017 0.001 TYR D 723 PHE 0.021 0.001 PHE D 57 TRP 0.024 0.002 TRP D 115 HIS 0.010 0.001 HIS B 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00220 / 0.11 (34687) covalent geometry : angle 0.49829 / 0.27 (47469) hydrogen bonds : bond 0.03156 / 2.18 ( 1438) hydrogen bonds : angle 4.00386 / 2.82 ( 4093) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7818 Ramachandran restraints generated. 3909 Oldfield, 0 Emsley, 3909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7818 Ramachandran restraints generated. 3909 Oldfield, 0 Emsley, 3909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 3358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 203 time to evaluate : 1.089 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 LEU cc_start: 0.9675 (mt) cc_final: 0.9420 (mt) REVERT: A 316 MET cc_start: 0.0850 (ptt) cc_final: 0.0606 (ptt) REVERT: C 545 PHE cc_start: 0.8080 (m-80) cc_final: 0.7564 (m-10) REVERT: C 587 LEU cc_start: 0.9094 (pt) cc_final: 0.8856 (pt) REVERT: C 681 MET cc_start: 0.8808 (mmm) cc_final: 0.8282 (ptp) REVERT: C 1107 MET cc_start: 0.8508 (ptm) cc_final: 0.8149 (pmm) REVERT: C 1131 MET cc_start: 0.9188 (mtp) cc_final: 0.8822 (mtt) REVERT: C 1180 MET cc_start: 0.7705 (ppp) cc_final: 0.7444 (ppp) REVERT: C 1290 MET cc_start: 0.7701 (mmt) cc_final: 0.7221 (mmt) REVERT: D 130 MET cc_start: 0.9174 (ttm) cc_final: 0.8635 (mmm) REVERT: D 151 MET cc_start: 0.3943 (pmm) cc_final: 0.3296 (pmm) REVERT: D 245 LEU cc_start: 0.9352 (tp) cc_final: 0.8989 (tp) REVERT: D 332 LYS cc_start: 0.7625 (tptt) cc_final: 0.7188 (tptp) REVERT: D 466 MET cc_start: 0.9194 (mmp) cc_final: 0.8871 (mmm) REVERT: D 485 MET cc_start: 0.8791 (tpt) cc_final: 0.8556 (tpt) REVERT: D 1040 MET cc_start: 0.0929 (ttt) cc_final: 0.0375 (ttp) REVERT: E 5 THR cc_start: 0.8836 (m) cc_final: 0.8554 (p) REVERT: E 30 MET cc_start: 0.8951 (tpp) cc_final: 0.8726 (tpp) REVERT: F 102 MET cc_start: 0.7524 (tpp) cc_final: 0.6985 (tpp) REVERT: F 105 MET cc_start: 0.8433 (ppp) cc_final: 0.8013 (ppp) REVERT: F 143 TYR cc_start: 0.9702 (t80) cc_final: 0.9488 (t80) REVERT: F 379 MET cc_start: 0.9484 (tpp) cc_final: 0.9249 (tpt) REVERT: F 413 MET cc_start: 0.9069 (ttm) cc_final: 0.8860 (tmm) REVERT: F 474 MET cc_start: 0.9248 (ptt) cc_final: 0.8110 (ppp) REVERT: F 487 MET cc_start: 0.8689 (tpt) cc_final: 0.8107 (tpp) REVERT: F 507 MET cc_start: 0.8541 (tpp) cc_final: 0.8139 (mtp) outliers start: 1 outliers final: 0 residues processed: 204 average time/residue: 0.2044 time to fit residues: 68.5305 Evaluate side-chains 175 residues out of total 3358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 175 time to evaluate : 1.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 9 optimal weight: 6.9990 chunk 403 optimal weight: 30.0000 chunk 298 optimal weight: 9.9990 chunk 151 optimal weight: 0.8980 chunk 388 optimal weight: 9.9990 chunk 241 optimal weight: 20.0000 chunk 295 optimal weight: 40.0000 chunk 14 optimal weight: 6.9990 chunk 192 optimal weight: 0.9980 chunk 271 optimal weight: 4.9990 chunk 284 optimal weight: 7.9990 overall best weight: 4.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 832 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 955 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 232 ASN ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 477 GLN ** D 936 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 954 ASN ** E 72 GLN ** 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 = 0.3591 r_free = 0.3591 target = 0.057690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.041903 restraints weight = 353724.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.042165 restraints weight = 275456.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.042643 restraints weight = 221044.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.043021 restraints weight = 188587.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.043089 restraints weight = 174840.336| |-----------------------------------------------------------------------------| r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.3075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.093 34687 Z= 0.165 Angle : 0.537 11.160 47469 Z= 0.287 Chirality : 0.041 0.223 5399 Planarity : 0.004 0.096 5694 Dihedral : 17.382 173.392 5939 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.14 % Favored : 94.78 % Rotamer: Outliers : 0.03 % Allowed : 1.58 % Favored : 98.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % 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: -0.27 (0.14), residues: 3909 helix: 1.67 (0.13), residues: 1637 sheet: -0.67 (0.26), residues: 352 loop : -1.83 (0.13), residues: 1920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG D 388 TYR 0.015 0.001 TYR D 46 PHE 0.057 0.001 PHE C 230 TRP 0.032 0.002 TRP D 115 HIS 0.023 0.001 HIS C 150 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.16 (34687) covalent geometry : angle 0.53684 / 0.29 (47469) hydrogen bonds : bond 0.03648 / 2.50 ( 1438) hydrogen bonds : angle 4.07662 / 2.88 ( 4093) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7818 Ramachandran restraints generated. 3909 Oldfield, 0 Emsley, 3909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7818 Ramachandran restraints generated. 3909 Oldfield, 0 Emsley, 3909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 3358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 198 time to evaluate : 1.246 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 LEU cc_start: 0.9690 (mt) cc_final: 0.9460 (mt) REVERT: A 316 MET cc_start: 0.0395 (ptt) cc_final: 0.0064 (ptt) REVERT: C 124 MET cc_start: 0.8309 (mpp) cc_final: 0.7879 (mpp) REVERT: C 545 PHE cc_start: 0.8144 (m-80) cc_final: 0.7623 (m-10) REVERT: C 681 MET cc_start: 0.8879 (mmm) cc_final: 0.8308 (ptp) REVERT: C 741 MET cc_start: 0.9088 (mmp) cc_final: 0.8883 (mmm) REVERT: C 1107 MET cc_start: 0.8555 (ptm) cc_final: 0.8248 (pmm) REVERT: C 1131 MET cc_start: 0.9236 (mtp) cc_final: 0.8830 (mtt) REVERT: C 1180 MET cc_start: 0.7869 (ppp) cc_final: 0.7570 (ppp) REVERT: C 1290 MET cc_start: 0.7746 (mmt) cc_final: 0.7208 (mmt) REVERT: D 130 MET cc_start: 0.9128 (ttm) cc_final: 0.8634 (mmm) REVERT: D 151 MET cc_start: 0.4218 (pmm) cc_final: 0.3641 (pmm) REVERT: D 245 LEU cc_start: 0.9358 (tp) cc_final: 0.9002 (tp) REVERT: D 332 LYS cc_start: 0.7751 (tptt) cc_final: 0.7412 (tptp) REVERT: D 466 MET cc_start: 0.9197 (mmp) cc_final: 0.8871 (mmm) REVERT: D 604 MET cc_start: 0.9347 (mmt) cc_final: 0.8684 (mmm) REVERT: E 5 THR cc_start: 0.8906 (m) cc_final: 0.8696 (p) REVERT: E 30 MET cc_start: 0.8970 (tpp) cc_final: 0.8643 (tpp) REVERT: E 58 LEU cc_start: 0.9290 (mp) cc_final: 0.9057 (tt) REVERT: E 67 ARG cc_start: 0.9026 (mpt-90) cc_final: 0.8792 (mtt180) REVERT: F 100 MET cc_start: 0.8692 (mtp) cc_final: 0.8488 (mtp) REVERT: F 102 MET cc_start: 0.7574 (tpp) cc_final: 0.6945 (tpp) REVERT: F 105 MET cc_start: 0.8510 (ppp) cc_final: 0.8124 (ppp) REVERT: F 137 TYR cc_start: 0.8685 (t80) cc_final: 0.8422 (t80) REVERT: F 379 MET cc_start: 0.9456 (tpp) cc_final: 0.9211 (tpt) REVERT: F 413 MET cc_start: 0.9078 (ttm) cc_final: 0.8696 (tpp) REVERT: F 474 MET cc_start: 0.9238 (ptt) cc_final: 0.8038 (tmm) REVERT: F 487 MET cc_start: 0.8672 (tpt) cc_final: 0.8070 (tpp) REVERT: F 507 MET cc_start: 0.8605 (tpp) cc_final: 0.8184 (mtp) REVERT: F 567 MET cc_start: 0.8805 (pmm) cc_final: 0.8086 (pmm) outliers start: 1 outliers final: 0 residues processed: 199 average time/residue: 0.1991 time to fit residues: 66.1723 Evaluate side-chains 170 residues out of total 3358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 170 time to evaluate : 1.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 190 optimal weight: 8.9990 chunk 183 optimal weight: 0.9990 chunk 354 optimal weight: 50.0000 chunk 62 optimal weight: 20.0000 chunk 394 optimal weight: 30.0000 chunk 66 optimal weight: 9.9990 chunk 216 optimal weight: 8.9990 chunk 44 optimal weight: 10.0000 chunk 34 optimal weight: 20.0000 chunk 293 optimal weight: 20.0000 chunk 388 optimal weight: 10.0000 overall best weight: 7.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 147 GLN A 276 HIS B 18 GLN B 37 HIS ** B 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 330 HIS C 462 ASN C 554 HIS C 658 GLN ** C 832 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1070 HIS ** C1134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1288 GLN ** D 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 409 ASN ** G 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.052522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.036401 restraints weight = 375200.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.037068 restraints weight = 272540.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.037525 restraints weight = 223215.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.037797 restraints weight = 196759.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.038016 restraints weight = 183076.135| |-----------------------------------------------------------------------------| r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.4401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.119 34687 Z= 0.294 Angle : 0.781 13.237 47469 Z= 0.405 Chirality : 0.045 0.309 5399 Planarity : 0.006 0.080 5694 Dihedral : 17.786 173.090 5939 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 18.58 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.75 % Favored : 93.12 % Rotamer: Outliers : 0.03 % Allowed : 2.21 % Favored : 97.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.65 (0.13), residues: 3909 helix: 1.16 (0.13), residues: 1638 sheet: -0.76 (0.26), residues: 373 loop : -1.87 (0.13), residues: 1898 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C1058 TYR 0.037 0.003 TYR D 772 PHE 0.021 0.003 PHE C 186 TRP 0.046 0.003 TRP D 115 HIS 0.027 0.003 HIS C 150 Details of bonding type rmsd/Z covalent geometry : bond 0.00601 / 0.29 (34687) covalent geometry : angle 0.78118 / 0.41 (47469) hydrogen bonds : bond 0.06329 / 4.36 ( 1438) hydrogen bonds : angle 4.69135 / 3.31 ( 4093) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7818 Ramachandran restraints generated. 3909 Oldfield, 0 Emsley, 3909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7818 Ramachandran restraints generated. 3909 Oldfield, 0 Emsley, 3909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 3358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 188 time to evaluate : 1.271 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 142 MET cc_start: 0.8738 (mmm) cc_final: 0.8288 (mmm) REVERT: A 316 MET cc_start: 0.2452 (ptt) cc_final: 0.1859 (ptt) REVERT: C 124 MET cc_start: 0.7977 (mpp) cc_final: 0.7540 (mpp) REVERT: C 545 PHE cc_start: 0.8390 (m-80) cc_final: 0.7869 (m-10) REVERT: C 681 MET cc_start: 0.8967 (mmm) cc_final: 0.8707 (mmm) REVERT: C 764 CYS cc_start: 0.8407 (t) cc_final: 0.7929 (p) REVERT: C 1126 ASP cc_start: 0.9345 (t0) cc_final: 0.8948 (m-30) REVERT: C 1131 MET cc_start: 0.9288 (mtp) cc_final: 0.8875 (mtt) REVERT: C 1180 MET cc_start: 0.8294 (ppp) cc_final: 0.7876 (ppp) REVERT: C 1273 MET cc_start: 0.8864 (mmt) cc_final: 0.8650 (mmm) REVERT: C 1290 MET cc_start: 0.7915 (mmt) cc_final: 0.7312 (mmt) REVERT: D 130 MET cc_start: 0.9124 (ttm) cc_final: 0.8696 (mmm) REVERT: D 151 MET cc_start: 0.5781 (pmm) cc_final: 0.5253 (pmm) REVERT: D 466 MET cc_start: 0.8903 (mmp) cc_final: 0.8420 (mmm) REVERT: D 604 MET cc_start: 0.9404 (mmt) cc_final: 0.8682 (mmm) REVERT: D 821 MET cc_start: 0.9232 (mmm) cc_final: 0.8945 (mmm) REVERT: E 25 ARG cc_start: 0.9201 (mmm160) cc_final: 0.8646 (tpm170) REVERT: E 30 MET cc_start: 0.8838 (tpp) cc_final: 0.8614 (tpp) REVERT: E 58 LEU cc_start: 0.9292 (mp) cc_final: 0.9085 (tt) REVERT: F 100 MET cc_start: 0.8521 (mtp) cc_final: 0.8260 (mtp) REVERT: F 102 MET cc_start: 0.7733 (tpp) cc_final: 0.7206 (tpp) REVERT: F 105 MET cc_start: 0.8827 (ppp) cc_final: 0.8452 (ppp) REVERT: F 365 MET cc_start: 0.9361 (ttp) cc_final: 0.9070 (ptm) REVERT: F 487 MET cc_start: 0.8828 (tpt) cc_final: 0.8223 (tpp) outliers start: 1 outliers final: 1 residues processed: 189 average time/residue: 0.1934 time to fit residues: 60.4738 Evaluate side-chains 149 residues out of total 3358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 148 time to evaluate : 1.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 151 optimal weight: 5.9990 chunk 254 optimal weight: 20.0000 chunk 355 optimal weight: 20.0000 chunk 49 optimal weight: 9.9990 chunk 348 optimal weight: 0.8980 chunk 318 optimal weight: 6.9990 chunk 67 optimal weight: 6.9990 chunk 36 optimal weight: 30.0000 chunk 139 optimal weight: 10.0000 chunk 15 optimal weight: 10.0000 chunk 267 optimal weight: 0.0670 overall best weight: 4.1924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 18 GLN B 37 HIS ** B 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 554 HIS ** C 832 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1070 HIS ** C1134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 495 ASN D1259 GLN ** E 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 45 GLN ** 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 = 0.3515 r_free = 0.3515 target = 0.053353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.038239 restraints weight = 369915.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 60)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.038594 restraints weight = 264862.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.039048 restraints weight = 205609.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.039460 restraints weight = 171600.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.039534 restraints weight = 156790.278| |-----------------------------------------------------------------------------| r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.4410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 34687 Z= 0.167 Angle : 0.589 9.737 47469 Z= 0.314 Chirality : 0.042 0.293 5399 Planarity : 0.004 0.094 5694 Dihedral : 17.775 172.486 5939 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 13.32 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.37 % Favored : 94.55 % Rotamer: Outliers : 0.03 % Allowed : 1.04 % Favored : 98.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.36 (0.14), residues: 3909 helix: 1.43 (0.13), residues: 1637 sheet: -0.65 (0.26), residues: 370 loop : -1.73 (0.14), residues: 1902 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG F 232 TYR 0.025 0.002 TYR F 143 PHE 0.014 0.001 PHE C 812 TRP 0.028 0.002 TRP D 115 HIS 0.015 0.001 HIS C 150 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.17 (34687) covalent geometry : angle 0.58938 / 0.31 (47469) hydrogen bonds : bond 0.04080 / 2.78 ( 1438) hydrogen bonds : angle 4.42551 / 3.13 ( 4093) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7818 Ramachandran restraints generated. 3909 Oldfield, 0 Emsley, 3909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7818 Ramachandran restraints generated. 3909 Oldfield, 0 Emsley, 3909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 3358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 180 time to evaluate : 1.134 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 LEU cc_start: 0.9733 (mt) cc_final: 0.9517 (mt) REVERT: A 142 MET cc_start: 0.8742 (mmm) cc_final: 0.8209 (mmm) REVERT: A 316 MET cc_start: 0.1742 (ptt) cc_final: 0.1229 (ptt) REVERT: C 124 MET cc_start: 0.7834 (mpp) cc_final: 0.7405 (mpp) REVERT: C 545 PHE cc_start: 0.8297 (m-80) cc_final: 0.7764 (m-10) REVERT: C 764 CYS cc_start: 0.8218 (t) cc_final: 0.7640 (p) REVERT: C 1131 MET cc_start: 0.9208 (mtp) cc_final: 0.8778 (mtt) REVERT: C 1180 MET cc_start: 0.8180 (ppp) cc_final: 0.7839 (ppp) REVERT: C 1290 MET cc_start: 0.8000 (mmt) cc_final: 0.7393 (mmt) REVERT: D 130 MET cc_start: 0.9071 (ttm) cc_final: 0.8710 (mmm) REVERT: D 151 MET cc_start: 0.5792 (pmm) cc_final: 0.5339 (pmm) REVERT: D 237 MET cc_start: 0.8618 (mpp) cc_final: 0.8351 (mpp) REVERT: D 466 MET cc_start: 0.9156 (mmp) cc_final: 0.8938 (mmm) REVERT: D 604 MET cc_start: 0.9383 (mmt) cc_final: 0.8856 (mmm) REVERT: D 698 MET cc_start: 0.9531 (mmp) cc_final: 0.9233 (ptp) REVERT: D 747 MET cc_start: 0.8809 (pmm) cc_final: 0.8470 (pmm) REVERT: D 821 MET cc_start: 0.9228 (mmm) cc_final: 0.8966 (mmm) REVERT: E 25 ARG cc_start: 0.9080 (mmm160) cc_final: 0.8554 (tpm170) REVERT: E 30 MET cc_start: 0.8838 (tpp) cc_final: 0.8611 (tpp) REVERT: E 58 LEU cc_start: 0.9249 (mp) cc_final: 0.9034 (tt) REVERT: F 100 MET cc_start: 0.8410 (mtp) cc_final: 0.8195 (mtp) REVERT: F 102 MET cc_start: 0.7622 (tpp) cc_final: 0.6997 (tpp) REVERT: F 105 MET cc_start: 0.8758 (ppp) cc_final: 0.8351 (ppp) REVERT: F 487 MET cc_start: 0.8724 (tpt) cc_final: 0.8142 (tpp) REVERT: F 507 MET cc_start: 0.8540 (tpp) cc_final: 0.8218 (mtp) REVERT: F 567 MET cc_start: 0.9066 (pmm) cc_final: 0.8580 (pmm) outliers start: 1 outliers final: 0 residues processed: 181 average time/residue: 0.2148 time to fit residues: 64.7620 Evaluate side-chains 158 residues out of total 3358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 158 time to evaluate : 1.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 257 optimal weight: 10.0000 chunk 40 optimal weight: 30.0000 chunk 18 optimal weight: 2.9990 chunk 152 optimal weight: 10.0000 chunk 145 optimal weight: 8.9990 chunk 157 optimal weight: 9.9990 chunk 389 optimal weight: 5.9990 chunk 51 optimal weight: 8.9990 chunk 118 optimal weight: 0.8980 chunk 47 optimal weight: 9.9990 chunk 285 optimal weight: 0.0060 overall best weight: 3.7802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 832 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1218 HIS E 60 ASN ** F 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.054558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.038814 restraints weight = 359277.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.038967 restraints weight = 275256.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.039335 restraints weight = 219115.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.039768 restraints weight = 190324.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.039862 restraints weight = 175408.185| |-----------------------------------------------------------------------------| r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.4548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 34687 Z= 0.159 Angle : 0.573 9.594 47469 Z= 0.305 Chirality : 0.041 0.207 5399 Planarity : 0.004 0.048 5694 Dihedral : 17.733 172.337 5939 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 12.84 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.86 % Favored : 94.06 % Rotamer: Outliers : 0.00 % Allowed : 0.60 % Favored : 99.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.22 (0.14), residues: 3909 helix: 1.54 (0.13), residues: 1635 sheet: -0.56 (0.27), residues: 370 loop : -1.64 (0.14), residues: 1904 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG D 388 TYR 0.015 0.001 TYR D 772 PHE 0.031 0.001 PHE D 461 TRP 0.022 0.002 TRP D 115 HIS 0.014 0.001 HIS C 150 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.16 (34687) covalent geometry : angle 0.57296 / 0.30 (47469) hydrogen bonds : bond 0.03941 / 2.69 ( 1438) hydrogen bonds : angle 4.35051 / 3.07 ( 4093) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7818 Ramachandran restraints generated. 3909 Oldfield, 0 Emsley, 3909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7818 Ramachandran restraints generated. 3909 Oldfield, 0 Emsley, 3909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 3358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 179 time to evaluate : 1.007 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 LEU cc_start: 0.9717 (mt) cc_final: 0.9497 (mt) REVERT: A 142 MET cc_start: 0.8739 (mmm) cc_final: 0.8286 (mmm) REVERT: A 316 MET cc_start: 0.1883 (ptt) cc_final: 0.1355 (ptt) REVERT: C 124 MET cc_start: 0.7819 (mpp) cc_final: 0.7350 (mpp) REVERT: C 545 PHE cc_start: 0.8260 (m-80) cc_final: 0.7697 (m-10) REVERT: C 681 MET cc_start: 0.8595 (mmp) cc_final: 0.7959 (ptp) REVERT: C 764 CYS cc_start: 0.8306 (t) cc_final: 0.7596 (p) REVERT: C 1085 MET cc_start: 0.8919 (mmt) cc_final: 0.8683 (mmt) REVERT: C 1131 MET cc_start: 0.9238 (mtp) cc_final: 0.8802 (mtt) REVERT: C 1180 MET cc_start: 0.8259 (ppp) cc_final: 0.7894 (ppp) REVERT: C 1290 MET cc_start: 0.7959 (mmt) cc_final: 0.7327 (mmt) REVERT: C 1315 MET cc_start: 0.6935 (tmm) cc_final: 0.6639 (tmm) REVERT: D 130 MET cc_start: 0.9153 (ttm) cc_final: 0.8752 (mmm) REVERT: D 151 MET cc_start: 0.5926 (pmm) cc_final: 0.5465 (pmm) REVERT: D 237 MET cc_start: 0.8676 (mpp) cc_final: 0.8412 (mpp) REVERT: D 372 MET cc_start: 0.9062 (mmm) cc_final: 0.8694 (mmp) REVERT: D 604 MET cc_start: 0.9310 (mmt) cc_final: 0.8800 (mmm) REVERT: D 698 MET cc_start: 0.9490 (mmp) cc_final: 0.9269 (ptt) REVERT: D 747 MET cc_start: 0.8796 (pmm) cc_final: 0.8393 (pmm) REVERT: D 821 MET cc_start: 0.9237 (mmm) cc_final: 0.8968 (mmm) REVERT: D 1040 MET cc_start: 0.0716 (tmm) cc_final: 0.0421 (tmm) REVERT: E 25 ARG cc_start: 0.9038 (mmm160) cc_final: 0.8418 (tpp-160) REVERT: E 30 MET cc_start: 0.8868 (tpp) cc_final: 0.8579 (tpp) REVERT: F 102 MET cc_start: 0.7750 (tpp) cc_final: 0.7141 (tpp) REVERT: F 105 MET cc_start: 0.8723 (ppp) cc_final: 0.8310 (ppp) REVERT: F 143 TYR cc_start: 0.9685 (t80) cc_final: 0.9453 (t80) REVERT: F 474 MET cc_start: 0.8952 (ppp) cc_final: 0.8740 (ppp) REVERT: F 487 MET cc_start: 0.8783 (tpt) cc_final: 0.8155 (tpp) REVERT: F 507 MET cc_start: 0.8433 (tpp) cc_final: 0.8199 (mtp) REVERT: F 567 MET cc_start: 0.9058 (pmm) cc_final: 0.8544 (pmm) outliers start: 0 outliers final: 0 residues processed: 179 average time/residue: 0.2008 time to fit residues: 59.5864 Evaluate side-chains 157 residues out of total 3358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 157 time to evaluate : 1.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 227 optimal weight: 10.0000 chunk 219 optimal weight: 0.7980 chunk 317 optimal weight: 2.9990 chunk 59 optimal weight: 20.0000 chunk 264 optimal weight: 0.9990 chunk 180 optimal weight: 6.9990 chunk 43 optimal weight: 4.9990 chunk 201 optimal weight: 3.9990 chunk 132 optimal weight: 0.7980 chunk 311 optimal weight: 20.0000 chunk 255 optimal weight: 7.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C1134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 113 HIS ** G 45 GLN ** 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 = 0.3529 r_free = 0.3529 target = 0.053725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.038365 restraints weight = 366775.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.038834 restraints weight = 263228.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.039337 restraints weight = 203016.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.039785 restraints weight = 172031.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 55)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.039915 restraints weight = 156563.647| |-----------------------------------------------------------------------------| r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.4529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 34687 Z= 0.115 Angle : 0.551 8.424 47469 Z= 0.292 Chirality : 0.042 0.346 5399 Planarity : 0.003 0.047 5694 Dihedral : 17.666 171.935 5939 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.91 % Favored : 95.01 % Rotamer: Outliers : 0.00 % Allowed : 0.57 % Favored : 99.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % 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: -0.07 (0.14), residues: 3909 helix: 1.65 (0.13), residues: 1631 sheet: -0.57 (0.26), residues: 374 loop : -1.53 (0.14), residues: 1904 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 200 TYR 0.013 0.001 TYR F 430 PHE 0.017 0.001 PHE C 812 TRP 0.016 0.001 TRP D 115 HIS 0.011 0.001 HIS C 150 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.11 (34687) covalent geometry : angle 0.55071 / 0.29 (47469) hydrogen bonds : bond 0.03256 / 2.20 ( 1438) hydrogen bonds : angle 4.21802 / 2.97 ( 4093) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7818 Ramachandran restraints generated. 3909 Oldfield, 0 Emsley, 3909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7818 Ramachandran restraints generated. 3909 Oldfield, 0 Emsley, 3909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 3358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 182 time to evaluate : 1.300 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 LEU cc_start: 0.9726 (mt) cc_final: 0.9488 (mt) REVERT: A 142 MET cc_start: 0.8767 (mmm) cc_final: 0.8354 (mmm) REVERT: A 316 MET cc_start: 0.2455 (ptt) cc_final: 0.1864 (ptt) REVERT: C 124 MET cc_start: 0.7707 (mpp) cc_final: 0.7219 (mpp) REVERT: C 545 PHE cc_start: 0.8240 (m-80) cc_final: 0.7731 (m-10) REVERT: C 681 MET cc_start: 0.8562 (mmp) cc_final: 0.8047 (mtp) REVERT: C 826 ASP cc_start: 0.8295 (m-30) cc_final: 0.8072 (m-30) REVERT: C 1085 MET cc_start: 0.8893 (mmt) cc_final: 0.8631 (mmt) REVERT: C 1131 MET cc_start: 0.9160 (mtp) cc_final: 0.8852 (mtp) REVERT: C 1180 MET cc_start: 0.8296 (ppp) cc_final: 0.7919 (ppp) REVERT: C 1290 MET cc_start: 0.7976 (mmt) cc_final: 0.7369 (mmt) REVERT: D 130 MET cc_start: 0.9091 (ttm) cc_final: 0.8590 (mmm) REVERT: D 151 MET cc_start: 0.5912 (pmm) cc_final: 0.5472 (pmm) REVERT: D 237 MET cc_start: 0.8755 (mpp) cc_final: 0.8499 (mpp) REVERT: D 466 MET cc_start: 0.9486 (mmp) cc_final: 0.9209 (mmm) REVERT: D 604 MET cc_start: 0.9235 (mmt) cc_final: 0.8746 (mmm) REVERT: D 698 MET cc_start: 0.9500 (mmp) cc_final: 0.9275 (ptt) REVERT: D 743 MET cc_start: 0.6438 (tpt) cc_final: 0.6135 (ttt) REVERT: D 821 MET cc_start: 0.9209 (mmm) cc_final: 0.8999 (mmm) REVERT: D 1040 MET cc_start: 0.0617 (tmm) cc_final: 0.0365 (tmm) REVERT: E 25 ARG cc_start: 0.9015 (mmm160) cc_final: 0.8393 (tpp-160) REVERT: E 30 MET cc_start: 0.8972 (tpp) cc_final: 0.8712 (tpp) REVERT: F 102 MET cc_start: 0.7742 (tpp) cc_final: 0.7139 (tpp) REVERT: F 105 MET cc_start: 0.8698 (ppp) cc_final: 0.8291 (ppp) REVERT: F 143 TYR cc_start: 0.9675 (t80) cc_final: 0.9440 (t80) REVERT: F 474 MET cc_start: 0.8971 (ppp) cc_final: 0.8738 (ppp) REVERT: F 487 MET cc_start: 0.8701 (tpt) cc_final: 0.8096 (tpp) REVERT: F 507 MET cc_start: 0.8608 (tpp) cc_final: 0.8260 (mtp) REVERT: F 567 MET cc_start: 0.9105 (pmm) cc_final: 0.8702 (pmm) outliers start: 0 outliers final: 0 residues processed: 182 average time/residue: 0.2158 time to fit residues: 65.4732 Evaluate side-chains 156 residues out of total 3358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 156 time to evaluate : 1.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 232 optimal weight: 2.9990 chunk 302 optimal weight: 0.6980 chunk 349 optimal weight: 0.0030 chunk 273 optimal weight: 5.9990 chunk 335 optimal weight: 5.9990 chunk 228 optimal weight: 6.9990 chunk 270 optimal weight: 9.9990 chunk 103 optimal weight: 6.9990 chunk 291 optimal weight: 4.9990 chunk 55 optimal weight: 9.9990 chunk 145 optimal weight: 0.9980 overall best weight: 1.9394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 194 GLN ** C1134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 60 ASN ** E 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.053742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.038197 restraints weight = 371238.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.038652 restraints weight = 263185.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.039063 restraints weight = 208238.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.039445 restraints weight = 180602.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.039467 restraints weight = 165528.124| |-----------------------------------------------------------------------------| r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.4564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 34687 Z= 0.115 Angle : 0.538 9.609 47469 Z= 0.286 Chirality : 0.041 0.199 5399 Planarity : 0.003 0.048 5694 Dihedral : 17.611 171.658 5939 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.14 % Favored : 94.78 % Rotamer: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 0.04 (0.14), residues: 3909 helix: 1.69 (0.13), residues: 1636 sheet: -0.52 (0.26), residues: 384 loop : -1.42 (0.14), residues: 1889 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 26 TYR 0.015 0.001 TYR D1282 PHE 0.015 0.001 PHE C 812 TRP 0.010 0.001 TRP D 115 HIS 0.012 0.001 HIS C 150 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.11 (34687) covalent geometry : angle 0.53798 / 0.29 (47469) hydrogen bonds : bond 0.03250 / 2.22 ( 1438) hydrogen bonds : angle 4.18078 / 2.94 ( 4093) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7818 Ramachandran restraints generated. 3909 Oldfield, 0 Emsley, 3909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7818 Ramachandran restraints generated. 3909 Oldfield, 0 Emsley, 3909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 3358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 184 time to evaluate : 1.303 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 LEU cc_start: 0.9707 (mt) cc_final: 0.9479 (mt) REVERT: A 142 MET cc_start: 0.8709 (mmm) cc_final: 0.8339 (mmm) REVERT: A 316 MET cc_start: 0.1979 (ptt) cc_final: 0.1410 (ptt) REVERT: C 124 MET cc_start: 0.7836 (mpp) cc_final: 0.7437 (mpp) REVERT: C 515 MET cc_start: 0.8513 (pmm) cc_final: 0.8130 (pmm) REVERT: C 545 PHE cc_start: 0.8180 (m-80) cc_final: 0.7645 (m-10) REVERT: C 681 MET cc_start: 0.8573 (mmp) cc_final: 0.8044 (mtm) REVERT: C 826 ASP cc_start: 0.8312 (m-30) cc_final: 0.8091 (m-30) REVERT: C 1085 MET cc_start: 0.8860 (mmt) cc_final: 0.8570 (mmt) REVERT: C 1131 MET cc_start: 0.9153 (mtp) cc_final: 0.8714 (mtt) REVERT: C 1180 MET cc_start: 0.8325 (ppp) cc_final: 0.7895 (ppp) REVERT: C 1290 MET cc_start: 0.7975 (mmt) cc_final: 0.7366 (mmt) REVERT: D 130 MET cc_start: 0.9098 (ttm) cc_final: 0.8597 (mmm) REVERT: D 151 MET cc_start: 0.5801 (pmm) cc_final: 0.5367 (pmm) REVERT: D 237 MET cc_start: 0.8729 (mpp) cc_final: 0.8498 (mpp) REVERT: D 332 LYS cc_start: 0.7918 (tptt) cc_final: 0.7473 (tptp) REVERT: D 466 MET cc_start: 0.9435 (mmp) cc_final: 0.9114 (mmm) REVERT: D 604 MET cc_start: 0.9141 (mmt) cc_final: 0.8722 (mmm) REVERT: D 698 MET cc_start: 0.9490 (mmp) cc_final: 0.9149 (ptp) REVERT: D 821 MET cc_start: 0.9225 (mmm) cc_final: 0.9019 (mmm) REVERT: D 1040 MET cc_start: 0.0275 (tmm) cc_final: 0.0062 (tmm) REVERT: E 25 ARG cc_start: 0.9051 (mmm160) cc_final: 0.8452 (tpp-160) REVERT: E 30 MET cc_start: 0.8918 (tpp) cc_final: 0.8418 (tpt) REVERT: E 58 LEU cc_start: 0.9222 (mp) cc_final: 0.9002 (tt) REVERT: F 100 MET cc_start: 0.8518 (mtp) cc_final: 0.8231 (mtp) REVERT: F 102 MET cc_start: 0.7731 (tpp) cc_final: 0.7157 (tpp) REVERT: F 105 MET cc_start: 0.8749 (ppp) cc_final: 0.8332 (ppp) REVERT: F 379 MET cc_start: 0.9392 (tpt) cc_final: 0.8994 (tpt) REVERT: F 474 MET cc_start: 0.8963 (ppp) cc_final: 0.8747 (ppp) REVERT: F 487 MET cc_start: 0.8742 (tpt) cc_final: 0.8106 (tpp) REVERT: F 507 MET cc_start: 0.8514 (tpp) cc_final: 0.8240 (mtp) REVERT: F 567 MET cc_start: 0.9228 (pmm) cc_final: 0.8596 (pmm) outliers start: 0 outliers final: 0 residues processed: 184 average time/residue: 0.2127 time to fit residues: 65.3392 Evaluate side-chains 158 residues out of total 3358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 158 time to evaluate : 1.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 263 optimal weight: 10.0000 chunk 330 optimal weight: 50.0000 chunk 107 optimal weight: 0.0030 chunk 67 optimal weight: 7.9990 chunk 318 optimal weight: 9.9990 chunk 243 optimal weight: 0.6980 chunk 320 optimal weight: 6.9990 chunk 224 optimal weight: 6.9990 chunk 96 optimal weight: 5.9990 chunk 321 optimal weight: 4.9990 chunk 198 optimal weight: 5.9990 overall best weight: 3.5396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 517 GLN C 832 HIS ** C1134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.053156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.037225 restraints weight = 371251.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.037791 restraints weight = 260919.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.038410 restraints weight = 211035.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.038786 restraints weight = 186473.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.038938 restraints weight = 169121.218| |-----------------------------------------------------------------------------| r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.4735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 34687 Z= 0.148 Angle : 0.567 11.093 47469 Z= 0.300 Chirality : 0.041 0.220 5399 Planarity : 0.004 0.047 5694 Dihedral : 17.631 171.703 5939 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 12.22 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.58 % Favored : 94.35 % Rotamer: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % 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: 0.06 (0.14), residues: 3909 helix: 1.71 (0.13), residues: 1629 sheet: -0.48 (0.27), residues: 374 loop : -1.40 (0.14), residues: 1906 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 26 TYR 0.018 0.001 TYR A 68 PHE 0.015 0.001 PHE C 812 TRP 0.011 0.001 TRP C1276 HIS 0.017 0.001 HIS A 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.15 (34687) covalent geometry : angle 0.56662 / 0.30 (47469) hydrogen bonds : bond 0.03594 / 2.44 ( 1438) hydrogen bonds : angle 4.26149 / 3.01 ( 4093) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6063.16 seconds wall clock time: 105 minutes 31.57 seconds (6331.57 seconds total)