Starting phenix.real_space_refine on Fri Mar 6 19:57:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7bef_12156/03_2026/7bef_12156.cif Found real_map, /net/cci-nas-00/data/ceres_data/7bef_12156/03_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 { model { file = "/net/cci-nas-00/data/ceres_data/7bef_12156/03_2026/7bef_12156.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7bef_12156/03_2026/7bef_12156.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7bef_12156/03_2026/7bef_12156.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7bef_12156/03_2026/7bef_12156.map" } 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-5986/lib/python3.9/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: 7.39, per 1000 atoms: 0.22 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: 2.60 Conformation dependent library (CDL) restraints added in 966.7 milliseconds 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: 4.20 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: 7.74 Time building geometry restraints manager: 3.28 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=" N LEU A 198 " pdb=" CA LEU A 198 " ideal model delta sigma weight residual 1.454 1.501 -0.047 1.34e-02 5.57e+03 1.25e+01 bond pdb=" C1' DA N -41 " pdb=" N9 DA N -41 " ideal model delta sigma weight residual 1.460 1.523 -0.063 2.00e-02 2.50e+03 9.84e+00 bond pdb=" N ARG G 30 " pdb=" CA ARG G 30 " ideal model delta sigma weight residual 1.457 1.496 -0.038 1.29e-02 6.01e+03 8.75e+00 ... (remaining 34682 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.83: 47266 2.83 - 5.67: 190 5.67 - 8.50: 8 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 113.50 103.54 9.96 1.50e+00 4.44e-01 4.41e+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: 5007 0.071 - 0.143: 377 0.143 - 0.214: 11 0.214 - 0.285: 1 0.285 - 0.357: 3 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 2.42 2.71 -0.30 2.00e-01 2.50e+01 2.18e+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: 1.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.550 Check model and map are aligned: 0.100 Set scattering table: 0.090 Process input model: 32.620 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6999 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 0.063 34687 Z= 0.141 Angle : 0.527 14.173 47469 Z= 0.342 Chirality : 0.039 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 covalent geometry : bond 0.00257 (34687) covalent geometry : angle 0.52732 (47469) hydrogen bonds : bond 0.12109 ( 1438) hydrogen bonds : angle 5.42221 ( 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 : 0.963 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: 0.2215 time to fit residues: 158.1501 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 : 1.276 ------------------------------------------------------------------------------- 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: 10.0000 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... Flipped N/Q/H residues before XYZ refinement: A 137 ASN A 147 GLN B 128 HIS B 186 ASN C 330 HIS C 406 ASN C 568 ASN C 760 ASN C 767 GLN ** C 832 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1256 GLN ** D 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 477 GLN D 489 ASN D 690 ASN D 700 ASN D 951 GLN D 954 ASN E 60 ASN G 45 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.055661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.039924 restraints weight = 368814.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.040401 restraints weight = 272138.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.040827 restraints weight = 215121.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.041339 restraints weight = 186570.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.041489 restraints weight = 168784.192| |-----------------------------------------------------------------------------| r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3104 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3104 r_free = 0.3104 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3104 r_free = 0.3104 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3104 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.2869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.105 34687 Z= 0.291 Angle : 0.728 11.465 47469 Z= 0.377 Chirality : 0.043 0.203 5399 Planarity : 0.005 0.074 5694 Dihedral : 17.212 179.217 5939 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 12.91 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.24 % Favored : 94.68 % Rotamer: Outliers : 0.09 % Allowed : 2.48 % Favored : 97.44 % 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: -1.06 (0.13), residues: 3909 helix: 1.03 (0.13), residues: 1627 sheet: -1.19 (0.25), residues: 359 loop : -2.24 (0.12), residues: 1923 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 996 TYR 0.023 0.002 TYR C1305 PHE 0.023 0.002 PHE C 186 TRP 0.033 0.003 TRP D 115 HIS 0.022 0.002 HIS C 150 Details of bonding type rmsd covalent geometry : bond 0.00607 (34687) covalent geometry : angle 0.72805 (47469) hydrogen bonds : bond 0.05850 ( 1438) hydrogen bonds : angle 4.49492 ( 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: 3 poor density : 224 time to evaluate : 1.243 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 156 SER cc_start: 0.8735 (p) cc_final: 0.8513 (t) REVERT: A 316 MET cc_start: 0.0894 (ptt) cc_final: 0.0510 (ptt) REVERT: C 545 PHE cc_start: 0.8074 (m-10) cc_final: 0.7781 (m-10) REVERT: C 681 MET cc_start: 0.8903 (mmm) cc_final: 0.8632 (mmp) REVERT: C 995 ASP cc_start: 0.9841 (t0) cc_final: 0.9618 (p0) REVERT: C 1107 MET cc_start: 0.8617 (ptm) cc_final: 0.8313 (pmm) REVERT: C 1131 MET cc_start: 0.9297 (mtp) cc_final: 0.8882 (mtt) REVERT: C 1180 MET cc_start: 0.7963 (ppp) cc_final: 0.7605 (ppp) REVERT: C 1290 MET cc_start: 0.7738 (mmt) cc_final: 0.7174 (mmt) REVERT: D 130 MET cc_start: 0.9095 (ttm) cc_final: 0.8630 (mmm) REVERT: D 151 MET cc_start: 0.4115 (pmm) cc_final: 0.3570 (pmm) REVERT: D 332 LYS cc_start: 0.7828 (tptt) cc_final: 0.7614 (tptp) REVERT: D 466 MET cc_start: 0.8807 (mmp) cc_final: 0.8396 (mmp) REVERT: D 485 MET cc_start: 0.8837 (tpt) cc_final: 0.8526 (tpt) REVERT: D 821 MET cc_start: 0.9363 (tpt) cc_final: 0.9038 (mmm) REVERT: D 1040 MET cc_start: 0.1355 (ttt) cc_final: 0.0985 (ttt) REVERT: E 5 THR cc_start: 0.8964 (m) cc_final: 0.8620 (p) REVERT: E 30 MET cc_start: 0.8792 (tpp) cc_final: 0.8365 (tpt) REVERT: E 49 ILE cc_start: 0.8776 (mt) cc_final: 0.8365 (tp) REVERT: F 102 MET cc_start: 0.7507 (tpp) cc_final: 0.6905 (tpp) REVERT: F 105 MET cc_start: 0.8386 (ppp) cc_final: 0.8033 (ppp) REVERT: F 413 MET cc_start: 0.9044 (ttm) cc_final: 0.8648 (tpp) REVERT: F 487 MET cc_start: 0.8747 (tpt) cc_final: 0.8157 (tpp) REVERT: F 507 MET cc_start: 0.8631 (tpp) cc_final: 0.8391 (tpp) outliers start: 3 outliers final: 2 residues processed: 226 average time/residue: 0.2264 time to fit residues: 82.0768 Evaluate side-chains 173 residues out of total 3358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 171 time to evaluate : 1.015 ------------------------------------------------------------------------------- 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: 0.8980 chunk 262 optimal weight: 1.9990 chunk 193 optimal weight: 9.9990 chunk 241 optimal weight: 20.0000 chunk 99 optimal weight: 5.9990 chunk 180 optimal weight: 2.9990 chunk 80 optimal weight: 30.0000 chunk 70 optimal weight: 8.9990 chunk 17 optimal weight: 10.0000 chunk 380 optimal weight: 40.0000 chunk 326 optimal weight: 5.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 554 HIS ** C 832 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 955 GLN C1220 GLN C1288 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** ** E 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 518 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.057219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.041427 restraints weight = 353356.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.041603 restraints weight = 267422.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.042079 restraints weight = 218571.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.042520 restraints weight = 187782.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.042619 restraints weight = 173077.825| |-----------------------------------------------------------------------------| r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.3165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 34687 Z= 0.154 Angle : 0.529 9.560 47469 Z= 0.284 Chirality : 0.040 0.239 5399 Planarity : 0.004 0.053 5694 Dihedral : 17.275 176.987 5939 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.43 % Favored : 95.50 % Rotamer: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % 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: -0.58 (0.13), residues: 3909 helix: 1.43 (0.13), residues: 1637 sheet: -0.93 (0.26), residues: 363 loop : -2.00 (0.13), residues: 1909 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 28 TYR 0.021 0.001 TYR F 143 PHE 0.019 0.001 PHE D 57 TRP 0.019 0.002 TRP F 315 HIS 0.015 0.001 HIS C 150 Details of bonding type rmsd covalent geometry : bond 0.00328 (34687) covalent geometry : angle 0.52916 (47469) hydrogen bonds : bond 0.03418 ( 1438) hydrogen bonds : angle 4.16400 ( 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 207 residues out of total 3358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 207 time to evaluate : 1.262 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 47 LEU cc_start: 0.9703 (mt) cc_final: 0.9483 (mt) REVERT: A 316 MET cc_start: 0.0808 (ptt) cc_final: 0.0392 (ptt) REVERT: C 928 VAL cc_start: 0.9679 (t) cc_final: 0.9479 (p) REVERT: C 1085 MET cc_start: 0.8813 (mmt) cc_final: 0.8595 (mmt) REVERT: C 1131 MET cc_start: 0.9229 (mtp) cc_final: 0.8822 (mtt) REVERT: C 1180 MET cc_start: 0.7949 (ppp) cc_final: 0.7648 (ppp) REVERT: C 1290 MET cc_start: 0.7807 (mmt) cc_final: 0.7265 (mmt) REVERT: D 130 MET cc_start: 0.9128 (ttm) cc_final: 0.8640 (mmm) REVERT: D 151 MET cc_start: 0.4373 (pmm) cc_final: 0.3833 (pmm) REVERT: D 466 MET cc_start: 0.9028 (mmp) cc_final: 0.8613 (mmm) REVERT: D 604 MET cc_start: 0.9408 (mmt) cc_final: 0.8717 (mmm) REVERT: E 5 THR cc_start: 0.8952 (m) cc_final: 0.8680 (p) REVERT: E 30 MET cc_start: 0.8862 (tpp) cc_final: 0.8608 (tpt) REVERT: E 64 LEU cc_start: 0.9402 (mm) cc_final: 0.9184 (mm) REVERT: F 100 MET cc_start: 0.8514 (mtp) cc_final: 0.8281 (mtp) REVERT: F 102 MET cc_start: 0.7556 (tpp) cc_final: 0.6941 (tpp) REVERT: F 105 MET cc_start: 0.8415 (ppp) cc_final: 0.8009 (ppp) REVERT: F 379 MET cc_start: 0.9459 (tpp) cc_final: 0.9153 (tpt) REVERT: F 413 MET cc_start: 0.9058 (ttm) cc_final: 0.8671 (tpp) REVERT: F 487 MET cc_start: 0.8708 (tpt) cc_final: 0.8156 (tpp) REVERT: F 507 MET cc_start: 0.8492 (tpp) cc_final: 0.8179 (mtp) outliers start: 0 outliers final: 0 residues processed: 207 average time/residue: 0.2119 time to fit residues: 71.8988 Evaluate side-chains 174 residues out of total 3358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 174 time to evaluate : 1.293 ------------------------------------------------------------------------------- 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: 40.0000 chunk 393 optimal weight: 10.0000 chunk 224 optimal weight: 6.9990 chunk 1 optimal weight: 20.0000 chunk 285 optimal weight: 20.0000 chunk 381 optimal weight: 0.2980 chunk 198 optimal weight: 6.9990 chunk 257 optimal weight: 8.9990 overall best weight: 4.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 ASN ** A 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 160 HIS C 462 ASN C 554 HIS ** C 832 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1268 GLN ** D 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 936 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1259 GLN ** E 72 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.055397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.039677 restraints weight = 359046.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.039920 restraints weight = 273824.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.040213 restraints weight = 220704.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.040529 restraints weight = 194108.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.040885 restraints weight = 178005.686| |-----------------------------------------------------------------------------| r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.3882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 34687 Z= 0.201 Angle : 0.586 9.252 47469 Z= 0.309 Chirality : 0.041 0.190 5399 Planarity : 0.004 0.053 5694 Dihedral : 17.328 175.255 5939 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 12.33 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.53 % Favored : 94.40 % Rotamer: Outliers : 0.03 % Allowed : 2.56 % Favored : 97.41 % 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: -0.37 (0.14), residues: 3909 helix: 1.54 (0.13), residues: 1642 sheet: -0.85 (0.26), residues: 366 loop : -1.82 (0.13), residues: 1901 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG D 311 TYR 0.020 0.002 TYR D 46 PHE 0.019 0.002 PHE C 35 TRP 0.022 0.002 TRP D 115 HIS 0.013 0.002 HIS C 150 Details of bonding type rmsd covalent geometry : bond 0.00419 (34687) covalent geometry : angle 0.58558 (47469) hydrogen bonds : bond 0.04306 ( 1438) hydrogen bonds : angle 4.24683 ( 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 195 residues out of total 3358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 194 time to evaluate : 1.321 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 LEU cc_start: 0.9723 (mt) cc_final: 0.9492 (mt) REVERT: A 316 MET cc_start: 0.1594 (ptt) cc_final: 0.0938 (ptt) REVERT: C 704 MET cc_start: 0.8553 (ptt) cc_final: 0.8297 (ptt) REVERT: C 1131 MET cc_start: 0.9250 (mtp) cc_final: 0.8857 (mtt) REVERT: C 1180 MET cc_start: 0.8152 (ppp) cc_final: 0.7808 (ppp) REVERT: C 1290 MET cc_start: 0.7821 (mmt) cc_final: 0.7219 (mmt) REVERT: D 130 MET cc_start: 0.9133 (ttm) cc_final: 0.8722 (mmm) REVERT: D 151 MET cc_start: 0.5091 (pmm) cc_final: 0.4570 (pmm) REVERT: D 180 MET cc_start: 0.7276 (mmp) cc_final: 0.6913 (mmp) REVERT: D 245 LEU cc_start: 0.9414 (tp) cc_final: 0.9203 (tp) REVERT: D 466 MET cc_start: 0.8974 (mmp) cc_final: 0.8479 (mmm) REVERT: E 30 MET cc_start: 0.8750 (tpp) cc_final: 0.8531 (tpt) REVERT: F 100 MET cc_start: 0.8563 (mtp) cc_final: 0.8355 (mtp) REVERT: F 102 MET cc_start: 0.7677 (tpp) cc_final: 0.7067 (tpp) REVERT: F 105 MET cc_start: 0.8675 (ppp) cc_final: 0.8279 (ppp) REVERT: F 379 MET cc_start: 0.9450 (tpp) cc_final: 0.9149 (tpt) REVERT: F 413 MET cc_start: 0.9095 (ttm) cc_final: 0.8676 (tpp) REVERT: F 487 MET cc_start: 0.8728 (tpt) cc_final: 0.8146 (tpp) REVERT: F 507 MET cc_start: 0.8511 (tpp) cc_final: 0.8288 (mtp) outliers start: 1 outliers final: 0 residues processed: 195 average time/residue: 0.2198 time to fit residues: 69.3548 Evaluate side-chains 164 residues out of total 3358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 164 time to evaluate : 1.164 ------------------------------------------------------------------------------- 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: 20.0000 chunk 403 optimal weight: 10.0000 chunk 298 optimal weight: 8.9990 chunk 151 optimal weight: 20.0000 chunk 388 optimal weight: 20.0000 chunk 241 optimal weight: 30.0000 chunk 295 optimal weight: 40.0000 chunk 14 optimal weight: 20.0000 chunk 192 optimal weight: 10.0000 chunk 271 optimal weight: 2.9990 chunk 284 optimal weight: 30.0000 overall best weight: 10.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 ASN A 276 HIS ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 37 HIS B 84 ASN ** B 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 658 GLN C 798 GLN ** C 832 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1099 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1136 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** ** D1218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 455 HIS ** F 461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 464 ASN ** G 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.048776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.033209 restraints weight = 392527.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.033565 restraints weight = 283473.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.033767 restraints weight = 224075.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.033984 restraints weight = 190853.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.033984 restraints weight = 173631.265| |-----------------------------------------------------------------------------| r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.5814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.136 34687 Z= 0.401 Angle : 0.912 15.175 47469 Z= 0.474 Chirality : 0.048 0.224 5399 Planarity : 0.006 0.070 5694 Dihedral : 18.040 177.280 5939 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 25.29 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.60 % Favored : 92.27 % Rotamer: Outliers : 0.06 % Allowed : 3.67 % Favored : 96.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -1.32 (0.13), residues: 3909 helix: 0.41 (0.13), residues: 1630 sheet: -1.30 (0.26), residues: 366 loop : -1.97 (0.13), residues: 1913 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C1246 TYR 0.035 0.003 TYR D 772 PHE 0.021 0.003 PHE C 186 TRP 0.022 0.003 TRP F 433 HIS 0.029 0.003 HIS C 150 Details of bonding type rmsd covalent geometry : bond 0.00833 (34687) covalent geometry : angle 0.91181 (47469) hydrogen bonds : bond 0.07606 ( 1438) hydrogen bonds : angle 5.39099 ( 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 167 residues out of total 3358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 165 time to evaluate : 1.296 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 316 MET cc_start: 0.2457 (ptt) cc_final: 0.1688 (ptt) REVERT: B 142 MET cc_start: 0.9269 (pmm) cc_final: 0.9014 (pmm) REVERT: C 403 MET cc_start: 0.9299 (ppp) cc_final: 0.9073 (ppp) REVERT: C 1131 MET cc_start: 0.9102 (mtp) cc_final: 0.8688 (mtt) REVERT: C 1180 MET cc_start: 0.8485 (ppp) cc_final: 0.8076 (ppp) REVERT: C 1290 MET cc_start: 0.8024 (mmt) cc_final: 0.7380 (mmt) REVERT: C 1315 MET cc_start: 0.7260 (tmm) cc_final: 0.6881 (tmm) REVERT: C 1319 MET cc_start: 0.7999 (tpp) cc_final: 0.7597 (tpp) REVERT: D 130 MET cc_start: 0.9115 (ttm) cc_final: 0.8814 (mmm) REVERT: D 151 MET cc_start: 0.5984 (pmm) cc_final: 0.5639 (pmm) REVERT: D 180 MET cc_start: 0.7712 (mmp) cc_final: 0.7156 (mmp) REVERT: D 332 LYS cc_start: 0.7689 (mmtt) cc_final: 0.7291 (tmtt) REVERT: D 466 MET cc_start: 0.8844 (mmp) cc_final: 0.8431 (mmm) REVERT: D 604 MET cc_start: 0.9405 (mmt) cc_final: 0.8824 (mmm) REVERT: F 100 MET cc_start: 0.8386 (mtp) cc_final: 0.8101 (mtp) REVERT: F 102 MET cc_start: 0.7861 (tpp) cc_final: 0.7217 (tpp) REVERT: F 105 MET cc_start: 0.8975 (ppp) cc_final: 0.8634 (ppp) REVERT: F 143 TYR cc_start: 0.9654 (t80) cc_final: 0.9434 (t80) REVERT: F 379 MET cc_start: 0.9456 (tpp) cc_final: 0.9155 (tpt) REVERT: F 413 MET cc_start: 0.9148 (ttm) cc_final: 0.8785 (tpp) REVERT: F 487 MET cc_start: 0.8872 (tpt) cc_final: 0.8330 (tpp) REVERT: F 507 MET cc_start: 0.8646 (tpp) cc_final: 0.8404 (tpp) outliers start: 2 outliers final: 1 residues processed: 167 average time/residue: 0.2106 time to fit residues: 58.1939 Evaluate side-chains 142 residues out of total 3358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 141 time to evaluate : 1.165 ------------------------------------------------------------------------------- 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: 1.9990 chunk 183 optimal weight: 0.8980 chunk 354 optimal weight: 20.0000 chunk 62 optimal weight: 0.0470 chunk 394 optimal weight: 7.9990 chunk 66 optimal weight: 7.9990 chunk 216 optimal weight: 8.9990 chunk 44 optimal weight: 6.9990 chunk 34 optimal weight: 7.9990 chunk 293 optimal weight: 20.0000 chunk 388 optimal weight: 10.0000 overall best weight: 3.5884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 ASN B 18 GLN B 84 ASN ** 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** C1312 ASN D 448 GLN ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 936 HIS D1218 HIS ** E 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.050373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.034827 restraints weight = 375006.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 60)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.034999 restraints weight = 264923.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.035473 restraints weight = 201874.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.035841 restraints weight = 170959.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.035895 restraints weight = 150850.976| |-----------------------------------------------------------------------------| r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.5566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.100 34687 Z= 0.166 Angle : 0.608 11.000 47469 Z= 0.323 Chirality : 0.042 0.203 5399 Planarity : 0.004 0.053 5694 Dihedral : 17.992 178.764 5939 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 14.98 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.81 % Favored : 94.09 % Rotamer: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -0.67 (0.13), residues: 3909 helix: 1.10 (0.13), residues: 1636 sheet: -1.10 (0.26), residues: 376 loop : -1.76 (0.14), residues: 1897 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 202 TYR 0.018 0.002 TYR D 631 PHE 0.015 0.001 PHE D 338 TRP 0.051 0.002 TRP D 115 HIS 0.017 0.001 HIS C 150 Details of bonding type rmsd covalent geometry : bond 0.00360 (34687) covalent geometry : angle 0.60818 (47469) hydrogen bonds : bond 0.04214 ( 1438) hydrogen bonds : angle 4.68509 ( 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 173 residues out of total 3358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 173 time to evaluate : 1.572 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: A 316 MET cc_start: 0.2692 (ptt) cc_final: 0.1762 (ptt) REVERT: B 142 MET cc_start: 0.9388 (pmm) cc_final: 0.9140 (pmm) REVERT: C 403 MET cc_start: 0.9251 (ppp) cc_final: 0.9022 (ppp) REVERT: C 515 MET cc_start: 0.8241 (ptt) cc_final: 0.7936 (ptt) REVERT: C 681 MET cc_start: 0.8881 (mmm) cc_final: 0.8516 (mtm) REVERT: C 1131 MET cc_start: 0.9148 (mtp) cc_final: 0.8705 (mtt) REVERT: C 1180 MET cc_start: 0.8356 (ppp) cc_final: 0.7983 (ppp) REVERT: C 1290 MET cc_start: 0.8042 (mmt) cc_final: 0.7419 (mmt) REVERT: D 130 MET cc_start: 0.9088 (ttm) cc_final: 0.8701 (mmm) REVERT: D 151 MET cc_start: 0.6099 (pmm) cc_final: 0.5817 (pmm) REVERT: D 180 MET cc_start: 0.7830 (mmp) cc_final: 0.7343 (mmp) REVERT: D 372 MET cc_start: 0.9002 (mmm) cc_final: 0.8587 (mmp) REVERT: D 604 MET cc_start: 0.9392 (mmt) cc_final: 0.8770 (mmm) REVERT: D 821 MET cc_start: 0.9382 (mmm) cc_final: 0.9156 (tpp) REVERT: E 58 LEU cc_start: 0.9325 (mp) cc_final: 0.9071 (tt) REVERT: F 102 MET cc_start: 0.7923 (tpp) cc_final: 0.7309 (tpp) REVERT: F 105 MET cc_start: 0.8904 (ppp) cc_final: 0.8515 (ppp) REVERT: F 379 MET cc_start: 0.9424 (tpp) cc_final: 0.9170 (tpt) REVERT: F 487 MET cc_start: 0.8823 (tpt) cc_final: 0.8178 (tpp) REVERT: F 507 MET cc_start: 0.8578 (tpp) cc_final: 0.8345 (mtp) REVERT: F 567 MET cc_start: 0.9134 (pmm) cc_final: 0.8793 (pmm) outliers start: 0 outliers final: 0 residues processed: 173 average time/residue: 0.2078 time to fit residues: 59.8538 Evaluate side-chains 145 residues out of total 3358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 145 time to evaluate : 1.375 ------------------------------------------------------------------------------- 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: 0.7980 chunk 254 optimal weight: 1.9990 chunk 355 optimal weight: 6.9990 chunk 49 optimal weight: 10.0000 chunk 348 optimal weight: 30.0000 chunk 318 optimal weight: 9.9990 chunk 67 optimal weight: 7.9990 chunk 36 optimal weight: 0.9980 chunk 139 optimal weight: 0.8980 chunk 15 optimal weight: 8.9990 chunk 267 optimal weight: 0.0170 overall best weight: 0.9420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 517 GLN ** C 811 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 113 HIS D 477 GLN D 921 GLN G 45 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.052586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.037580 restraints weight = 356179.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.038168 restraints weight = 248355.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.038687 restraints weight = 191605.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.038951 restraints weight = 164583.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.039219 restraints weight = 149772.686| |-----------------------------------------------------------------------------| r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.5304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 34687 Z= 0.116 Angle : 0.560 11.105 47469 Z= 0.297 Chirality : 0.041 0.171 5399 Planarity : 0.004 0.048 5694 Dihedral : 17.659 178.234 5939 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.12 % Favored : 94.81 % Rotamer: Outliers : 0.03 % Allowed : 1.01 % Favored : 98.96 % 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: -0.24 (0.14), residues: 3909 helix: 1.50 (0.13), residues: 1631 sheet: -0.86 (0.26), residues: 365 loop : -1.55 (0.14), residues: 1913 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 933 TYR 0.017 0.001 TYR D 144 PHE 0.038 0.001 PHE D 461 TRP 0.028 0.001 TRP D 115 HIS 0.009 0.001 HIS C 150 Details of bonding type rmsd covalent geometry : bond 0.00249 (34687) covalent geometry : angle 0.55994 (47469) hydrogen bonds : bond 0.03200 ( 1438) hydrogen bonds : angle 4.30781 ( 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 185 residues out of total 3358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 184 time to evaluate : 1.305 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 316 MET cc_start: 0.1419 (ptt) cc_final: 0.0581 (ptt) REVERT: C 681 MET cc_start: 0.8899 (mmm) cc_final: 0.8401 (mtm) REVERT: C 1131 MET cc_start: 0.9130 (mtp) cc_final: 0.8721 (mtt) REVERT: C 1180 MET cc_start: 0.8385 (ppp) cc_final: 0.7906 (ppp) REVERT: C 1290 MET cc_start: 0.8118 (mmt) cc_final: 0.7593 (mmt) REVERT: C 1295 SER cc_start: 0.8807 (m) cc_final: 0.8515 (p) REVERT: C 1315 MET cc_start: 0.6977 (tmm) cc_final: 0.6745 (tmm) REVERT: D 130 MET cc_start: 0.9054 (ttm) cc_final: 0.8697 (mmm) REVERT: D 151 MET cc_start: 0.6065 (pmm) cc_final: 0.5752 (pmm) REVERT: D 180 MET cc_start: 0.7699 (mmp) cc_final: 0.7243 (mmp) REVERT: D 245 LEU cc_start: 0.9639 (tp) cc_final: 0.9407 (tp) REVERT: D 466 MET cc_start: 0.9389 (mmm) cc_final: 0.9148 (mmm) REVERT: D 604 MET cc_start: 0.9267 (mmt) cc_final: 0.8767 (mmm) REVERT: D 821 MET cc_start: 0.9435 (mmm) cc_final: 0.9211 (tpp) REVERT: E 30 MET cc_start: 0.8888 (tpp) cc_final: 0.8652 (tpp) REVERT: F 102 MET cc_start: 0.7894 (tpp) cc_final: 0.7275 (tpp) REVERT: F 105 MET cc_start: 0.8830 (ppp) cc_final: 0.8444 (ppp) REVERT: F 379 MET cc_start: 0.9441 (tpp) cc_final: 0.9183 (tpt) REVERT: F 474 MET cc_start: 0.9000 (ppp) cc_final: 0.8798 (ppp) REVERT: F 487 MET cc_start: 0.8819 (tpt) cc_final: 0.8158 (tpp) REVERT: F 507 MET cc_start: 0.8607 (tpp) cc_final: 0.8273 (mtp) REVERT: F 567 MET cc_start: 0.9183 (pmm) cc_final: 0.8897 (pmm) outliers start: 1 outliers final: 0 residues processed: 185 average time/residue: 0.2045 time to fit residues: 62.7811 Evaluate side-chains 143 residues out of total 3358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 143 time to evaluate : 1.207 ------------------------------------------------------------------------------- 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: 7.9990 chunk 40 optimal weight: 30.0000 chunk 18 optimal weight: 20.0000 chunk 152 optimal weight: 5.9990 chunk 145 optimal weight: 7.9990 chunk 157 optimal weight: 5.9990 chunk 389 optimal weight: 5.9990 chunk 51 optimal weight: 20.0000 chunk 118 optimal weight: 0.9980 chunk 47 optimal weight: 30.0000 chunk 285 optimal weight: 10.0000 overall best weight: 5.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 ASN B 18 GLN ** B 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 194 GLN C 31 GLN ** C 517 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** D 153 ASN ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.050234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.033451 restraints weight = 378781.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.034122 restraints weight = 265333.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.034469 restraints weight = 208488.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 18)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.034668 restraints weight = 179413.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.034903 restraints weight = 167449.995| |-----------------------------------------------------------------------------| r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.5740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 34687 Z= 0.206 Angle : 0.618 11.759 47469 Z= 0.327 Chirality : 0.041 0.202 5399 Planarity : 0.004 0.050 5694 Dihedral : 17.681 178.701 5939 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 15.43 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.11 % Favored : 93.78 % Rotamer: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % 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: -0.28 (0.14), residues: 3909 helix: 1.45 (0.13), residues: 1636 sheet: -0.87 (0.26), residues: 377 loop : -1.57 (0.14), residues: 1896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 26 TYR 0.031 0.002 TYR C1229 PHE 0.015 0.002 PHE D 338 TRP 0.017 0.002 TRP D 115 HIS 0.017 0.002 HIS C 150 Details of bonding type rmsd covalent geometry : bond 0.00435 (34687) covalent geometry : angle 0.61820 (47469) hydrogen bonds : bond 0.04531 ( 1438) hydrogen bonds : angle 4.57247 ( 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 166 residues out of total 3358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 166 time to evaluate : 1.256 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 316 MET cc_start: 0.3528 (ptt) cc_final: 0.2587 (ptt) REVERT: B 142 MET cc_start: 0.9299 (pmm) cc_final: 0.9078 (pmm) REVERT: C 124 MET cc_start: 0.8176 (mpp) cc_final: 0.7772 (mpp) REVERT: C 681 MET cc_start: 0.8928 (mmm) cc_final: 0.8468 (mtm) REVERT: C 1131 MET cc_start: 0.9123 (mtp) cc_final: 0.8742 (mtt) REVERT: C 1180 MET cc_start: 0.8472 (ppp) cc_final: 0.8107 (ppp) REVERT: C 1290 MET cc_start: 0.8006 (mmt) cc_final: 0.7290 (mmt) REVERT: D 130 MET cc_start: 0.9104 (ttm) cc_final: 0.8722 (mmm) REVERT: D 151 MET cc_start: 0.6218 (pmm) cc_final: 0.5901 (pmm) REVERT: D 180 MET cc_start: 0.7668 (mmp) cc_final: 0.7344 (mmp) REVERT: D 466 MET cc_start: 0.9292 (mmm) cc_final: 0.9061 (mmm) REVERT: D 604 MET cc_start: 0.9256 (mmt) cc_final: 0.8766 (mmp) REVERT: D 785 ASP cc_start: 0.8999 (t70) cc_final: 0.8745 (t0) REVERT: E 30 MET cc_start: 0.8993 (tpp) cc_final: 0.8745 (tpp) REVERT: F 102 MET cc_start: 0.7899 (tpp) cc_final: 0.7353 (tpp) REVERT: F 105 MET cc_start: 0.9009 (ppp) cc_final: 0.8638 (ppp) REVERT: F 487 MET cc_start: 0.8891 (tpt) cc_final: 0.8298 (tpp) REVERT: F 507 MET cc_start: 0.8528 (tpp) cc_final: 0.8286 (tpp) REVERT: F 567 MET cc_start: 0.9174 (pmm) cc_final: 0.8873 (pmm) outliers start: 0 outliers final: 0 residues processed: 166 average time/residue: 0.2053 time to fit residues: 57.5097 Evaluate side-chains 138 residues out of total 3358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 138 time to evaluate : 1.229 ------------------------------------------------------------------------------- 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: 0.0270 chunk 219 optimal weight: 1.9990 chunk 317 optimal weight: 3.9990 chunk 59 optimal weight: 8.9990 chunk 264 optimal weight: 2.9990 chunk 180 optimal weight: 0.9980 chunk 43 optimal weight: 20.0000 chunk 201 optimal weight: 3.9990 chunk 132 optimal weight: 3.9990 chunk 311 optimal weight: 30.0000 chunk 255 optimal weight: 8.9990 overall best weight: 2.0044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 ASN ** B 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 517 GLN ** C1134 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** ** E 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 45 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.051184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.035292 restraints weight = 373768.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.035633 restraints weight = 261463.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.036081 restraints weight = 196227.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 76)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.036191 restraints weight = 168702.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.036267 restraints weight = 151914.449| |-----------------------------------------------------------------------------| r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.5659 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= 0.121 Angle : 0.565 9.500 47469 Z= 0.299 Chirality : 0.041 0.175 5399 Planarity : 0.004 0.063 5694 Dihedral : 17.674 178.555 5939 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.40 % Favored : 94.53 % Rotamer: Outliers : 0.03 % Allowed : 0.42 % Favored : 99.55 % 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: -0.10 (0.14), residues: 3909 helix: 1.60 (0.13), residues: 1631 sheet: -0.79 (0.26), residues: 386 loop : -1.46 (0.14), residues: 1892 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 996 TYR 0.031 0.001 TYR C1229 PHE 0.019 0.001 PHE C 464 TRP 0.010 0.001 TRP D 580 HIS 0.010 0.001 HIS C 150 Details of bonding type rmsd covalent geometry : bond 0.00265 (34687) covalent geometry : angle 0.56533 (47469) hydrogen bonds : bond 0.03301 ( 1438) hydrogen bonds : angle 4.37148 ( 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 170 residues out of total 3358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 169 time to evaluate : 1.270 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 316 MET cc_start: 0.2585 (ptt) cc_final: 0.1548 (ptt) REVERT: B 142 MET cc_start: 0.9333 (pmm) cc_final: 0.9130 (pmm) REVERT: C 124 MET cc_start: 0.8065 (mpp) cc_final: 0.7596 (mpp) REVERT: C 681 MET cc_start: 0.8926 (mmm) cc_final: 0.8456 (mtm) REVERT: C 800 MET cc_start: 0.8020 (mmm) cc_final: 0.7789 (mmm) REVERT: C 1131 MET cc_start: 0.9085 (mtp) cc_final: 0.8649 (mtt) REVERT: C 1180 MET cc_start: 0.8440 (ppp) cc_final: 0.8017 (ppp) REVERT: C 1290 MET cc_start: 0.8037 (mmt) cc_final: 0.7548 (mmt) REVERT: C 1295 SER cc_start: 0.8972 (m) cc_final: 0.8729 (p) REVERT: C 1315 MET cc_start: 0.7246 (tmm) cc_final: 0.6848 (tmm) REVERT: D 130 MET cc_start: 0.9087 (ttm) cc_final: 0.8752 (mmm) REVERT: D 151 MET cc_start: 0.6260 (pmm) cc_final: 0.5934 (pmm) REVERT: D 180 MET cc_start: 0.7890 (mmp) cc_final: 0.7299 (mmp) REVERT: D 245 LEU cc_start: 0.9618 (tp) cc_final: 0.9375 (tp) REVERT: D 604 MET cc_start: 0.9181 (mmt) cc_final: 0.8749 (mmp) REVERT: E 30 MET cc_start: 0.8996 (tpp) cc_final: 0.8792 (tpp) REVERT: F 100 MET cc_start: 0.8226 (mtp) cc_final: 0.7935 (mtp) REVERT: F 102 MET cc_start: 0.7888 (tpp) cc_final: 0.7346 (tpp) REVERT: F 105 MET cc_start: 0.8939 (ppp) cc_final: 0.8564 (ppp) REVERT: F 487 MET cc_start: 0.8883 (tpt) cc_final: 0.8229 (tpp) REVERT: F 507 MET cc_start: 0.8605 (tpp) cc_final: 0.8262 (mtp) REVERT: F 567 MET cc_start: 0.9219 (pmm) cc_final: 0.8971 (pmm) outliers start: 1 outliers final: 0 residues processed: 170 average time/residue: 0.2088 time to fit residues: 59.0286 Evaluate side-chains 146 residues out of total 3358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 146 time to evaluate : 1.167 ------------------------------------------------------------------------------- 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: 6.9990 chunk 302 optimal weight: 5.9990 chunk 349 optimal weight: 8.9990 chunk 273 optimal weight: 6.9990 chunk 335 optimal weight: 9.9990 chunk 228 optimal weight: 0.9990 chunk 270 optimal weight: 4.9990 chunk 103 optimal weight: 0.0980 chunk 291 optimal weight: 0.6980 chunk 55 optimal weight: 9.9990 chunk 145 optimal weight: 6.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 ASN ** B 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 45 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.051032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.035072 restraints weight = 377682.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.035386 restraints weight = 264779.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.035808 restraints weight = 201709.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.035986 restraints weight = 171078.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 16)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.036178 restraints weight = 157315.228| |-----------------------------------------------------------------------------| r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.5738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 34687 Z= 0.134 Angle : 0.569 10.708 47469 Z= 0.300 Chirality : 0.041 0.306 5399 Planarity : 0.004 0.049 5694 Dihedral : 17.610 178.229 5939 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 12.60 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.81 % Favored : 94.12 % Rotamer: Outliers : 0.03 % Allowed : 0.21 % Favored : 99.76 % 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: -0.01 (0.14), residues: 3909 helix: 1.65 (0.13), residues: 1631 sheet: -0.76 (0.26), residues: 389 loop : -1.38 (0.14), residues: 1889 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 26 TYR 0.026 0.001 TYR C1229 PHE 0.016 0.001 PHE C 812 TRP 0.009 0.001 TRP D 580 HIS 0.015 0.001 HIS C 150 Details of bonding type rmsd covalent geometry : bond 0.00291 (34687) covalent geometry : angle 0.56876 (47469) hydrogen bonds : bond 0.03482 ( 1438) hydrogen bonds : angle 4.36649 ( 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 165 residues out of total 3358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 164 time to evaluate : 1.310 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 316 MET cc_start: 0.3377 (ptt) cc_final: 0.2454 (ptt) REVERT: C 124 MET cc_start: 0.7916 (mpp) cc_final: 0.7526 (mpp) REVERT: C 681 MET cc_start: 0.8945 (mmm) cc_final: 0.8461 (mtm) REVERT: C 1131 MET cc_start: 0.9086 (mtp) cc_final: 0.8657 (mtt) REVERT: C 1180 MET cc_start: 0.8448 (ppp) cc_final: 0.8031 (ppp) REVERT: C 1290 MET cc_start: 0.7969 (mmt) cc_final: 0.7574 (mmt) REVERT: C 1295 SER cc_start: 0.8945 (m) cc_final: 0.8725 (p) REVERT: C 1315 MET cc_start: 0.7177 (tmm) cc_final: 0.6794 (tmm) REVERT: D 130 MET cc_start: 0.9060 (ttm) cc_final: 0.8736 (mmm) REVERT: D 151 MET cc_start: 0.6291 (pmm) cc_final: 0.5997 (pmm) REVERT: D 180 MET cc_start: 0.7622 (mmp) cc_final: 0.7369 (mmp) REVERT: D 245 LEU cc_start: 0.9625 (tp) cc_final: 0.9379 (tp) REVERT: D 604 MET cc_start: 0.9403 (mmm) cc_final: 0.8899 (mmp) REVERT: D 785 ASP cc_start: 0.8901 (t70) cc_final: 0.8671 (t0) REVERT: D 822 MET cc_start: 0.8273 (mpp) cc_final: 0.7655 (mpp) REVERT: E 30 MET cc_start: 0.9128 (tpp) cc_final: 0.8920 (tpp) REVERT: F 100 MET cc_start: 0.8442 (mtp) cc_final: 0.8147 (mtp) REVERT: F 102 MET cc_start: 0.7871 (tpp) cc_final: 0.7322 (tpp) REVERT: F 105 MET cc_start: 0.8911 (ppp) cc_final: 0.8547 (ppp) REVERT: F 137 TYR cc_start: 0.9126 (t80) cc_final: 0.8912 (t80) REVERT: F 143 TYR cc_start: 0.9697 (t80) cc_final: 0.9480 (t80) REVERT: F 379 MET cc_start: 0.9425 (tpt) cc_final: 0.9058 (tpt) REVERT: F 487 MET cc_start: 0.8848 (tpt) cc_final: 0.8219 (tpp) REVERT: F 507 MET cc_start: 0.8597 (tpp) cc_final: 0.8307 (mtp) REVERT: F 567 MET cc_start: 0.9233 (pmm) cc_final: 0.8893 (pmm) outliers start: 1 outliers final: 0 residues processed: 165 average time/residue: 0.2100 time to fit residues: 57.9677 Evaluate side-chains 146 residues out of total 3358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 146 time to evaluate : 1.075 ------------------------------------------------------------------------------- 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: 9.9990 chunk 330 optimal weight: 8.9990 chunk 107 optimal weight: 3.9990 chunk 67 optimal weight: 5.9990 chunk 318 optimal weight: 20.0000 chunk 243 optimal weight: 8.9990 chunk 320 optimal weight: 0.0370 chunk 224 optimal weight: 5.9990 chunk 96 optimal weight: 6.9990 chunk 321 optimal weight: 6.9990 chunk 198 optimal weight: 9.9990 overall best weight: 4.6066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 ASN ** 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** ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3454 r_free = 0.3454 target = 0.050275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.034641 restraints weight = 378976.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 62)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.034926 restraints weight = 272074.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.035318 restraints weight = 211123.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.035601 restraints weight = 182025.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.035712 restraints weight = 165910.562| |-----------------------------------------------------------------------------| r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.6039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 34687 Z= 0.179 Angle : 0.599 11.784 47469 Z= 0.317 Chirality : 0.041 0.190 5399 Planarity : 0.004 0.049 5694 Dihedral : 17.694 178.729 5939 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 14.98 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.37 % Favored : 93.55 % Rotamer: Outliers : 0.00 % Allowed : 0.21 % Favored : 99.79 % 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: -0.09 (0.14), residues: 3909 helix: 1.58 (0.13), residues: 1634 sheet: -0.76 (0.27), residues: 372 loop : -1.42 (0.14), residues: 1903 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG E 67 TYR 0.030 0.001 TYR C1229 PHE 0.017 0.001 PHE C 812 TRP 0.009 0.002 TRP D 580 HIS 0.013 0.001 HIS C 150 Details of bonding type rmsd covalent geometry : bond 0.00382 (34687) covalent geometry : angle 0.59935 (47469) hydrogen bonds : bond 0.04019 ( 1438) hydrogen bonds : angle 4.53973 ( 4093) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6291.25 seconds wall clock time: 109 minutes 12.62 seconds (6552.62 seconds total)