Starting phenix.real_space_refine on Fri Jul 3 06:27:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7w02_32234/07_2026/7w02_32234.cif Found real_map, /net/cci-nas-00/data/ceres_data/7w02_32234/07_2026/7w02_32234.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7w02_32234/07_2026/7w02_32234.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7w02_32234/07_2026/7w02_32234.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7w02_32234/07_2026/7w02_32234.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7w02_32234/07_2026/7w02_32234.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7w02_32234/07_2026/7w02_32234.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7w02_32234/07_2026/7w02_32234.cif" } resolution = 3.3 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= -0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 68 5.16 5 C 7985 2.51 5 N 2063 2.21 5 O 2202 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 114 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12326 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 12234 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1566, 12234 Classifications: {'peptide': 1566} Incomplete info: {'truncation_to_alanine': 46} Link IDs: {'PTRANS': 69, 'TRANS': 1496} Chain breaks: 8 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 191 Unresolved non-hydrogen angles: 234 Unresolved non-hydrogen dihedrals: 168 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLU:plan': 9, 'HIS:plan': 6, 'ASN:plan1': 2, 'ARG:plan': 2, 'GLN:plan1': 3, 'PHE:plan': 1, 'ASP:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 110 Chain: "A" Number of atoms: 92 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 92 Unusual residues: {' MG': 2, 'ATP': 2, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 2.29, per 1000 atoms: 0.19 Number of scatterers: 12326 At special positions: 0 Unit cell: (97.2, 145.8, 138.24, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 68 16.00 P 6 15.00 Mg 2 11.99 O 2202 8.00 N 2063 7.00 C 7985 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A1274 " - pdb=" SG CYS A1284 " distance=2.03 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 Links applied NAG-ASN " NAG A1805 " - " ASN A 124 " " NAG A1806 " - " ASN A 140 " Time building additional restraints: 0.80 Conformation dependent library (CDL) restraints added in 552.8 milliseconds 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2932 Finding SS restraints... Secondary structure from input PDB file: 67 helices and 9 sheets defined 50.8% alpha, 8.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.41 Creating SS restraints... Processing helix chain 'A' and resid 1 through 20 removed outlier: 3.991A pdb=" N LEU A 9 " --> pdb=" O ARG A 5 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ARG A 20 " --> pdb=" O THR A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 21 through 30 Processing helix chain 'A' and resid 36 through 46 removed outlier: 3.668A pdb=" N ILE A 40 " --> pdb=" O SER A 36 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LEU A 44 " --> pdb=" O ILE A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 101 removed outlier: 3.871A pdb=" N THR A 94 " --> pdb=" O ALA A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 122 removed outlier: 3.710A pdb=" N PHE A 116 " --> pdb=" O SER A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 143 removed outlier: 4.453A pdb=" N SER A 142 " --> pdb=" O PHE A 139 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LYS A 143 " --> pdb=" O ASN A 140 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 139 through 143' Processing helix chain 'A' and resid 210 through 227 removed outlier: 3.677A pdb=" N MET A 223 " --> pdb=" O ASP A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 235 removed outlier: 3.667A pdb=" N GLN A 233 " --> pdb=" O ALA A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 284 removed outlier: 3.609A pdb=" N LEU A 269 " --> pdb=" O LEU A 265 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N SER A 270 " --> pdb=" O LEU A 266 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N PHE A 271 " --> pdb=" O LEU A 267 " (cutoff:3.500A) removed outlier: 5.448A pdb=" N TYR A 273 " --> pdb=" O LEU A 269 " (cutoff:3.500A) removed outlier: 5.208A pdb=" N THR A 274 " --> pdb=" O SER A 270 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ALA A 279 " --> pdb=" O ALA A 275 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ARG A 280 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL A 283 " --> pdb=" O ALA A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 299 removed outlier: 3.655A pdb=" N MET A 294 " --> pdb=" O LEU A 290 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N LEU A 299 " --> pdb=" O ARG A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 326 removed outlier: 3.812A pdb=" N TRP A 305 " --> pdb=" O SER A 301 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N SER A 306 " --> pdb=" O TRP A 302 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ALA A 307 " --> pdb=" O LEU A 303 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LEU A 314 " --> pdb=" O LEU A 310 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N PHE A 315 " --> pdb=" O LEU A 311 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU A 316 " --> pdb=" O PHE A 312 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N THR A 324 " --> pdb=" O ALA A 320 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 365 removed outlier: 3.871A pdb=" N VAL A 346 " --> pdb=" O ASP A 342 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N SER A 356 " --> pdb=" O CYS A 352 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N SER A 361 " --> pdb=" O THR A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 385 removed outlier: 3.853A pdb=" N GLY A 379 " --> pdb=" O ALA A 375 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N PHE A 380 " --> pdb=" O ALA A 376 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU A 381 " --> pdb=" O PHE A 377 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N TYR A 382 " --> pdb=" O GLY A 378 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N PHE A 383 " --> pdb=" O GLY A 379 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 390 Processing helix chain 'A' and resid 393 through 397 removed outlier: 3.813A pdb=" N TYR A 396 " --> pdb=" O ALA A 393 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N ASN A 397 " --> pdb=" O PRO A 394 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 393 through 397' Processing helix chain 'A' and resid 400 through 406 Processing helix chain 'A' and resid 407 through 409 No H-bonds generated for 'chain 'A' and resid 407 through 409' Processing helix chain 'A' and resid 410 through 427 removed outlier: 3.530A pdb=" N GLY A 418 " --> pdb=" O ALA A 414 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N LEU A 421 " --> pdb=" O MET A 417 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLY A 423 " --> pdb=" O ALA A 419 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 474 removed outlier: 3.654A pdb=" N LEU A 453 " --> pdb=" O PHE A 449 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N MET A 455 " --> pdb=" O GLN A 451 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N SER A 460 " --> pdb=" O LEU A 456 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N VAL A 461 " --> pdb=" O LEU A 457 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N VAL A 466 " --> pdb=" O LEU A 462 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N TYR A 469 " --> pdb=" O LEU A 465 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLU A 471 " --> pdb=" O THR A 467 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ALA A 472 " --> pdb=" O TRP A 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 575 through 580 Processing helix chain 'A' and resid 600 through 605 removed outlier: 4.205A pdb=" N ILE A 604 " --> pdb=" O ASP A 600 " (cutoff:3.500A) Processing helix chain 'A' and resid 622 through 635 removed outlier: 3.830A pdb=" N LYS A 634 " --> pdb=" O TYR A 630 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLY A 635 " --> pdb=" O ALA A 631 " (cutoff:3.500A) Processing helix chain 'A' and resid 640 through 653 removed outlier: 3.969A pdb=" N GLU A 644 " --> pdb=" O LYS A 640 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLY A 653 " --> pdb=" O LEU A 649 " (cutoff:3.500A) Processing helix chain 'A' and resid 668 through 680 removed outlier: 3.757A pdb=" N LYS A 672 " --> pdb=" O GLY A 668 " (cutoff:3.500A) Processing helix chain 'A' and resid 696 through 710 removed outlier: 4.217A pdb=" N ALA A 702 " --> pdb=" O ILE A 698 " (cutoff:3.500A) Processing helix chain 'A' and resid 724 through 729 Processing helix chain 'A' and resid 750 through 755 removed outlier: 3.574A pdb=" N TYR A 754 " --> pdb=" O LEU A 750 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLY A 755 " --> pdb=" O LYS A 751 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 750 through 755' Processing helix chain 'A' and resid 769 through 781 removed outlier: 3.949A pdb=" N ILE A 773 " --> pdb=" O ASN A 769 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU A 776 " --> pdb=" O ASP A 772 " (cutoff:3.500A) Processing helix chain 'A' and resid 803 through 805 No H-bonds generated for 'chain 'A' and resid 803 through 805' Processing helix chain 'A' and resid 806 through 816 removed outlier: 3.534A pdb=" N LYS A 816 " --> pdb=" O LYS A 812 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 821 removed outlier: 3.856A pdb=" N LEU A 820 " --> pdb=" O LYS A 816 " (cutoff:3.500A) Processing helix chain 'A' and resid 831 through 843 removed outlier: 4.006A pdb=" N VAL A 835 " --> pdb=" O THR A 831 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N PHE A 836 " --> pdb=" O MET A 832 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LEU A 837 " --> pdb=" O GLU A 833 " (cutoff:3.500A) Processing helix chain 'A' and resid 900 through 917 removed outlier: 3.663A pdb=" N HIS A 904 " --> pdb=" O GLY A 900 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N TRP A 909 " --> pdb=" O CYS A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 917 through 922 removed outlier: 3.851A pdb=" N ARG A 921 " --> pdb=" O ALA A 917 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLU A 922 " --> pdb=" O TYR A 918 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 917 through 922' Processing helix chain 'A' and resid 922 through 936 removed outlier: 4.022A pdb=" N VAL A 926 " --> pdb=" O GLU A 922 " (cutoff:3.500A) Proline residue: A 933 - end of helix removed outlier: 3.628A pdb=" N CYS A 936 " --> pdb=" O VAL A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 941 through 946 Processing helix chain 'A' and resid 979 through 994 removed outlier: 3.958A pdb=" N HIS A 985 " --> pdb=" O GLN A 981 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLN A 991 " --> pdb=" O LYS A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1003 through 1016 removed outlier: 3.862A pdb=" N GLY A1016 " --> pdb=" O ALA A1012 " (cutoff:3.500A) Processing helix chain 'A' and resid 1017 through 1022 removed outlier: 3.829A pdb=" N ASN A1020 " --> pdb=" O GLY A1017 " (cutoff:3.500A) Processing helix chain 'A' and resid 1048 through 1066 removed outlier: 3.813A pdb=" N THR A1052 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU A1060 " --> pdb=" O VAL A1056 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LEU A1065 " --> pdb=" O LEU A1061 " (cutoff:3.500A) Processing helix chain 'A' and resid 1095 through 1112 removed outlier: 4.020A pdb=" N ILE A1100 " --> pdb=" O LYS A1096 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ALA A1107 " --> pdb=" O ASN A1103 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N PHE A1110 " --> pdb=" O PHE A1106 " (cutoff:3.500A) Processing helix chain 'A' and resid 1113 through 1115 No H-bonds generated for 'chain 'A' and resid 1113 through 1115' Processing helix chain 'A' and resid 1116 through 1125 removed outlier: 4.100A pdb=" N ARG A1123 " --> pdb=" O ALA A1119 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N VAL A1125 " --> pdb=" O SER A1121 " (cutoff:3.500A) Processing helix chain 'A' and resid 1126 through 1134 removed outlier: 4.024A pdb=" N VAL A1130 " --> pdb=" O GLN A1126 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLN A1131 " --> pdb=" O ALA A1127 " (cutoff:3.500A) Processing helix chain 'A' and resid 1137 through 1167 removed outlier: 3.785A pdb=" N SER A1144 " --> pdb=" O SER A1140 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ALA A1145 " --> pdb=" O PHE A1141 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ILE A1155 " --> pdb=" O ILE A1151 " (cutoff:3.500A) Proline residue: A1156 - end of helix removed outlier: 4.101A pdb=" N LEU A1161 " --> pdb=" O SER A1157 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N VAL A1162 " --> pdb=" O LEU A1158 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL A1163 " --> pdb=" O LEU A1159 " (cutoff:3.500A) Processing helix chain 'A' and resid 1169 through 1173 Processing helix chain 'A' and resid 1176 through 1199 removed outlier: 4.072A pdb=" N ASP A1180 " --> pdb=" O GLY A1176 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ILE A1193 " --> pdb=" O GLY A1189 " (cutoff:3.500A) Proline residue: A1194 - end of helix Processing helix chain 'A' and resid 1200 through 1202 No H-bonds generated for 'chain 'A' and resid 1200 through 1202' Processing helix chain 'A' and resid 1206 through 1220 removed outlier: 3.622A pdb=" N TYR A1210 " --> pdb=" O ALA A1206 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N THR A1211 " --> pdb=" O ALA A1207 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ARG A1212 " --> pdb=" O THR A1208 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N ILE A1215 " --> pdb=" O THR A1211 " (cutoff:3.500A) Processing helix chain 'A' and resid 1221 through 1231 Processing helix chain 'A' and resid 1240 through 1245 removed outlier: 3.734A pdb=" N THR A1244 " --> pdb=" O GLU A1240 " (cutoff:3.500A) Processing helix chain 'A' and resid 1248 through 1251 removed outlier: 3.760A pdb=" N VAL A1251 " --> pdb=" O VAL A1248 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1248 through 1251' Processing helix chain 'A' and resid 1252 through 1274 removed outlier: 3.733A pdb=" N LEU A1257 " --> pdb=" O PRO A1253 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N CYS A1274 " --> pdb=" O THR A1270 " (cutoff:3.500A) Processing helix chain 'A' and resid 1277 through 1287 removed outlier: 4.238A pdb=" N TYR A1283 " --> pdb=" O VAL A1279 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LYS A1285 " --> pdb=" O ALA A1281 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N TYR A1287 " --> pdb=" O TYR A1283 " (cutoff:3.500A) Processing helix chain 'A' and resid 1304 through 1325 removed outlier: 3.822A pdb=" N GLY A1314 " --> pdb=" O MET A1310 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N CYS A1315 " --> pdb=" O ALA A1311 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ALA A1316 " --> pdb=" O ALA A1312 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU A1320 " --> pdb=" O ALA A1316 " (cutoff:3.500A) Processing helix chain 'A' and resid 1358 through 1368 removed outlier: 3.610A pdb=" N GLU A1364 " --> pdb=" O ASP A1360 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ARG A1365 " --> pdb=" O VAL A1361 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N THR A1366 " --> pdb=" O ALA A1362 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ILE A1368 " --> pdb=" O GLU A1364 " (cutoff:3.500A) Processing helix chain 'A' and resid 1421 through 1431 removed outlier: 3.779A pdb=" N MET A1428 " --> pdb=" O THR A1424 " (cutoff:3.500A) Processing helix chain 'A' and resid 1472 through 1484 removed outlier: 3.520A pdb=" N LEU A1477 " --> pdb=" O GLY A1473 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N TYR A1480 " --> pdb=" O MET A1476 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ARG A1484 " --> pdb=" O TYR A1480 " (cutoff:3.500A) Processing helix chain 'A' and resid 1487 through 1490 Processing helix chain 'A' and resid 1491 through 1501 removed outlier: 3.856A pdb=" N THR A1498 " --> pdb=" O CYS A1494 " (cutoff:3.500A) Processing helix chain 'A' and resid 1518 through 1528 removed outlier: 3.756A pdb=" N LEU A1523 " --> pdb=" O ASN A1519 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ALA A1528 " --> pdb=" O SER A1524 " (cutoff:3.500A) Processing helix chain 'A' and resid 1546 through 1562 removed outlier: 3.519A pdb=" N TRP A1554 " --> pdb=" O ARG A1550 " (cutoff:3.500A) Processing helix chain 'A' and resid 1597 through 1603 Processing helix chain 'A' and resid 1622 through 1635 removed outlier: 3.553A pdb=" N ALA A1629 " --> pdb=" O GLU A1625 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N PHE A1630 " --> pdb=" O GLU A1626 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N VAL A1631 " --> pdb=" O PHE A1627 " (cutoff:3.500A) Processing helix chain 'A' and resid 1660 through 1664 Processing helix chain 'A' and resid 1665 through 1668 removed outlier: 3.656A pdb=" N LYS A1668 " --> pdb=" O ILE A1665 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1665 through 1668' Processing helix chain 'A' and resid 1684 through 1691 removed outlier: 3.617A pdb=" N VAL A1688 " --> pdb=" O SER A1684 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 105 through 106 removed outlier: 7.714A pdb=" N GLU A 79 " --> pdb=" O LEU A 130 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ALA A 132 " --> pdb=" O GLU A 79 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ALA A 81 " --> pdb=" O ALA A 132 " (cutoff:3.500A) removed outlier: 5.879A pdb=" N VAL A 134 " --> pdb=" O ALA A 81 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N VAL A 134 " --> pdb=" O HIS A 153 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU A 154 " --> pdb=" O SER A1075 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N VAL A1074 " --> pdb=" O LEU A 958 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 238 through 241 removed outlier: 3.550A pdb=" N ARG A1035 " --> pdb=" O VAL A1032 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N VAL A 967 " --> pdb=" O VAL A1025 " (cutoff:3.500A) removed outlier: 8.533A pdb=" N ALA A1027 " --> pdb=" O VAL A 967 " (cutoff:3.500A) removed outlier: 8.386A pdb=" N PHE A1029 " --> pdb=" O PRO A 969 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N SER A 971 " --> pdb=" O PHE A1029 " (cutoff:3.500A) removed outlier: 8.484A pdb=" N ASP A1031 " --> pdb=" O SER A 971 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ARG A 998 " --> pdb=" O VAL A 968 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 547 through 557 removed outlier: 6.452A pdb=" N ALA A 548 " --> pdb=" O VAL A 538 " (cutoff:3.500A) removed outlier: 7.596A pdb=" N VAL A 538 " --> pdb=" O ALA A 548 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N ARG A 550 " --> pdb=" O SER A 536 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N SER A 536 " --> pdb=" O ARG A 550 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N LEU A 552 " --> pdb=" O HIS A 534 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N LEU A 535 " --> pdb=" O SER A 587 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N SER A 587 " --> pdb=" O LEU A 535 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 608 through 611 removed outlier: 6.717A pdb=" N GLY A 609 " --> pdb=" O ILE A 687 " (cutoff:3.500A) removed outlier: 8.127A pdb=" N ASP A 689 " --> pdb=" O GLY A 609 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N CYS A 611 " --> pdb=" O ASP A 689 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ARG A 732 " --> pdb=" O ILE A 561 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ILE A 733 " --> pdb=" O CYS A 744 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N CYS A 744 " --> pdb=" O ILE A 733 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N ILE A 735 " --> pdb=" O GLN A 742 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 785 through 786 removed outlier: 3.609A pdb=" N THR A 785 " --> pdb=" O ILE A 797 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N MET A 760 " --> pdb=" O PHE A 796 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU A 798 " --> pdb=" O TYR A 758 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N ASP A1677 " --> pdb=" O LYS A1614 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N SER A1681 " --> pdb=" O SER A1610 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1404 through 1406 removed outlier: 3.743A pdb=" N LEU A1381 " --> pdb=" O VAL A1406 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1386 through 1390 removed outlier: 6.363A pdb=" N LEU A1386 " --> pdb=" O ASP A1400 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ASP A1400 " --> pdb=" O LEU A1386 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N LYS A1388 " --> pdb=" O ALA A1398 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1411 through 1412 removed outlier: 6.878A pdb=" N ILE A1536 " --> pdb=" O ILE A1568 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1415 through 1416 removed outlier: 6.419A pdb=" N LEU A1415 " --> pdb=" O MET A1587 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N ILE A1586 " --> pdb=" O LYS A1593 " (cutoff:3.500A) 480 hydrogen bonds defined for protein. 1395 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.13 Time building geometry restraints manager: 1.13 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: 3886 1.34 - 1.46: 2654 1.46 - 1.58: 5957 1.58 - 1.69: 10 1.69 - 1.81: 112 Bond restraints: 12619 Sorted by residual: bond pdb=" C4 ATP A1802 " pdb=" C5 ATP A1802 " ideal model delta sigma weight residual 1.388 1.466 -0.078 1.00e-02 1.00e+04 6.01e+01 bond pdb=" C4 ATP A1801 " pdb=" C5 ATP A1801 " ideal model delta sigma weight residual 1.388 1.464 -0.076 1.00e-02 1.00e+04 5.79e+01 bond pdb=" C5 ATP A1801 " pdb=" C6 ATP A1801 " ideal model delta sigma weight residual 1.409 1.477 -0.068 1.00e-02 1.00e+04 4.56e+01 bond pdb=" C5 ATP A1802 " pdb=" C6 ATP A1802 " ideal model delta sigma weight residual 1.409 1.475 -0.066 1.00e-02 1.00e+04 4.38e+01 bond pdb=" C4 ATP A1801 " pdb=" N9 ATP A1801 " ideal model delta sigma weight residual 1.374 1.327 0.047 1.00e-02 1.00e+04 2.18e+01 ... (remaining 12614 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.06: 17032 4.06 - 8.12: 89 8.12 - 12.18: 6 12.18 - 16.23: 4 16.23 - 20.29: 2 Bond angle restraints: 17133 Sorted by residual: angle pdb=" PB ATP A1801 " pdb=" O3B ATP A1801 " pdb=" PG ATP A1801 " ideal model delta sigma weight residual 139.87 119.58 20.29 1.00e+00 1.00e+00 4.12e+02 angle pdb=" PB ATP A1802 " pdb=" O3B ATP A1802 " pdb=" PG ATP A1802 " ideal model delta sigma weight residual 139.87 120.09 19.78 1.00e+00 1.00e+00 3.91e+02 angle pdb=" PA ATP A1802 " pdb=" O3A ATP A1802 " pdb=" PB ATP A1802 " ideal model delta sigma weight residual 136.83 121.88 14.95 1.00e+00 1.00e+00 2.23e+02 angle pdb=" PA ATP A1801 " pdb=" O3A ATP A1801 " pdb=" PB ATP A1801 " ideal model delta sigma weight residual 136.83 122.86 13.97 1.00e+00 1.00e+00 1.95e+02 angle pdb=" C5 ATP A1801 " pdb=" C4 ATP A1801 " pdb=" N3 ATP A1801 " ideal model delta sigma weight residual 126.80 118.97 7.83 1.00e+00 1.00e+00 6.13e+01 ... (remaining 17128 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 6634 17.97 - 35.94: 639 35.94 - 53.91: 109 53.91 - 71.88: 21 71.88 - 89.85: 10 Dihedral angle restraints: 7413 sinusoidal: 2872 harmonic: 4541 Sorted by residual: dihedral pdb=" CA ARG A1174 " pdb=" C ARG A1174 " pdb=" N ASP A1175 " pdb=" CA ASP A1175 " ideal model delta harmonic sigma weight residual -180.00 -142.34 -37.66 0 5.00e+00 4.00e-02 5.67e+01 dihedral pdb=" CA ARG A1401 " pdb=" C ARG A1401 " pdb=" N LEU A1402 " pdb=" CA LEU A1402 " ideal model delta harmonic sigma weight residual 180.00 154.95 25.05 0 5.00e+00 4.00e-02 2.51e+01 dihedral pdb=" CA LEU A1001 " pdb=" C LEU A1001 " pdb=" N GLY A1002 " pdb=" CA GLY A1002 " ideal model delta harmonic sigma weight residual -180.00 -156.03 -23.97 0 5.00e+00 4.00e-02 2.30e+01 ... (remaining 7410 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 1673 0.067 - 0.134: 265 0.134 - 0.201: 9 0.201 - 0.268: 2 0.268 - 0.334: 2 Chirality restraints: 1951 Sorted by residual: chirality pdb=" C1 NAG A1805 " pdb=" ND2 ASN A 124 " pdb=" C2 NAG A1805 " pdb=" O5 NAG A1805 " both_signs ideal model delta sigma weight residual False -2.40 -2.07 -0.33 2.00e-01 2.50e+01 2.80e+00 chirality pdb=" C1 NAG A1806 " pdb=" ND2 ASN A 140 " pdb=" C2 NAG A1806 " pdb=" O5 NAG A1806 " both_signs ideal model delta sigma weight residual False -2.40 -2.10 -0.30 2.00e-01 2.50e+01 2.22e+00 chirality pdb=" CB ILE A 829 " pdb=" CA ILE A 829 " pdb=" CG1 ILE A 829 " pdb=" CG2 ILE A 829 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.24 2.00e-01 2.50e+01 1.38e+00 ... (remaining 1948 not shown) Planarity restraints: 2150 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE A 110 " -0.033 5.00e-02 4.00e+02 4.96e-02 3.94e+00 pdb=" N PRO A 111 " 0.086 5.00e-02 4.00e+02 pdb=" CA PRO A 111 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 111 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A1546 " 0.030 5.00e-02 4.00e+02 4.62e-02 3.41e+00 pdb=" N PRO A1547 " -0.080 5.00e-02 4.00e+02 pdb=" CA PRO A1547 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A1547 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 31 " 0.030 5.00e-02 4.00e+02 4.47e-02 3.20e+00 pdb=" N PRO A 32 " -0.077 5.00e-02 4.00e+02 pdb=" CA PRO A 32 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 32 " 0.025 5.00e-02 4.00e+02 ... (remaining 2147 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.49: 54 2.49 - 3.10: 8562 3.10 - 3.70: 17212 3.70 - 4.30: 25123 4.30 - 4.90: 43378 Nonbonded interactions: 94329 Sorted by model distance: nonbonded pdb=" OE1 GLN A 613 " pdb="MG MG A1803 " model vdw 1.892 2.170 nonbonded pdb=" O2B ATP A1801 " pdb="MG MG A1803 " model vdw 2.000 2.170 nonbonded pdb=" OG1 THR A1423 " pdb="MG MG A1804 " model vdw 2.052 2.170 nonbonded pdb=" OD2 ASP A1149 " pdb=" OH TYR A1197 " model vdw 2.054 3.040 nonbonded pdb=" O2B ATP A1802 " pdb="MG MG A1804 " model vdw 2.061 2.170 ... (remaining 94324 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.790 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: 0.010 Extract box with map and model: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 10.730 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 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:1.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 12.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8723 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 : 0.007 0.078 12622 Z= 0.329 Angle : 0.891 20.293 17141 Z= 0.555 Chirality : 0.049 0.334 1951 Planarity : 0.004 0.050 2148 Dihedral : 14.649 89.849 4478 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.06 % Allowed : 10.85 % Favored : 89.08 % Rotamer: Outliers : 0.23 % Allowed : 0.70 % Favored : 99.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.18 (0.20), residues: 1548 helix: -1.38 (0.18), residues: 776 sheet: -2.40 (0.45), residues: 123 loop : -2.93 (0.21), residues: 649 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A1305 TYR 0.012 0.002 TYR A 386 PHE 0.024 0.002 PHE A 156 TRP 0.020 0.002 TRP A 658 HIS 0.006 0.001 HIS A 304 Details of bonding type rmsd/Z covalent geometry : bond 0.00673 / 0.33 (12619) covalent geometry : angle 0.88837 / 0.55 (17133) SS BOND : bond 0.00477 / 0.25 ( 1) SS BOND : angle 0.70695 / 0.38 ( 2) hydrogen bonds : bond 0.20722 / 13.02 ( 480) hydrogen bonds : angle 7.06224 / 4.84 ( 1395) link_NAG-ASN : bond 0.00774 / 0.39 ( 2) link_NAG-ASN : angle 3.98860 / 1.70 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 136 time to evaluate : 0.454 Fit side-chains REVERT: A 417 MET cc_start: 0.9019 (mtm) cc_final: 0.8751 (mtm) REVERT: A 1231 MET cc_start: 0.9122 (ttp) cc_final: 0.8794 (ttp) outliers start: 3 outliers final: 0 residues processed: 138 average time/residue: 0.0897 time to fit residues: 18.5463 Evaluate side-chains 110 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 110 time to evaluate : 0.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 98 optimal weight: 7.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 6.9990 chunk 149 optimal weight: 30.0000 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.121760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.087324 restraints weight = 18718.114| |-----------------------------------------------------------------------------| r_work (start): 0.2882 rms_B_bonded: 2.16 r_work: 0.2748 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2627 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8854 moved from start: 0.0797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 12622 Z= 0.236 Angle : 0.736 13.749 17141 Z= 0.370 Chirality : 0.048 0.543 1951 Planarity : 0.005 0.060 2148 Dihedral : 5.138 33.135 1693 Min Nonbonded Distance : 1.839 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.85 % Favored : 89.15 % Rotamer: Outliers : 0.62 % Allowed : 9.16 % Favored : 90.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -2.78 (0.20), residues: 1548 helix: -1.00 (0.18), residues: 782 sheet: -1.79 (0.50), residues: 119 loop : -2.91 (0.21), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 670 TYR 0.016 0.002 TYR A1283 PHE 0.020 0.002 PHE A 583 TRP 0.019 0.001 TRP A 658 HIS 0.007 0.001 HIS A 141 Details of bonding type rmsd/Z covalent geometry : bond 0.00575 / 0.24 (12619) covalent geometry : angle 0.72357 / 0.37 (17133) SS BOND : bond 0.00662 / 0.35 ( 1) SS BOND : angle 1.19064 / 0.63 ( 2) hydrogen bonds : bond 0.05446 / 3.46 ( 480) hydrogen bonds : angle 4.68528 / 3.27 ( 1395) link_NAG-ASN : bond 0.01494 / 0.72 ( 2) link_NAG-ASN : angle 7.13058 / 2.60 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 124 time to evaluate : 0.465 Fit side-chains REVERT: A 522 GLU cc_start: 0.7985 (mt-10) cc_final: 0.7745 (tt0) REVERT: A 1239 GLU cc_start: 0.8452 (tm-30) cc_final: 0.8209 (tm-30) outliers start: 8 outliers final: 5 residues processed: 127 average time/residue: 0.0987 time to fit residues: 18.8064 Evaluate side-chains 120 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 115 time to evaluate : 0.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 950 LEU Chi-restraints excluded: chain A residue 1219 LEU Chi-restraints excluded: chain A residue 1569 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 98 optimal weight: 0.5980 chunk 24 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 65 optimal weight: 0.5980 chunk 25 optimal weight: 2.9990 chunk 72 optimal weight: 9.9990 chunk 43 optimal weight: 4.9990 chunk 143 optimal weight: 0.9980 chunk 34 optimal weight: 0.7980 chunk 147 optimal weight: 9.9990 chunk 116 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.125600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.091795 restraints weight = 18553.007| |-----------------------------------------------------------------------------| r_work (start): 0.2954 rms_B_bonded: 2.21 r_work: 0.2823 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2702 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8794 moved from start: 0.1225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 12622 Z= 0.115 Angle : 0.610 12.269 17141 Z= 0.306 Chirality : 0.043 0.390 1951 Planarity : 0.004 0.052 2148 Dihedral : 4.679 31.452 1693 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.07 % Favored : 91.86 % Rotamer: Outliers : 1.86 % Allowed : 10.64 % Favored : 87.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -2.23 (0.21), residues: 1548 helix: -0.49 (0.19), residues: 779 sheet: -1.37 (0.50), residues: 117 loop : -2.75 (0.21), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 670 TYR 0.011 0.001 TYR A1287 PHE 0.010 0.001 PHE A 583 TRP 0.013 0.001 TRP A1148 HIS 0.004 0.001 HIS A 141 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.11 (12619) covalent geometry : angle 0.59901 / 0.30 (17133) SS BOND : bond 0.00187 / 0.10 ( 1) SS BOND : angle 0.57036 / 0.31 ( 2) hydrogen bonds : bond 0.03786 / 2.43 ( 480) hydrogen bonds : angle 4.11661 / 2.87 ( 1395) link_NAG-ASN : bond 0.01335 / 0.64 ( 2) link_NAG-ASN : angle 6.20143 / 2.24 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 131 time to evaluate : 0.328 Fit side-chains REVERT: A 729 LEU cc_start: 0.9215 (OUTLIER) cc_final: 0.8939 (pp) REVERT: A 1283 TYR cc_start: 0.8182 (t80) cc_final: 0.7964 (t80) REVERT: A 1436 THR cc_start: 0.6827 (OUTLIER) cc_final: 0.6351 (p) REVERT: A 1589 GLN cc_start: 0.8307 (mm110) cc_final: 0.8106 (mm110) outliers start: 24 outliers final: 12 residues processed: 144 average time/residue: 0.0856 time to fit residues: 18.5858 Evaluate side-chains 128 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 114 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 294 MET Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 658 TRP Chi-restraints excluded: chain A residue 665 LEU Chi-restraints excluded: chain A residue 729 LEU Chi-restraints excluded: chain A residue 950 LEU Chi-restraints excluded: chain A residue 968 VAL Chi-restraints excluded: chain A residue 1436 THR Chi-restraints excluded: chain A residue 1512 VAL Chi-restraints excluded: chain A residue 1569 ILE Chi-restraints excluded: chain A residue 1639 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 110 optimal weight: 0.5980 chunk 86 optimal weight: 2.9990 chunk 127 optimal weight: 6.9990 chunk 18 optimal weight: 9.9990 chunk 1 optimal weight: 4.9990 chunk 117 optimal weight: 0.8980 chunk 21 optimal weight: 10.0000 chunk 53 optimal weight: 3.9990 chunk 145 optimal weight: 10.0000 chunk 78 optimal weight: 6.9990 chunk 63 optimal weight: 3.9990 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.122927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.088566 restraints weight = 18565.868| |-----------------------------------------------------------------------------| r_work (start): 0.2880 rms_B_bonded: 2.05 r_work: 0.2747 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2629 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8834 moved from start: 0.1256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 12622 Z= 0.198 Angle : 0.657 12.199 17141 Z= 0.329 Chirality : 0.045 0.386 1951 Planarity : 0.004 0.046 2148 Dihedral : 4.704 29.837 1693 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.43 % Favored : 90.50 % Rotamer: Outliers : 1.94 % Allowed : 12.34 % Favored : 85.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.17 (0.21), residues: 1548 helix: -0.39 (0.19), residues: 779 sheet: -1.57 (0.48), residues: 122 loop : -2.74 (0.22), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 670 TYR 0.010 0.002 TYR A 386 PHE 0.018 0.001 PHE A 583 TRP 0.012 0.001 TRP A 308 HIS 0.004 0.001 HIS A 141 Details of bonding type rmsd/Z covalent geometry : bond 0.00484 / 0.20 (12619) covalent geometry : angle 0.64776 / 0.33 (17133) SS BOND : bond 0.00461 / 0.24 ( 1) SS BOND : angle 0.35518 / 0.19 ( 2) hydrogen bonds : bond 0.04550 / 2.91 ( 480) hydrogen bonds : angle 4.06598 / 2.84 ( 1395) link_NAG-ASN : bond 0.01272 / 0.61 ( 2) link_NAG-ASN : angle 5.95044 / 2.15 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 119 time to evaluate : 0.480 Fit side-chains REVERT: A 729 LEU cc_start: 0.9223 (OUTLIER) cc_final: 0.8919 (pp) REVERT: A 794 LEU cc_start: 0.7257 (OUTLIER) cc_final: 0.6966 (tt) REVERT: A 1239 GLU cc_start: 0.8423 (tm-30) cc_final: 0.8211 (tm-30) REVERT: A 1283 TYR cc_start: 0.8188 (t80) cc_final: 0.7910 (t80) REVERT: A 1436 THR cc_start: 0.6809 (OUTLIER) cc_final: 0.6284 (p) outliers start: 25 outliers final: 14 residues processed: 136 average time/residue: 0.0882 time to fit residues: 18.3234 Evaluate side-chains 133 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 116 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 327 PHE Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 658 TRP Chi-restraints excluded: chain A residue 729 LEU Chi-restraints excluded: chain A residue 794 LEU Chi-restraints excluded: chain A residue 950 LEU Chi-restraints excluded: chain A residue 968 VAL Chi-restraints excluded: chain A residue 1138 VAL Chi-restraints excluded: chain A residue 1436 THR Chi-restraints excluded: chain A residue 1569 ILE Chi-restraints excluded: chain A residue 1639 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 18 optimal weight: 10.0000 chunk 46 optimal weight: 0.0770 chunk 76 optimal weight: 7.9990 chunk 53 optimal weight: 3.9990 chunk 102 optimal weight: 2.9990 chunk 150 optimal weight: 2.9990 chunk 124 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 134 optimal weight: 4.9990 chunk 125 optimal weight: 0.8980 chunk 31 optimal weight: 5.9990 overall best weight: 1.7944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.124069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.089888 restraints weight = 18613.205| |-----------------------------------------------------------------------------| r_work (start): 0.2908 rms_B_bonded: 2.22 r_work: 0.2774 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2654 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8814 moved from start: 0.1430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 12622 Z= 0.151 Angle : 0.626 11.821 17141 Z= 0.312 Chirality : 0.044 0.377 1951 Planarity : 0.004 0.044 2148 Dihedral : 4.577 29.819 1693 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.53 % Favored : 91.41 % Rotamer: Outliers : 2.33 % Allowed : 12.97 % Favored : 84.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.99 (0.21), residues: 1548 helix: -0.20 (0.19), residues: 773 sheet: -1.48 (0.48), residues: 122 loop : -2.70 (0.21), residues: 653 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1305 TYR 0.010 0.001 TYR A1287 PHE 0.015 0.001 PHE A 583 TRP 0.012 0.001 TRP A1148 HIS 0.005 0.001 HIS A 141 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.15 (12619) covalent geometry : angle 0.61740 / 0.31 (17133) SS BOND : bond 0.00283 / 0.15 ( 1) SS BOND : angle 0.35401 / 0.20 ( 2) hydrogen bonds : bond 0.03982 / 2.55 ( 480) hydrogen bonds : angle 3.90013 / 2.73 ( 1395) link_NAG-ASN : bond 0.01214 / 0.58 ( 2) link_NAG-ASN : angle 5.60696 / 2.02 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 123 time to evaluate : 0.395 Fit side-chains revert: symmetry clash REVERT: A 718 LEU cc_start: 0.9066 (OUTLIER) cc_final: 0.8832 (mt) REVERT: A 729 LEU cc_start: 0.9210 (OUTLIER) cc_final: 0.8915 (pp) REVERT: A 794 LEU cc_start: 0.7228 (OUTLIER) cc_final: 0.6952 (tt) REVERT: A 1283 TYR cc_start: 0.8223 (t80) cc_final: 0.7955 (t80) REVERT: A 1436 THR cc_start: 0.6828 (OUTLIER) cc_final: 0.6301 (p) outliers start: 30 outliers final: 19 residues processed: 141 average time/residue: 0.0966 time to fit residues: 20.4548 Evaluate side-chains 146 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 123 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 262 GLN Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 284 GLN Chi-restraints excluded: chain A residue 294 MET Chi-restraints excluded: chain A residue 327 PHE Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 658 TRP Chi-restraints excluded: chain A residue 718 LEU Chi-restraints excluded: chain A residue 729 LEU Chi-restraints excluded: chain A residue 794 LEU Chi-restraints excluded: chain A residue 950 LEU Chi-restraints excluded: chain A residue 968 VAL Chi-restraints excluded: chain A residue 1138 VAL Chi-restraints excluded: chain A residue 1402 LEU Chi-restraints excluded: chain A residue 1436 THR Chi-restraints excluded: chain A residue 1512 VAL Chi-restraints excluded: chain A residue 1569 ILE Chi-restraints excluded: chain A residue 1639 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 147 optimal weight: 6.9990 chunk 151 optimal weight: 4.9990 chunk 111 optimal weight: 3.9990 chunk 70 optimal weight: 5.9990 chunk 6 optimal weight: 0.0040 chunk 134 optimal weight: 0.4980 chunk 56 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 chunk 16 optimal weight: 0.0670 chunk 102 optimal weight: 2.9990 chunk 100 optimal weight: 0.0050 overall best weight: 0.7146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1090 GLN A1600 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.127149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.092683 restraints weight = 18465.281| |-----------------------------------------------------------------------------| r_work (start): 0.2972 rms_B_bonded: 2.12 r_work: 0.2849 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2729 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8775 moved from start: 0.1762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 12622 Z= 0.103 Angle : 0.577 13.526 17141 Z= 0.287 Chirality : 0.041 0.365 1951 Planarity : 0.003 0.043 2148 Dihedral : 4.248 26.985 1693 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.01 % Favored : 91.93 % Rotamer: Outliers : 2.17 % Allowed : 13.98 % Favored : 83.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.63 (0.21), residues: 1548 helix: 0.14 (0.19), residues: 767 sheet: -1.19 (0.47), residues: 120 loop : -2.58 (0.22), residues: 661 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1305 TYR 0.010 0.001 TYR A1650 PHE 0.013 0.001 PHE A1062 TRP 0.012 0.001 TRP A1148 HIS 0.005 0.001 HIS A 141 Details of bonding type rmsd/Z covalent geometry : bond 0.00227 / 0.10 (12619) covalent geometry : angle 0.56880 / 0.28 (17133) SS BOND : bond 0.00067 / 0.04 ( 1) SS BOND : angle 0.42121 / 0.24 ( 2) hydrogen bonds : bond 0.03101 / 1.99 ( 480) hydrogen bonds : angle 3.67835 / 2.57 ( 1395) link_NAG-ASN : bond 0.01145 / 0.55 ( 2) link_NAG-ASN : angle 5.24282 / 1.88 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 132 time to evaluate : 0.394 Fit side-chains revert: symmetry clash REVERT: A 718 LEU cc_start: 0.9009 (OUTLIER) cc_final: 0.8739 (mt) REVERT: A 729 LEU cc_start: 0.9215 (OUTLIER) cc_final: 0.8952 (pp) REVERT: A 794 LEU cc_start: 0.7256 (OUTLIER) cc_final: 0.6986 (tt) REVERT: A 1436 THR cc_start: 0.6860 (OUTLIER) cc_final: 0.6384 (p) REVERT: A 1682 GLN cc_start: 0.6419 (tm-30) cc_final: 0.5891 (tm-30) outliers start: 28 outliers final: 17 residues processed: 150 average time/residue: 0.0921 time to fit residues: 20.7802 Evaluate side-chains 142 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 121 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 284 GLN Chi-restraints excluded: chain A residue 294 MET Chi-restraints excluded: chain A residue 327 PHE Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 400 THR Chi-restraints excluded: chain A residue 658 TRP Chi-restraints excluded: chain A residue 718 LEU Chi-restraints excluded: chain A residue 729 LEU Chi-restraints excluded: chain A residue 794 LEU Chi-restraints excluded: chain A residue 968 VAL Chi-restraints excluded: chain A residue 1138 VAL Chi-restraints excluded: chain A residue 1190 TRP Chi-restraints excluded: chain A residue 1402 LEU Chi-restraints excluded: chain A residue 1436 THR Chi-restraints excluded: chain A residue 1512 VAL Chi-restraints excluded: chain A residue 1569 ILE Chi-restraints excluded: chain A residue 1639 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 95 optimal weight: 0.8980 chunk 75 optimal weight: 20.0000 chunk 73 optimal weight: 0.7980 chunk 34 optimal weight: 2.9990 chunk 47 optimal weight: 0.8980 chunk 67 optimal weight: 5.9990 chunk 55 optimal weight: 0.9980 chunk 3 optimal weight: 2.9990 chunk 82 optimal weight: 3.9990 chunk 123 optimal weight: 2.9990 chunk 21 optimal weight: 8.9990 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 226 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.125931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.091499 restraints weight = 18511.776| |-----------------------------------------------------------------------------| r_work (start): 0.2947 rms_B_bonded: 2.08 r_work: 0.2823 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2704 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8794 moved from start: 0.1775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12622 Z= 0.126 Angle : 0.593 13.460 17141 Z= 0.293 Chirality : 0.042 0.356 1951 Planarity : 0.003 0.044 2148 Dihedral : 4.238 26.451 1693 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.27 % Favored : 91.67 % Rotamer: Outliers : 2.87 % Allowed : 14.29 % Favored : 82.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.60 (0.21), residues: 1548 helix: 0.15 (0.19), residues: 776 sheet: -1.16 (0.47), residues: 120 loop : -2.60 (0.22), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1305 TYR 0.023 0.001 TYR A1283 PHE 0.014 0.001 PHE A1062 TRP 0.010 0.001 TRP A1148 HIS 0.004 0.001 HIS A 141 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 (12619) covalent geometry : angle 0.58495 / 0.29 (17133) SS BOND : bond 0.00182 / 0.10 ( 1) SS BOND : angle 0.29224 / 0.17 ( 2) hydrogen bonds : bond 0.03462 / 2.22 ( 480) hydrogen bonds : angle 3.67743 / 2.60 ( 1395) link_NAG-ASN : bond 0.01148 / 0.55 ( 2) link_NAG-ASN : angle 5.09959 / 1.83 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 123 time to evaluate : 0.427 Fit side-chains revert: symmetry clash REVERT: A 5 ARG cc_start: 0.8881 (ttp-110) cc_final: 0.8578 (ttp80) REVERT: A 304 HIS cc_start: 0.8274 (OUTLIER) cc_final: 0.7852 (t-170) REVERT: A 718 LEU cc_start: 0.9009 (OUTLIER) cc_final: 0.8728 (mt) REVERT: A 729 LEU cc_start: 0.9259 (OUTLIER) cc_final: 0.8974 (pp) REVERT: A 794 LEU cc_start: 0.7271 (OUTLIER) cc_final: 0.7036 (tt) REVERT: A 1436 THR cc_start: 0.6885 (OUTLIER) cc_final: 0.6401 (p) REVERT: A 1682 GLN cc_start: 0.6402 (tm-30) cc_final: 0.5849 (tm-30) outliers start: 37 outliers final: 25 residues processed: 148 average time/residue: 0.0910 time to fit residues: 19.9109 Evaluate side-chains 151 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 121 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 226 HIS Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 262 GLN Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 284 GLN Chi-restraints excluded: chain A residue 304 HIS Chi-restraints excluded: chain A residue 327 PHE Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 400 THR Chi-restraints excluded: chain A residue 658 TRP Chi-restraints excluded: chain A residue 675 ILE Chi-restraints excluded: chain A residue 718 LEU Chi-restraints excluded: chain A residue 729 LEU Chi-restraints excluded: chain A residue 794 LEU Chi-restraints excluded: chain A residue 950 LEU Chi-restraints excluded: chain A residue 968 VAL Chi-restraints excluded: chain A residue 1031 ASP Chi-restraints excluded: chain A residue 1138 VAL Chi-restraints excluded: chain A residue 1190 TRP Chi-restraints excluded: chain A residue 1402 LEU Chi-restraints excluded: chain A residue 1436 THR Chi-restraints excluded: chain A residue 1512 VAL Chi-restraints excluded: chain A residue 1569 ILE Chi-restraints excluded: chain A residue 1595 LEU Chi-restraints excluded: chain A residue 1639 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 48 optimal weight: 0.2980 chunk 129 optimal weight: 0.9990 chunk 121 optimal weight: 0.4980 chunk 137 optimal weight: 0.7980 chunk 50 optimal weight: 0.8980 chunk 63 optimal weight: 0.9980 chunk 153 optimal weight: 7.9990 chunk 152 optimal weight: 20.0000 chunk 76 optimal weight: 9.9990 chunk 104 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.127200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.092719 restraints weight = 18359.389| |-----------------------------------------------------------------------------| r_work (start): 0.2955 rms_B_bonded: 2.10 r_work: 0.2830 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2709 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8776 moved from start: 0.1886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 12622 Z= 0.101 Angle : 0.578 13.204 17141 Z= 0.285 Chirality : 0.041 0.352 1951 Planarity : 0.003 0.043 2148 Dihedral : 4.155 26.769 1693 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.20 % Favored : 91.73 % Rotamer: Outliers : 2.64 % Allowed : 14.44 % Favored : 82.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.41 (0.21), residues: 1548 helix: 0.34 (0.20), residues: 768 sheet: -1.09 (0.46), residues: 120 loop : -2.52 (0.22), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1305 TYR 0.011 0.001 TYR A1287 PHE 0.013 0.001 PHE A1062 TRP 0.012 0.001 TRP A1148 HIS 0.009 0.001 HIS A 226 Details of bonding type rmsd/Z covalent geometry : bond 0.00220 / 0.10 (12619) covalent geometry : angle 0.57050 / 0.28 (17133) SS BOND : bond 0.00063 / 0.03 ( 1) SS BOND : angle 0.45242 / 0.25 ( 2) hydrogen bonds : bond 0.03104 / 1.99 ( 480) hydrogen bonds : angle 3.60405 / 2.54 ( 1395) link_NAG-ASN : bond 0.01134 / 0.55 ( 2) link_NAG-ASN : angle 4.96446 / 1.78 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 129 time to evaluate : 0.312 Fit side-chains revert: symmetry clash REVERT: A 5 ARG cc_start: 0.8862 (ttp-110) cc_final: 0.8515 (ttp80) REVERT: A 304 HIS cc_start: 0.8225 (OUTLIER) cc_final: 0.7797 (t-170) REVERT: A 718 LEU cc_start: 0.8973 (OUTLIER) cc_final: 0.8687 (mt) REVERT: A 729 LEU cc_start: 0.9239 (OUTLIER) cc_final: 0.8972 (pp) REVERT: A 794 LEU cc_start: 0.7232 (OUTLIER) cc_final: 0.6995 (tt) REVERT: A 1436 THR cc_start: 0.6766 (OUTLIER) cc_final: 0.6328 (p) REVERT: A 1682 GLN cc_start: 0.6368 (tm-30) cc_final: 0.5827 (tm-30) outliers start: 34 outliers final: 20 residues processed: 152 average time/residue: 0.0947 time to fit residues: 21.4050 Evaluate side-chains 147 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 122 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 262 GLN Chi-restraints excluded: chain A residue 294 MET Chi-restraints excluded: chain A residue 304 HIS Chi-restraints excluded: chain A residue 327 PHE Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 400 THR Chi-restraints excluded: chain A residue 658 TRP Chi-restraints excluded: chain A residue 718 LEU Chi-restraints excluded: chain A residue 729 LEU Chi-restraints excluded: chain A residue 794 LEU Chi-restraints excluded: chain A residue 950 LEU Chi-restraints excluded: chain A residue 968 VAL Chi-restraints excluded: chain A residue 1190 TRP Chi-restraints excluded: chain A residue 1402 LEU Chi-restraints excluded: chain A residue 1436 THR Chi-restraints excluded: chain A residue 1512 VAL Chi-restraints excluded: chain A residue 1569 ILE Chi-restraints excluded: chain A residue 1595 LEU Chi-restraints excluded: chain A residue 1639 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 32 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 chunk 90 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 151 optimal weight: 6.9990 chunk 93 optimal weight: 8.9990 chunk 123 optimal weight: 0.7980 chunk 21 optimal weight: 9.9990 chunk 85 optimal weight: 0.6980 chunk 108 optimal weight: 0.9980 chunk 13 optimal weight: 3.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 226 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.125319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.090769 restraints weight = 18460.804| |-----------------------------------------------------------------------------| r_work (start): 0.2949 rms_B_bonded: 2.11 r_work: 0.2822 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2701 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8801 moved from start: 0.1840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12622 Z= 0.135 Angle : 0.602 13.192 17141 Z= 0.297 Chirality : 0.043 0.349 1951 Planarity : 0.003 0.043 2148 Dihedral : 4.218 26.633 1693 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.46 % Favored : 91.47 % Rotamer: Outliers : 2.48 % Allowed : 14.75 % Favored : 82.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.46 (0.21), residues: 1548 helix: 0.29 (0.19), residues: 770 sheet: -1.06 (0.47), residues: 120 loop : -2.55 (0.21), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1305 TYR 0.013 0.001 TYR A1287 PHE 0.013 0.001 PHE A1062 TRP 0.010 0.001 TRP A1148 HIS 0.004 0.001 HIS A 141 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.13 (12619) covalent geometry : angle 0.59552 / 0.30 (17133) SS BOND : bond 0.00249 / 0.13 ( 1) SS BOND : angle 0.55166 / 0.29 ( 2) hydrogen bonds : bond 0.03597 / 2.31 ( 480) hydrogen bonds : angle 3.64280 / 2.57 ( 1395) link_NAG-ASN : bond 0.01120 / 0.54 ( 2) link_NAG-ASN : angle 4.91224 / 1.76 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 122 time to evaluate : 0.474 Fit side-chains revert: symmetry clash REVERT: A 67 LEU cc_start: 0.8406 (OUTLIER) cc_final: 0.8202 (mm) REVERT: A 304 HIS cc_start: 0.8280 (OUTLIER) cc_final: 0.7863 (t-170) REVERT: A 718 LEU cc_start: 0.9017 (OUTLIER) cc_final: 0.8717 (mt) REVERT: A 729 LEU cc_start: 0.9261 (OUTLIER) cc_final: 0.8978 (pp) REVERT: A 1436 THR cc_start: 0.6838 (OUTLIER) cc_final: 0.6364 (p) REVERT: A 1682 GLN cc_start: 0.6342 (tm-30) cc_final: 0.5752 (tm-30) outliers start: 32 outliers final: 22 residues processed: 144 average time/residue: 0.1034 time to fit residues: 22.1881 Evaluate side-chains 148 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 121 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 226 HIS Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 262 GLN Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 294 MET Chi-restraints excluded: chain A residue 304 HIS Chi-restraints excluded: chain A residue 327 PHE Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 400 THR Chi-restraints excluded: chain A residue 658 TRP Chi-restraints excluded: chain A residue 718 LEU Chi-restraints excluded: chain A residue 729 LEU Chi-restraints excluded: chain A residue 950 LEU Chi-restraints excluded: chain A residue 968 VAL Chi-restraints excluded: chain A residue 1031 ASP Chi-restraints excluded: chain A residue 1238 LEU Chi-restraints excluded: chain A residue 1402 LEU Chi-restraints excluded: chain A residue 1436 THR Chi-restraints excluded: chain A residue 1512 VAL Chi-restraints excluded: chain A residue 1569 ILE Chi-restraints excluded: chain A residue 1595 LEU Chi-restraints excluded: chain A residue 1639 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 137 optimal weight: 0.8980 chunk 49 optimal weight: 0.0370 chunk 134 optimal weight: 0.7980 chunk 122 optimal weight: 2.9990 chunk 42 optimal weight: 4.9990 chunk 38 optimal weight: 0.0870 chunk 33 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 70 optimal weight: 5.9990 chunk 147 optimal weight: 10.0000 overall best weight: 0.5636 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 226 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.127844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.092324 restraints weight = 18558.701| |-----------------------------------------------------------------------------| r_work (start): 0.2971 rms_B_bonded: 2.20 r_work: 0.2851 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2731 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8764 moved from start: 0.2016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 12622 Z= 0.099 Angle : 0.580 12.978 17141 Z= 0.287 Chirality : 0.041 0.344 1951 Planarity : 0.003 0.042 2148 Dihedral : 4.118 26.782 1693 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.07 % Favored : 91.86 % Rotamer: Outliers : 2.10 % Allowed : 15.30 % Favored : 82.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.27 (0.21), residues: 1548 helix: 0.47 (0.20), residues: 768 sheet: -0.93 (0.47), residues: 120 loop : -2.48 (0.22), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1305 TYR 0.013 0.001 TYR A 225 PHE 0.013 0.001 PHE A1062 TRP 0.014 0.001 TRP A 434 HIS 0.010 0.001 HIS A 226 Details of bonding type rmsd/Z covalent geometry : bond 0.00214 / 0.10 (12619) covalent geometry : angle 0.57326 / 0.29 (17133) SS BOND : bond 0.00085 / 0.04 ( 1) SS BOND : angle 0.68599 / 0.37 ( 2) hydrogen bonds : bond 0.03026 / 1.94 ( 480) hydrogen bonds : angle 3.57079 / 2.52 ( 1395) link_NAG-ASN : bond 0.01115 / 0.54 ( 2) link_NAG-ASN : angle 4.82429 / 1.72 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 130 time to evaluate : 0.444 Fit side-chains revert: symmetry clash REVERT: A 304 HIS cc_start: 0.8298 (OUTLIER) cc_final: 0.7845 (t-170) REVERT: A 718 LEU cc_start: 0.8981 (OUTLIER) cc_final: 0.8671 (mt) REVERT: A 729 LEU cc_start: 0.9231 (OUTLIER) cc_final: 0.8952 (pp) REVERT: A 1436 THR cc_start: 0.6716 (OUTLIER) cc_final: 0.6282 (p) REVERT: A 1682 GLN cc_start: 0.6307 (tm-30) cc_final: 0.5726 (tm-30) outliers start: 27 outliers final: 21 residues processed: 148 average time/residue: 0.0988 time to fit residues: 22.0969 Evaluate side-chains 151 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 126 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 226 HIS Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 262 GLN Chi-restraints excluded: chain A residue 294 MET Chi-restraints excluded: chain A residue 304 HIS Chi-restraints excluded: chain A residue 327 PHE Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 400 THR Chi-restraints excluded: chain A residue 658 TRP Chi-restraints excluded: chain A residue 718 LEU Chi-restraints excluded: chain A residue 729 LEU Chi-restraints excluded: chain A residue 950 LEU Chi-restraints excluded: chain A residue 968 VAL Chi-restraints excluded: chain A residue 1190 TRP Chi-restraints excluded: chain A residue 1238 LEU Chi-restraints excluded: chain A residue 1402 LEU Chi-restraints excluded: chain A residue 1436 THR Chi-restraints excluded: chain A residue 1512 VAL Chi-restraints excluded: chain A residue 1569 ILE Chi-restraints excluded: chain A residue 1595 LEU Chi-restraints excluded: chain A residue 1639 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 60 optimal weight: 2.9990 chunk 15 optimal weight: 0.9990 chunk 103 optimal weight: 0.9980 chunk 111 optimal weight: 0.7980 chunk 70 optimal weight: 4.9990 chunk 27 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 94 optimal weight: 9.9990 chunk 104 optimal weight: 0.9990 chunk 95 optimal weight: 0.8980 chunk 102 optimal weight: 0.9980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.127090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.092697 restraints weight = 18320.150| |-----------------------------------------------------------------------------| r_work (start): 0.2982 rms_B_bonded: 2.10 r_work: 0.2854 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2733 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8776 moved from start: 0.2015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 12622 Z= 0.109 Angle : 0.587 12.984 17141 Z= 0.288 Chirality : 0.042 0.342 1951 Planarity : 0.003 0.042 2148 Dihedral : 4.097 26.867 1693 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.20 % Favored : 91.73 % Rotamer: Outliers : 2.17 % Allowed : 15.45 % Favored : 82.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.24 (0.21), residues: 1548 helix: 0.51 (0.20), residues: 770 sheet: -0.89 (0.47), residues: 120 loop : -2.50 (0.22), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1305 TYR 0.013 0.001 TYR A1287 PHE 0.013 0.001 PHE A1062 TRP 0.011 0.001 TRP A1148 HIS 0.004 0.001 HIS A 141 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.11 (12619) covalent geometry : angle 0.58017 / 0.29 (17133) SS BOND : bond 0.00132 / 0.07 ( 1) SS BOND : angle 0.78609 / 0.42 ( 2) hydrogen bonds : bond 0.03172 / 2.04 ( 480) hydrogen bonds : angle 3.54720 / 2.50 ( 1395) link_NAG-ASN : bond 0.01099 / 0.53 ( 2) link_NAG-ASN : angle 4.75424 / 1.70 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2888.70 seconds wall clock time: 50 minutes 4.89 seconds (3004.89 seconds total)