Starting phenix.real_space_refine on Wed Jun 11 07:54:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7w02_32234/06_2025/7w02_32234.cif Found real_map, /net/cci-nas-00/data/ceres_data/7w02_32234/06_2025/7w02_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7w02_32234/06_2025/7w02_32234.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7w02_32234/06_2025/7w02_32234.map" model { file = "/net/cci-nas-00/data/ceres_data/7w02_32234/06_2025/7w02_32234.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7w02_32234/06_2025/7w02_32234.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'GLN:plan1': 3, 'ASP:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'HIS:plan': 6, 'PHE:plan': 1, 'GLU:plan': 9, 'ARG:plan': 2} 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 7.28, per 1000 atoms: 0.59 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: 2.74 Conformation dependent library (CDL) restraints added in 1.6 seconds 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: 1.69 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: 5.31 Time building geometry restraints manager: 3.36 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: 6682 17.97 - 35.94: 665 35.94 - 53.91: 135 53.91 - 71.88: 23 71.88 - 89.85: 12 Dihedral angle restraints: 7517 sinusoidal: 2976 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 7514 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: 1.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.480 Check model and map are aligned: 0.080 Set scattering table: 0.120 Process input model: 31.670 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 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 : 15.175 89.849 4582 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 7.36 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.020 0.002 TRP A 658 HIS 0.006 0.001 HIS A 304 PHE 0.024 0.002 PHE A 156 TYR 0.012 0.002 TYR A 386 ARG 0.008 0.001 ARG A1305 Details of bonding type rmsd link_NAG-ASN : bond 0.00774 ( 2) link_NAG-ASN : angle 3.98860 ( 6) hydrogen bonds : bond 0.20722 ( 480) hydrogen bonds : angle 7.06224 ( 1395) SS BOND : bond 0.00477 ( 1) SS BOND : angle 0.70695 ( 2) covalent geometry : bond 0.00673 (12619) covalent geometry : angle 0.88837 (17133) *********************** 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 : 1.352 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: 0.2488 time to fit residues: 50.5214 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 : 1.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 9.9990 chunk 118 optimal weight: 0.6980 chunk 65 optimal weight: 3.9990 chunk 40 optimal weight: 0.8980 chunk 79 optimal weight: 10.0000 chunk 63 optimal weight: 0.9980 chunk 122 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 chunk 74 optimal weight: 5.9990 chunk 91 optimal weight: 6.9990 chunk 141 optimal weight: 0.0020 overall best weight: 0.9190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3440 r_free = 0.3440 target = 0.125336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.091016 restraints weight = 18435.805| |-----------------------------------------------------------------------------| r_work (start): 0.2946 rms_B_bonded: 2.10 r_work: 0.2811 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2692 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8619 moved from start: 0.0972 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= 0.125 Angle : 0.664 13.382 17141 Z= 0.334 Chirality : 0.045 0.539 1951 Planarity : 0.004 0.055 2148 Dihedral : 8.032 88.671 1797 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.56 % Favored : 90.44 % Rotamer: Outliers : 0.78 % Allowed : 7.61 % Favored : 91.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.50 (0.20), residues: 1548 helix: -0.77 (0.19), residues: 777 sheet: -1.66 (0.50), residues: 121 loop : -2.76 (0.21), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 658 HIS 0.008 0.001 HIS A 141 PHE 0.011 0.001 PHE A 583 TYR 0.014 0.001 TYR A1283 ARG 0.007 0.000 ARG A 670 Details of bonding type rmsd link_NAG-ASN : bond 0.01637 ( 2) link_NAG-ASN : angle 7.03605 ( 6) hydrogen bonds : bond 0.04353 ( 480) hydrogen bonds : angle 4.54209 ( 1395) SS BOND : bond 0.00328 ( 1) SS BOND : angle 1.14093 ( 2) covalent geometry : bond 0.00272 (12619) covalent geometry : angle 0.65057 (17133) *********************** 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 142 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 132 time to evaluate : 1.383 Fit side-chains REVERT: A 1239 GLU cc_start: 0.8335 (tm-30) cc_final: 0.8112 (tm-30) outliers start: 10 outliers final: 5 residues processed: 135 average time/residue: 0.2443 time to fit residues: 48.9889 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 : 1.381 ------------------------------------------------------------------------------- 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 1512 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 127 optimal weight: 6.9990 chunk 41 optimal weight: 2.9990 chunk 50 optimal weight: 0.0870 chunk 62 optimal weight: 0.1980 chunk 47 optimal weight: 0.7980 chunk 16 optimal weight: 7.9990 chunk 73 optimal weight: 9.9990 chunk 20 optimal weight: 3.9990 chunk 83 optimal weight: 0.0040 chunk 137 optimal weight: 0.6980 chunk 100 optimal weight: 20.0000 overall best weight: 0.3570 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1103 ASN A1600 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.129150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.092933 restraints weight = 18413.683| |-----------------------------------------------------------------------------| r_work (start): 0.2976 rms_B_bonded: 2.00 r_work: 0.2866 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2746 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8566 moved from start: 0.1581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 12622 Z= 0.099 Angle : 0.579 12.204 17141 Z= 0.289 Chirality : 0.041 0.387 1951 Planarity : 0.003 0.043 2148 Dihedral : 6.930 85.897 1797 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.36 % Favored : 92.57 % Rotamer: Outliers : 1.71 % Allowed : 8.93 % Favored : 89.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.89 (0.21), residues: 1548 helix: -0.19 (0.19), residues: 767 sheet: -1.11 (0.48), residues: 130 loop : -2.61 (0.22), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 658 HIS 0.004 0.001 HIS A 141 PHE 0.007 0.001 PHE A 583 TYR 0.013 0.001 TYR A1287 ARG 0.006 0.000 ARG A 670 Details of bonding type rmsd link_NAG-ASN : bond 0.01376 ( 2) link_NAG-ASN : angle 6.01188 ( 6) hydrogen bonds : bond 0.03197 ( 480) hydrogen bonds : angle 3.94016 ( 1395) SS BOND : bond 0.00076 ( 1) SS BOND : angle 0.60546 ( 2) covalent geometry : bond 0.00201 (12619) covalent geometry : angle 0.56804 (17133) *********************** 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: 22 poor density : 133 time to evaluate : 1.259 Fit side-chains REVERT: A 1436 THR cc_start: 0.6677 (OUTLIER) cc_final: 0.6283 (p) outliers start: 22 outliers final: 10 residues processed: 149 average time/residue: 0.2465 time to fit residues: 54.3713 Evaluate side-chains 126 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 115 time to evaluate : 1.247 ------------------------------------------------------------------------------- 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 335 VAL Chi-restraints excluded: chain A residue 658 TRP Chi-restraints excluded: chain A residue 665 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 140 optimal weight: 3.9990 chunk 89 optimal weight: 4.9990 chunk 95 optimal weight: 3.9990 chunk 12 optimal weight: 9.9990 chunk 14 optimal weight: 7.9990 chunk 42 optimal weight: 0.0050 chunk 66 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 53 optimal weight: 4.9990 chunk 72 optimal weight: 20.0000 chunk 78 optimal weight: 2.9990 overall best weight: 2.2002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3428 r_free = 0.3428 target = 0.124269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.089882 restraints weight = 18332.474| |-----------------------------------------------------------------------------| r_work (start): 0.2918 rms_B_bonded: 2.09 r_work: 0.2789 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2669 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2669 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8647 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 0.033 12622 Z= 0.179 Angle : 0.647 14.224 17141 Z= 0.321 Chirality : 0.045 0.377 1951 Planarity : 0.004 0.043 2148 Dihedral : 6.822 69.207 1797 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.17 % Favored : 90.76 % Rotamer: Outliers : 2.41 % Allowed : 11.18 % Favored : 86.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.93 (0.21), residues: 1548 helix: -0.16 (0.19), residues: 773 sheet: -1.44 (0.48), residues: 122 loop : -2.65 (0.22), residues: 653 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1148 HIS 0.004 0.001 HIS A 141 PHE 0.019 0.001 PHE A 583 TYR 0.024 0.002 TYR A1283 ARG 0.005 0.000 ARG A 280 Details of bonding type rmsd link_NAG-ASN : bond 0.01289 ( 2) link_NAG-ASN : angle 5.81632 ( 6) hydrogen bonds : bond 0.04331 ( 480) hydrogen bonds : angle 3.92860 ( 1395) SS BOND : bond 0.00479 ( 1) SS BOND : angle 0.38866 ( 2) covalent geometry : bond 0.00432 (12619) covalent geometry : angle 0.63834 (17133) *********************** 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 156 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 125 time to evaluate : 1.389 Fit side-chains revert: symmetry clash REVERT: A 794 LEU cc_start: 0.7246 (OUTLIER) cc_final: 0.6967 (tt) REVERT: A 1239 GLU cc_start: 0.8335 (tm-30) cc_final: 0.8059 (tm-30) REVERT: A 1436 THR cc_start: 0.6735 (OUTLIER) cc_final: 0.6279 (p) outliers start: 31 outliers final: 17 residues processed: 144 average time/residue: 0.2602 time to fit residues: 56.7627 Evaluate side-chains 139 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 120 time to evaluate : 1.381 ------------------------------------------------------------------------------- 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 67 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 327 PHE Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 480 VAL Chi-restraints excluded: chain A residue 658 TRP 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 1190 TRP 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 140 optimal weight: 0.7980 chunk 70 optimal weight: 5.9990 chunk 10 optimal weight: 0.0670 chunk 40 optimal weight: 0.5980 chunk 28 optimal weight: 1.9990 chunk 93 optimal weight: 3.9990 chunk 99 optimal weight: 9.9990 chunk 7 optimal weight: 9.9990 chunk 116 optimal weight: 1.9990 chunk 3 optimal weight: 5.9990 chunk 134 optimal weight: 0.8980 overall best weight: 0.8720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1090 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.126693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.090182 restraints weight = 18357.074| |-----------------------------------------------------------------------------| r_work (start): 0.2936 rms_B_bonded: 2.00 r_work: 0.2828 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2708 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8604 moved from start: 0.1665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 12622 Z= 0.110 Angle : 0.597 14.114 17141 Z= 0.294 Chirality : 0.041 0.232 1951 Planarity : 0.003 0.042 2148 Dihedral : 6.570 64.945 1797 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.20 % Favored : 91.73 % Rotamer: Outliers : 2.02 % Allowed : 12.42 % Favored : 85.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.68 (0.21), residues: 1548 helix: 0.09 (0.19), residues: 770 sheet: -1.18 (0.48), residues: 120 loop : -2.62 (0.21), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1148 HIS 0.003 0.001 HIS A1600 PHE 0.011 0.001 PHE A 583 TYR 0.011 0.001 TYR A 946 ARG 0.006 0.000 ARG A1305 Details of bonding type rmsd link_NAG-ASN : bond 0.00839 ( 2) link_NAG-ASN : angle 3.68151 ( 6) hydrogen bonds : bond 0.03396 ( 480) hydrogen bonds : angle 3.75298 ( 1395) SS BOND : bond 0.00131 ( 1) SS BOND : angle 0.38383 ( 2) covalent geometry : bond 0.00245 (12619) covalent geometry : angle 0.59288 (17133) *********************** 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 148 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 122 time to evaluate : 1.364 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 794 LEU cc_start: 0.7285 (OUTLIER) cc_final: 0.7008 (tt) REVERT: A 1436 THR cc_start: 0.6732 (OUTLIER) cc_final: 0.6281 (p) outliers start: 26 outliers final: 19 residues processed: 137 average time/residue: 0.2348 time to fit residues: 48.6298 Evaluate side-chains 139 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 118 time to evaluate : 1.214 ------------------------------------------------------------------------------- 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 284 GLN 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 665 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 14 optimal weight: 6.9990 chunk 9 optimal weight: 4.9990 chunk 119 optimal weight: 4.9990 chunk 16 optimal weight: 5.9990 chunk 33 optimal weight: 0.5980 chunk 146 optimal weight: 10.0000 chunk 56 optimal weight: 3.9990 chunk 128 optimal weight: 10.0000 chunk 8 optimal weight: 0.9980 chunk 108 optimal weight: 0.9980 chunk 129 optimal weight: 0.8980 overall best weight: 1.4982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 226 HIS A1600 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.125599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.091017 restraints weight = 18641.934| |-----------------------------------------------------------------------------| r_work (start): 0.2945 rms_B_bonded: 2.17 r_work: 0.2813 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2693 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8617 moved from start: 0.1694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12622 Z= 0.136 Angle : 0.603 14.214 17141 Z= 0.299 Chirality : 0.043 0.259 1951 Planarity : 0.003 0.042 2148 Dihedral : 6.522 60.979 1797 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.72 % Favored : 91.21 % Rotamer: Outliers : 2.41 % Allowed : 12.66 % Favored : 84.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.64 (0.21), residues: 1548 helix: 0.14 (0.19), residues: 771 sheet: -1.12 (0.48), residues: 118 loop : -2.63 (0.21), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1148 HIS 0.003 0.001 HIS A 141 PHE 0.014 0.001 PHE A 583 TYR 0.011 0.001 TYR A 946 ARG 0.004 0.000 ARG A1305 Details of bonding type rmsd link_NAG-ASN : bond 0.00723 ( 2) link_NAG-ASN : angle 3.15860 ( 6) hydrogen bonds : bond 0.03683 ( 480) hydrogen bonds : angle 3.71736 ( 1395) SS BOND : bond 0.00251 ( 1) SS BOND : angle 0.28669 ( 2) covalent geometry : bond 0.00321 (12619) covalent geometry : angle 0.59994 (17133) *********************** 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 155 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 124 time to evaluate : 1.274 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 160 ARG cc_start: 0.8135 (OUTLIER) cc_final: 0.7930 (tpt-90) REVERT: A 1436 THR cc_start: 0.6700 (OUTLIER) cc_final: 0.6209 (p) REVERT: A 1682 GLN cc_start: 0.6417 (tm-30) cc_final: 0.5875 (tm-30) outliers start: 31 outliers final: 23 residues processed: 145 average time/residue: 0.2503 time to fit residues: 52.9645 Evaluate side-chains 146 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 121 time to evaluate : 1.449 ------------------------------------------------------------------------------- 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 160 ARG 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 327 PHE Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 480 VAL Chi-restraints excluded: chain A residue 658 TRP 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 1639 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 137 optimal weight: 0.2980 chunk 111 optimal weight: 3.9990 chunk 24 optimal weight: 0.4980 chunk 124 optimal weight: 7.9990 chunk 26 optimal weight: 2.9990 chunk 8 optimal weight: 4.9990 chunk 92 optimal weight: 0.5980 chunk 60 optimal weight: 10.0000 chunk 46 optimal weight: 0.0570 chunk 155 optimal weight: 10.0000 chunk 151 optimal weight: 8.9990 overall best weight: 0.8900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3462 r_free = 0.3462 target = 0.126928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.091967 restraints weight = 18433.820| |-----------------------------------------------------------------------------| r_work (start): 0.2961 rms_B_bonded: 2.14 r_work: 0.2839 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2719 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8586 moved from start: 0.1818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 12622 Z= 0.108 Angle : 0.585 15.071 17141 Z= 0.289 Chirality : 0.041 0.256 1951 Planarity : 0.003 0.041 2148 Dihedral : 6.393 59.312 1797 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.14 % Favored : 91.80 % Rotamer: Outliers : 2.33 % Allowed : 13.12 % Favored : 84.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.49 (0.21), residues: 1548 helix: 0.28 (0.19), residues: 770 sheet: -1.08 (0.47), residues: 120 loop : -2.58 (0.22), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1148 HIS 0.010 0.001 HIS A 226 PHE 0.010 0.001 PHE A 583 TYR 0.010 0.001 TYR A 946 ARG 0.005 0.000 ARG A1305 Details of bonding type rmsd link_NAG-ASN : bond 0.00666 ( 2) link_NAG-ASN : angle 2.95043 ( 6) hydrogen bonds : bond 0.03302 ( 480) hydrogen bonds : angle 3.63911 ( 1395) SS BOND : bond 0.00155 ( 1) SS BOND : angle 0.23106 ( 2) covalent geometry : bond 0.00240 (12619) covalent geometry : angle 0.58255 (17133) *********************** 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 155 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 125 time to evaluate : 1.263 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 67 LEU cc_start: 0.8362 (OUTLIER) cc_final: 0.8127 (mm) REVERT: A 1436 THR cc_start: 0.6674 (OUTLIER) cc_final: 0.6233 (p) REVERT: A 1682 GLN cc_start: 0.6397 (tm-30) cc_final: 0.5839 (tm-30) outliers start: 30 outliers final: 20 residues processed: 143 average time/residue: 0.2367 time to fit residues: 50.9008 Evaluate side-chains 143 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 121 time to evaluate : 1.430 ------------------------------------------------------------------------------- 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 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 480 VAL Chi-restraints excluded: chain A residue 658 TRP Chi-restraints excluded: chain A residue 968 VAL Chi-restraints excluded: chain A residue 1031 ASP 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 5 optimal weight: 4.9990 chunk 108 optimal weight: 2.9990 chunk 47 optimal weight: 0.0570 chunk 8 optimal weight: 0.7980 chunk 101 optimal weight: 4.9990 chunk 53 optimal weight: 0.2980 chunk 95 optimal weight: 0.9980 chunk 62 optimal weight: 0.9990 chunk 59 optimal weight: 1.9990 chunk 78 optimal weight: 9.9990 chunk 139 optimal weight: 0.8980 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3490 r_free = 0.3490 target = 0.129155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.095231 restraints weight = 18513.654| |-----------------------------------------------------------------------------| r_work (start): 0.3009 rms_B_bonded: 2.18 r_work: 0.2873 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2752 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 moved from start: 0.2069 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= 0.097 Angle : 0.564 15.123 17141 Z= 0.278 Chirality : 0.041 0.244 1951 Planarity : 0.003 0.041 2148 Dihedral : 6.102 81.408 1797 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.75 % Favored : 92.18 % Rotamer: Outliers : 2.33 % Allowed : 13.28 % Favored : 84.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (0.21), residues: 1548 helix: 0.55 (0.20), residues: 765 sheet: -0.93 (0.47), residues: 118 loop : -2.54 (0.21), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 434 HIS 0.004 0.001 HIS A1600 PHE 0.007 0.001 PHE A1153 TYR 0.009 0.001 TYR A 225 ARG 0.005 0.000 ARG A1305 Details of bonding type rmsd link_NAG-ASN : bond 0.00596 ( 2) link_NAG-ASN : angle 2.65868 ( 6) hydrogen bonds : bond 0.02854 ( 480) hydrogen bonds : angle 3.52597 ( 1395) SS BOND : bond 0.00054 ( 1) SS BOND : angle 0.27242 ( 2) covalent geometry : bond 0.00208 (12619) covalent geometry : angle 0.56194 (17133) *********************** 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 167 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 137 time to evaluate : 1.358 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 67 LEU cc_start: 0.8463 (OUTLIER) cc_final: 0.8202 (mm) REVERT: A 446 ASP cc_start: 0.8100 (t0) cc_final: 0.7746 (p0) REVERT: A 1239 GLU cc_start: 0.8391 (tm-30) cc_final: 0.8161 (tm-30) REVERT: A 1436 THR cc_start: 0.6635 (OUTLIER) cc_final: 0.6215 (p) REVERT: A 1682 GLN cc_start: 0.6232 (tm-30) cc_final: 0.5659 (tm-30) outliers start: 30 outliers final: 18 residues processed: 157 average time/residue: 0.2118 time to fit residues: 50.7221 Evaluate side-chains 144 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 124 time to evaluate : 1.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 480 VAL Chi-restraints excluded: chain A residue 658 TRP 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 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 1639 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 3 optimal weight: 6.9990 chunk 13 optimal weight: 0.9990 chunk 149 optimal weight: 3.9990 chunk 101 optimal weight: 2.9990 chunk 1 optimal weight: 0.9980 chunk 123 optimal weight: 1.9990 chunk 131 optimal weight: 0.8980 chunk 33 optimal weight: 0.7980 chunk 116 optimal weight: 0.9980 chunk 136 optimal weight: 4.9990 chunk 154 optimal weight: 6.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3479 r_free = 0.3479 target = 0.128270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.094560 restraints weight = 18461.904| |-----------------------------------------------------------------------------| r_work (start): 0.3002 rms_B_bonded: 2.19 r_work: 0.2864 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2745 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.2106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 12622 Z= 0.109 Angle : 0.583 15.836 17141 Z= 0.286 Chirality : 0.041 0.242 1951 Planarity : 0.003 0.041 2148 Dihedral : 6.122 85.038 1797 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.82 % Favored : 92.12 % Rotamer: Outliers : 1.71 % Allowed : 13.66 % Favored : 84.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (0.21), residues: 1548 helix: 0.65 (0.20), residues: 765 sheet: -0.87 (0.48), residues: 118 loop : -2.54 (0.21), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 658 HIS 0.007 0.001 HIS A 226 PHE 0.009 0.001 PHE A 583 TYR 0.028 0.001 TYR A1283 ARG 0.004 0.000 ARG A1305 Details of bonding type rmsd link_NAG-ASN : bond 0.00617 ( 2) link_NAG-ASN : angle 2.57696 ( 6) hydrogen bonds : bond 0.03064 ( 480) hydrogen bonds : angle 3.50746 ( 1395) SS BOND : bond 0.00139 ( 1) SS BOND : angle 0.12774 ( 2) covalent geometry : bond 0.00250 (12619) covalent geometry : angle 0.58143 (17133) *********************** 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 147 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 125 time to evaluate : 1.235 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 67 LEU cc_start: 0.8429 (OUTLIER) cc_final: 0.8172 (mm) REVERT: A 446 ASP cc_start: 0.8137 (t0) cc_final: 0.7771 (p0) REVERT: A 1436 THR cc_start: 0.6672 (OUTLIER) cc_final: 0.6253 (p) REVERT: A 1682 GLN cc_start: 0.6200 (tm-30) cc_final: 0.5607 (tm-30) outliers start: 22 outliers final: 19 residues processed: 140 average time/residue: 0.2207 time to fit residues: 46.7345 Evaluate side-chains 144 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 123 time to evaluate : 1.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 480 VAL Chi-restraints excluded: chain A residue 658 TRP Chi-restraints excluded: chain A residue 675 ILE 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 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 1639 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 123 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 chunk 83 optimal weight: 3.9990 chunk 24 optimal weight: 0.0000 chunk 95 optimal weight: 1.9990 chunk 90 optimal weight: 3.9990 chunk 74 optimal weight: 0.9990 chunk 80 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 21 optimal weight: 5.9990 chunk 12 optimal weight: 3.9990 overall best weight: 1.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.127041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.092301 restraints weight = 18324.813| |-----------------------------------------------------------------------------| r_work (start): 0.2967 rms_B_bonded: 2.23 r_work: 0.2835 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2712 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.2045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12622 Z= 0.131 Angle : 0.600 15.731 17141 Z= 0.296 Chirality : 0.042 0.234 1951 Planarity : 0.003 0.041 2148 Dihedral : 6.217 87.971 1797 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.01 % Favored : 91.93 % Rotamer: Outliers : 2.02 % Allowed : 13.90 % Favored : 84.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.16 (0.21), residues: 1548 helix: 0.65 (0.20), residues: 764 sheet: -0.84 (0.48), residues: 120 loop : -2.54 (0.21), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 658 HIS 0.012 0.001 HIS A 226 PHE 0.012 0.001 PHE A 583 TYR 0.011 0.001 TYR A 946 ARG 0.004 0.000 ARG A1305 Details of bonding type rmsd link_NAG-ASN : bond 0.00692 ( 2) link_NAG-ASN : angle 2.62134 ( 6) hydrogen bonds : bond 0.03378 ( 480) hydrogen bonds : angle 3.53953 ( 1395) SS BOND : bond 0.00273 ( 1) SS BOND : angle 0.12803 ( 2) covalent geometry : bond 0.00309 (12619) covalent geometry : angle 0.59791 (17133) ********************** 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 149 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 123 time to evaluate : 1.406 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 67 LEU cc_start: 0.8480 (OUTLIER) cc_final: 0.8215 (mm) REVERT: A 446 ASP cc_start: 0.8090 (t0) cc_final: 0.7745 (p0) REVERT: A 1436 THR cc_start: 0.6660 (OUTLIER) cc_final: 0.6241 (p) REVERT: A 1682 GLN cc_start: 0.6183 (tm-30) cc_final: 0.5586 (tm-30) outliers start: 26 outliers final: 20 residues processed: 141 average time/residue: 0.2414 time to fit residues: 51.7910 Evaluate side-chains 144 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 122 time to evaluate : 1.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 277 THR 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 480 VAL Chi-restraints excluded: chain A residue 658 TRP Chi-restraints excluded: chain A residue 950 LEU Chi-restraints excluded: chain A residue 968 VAL Chi-restraints excluded: chain A residue 1000 VAL Chi-restraints excluded: chain A residue 1031 ASP 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 1639 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 1 optimal weight: 0.9990 chunk 27 optimal weight: 0.7980 chunk 28 optimal weight: 3.9990 chunk 135 optimal weight: 0.0470 chunk 73 optimal weight: 0.8980 chunk 66 optimal weight: 0.2980 chunk 47 optimal weight: 0.0070 chunk 127 optimal weight: 10.0000 chunk 114 optimal weight: 0.7980 chunk 137 optimal weight: 0.7980 chunk 14 optimal weight: 0.7980 overall best weight: 0.3896 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 HIS A1418 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.130046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.096109 restraints weight = 18417.529| |-----------------------------------------------------------------------------| r_work (start): 0.3037 rms_B_bonded: 2.29 r_work: 0.2895 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2775 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8566 moved from start: 0.2315 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= 0.096 Angle : 0.569 16.223 17141 Z= 0.279 Chirality : 0.041 0.230 1951 Planarity : 0.003 0.041 2148 Dihedral : 5.912 83.057 1797 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.49 % Favored : 92.44 % Rotamer: Outliers : 1.55 % Allowed : 14.13 % Favored : 84.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.21), residues: 1548 helix: 0.88 (0.20), residues: 764 sheet: -0.71 (0.51), residues: 107 loop : -2.45 (0.21), residues: 677 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 434 HIS 0.003 0.001 HIS A1600 PHE 0.006 0.001 PHE A1153 TYR 0.008 0.001 TYR A 918 ARG 0.004 0.000 ARG A 106 Details of bonding type rmsd link_NAG-ASN : bond 0.00630 ( 2) link_NAG-ASN : angle 2.42626 ( 6) hydrogen bonds : bond 0.02658 ( 480) hydrogen bonds : angle 3.45706 ( 1395) SS BOND : bond 0.00002 ( 1) SS BOND : angle 0.15964 ( 2) covalent geometry : bond 0.00204 (12619) covalent geometry : angle 0.56763 (17133) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6687.34 seconds wall clock time: 115 minutes 52.27 seconds (6952.27 seconds total)