Starting phenix.real_space_refine on Fri Sep 11 22:14:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6nt3_0500/09_2026/6nt3_0500_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6nt3_0500/09_2026/6nt3_0500.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6nt3_0500/09_2026/6nt3_0500_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6nt3_0500/09_2026/6nt3_0500_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6nt3_0500/09_2026/6nt3_0500.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6nt3_0500/09_2026/6nt3_0500.map" } resolution = 3.4 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= 0.048 sd= 1.104 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 5 5.49 5 S 68 5.16 5 C 7275 2.51 5 N 1685 2.21 5 O 1901 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 36 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10934 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 10440 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1278, 10429 Classifications: {'peptide': 1278} Link IDs: {'PTRANS': 41, 'TRANS': 1236} Chain breaks: 4 Conformer: "B" Number of residues, atoms: 1278, 10429 Classifications: {'peptide': 1278} Link IDs: {'PTRANS': 41, 'TRANS': 1236} Chain breaks: 4 bond proxies already assigned to first conformer: 10700 Chain: "B" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 3, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 377 Unusual residues: {'76F': 4, 'AJP': 1, 'LHG': 1, 'NAG': 4, 'Y01': 1} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 64 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'76F:plan-1': 2, '76F:plan-2': 1, '76F:plan-3': 2} Unresolved non-hydrogen planarities: 16 Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AARG A1293 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG A1293 " occ=0.50 Time building chain proxies: 3.27, per 1000 atoms: 0.30 Number of scatterers: 10934 At special positions: 0 Unit cell: (134, 136, 125, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 68 16.00 P 5 15.00 O 1901 8.00 N 1685 7.00 C 7275 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 288 " - pdb=" SG CYS A 337 " distance=2.03 Simple disulfide: pdb=" SG CYS A 328 " - pdb=" SG CYS A 343 " distance=2.03 Simple disulfide: pdb=" SG CYS A 709 " - pdb=" SG CYS A 717 " distance=2.03 Simple disulfide: pdb=" SG CYS A1011 " - pdb=" SG CYS A1030 " distance=2.03 Simple disulfide: pdb=" SG CYS A1368 " - pdb=" SG CYS A1381 " 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 BETA1-3 " NAG B 1 " - " NAG B 2 " " NAG B 2 " - " BMA B 3 " " BMA B 3 " - " BMA B 4 " BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " BETA1-6 " BMA B 3 " - " BMA B 5 " NAG-ASN " NAG A1606 " - " ASN A1028 " " NAG A1608 " - " ASN A1015 " " NAG A1613 " - " ASN A 300 " " NAG B 1 " - " ASN A 330 " " NAG C 1 " - " ASN A 312 " " NAG D 1 " - " ASN A 308 " Time building additional restraints: 1.06 Conformation dependent library (CDL) restraints added in 775.0 milliseconds 2542 Ramachandran restraints generated. 1271 Oldfield, 0 Emsley, 1271 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2426 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 2 sheets defined 67.3% alpha, 0.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.36 Creating SS restraints... Processing helix chain 'A' and resid 52 through 57 removed outlier: 4.135A pdb=" N ARG A 56 " --> pdb=" O ALA A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 108 Processing helix chain 'A' and resid 129 through 138 removed outlier: 3.537A pdb=" N VAL A 138 " --> pdb=" O ILE A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 158 Processing helix chain 'A' and resid 164 through 186 removed outlier: 3.994A pdb=" N LEU A 168 " --> pdb=" O THR A 164 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N TYR A 176 " --> pdb=" O PHE A 172 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N THR A 177 " --> pdb=" O LEU A 173 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ILE A 178 " --> pdb=" O SER A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 198 removed outlier: 4.235A pdb=" N ARG A 198 " --> pdb=" O ALA A 195 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 195 through 198' Processing helix chain 'A' and resid 199 through 217 removed outlier: 4.012A pdb=" N TRP A 203 " --> pdb=" O ASP A 199 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N THR A 209 " --> pdb=" O ASP A 205 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU A 216 " --> pdb=" O GLY A 212 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N VAL A 217 " --> pdb=" O TYR A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 240 removed outlier: 3.696A pdb=" N TRP A 235 " --> pdb=" O LEU A 232 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N THR A 239 " --> pdb=" O ARG A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 280 removed outlier: 3.574A pdb=" N VAL A 248 " --> pdb=" O TRP A 244 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ASP A 249 " --> pdb=" O ARG A 245 " (cutoff:3.500A) removed outlier: 5.045A pdb=" N ALA A 250 " --> pdb=" O THR A 246 " (cutoff:3.500A) removed outlier: 5.561A pdb=" N ASP A 260 " --> pdb=" O THR A 256 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N LEU A 261 " --> pdb=" O SER A 257 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LEU A 264 " --> pdb=" O ASP A 260 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLN A 278 " --> pdb=" O LEU A 274 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU A 279 " --> pdb=" O ILE A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 310 Processing helix chain 'A' and resid 311 through 316 removed outlier: 5.772A pdb=" N SER A 314 " --> pdb=" O SER A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 360 through 373 Processing helix chain 'A' and resid 376 through 388 removed outlier: 4.495A pdb=" N LEU A 380 " --> pdb=" O TYR A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 391 No H-bonds generated for 'chain 'A' and resid 389 through 391' Processing helix chain 'A' and resid 392 through 404 removed outlier: 3.882A pdb=" N PHE A 396 " --> pdb=" O HIS A 392 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N ILE A 398 " --> pdb=" O LEU A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 432 removed outlier: 3.916A pdb=" N LYS A 424 " --> pdb=" O THR A 420 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N ARG A 425 " --> pdb=" O HIS A 421 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ALA A 426 " --> pdb=" O MET A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 503 through 515 Processing helix chain 'A' and resid 518 through 536 removed outlier: 4.150A pdb=" N GLU A 522 " --> pdb=" O SER A 518 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEU A 523 " --> pdb=" O PRO A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 544 through 571 Processing helix chain 'A' and resid 584 through 603 removed outlier: 3.689A pdb=" N GLU A 601 " --> pdb=" O GLU A 597 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLY A 602 " --> pdb=" O LEU A 598 " (cutoff:3.500A) Processing helix chain 'A' and resid 611 through 620 removed outlier: 3.674A pdb=" N ARG A 616 " --> pdb=" O ARG A 613 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N PHE A 618 " --> pdb=" O LEU A 615 " (cutoff:3.500A) Processing helix chain 'A' and resid 624 through 636 removed outlier: 3.821A pdb=" N MET A 634 " --> pdb=" O PHE A 630 " (cutoff:3.500A) Processing helix chain 'A' and resid 638 through 663 Processing helix chain 'A' and resid 665 through 670 removed outlier: 3.881A pdb=" N ASN A 670 " --> pdb=" O ASN A 666 " (cutoff:3.500A) Processing helix chain 'A' and resid 686 through 699 Processing helix chain 'A' and resid 702 through 713 removed outlier: 3.641A pdb=" N MET A 706 " --> pdb=" O TRP A 702 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N ASP A 708 " --> pdb=" O GLU A 704 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL A 712 " --> pdb=" O ASP A 708 " (cutoff:3.500A) Processing helix chain 'A' and resid 717 through 727 removed outlier: 3.506A pdb=" N PHE A 721 " --> pdb=" O CYS A 717 " (cutoff:3.500A) Processing helix chain 'A' and resid 728 through 738 removed outlier: 4.456A pdb=" N ASN A 734 " --> pdb=" O LEU A 730 " (cutoff:3.500A) Processing helix chain 'A' and resid 838 through 854 removed outlier: 3.947A pdb=" N LYS A 854 " --> pdb=" O PHE A 850 " (cutoff:3.500A) Processing helix chain 'A' and resid 855 through 872 removed outlier: 3.506A pdb=" N GLN A 859 " --> pdb=" O ASN A 855 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N LEU A 872 " --> pdb=" O ILE A 868 " (cutoff:3.500A) Processing helix chain 'A' and resid 883 through 913 removed outlier: 4.185A pdb=" N VAL A 887 " --> pdb=" O ARG A 883 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N ASN A 888 " --> pdb=" O PRO A 884 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLY A 913 " --> pdb=" O LEU A 909 " (cutoff:3.500A) Processing helix chain 'A' and resid 914 through 919 removed outlier: 3.684A pdb=" N PHE A 918 " --> pdb=" O PHE A 914 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N THR A 919 " --> pdb=" O LYS A 915 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 914 through 919' Processing helix chain 'A' and resid 920 through 938 removed outlier: 3.954A pdb=" N TRP A 924 " --> pdb=" O SER A 920 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N LEU A 925 " --> pdb=" O LYS A 921 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ASP A 926 " --> pdb=" O TRP A 922 " (cutoff:3.500A) Processing helix chain 'A' and resid 947 through 952 removed outlier: 4.085A pdb=" N ARG A 951 " --> pdb=" O LEU A 947 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU A 952 " --> pdb=" O GLN A 948 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 947 through 952' Processing helix chain 'A' and resid 953 through 957 removed outlier: 3.634A pdb=" N PHE A 956 " --> pdb=" O LEU A 953 " (cutoff:3.500A) Processing helix chain 'A' and resid 958 through 963 removed outlier: 3.976A pdb=" N LEU A 962 " --> pdb=" O LEU A 958 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N SER A 963 " --> pdb=" O PHE A 959 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 958 through 963' Processing helix chain 'A' and resid 968 through 1005 removed outlier: 3.916A pdb=" N THR A 972 " --> pdb=" O MET A 968 " (cutoff:3.500A) Proline residue: A 980 - end of helix removed outlier: 3.767A pdb=" N ASN A 984 " --> pdb=" O PRO A 980 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N MET A 999 " --> pdb=" O VAL A 995 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N GLN A1002 " --> pdb=" O ILE A 998 " (cutoff:3.500A) Processing helix chain 'A' and resid 1026 through 1033 removed outlier: 3.899A pdb=" N GLU A1033 " --> pdb=" O ASP A1029 " (cutoff:3.500A) Processing helix chain 'A' and resid 1047 through 1058 Processing helix chain 'A' and resid 1063 through 1073 removed outlier: 3.716A pdb=" N MET A1067 " --> pdb=" O TRP A1063 " (cutoff:3.500A) Processing helix chain 'A' and resid 1085 through 1087 No H-bonds generated for 'chain 'A' and resid 1085 through 1087' Processing helix chain 'A' and resid 1088 through 1100 removed outlier: 4.511A pdb=" N PHE A1092 " --> pdb=" O MET A1088 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N PHE A1098 " --> pdb=" O PHE A1094 " (cutoff:3.500A) Processing helix chain 'A' and resid 1103 through 1110 removed outlier: 3.967A pdb=" N PHE A1107 " --> pdb=" O LEU A1104 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N VAL A1108 " --> pdb=" O LYS A1105 " (cutoff:3.500A) Processing helix chain 'A' and resid 1111 through 1123 Processing helix chain 'A' and resid 1132 through 1142 removed outlier: 3.936A pdb=" N TYR A1136 " --> pdb=" O THR A1132 " (cutoff:3.500A) Processing helix chain 'A' and resid 1157 through 1162 Processing helix chain 'A' and resid 1163 through 1168 removed outlier: 3.761A pdb=" N VAL A1167 " --> pdb=" O ILE A1163 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N THR A1168 " --> pdb=" O PHE A1164 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1163 through 1168' Processing helix chain 'A' and resid 1176 through 1187 removed outlier: 4.063A pdb=" N CYS A1181 " --> pdb=" O MET A1177 " (cutoff:3.500A) Processing helix chain 'A' and resid 1195 through 1224 removed outlier: 3.941A pdb=" N THR A1199 " --> pdb=" O SER A1195 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N GLU A1200 " --> pdb=" O GLN A1196 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N VAL A1207 " --> pdb=" O TYR A1203 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N VAL A1208 " --> pdb=" O TRP A1204 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N PHE A1209 " --> pdb=" O ILE A1205 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N THR A1214 " --> pdb=" O ILE A1210 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU A1224 " --> pdb=" O LYS A1220 " (cutoff:3.500A) Processing helix chain 'A' and resid 1231 through 1251 removed outlier: 3.632A pdb=" N ILE A1235 " --> pdb=" O VAL A1231 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N PHE A1249 " --> pdb=" O ILE A1245 " (cutoff:3.500A) Processing helix chain 'A' and resid 1260 through 1268 removed outlier: 3.538A pdb=" N PHE A1264 " --> pdb=" O SER A1260 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N VAL A1266 " --> pdb=" O THR A1262 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ARG A1268 " --> pdb=" O PHE A1264 " (cutoff:3.500A) Processing helix chain 'A' and resid 1269 through 1280 removed outlier: 3.736A pdb=" N ARG A1274 " --> pdb=" O ARG A1271 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ILE A1275 " --> pdb=" O ILE A1272 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N ARG A1277 " --> pdb=" O ARG A1274 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N VAL A1279 " --> pdb=" O LEU A1276 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LYS A1280 " --> pdb=" O ARG A1277 " (cutoff:3.500A) Processing helix chain 'A' and resid 1283 through 1294 removed outlier: 4.025A pdb=" N LEU A1289 " --> pdb=" O ILE A1285 " (cutoff:3.500A) Processing helix chain 'A' and resid 1296 through 1321 removed outlier: 3.928A pdb=" N GLU A1319 " --> pdb=" O VAL A1315 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N PHE A1320 " --> pdb=" O PHE A1316 " (cutoff:3.500A) Processing helix chain 'A' and resid 1338 through 1350 removed outlier: 4.103A pdb=" N GLN A1348 " --> pdb=" O ILE A1344 " (cutoff:3.500A) Processing helix chain 'A' and resid 1354 through 1363 removed outlier: 3.923A pdb=" N VAL A1358 " --> pdb=" O GLY A1354 " (cutoff:3.500A) Processing helix chain 'A' and resid 1384 through 1392 removed outlier: 3.812A pdb=" N TYR A1390 " --> pdb=" O LEU A1386 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU A1391 " --> pdb=" O GLY A1387 " (cutoff:3.500A) Processing helix chain 'A' and resid 1402 through 1423 removed outlier: 4.119A pdb=" N ALA A1407 " --> pdb=" O ILE A1403 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLU A1416 " --> pdb=" O ASP A1412 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N GLU A1423 " --> pdb=" O GLU A1419 " (cutoff:3.500A) Processing helix chain 'A' and resid 1428 through 1436 removed outlier: 4.278A pdb=" N VAL A1436 " --> pdb=" O MET A1432 " (cutoff:3.500A) Processing helix chain 'A' and resid 1452 through 1457 Processing helix chain 'A' and resid 1461 through 1465 removed outlier: 3.587A pdb=" N GLN A1465 " --> pdb=" O PRO A1462 " (cutoff:3.500A) Processing helix chain 'A' and resid 1470 through 1477 Processing helix chain 'A' and resid 1488 through 1505 removed outlier: 4.146A pdb=" N VAL A1492 " --> pdb=" O PHE A1488 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 287 through 290 Processing sheet with id=AA2, first strand: chain 'A' and resid 1009 through 1011 521 hydrogen bonds defined for protein. 1495 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: 1.53 Time building geometry restraints manager: 1.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1610 1.31 - 1.44: 3265 1.44 - 1.57: 6218 1.57 - 1.71: 18 1.71 - 1.84: 115 Bond restraints: 11226 Sorted by residual: bond pdb=" C06 AJP A1620 " pdb=" C07 AJP A1620 " ideal model delta sigma weight residual 1.530 1.308 0.222 2.00e-02 2.50e+03 1.23e+02 bond pdb=" C40 76F A1616 " pdb=" C41 76F A1616 " ideal model delta sigma weight residual 1.330 1.531 -0.201 2.00e-02 2.50e+03 1.01e+02 bond pdb=" C21 76F A1618 " pdb=" C22 76F A1618 " ideal model delta sigma weight residual 1.330 1.525 -0.195 2.00e-02 2.50e+03 9.49e+01 bond pdb=" C21 76F A1617 " pdb=" C22 76F A1617 " ideal model delta sigma weight residual 1.330 1.524 -0.194 2.00e-02 2.50e+03 9.44e+01 bond pdb=" C21 76F A1616 " pdb=" C22 76F A1616 " ideal model delta sigma weight residual 1.330 1.524 -0.194 2.00e-02 2.50e+03 9.39e+01 ... (remaining 11221 not shown) Histogram of bond angle deviations from ideal: 0.00 - 9.10: 15189 9.10 - 18.20: 34 18.20 - 27.31: 5 27.31 - 36.41: 1 36.41 - 45.51: 1 Bond angle restraints: 15230 Sorted by residual: angle pdb=" O09 AJP A1620 " pdb=" C05 AJP A1620 " pdb=" O84 AJP A1620 " ideal model delta sigma weight residual 110.48 64.97 45.51 3.00e+00 1.11e-01 2.30e+02 angle pdb=" C04 AJP A1620 " pdb=" C05 AJP A1620 " pdb=" C06 AJP A1620 " ideal model delta sigma weight residual 114.54 145.42 -30.88 3.00e+00 1.11e-01 1.06e+02 angle pdb=" C17 76F A1617 " pdb=" C18 76F A1617 " pdb=" C19 76F A1617 " ideal model delta sigma weight residual 128.07 108.05 20.02 3.00e+00 1.11e-01 4.45e+01 angle pdb=" C17 76F A1618 " pdb=" C18 76F A1618 " pdb=" C19 76F A1618 " ideal model delta sigma weight residual 128.07 109.24 18.83 3.00e+00 1.11e-01 3.94e+01 angle pdb=" C17 76F A1616 " pdb=" C18 76F A1616 " pdb=" C19 76F A1616 " ideal model delta sigma weight residual 128.07 109.36 18.71 3.00e+00 1.11e-01 3.89e+01 ... (remaining 15225 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.72: 6529 33.72 - 67.43: 292 67.43 - 101.15: 94 101.15 - 134.86: 60 134.86 - 168.58: 18 Dihedral angle restraints: 6993 sinusoidal: 3236 harmonic: 3757 Sorted by residual: dihedral pdb=" CA HIS A 315 " pdb=" C HIS A 315 " pdb=" N TRP A 316 " pdb=" CA TRP A 316 " ideal model delta harmonic sigma weight residual 180.00 151.20 28.80 0 5.00e+00 4.00e-02 3.32e+01 dihedral pdb=" CA PRO A 338 " pdb=" C PRO A 338 " pdb=" N PRO A 339 " pdb=" CA PRO A 339 " ideal model delta harmonic sigma weight residual 180.00 151.40 28.60 0 5.00e+00 4.00e-02 3.27e+01 dihedral pdb=" CA MET A 336 " pdb=" C MET A 336 " pdb=" N CYS A 337 " pdb=" CA CYS A 337 " ideal model delta harmonic sigma weight residual 180.00 -152.97 -27.03 0 5.00e+00 4.00e-02 2.92e+01 ... (remaining 6990 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.158: 1750 1.158 - 2.316: 0 2.316 - 3.473: 0 3.473 - 4.631: 3 4.631 - 5.789: 17 Chirality restraints: 1770 Sorted by residual: chirality pdb=" C08 AJP A1620 " pdb=" C07 AJP A1620 " pdb=" C10 AJP A1620 " pdb=" O09 AJP A1620 " both_signs ideal model delta sigma weight residual False 2.56 -3.23 5.79 2.00e-01 2.50e+01 8.38e+02 chirality pdb=" C12 AJP A1620 " pdb=" C07 AJP A1620 " pdb=" C11 AJP A1620 " pdb=" C13 AJP A1620 " both_signs ideal model delta sigma weight residual False 3.01 -2.58 5.59 2.00e-01 2.50e+01 7.81e+02 chirality pdb=" C16 AJP A1620 " pdb=" C11 AJP A1620 " pdb=" C15 AJP A1620 " pdb=" C17 AJP A1620 " both_signs ideal model delta sigma weight residual False -2.70 2.64 -5.35 2.00e-01 2.50e+01 7.15e+02 ... (remaining 1767 not shown) Planarity restraints: 1826 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C20 76F A1616 " 0.165 2.00e-02 2.50e+03 3.26e-01 1.06e+03 pdb=" C21 76F A1616 " -0.433 2.00e-02 2.50e+03 pdb=" C22 76F A1616 " 0.430 2.00e-02 2.50e+03 pdb=" C23 76F A1616 " -0.163 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C17 76F A1618 " 0.160 2.00e-02 2.50e+03 2.87e-01 8.21e+02 pdb=" C18 76F A1618 " -0.372 2.00e-02 2.50e+03 pdb=" C19 76F A1618 " 0.372 2.00e-02 2.50e+03 pdb=" C20 76F A1618 " -0.161 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C39 76F A1616 " -0.187 2.00e-02 2.50e+03 1.88e-01 3.52e+02 pdb=" C40 76F A1616 " 0.184 2.00e-02 2.50e+03 pdb=" C41 76F A1616 " 0.191 2.00e-02 2.50e+03 pdb=" C42 76F A1616 " -0.188 2.00e-02 2.50e+03 ... (remaining 1823 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 402 2.69 - 3.24: 11372 3.24 - 3.80: 15669 3.80 - 4.35: 19371 4.35 - 4.90: 31526 Nonbonded interactions: 78340 Sorted by model distance: nonbonded pdb=" O ASP A 205 " pdb=" OD1 ASP A 205 " model vdw 2.140 3.040 nonbonded pdb=" O ASP A 303 " pdb=" N TRP A 306 " model vdw 2.220 3.120 nonbonded pdb=" O25 AJP A1620 " pdb=" O77 AJP A1620 " model vdw 2.241 3.040 nonbonded pdb=" N LYS A1150 " pdb=" OE1 GLU A1443 " model vdw 2.253 3.120 nonbonded pdb=" O GLN A 64 " pdb=" N ARG A 75 " model vdw 2.276 3.120 ... (remaining 78335 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 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: 1.510 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: 0.240 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.810 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 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 : 0.011 0.222 11243 Z= 0.531 Angle : 1.404 45.510 15276 Z= 0.622 Chirality : 0.531 5.789 1770 Planarity : 0.014 0.326 1820 Dihedral : 26.015 168.577 4552 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.47 % Allowed : 13.25 % Favored : 86.28 % Rotamer: Outliers : 0.53 % Allowed : 7.12 % Favored : 92.35 % 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: -4.75 (0.19), residues: 1271 helix: -2.48 (0.15), residues: 786 sheet: -4.28 (0.95), residues: 20 loop : -4.18 (0.24), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 233 TYR 0.024 0.002 TYR A1051 PHE 0.023 0.002 PHE A 684 TRP 0.024 0.002 TRP A1437 HIS 0.008 0.001 HIS A 541 Details of bonding type rmsd/Z covalent geometry : bond 0.01123 / 0.53 (11226) covalent geometry : angle 1.39002 / 0.62 (15230) SS BOND : bond 0.00334 / 0.17 ( 5) SS BOND : angle 1.69551 / 1.53 ( 10) hydrogen bonds : bond 0.15673 / 10.29 ( 521) hydrogen bonds : angle 6.28227 / 4.43 ( 1495) link_BETA1-3 : bond 0.01948 / 0.96 ( 3) link_BETA1-3 : angle 6.70524 / 4.15 ( 9) link_BETA1-4 : bond 0.00807 / 0.42 ( 2) link_BETA1-4 : angle 1.39400 / 0.87 ( 6) link_BETA1-6 : bond 0.00186 / 0.10 ( 1) link_BETA1-6 : angle 2.45805 / 1.43 ( 3) link_NAG-ASN : bond 0.00520 / 0.27 ( 6) link_NAG-ASN : angle 3.61649 / 2.81 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2542 Ramachandran restraints generated. 1271 Oldfield, 0 Emsley, 1271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2542 Ramachandran restraints generated. 1271 Oldfield, 0 Emsley, 1271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 220 time to evaluate : 0.356 Fit side-chains revert: symmetry clash REVERT: A 159 MET cc_start: 0.7523 (ptp) cc_final: 0.6616 (tmm) REVERT: A 178 ILE cc_start: 0.8788 (tt) cc_final: 0.8544 (pt) REVERT: A 236 ARG cc_start: 0.8527 (OUTLIER) cc_final: 0.8139 (ttt180) REVERT: A 278 GLN cc_start: 0.7926 (mm-40) cc_final: 0.7668 (mm-40) REVERT: A 854 LYS cc_start: 0.5883 (mmtp) cc_final: 0.4700 (ptpt) REVERT: A 905 MET cc_start: 0.7706 (tmm) cc_final: 0.7323 (tmm) REVERT: A 914 PHE cc_start: 0.8323 (t80) cc_final: 0.8015 (m-80) REVERT: A 1184 MET cc_start: 0.7715 (ttp) cc_final: 0.7450 (ttm) REVERT: A 1228 TYR cc_start: 0.8069 (t80) cc_final: 0.7763 (t80) REVERT: A 1248 MET cc_start: 0.7878 (tpp) cc_final: 0.6624 (tmm) REVERT: A 1432 MET cc_start: 0.8332 (ttp) cc_final: 0.7719 (tmm) REVERT: A 1447 TYR cc_start: 0.5508 (m-80) cc_final: 0.5171 (m-80) outliers start: 6 outliers final: 2 residues processed: 224 average time/residue: 0.0900 time to fit residues: 28.9963 Evaluate side-chains 170 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 167 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 GLU Chi-restraints excluded: chain A residue 236 ARG Chi-restraints excluded: chain A residue 1268 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 108 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 10.0000 chunk 113 optimal weight: 2.9990 chunk 53 optimal weight: 0.4980 chunk 5 optimal weight: 9.9990 chunk 33 optimal weight: 0.7980 chunk 123 optimal weight: 0.1980 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 0.8980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 532 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1077 HIS A1461 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.161206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.115385 restraints weight = 40781.101| |-----------------------------------------------------------------------------| r_work (start): 0.3408 rms_B_bonded: 5.38 r_work (final): 0.3408 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3407 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3407 r_free = 0.3407 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3407 r_free = 0.3407 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3407 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.1591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 11243 Z= 0.168 Angle : 1.140 34.535 15276 Z= 0.480 Chirality : 0.095 2.191 1770 Planarity : 0.005 0.068 1820 Dihedral : 23.652 175.468 2163 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.86 % Favored : 90.14 % Rotamer: Outliers : 2.02 % Allowed : 14.07 % Favored : 83.91 % 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: -3.04 (0.22), residues: 1271 helix: -1.00 (0.17), residues: 798 sheet: -3.50 (1.16), residues: 20 loop : -3.80 (0.26), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 233 TYR 0.019 0.001 TYR A 176 PHE 0.037 0.002 PHE A1440 TRP 0.018 0.001 TRP A1437 HIS 0.004 0.001 HIS A 541 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.17 (11226) covalent geometry : angle 1.12790 / 0.48 (15230) SS BOND : bond 0.00385 / 0.20 ( 5) SS BOND : angle 1.49890 / 1.17 ( 10) hydrogen bonds : bond 0.06087 / 4.41 ( 521) hydrogen bonds : angle 4.56085 / 3.22 ( 1495) link_BETA1-3 : bond 0.01674 / 0.76 ( 3) link_BETA1-3 : angle 4.92098 / 3.04 ( 9) link_BETA1-4 : bond 0.00817 / 0.41 ( 2) link_BETA1-4 : angle 1.42904 / 0.92 ( 6) link_BETA1-6 : bond 0.00824 / 0.43 ( 1) link_BETA1-6 : angle 3.58361 / 2.27 ( 3) link_NAG-ASN : bond 0.00687 / 0.37 ( 6) link_NAG-ASN : angle 3.31589 / 2.58 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2542 Ramachandran restraints generated. 1271 Oldfield, 0 Emsley, 1271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2542 Ramachandran restraints generated. 1271 Oldfield, 0 Emsley, 1271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 189 time to evaluate : 0.398 Fit side-chains revert: symmetry clash REVERT: A 122 MET cc_start: 0.5628 (OUTLIER) cc_final: 0.5139 (tmm) REVERT: A 159 MET cc_start: 0.7624 (ptp) cc_final: 0.6722 (tmm) REVERT: A 179 GLU cc_start: 0.8650 (OUTLIER) cc_final: 0.8309 (tt0) REVERT: A 224 TYR cc_start: 0.7884 (m-80) cc_final: 0.6088 (p90) REVERT: A 227 ARG cc_start: 0.8216 (ttp-170) cc_final: 0.7981 (ttp-170) REVERT: A 236 ARG cc_start: 0.8796 (OUTLIER) cc_final: 0.8136 (ttt-90) REVERT: A 278 GLN cc_start: 0.8107 (mm-40) cc_final: 0.7845 (mm-40) REVERT: A 521 PHE cc_start: 0.7450 (OUTLIER) cc_final: 0.6946 (t80) REVERT: A 854 LYS cc_start: 0.5681 (mmtp) cc_final: 0.4545 (ptpt) REVERT: A 905 MET cc_start: 0.7656 (tmm) cc_final: 0.7181 (tmm) REVERT: A 914 PHE cc_start: 0.8126 (t80) cc_final: 0.7694 (m-80) REVERT: A 1014 GLU cc_start: 0.8447 (mp0) cc_final: 0.8211 (mp0) REVERT: A 1085 ASN cc_start: 0.8668 (t0) cc_final: 0.8323 (t0) REVERT: A 1141 MET cc_start: 0.8476 (tpp) cc_final: 0.8042 (tpt) REVERT: A 1184 MET cc_start: 0.7400 (ttp) cc_final: 0.7123 (ttp) REVERT: A 1248 MET cc_start: 0.7697 (tpp) cc_final: 0.6544 (tmm) REVERT: A 1432 MET cc_start: 0.8231 (ttp) cc_final: 0.7379 (tmm) outliers start: 23 outliers final: 8 residues processed: 203 average time/residue: 0.0904 time to fit residues: 27.1126 Evaluate side-chains 172 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 160 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 MET Chi-restraints excluded: chain A residue 179 GLU Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 236 ARG Chi-restraints excluded: chain A residue 521 PHE Chi-restraints excluded: chain A residue 534 THR Chi-restraints excluded: chain A residue 586 PHE Chi-restraints excluded: chain A residue 912 VAL Chi-restraints excluded: chain A residue 966 ASN Chi-restraints excluded: chain A residue 1198 MET Chi-restraints excluded: chain A residue 1268 ARG Chi-restraints excluded: chain A residue 1419 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 37 optimal weight: 6.9990 chunk 117 optimal weight: 6.9990 chunk 55 optimal weight: 0.9990 chunk 121 optimal weight: 5.9990 chunk 32 optimal weight: 6.9990 chunk 36 optimal weight: 0.9990 chunk 62 optimal weight: 2.9990 chunk 77 optimal weight: 0.8980 chunk 12 optimal weight: 0.3980 chunk 94 optimal weight: 7.9990 chunk 89 optimal weight: 6.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 291 HIS ** A 532 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 683 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.162333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.117533 restraints weight = 31936.505| |-----------------------------------------------------------------------------| r_work (start): 0.3431 rms_B_bonded: 4.72 r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3430 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3430 r_free = 0.3430 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3430 r_free = 0.3430 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3430 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.2094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11243 Z= 0.148 Angle : 0.982 31.416 15276 Z= 0.421 Chirality : 0.088 2.181 1770 Planarity : 0.005 0.062 1820 Dihedral : 20.702 174.434 2163 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.49 % Favored : 89.51 % Rotamer: Outliers : 2.81 % Allowed : 15.13 % Favored : 82.06 % 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: -2.32 (0.23), residues: 1271 helix: -0.47 (0.18), residues: 812 sheet: -3.21 (1.21), residues: 20 loop : -3.50 (0.27), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 233 TYR 0.021 0.001 TYR A 176 PHE 0.021 0.001 PHE A1440 TRP 0.016 0.001 TRP A1437 HIS 0.004 0.001 HIS A 541 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.15 (11226) covalent geometry : angle 0.96869 / 0.42 (15230) SS BOND : bond 0.00328 / 0.18 ( 5) SS BOND : angle 1.20243 / 1.00 ( 10) hydrogen bonds : bond 0.05333 / 3.87 ( 521) hydrogen bonds : angle 4.24717 / 3.01 ( 1495) link_BETA1-3 : bond 0.01736 / 0.82 ( 3) link_BETA1-3 : angle 4.74286 / 2.88 ( 9) link_BETA1-4 : bond 0.00643 / 0.32 ( 2) link_BETA1-4 : angle 1.30511 / 0.84 ( 6) link_BETA1-6 : bond 0.00154 / 0.08 ( 1) link_BETA1-6 : angle 2.70974 / 1.62 ( 3) link_NAG-ASN : bond 0.00518 / 0.29 ( 6) link_NAG-ASN : angle 3.20743 / 2.47 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2542 Ramachandran restraints generated. 1271 Oldfield, 0 Emsley, 1271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2542 Ramachandran restraints generated. 1271 Oldfield, 0 Emsley, 1271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 184 time to evaluate : 0.424 Fit side-chains revert: symmetry clash REVERT: A 122 MET cc_start: 0.5268 (ttp) cc_final: 0.4810 (tmm) REVERT: A 147 MET cc_start: 0.7636 (OUTLIER) cc_final: 0.7214 (mpp) REVERT: A 159 MET cc_start: 0.7291 (ptp) cc_final: 0.6556 (tmm) REVERT: A 179 GLU cc_start: 0.8728 (OUTLIER) cc_final: 0.8517 (tt0) REVERT: A 205 ASP cc_start: 0.8968 (OUTLIER) cc_final: 0.8745 (t0) REVERT: A 224 TYR cc_start: 0.7972 (m-80) cc_final: 0.6123 (p90) REVERT: A 236 ARG cc_start: 0.8925 (OUTLIER) cc_final: 0.8637 (ttt180) REVERT: A 854 LYS cc_start: 0.5659 (mmtp) cc_final: 0.4576 (ptpt) REVERT: A 905 MET cc_start: 0.7648 (tmm) cc_final: 0.7267 (tmm) REVERT: A 914 PHE cc_start: 0.8038 (t80) cc_final: 0.7512 (m-80) REVERT: A 1085 ASN cc_start: 0.8742 (t0) cc_final: 0.8403 (t0) REVERT: A 1141 MET cc_start: 0.8477 (tpp) cc_final: 0.8017 (tpt) REVERT: A 1248 MET cc_start: 0.7673 (tpp) cc_final: 0.6454 (tmm) REVERT: A 1419 GLU cc_start: 0.8338 (OUTLIER) cc_final: 0.7992 (tt0) REVERT: A 1432 MET cc_start: 0.8185 (ttp) cc_final: 0.7951 (tpp) outliers start: 32 outliers final: 16 residues processed: 200 average time/residue: 0.1008 time to fit residues: 29.2632 Evaluate side-chains 181 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 160 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 MET Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 179 GLU Chi-restraints excluded: chain A residue 205 ASP Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 236 ARG Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 268 SER Chi-restraints excluded: chain A residue 393 ILE Chi-restraints excluded: chain A residue 586 PHE Chi-restraints excluded: chain A residue 624 TRP Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 912 VAL Chi-restraints excluded: chain A residue 1046 HIS Chi-restraints excluded: chain A residue 1198 MET Chi-restraints excluded: chain A residue 1224 LEU Chi-restraints excluded: chain A residue 1322 MET Chi-restraints excluded: chain A residue 1349 LEU Chi-restraints excluded: chain A residue 1419 GLU Chi-restraints excluded: chain A residue 1436 VAL Chi-restraints excluded: chain A residue 1464 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 70 optimal weight: 2.9990 chunk 103 optimal weight: 8.9990 chunk 54 optimal weight: 6.9990 chunk 105 optimal weight: 0.0770 chunk 66 optimal weight: 1.9990 chunk 48 optimal weight: 5.9990 chunk 20 optimal weight: 0.8980 chunk 9 optimal weight: 0.9990 chunk 112 optimal weight: 5.9990 chunk 63 optimal weight: 0.8980 chunk 28 optimal weight: 5.9990 overall best weight: 0.9742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 153 HIS A 291 HIS ** A 532 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.165153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.119568 restraints weight = 33794.254| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 4.91 r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3458 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3458 r_free = 0.3458 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3458 r_free = 0.3458 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.3458 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.2562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11243 Z= 0.134 Angle : 0.964 32.911 15276 Z= 0.408 Chirality : 0.081 2.035 1770 Planarity : 0.005 0.077 1820 Dihedral : 18.834 176.124 2159 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.62 % Favored : 90.38 % Rotamer: Outliers : 2.11 % Allowed : 17.68 % Favored : 80.21 % 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: -1.92 (0.24), residues: 1271 helix: -0.19 (0.18), residues: 823 sheet: -3.19 (1.23), residues: 20 loop : -3.35 (0.28), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 227 TYR 0.017 0.001 TYR A1227 PHE 0.026 0.001 PHE A 623 TRP 0.019 0.001 TRP A 715 HIS 0.004 0.001 HIS A 291 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.13 (11226) covalent geometry : angle 0.95099 / 0.40 (15230) SS BOND : bond 0.00395 / 0.21 ( 5) SS BOND : angle 1.19195 / 0.93 ( 10) hydrogen bonds : bond 0.04699 / 3.42 ( 521) hydrogen bonds : angle 4.03783 / 2.86 ( 1495) link_BETA1-3 : bond 0.01736 / 0.83 ( 3) link_BETA1-3 : angle 4.50789 / 2.72 ( 9) link_BETA1-4 : bond 0.00654 / 0.33 ( 2) link_BETA1-4 : angle 1.21431 / 0.78 ( 6) link_BETA1-6 : bond 0.00284 / 0.15 ( 1) link_BETA1-6 : angle 2.27601 / 1.37 ( 3) link_NAG-ASN : bond 0.00533 / 0.31 ( 6) link_NAG-ASN : angle 3.23750 / 2.46 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2542 Ramachandran restraints generated. 1271 Oldfield, 0 Emsley, 1271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2542 Ramachandran restraints generated. 1271 Oldfield, 0 Emsley, 1271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 177 time to evaluate : 0.399 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 159 MET cc_start: 0.7097 (ptp) cc_final: 0.6463 (tmm) REVERT: A 179 GLU cc_start: 0.8753 (OUTLIER) cc_final: 0.8513 (tt0) REVERT: A 187 ARG cc_start: 0.7906 (mtt180) cc_final: 0.7665 (mtt180) REVERT: A 205 ASP cc_start: 0.9145 (OUTLIER) cc_final: 0.8837 (t0) REVERT: A 224 TYR cc_start: 0.7977 (m-80) cc_final: 0.6073 (p90) REVERT: A 236 ARG cc_start: 0.8885 (OUTLIER) cc_final: 0.8649 (ttt180) REVERT: A 613 ARG cc_start: 0.8521 (ttt90) cc_final: 0.8274 (ttt90) REVERT: A 854 LYS cc_start: 0.5525 (mmtp) cc_final: 0.4495 (ptpt) REVERT: A 905 MET cc_start: 0.7622 (tmm) cc_final: 0.7339 (tmm) REVERT: A 914 PHE cc_start: 0.8091 (t80) cc_final: 0.7481 (m-80) REVERT: A 1085 ASN cc_start: 0.8596 (t0) cc_final: 0.8349 (t0) REVERT: A 1141 MET cc_start: 0.8476 (tpp) cc_final: 0.8023 (tpt) REVERT: A 1245 ILE cc_start: 0.8699 (tp) cc_final: 0.8468 (tp) REVERT: A 1248 MET cc_start: 0.7697 (tpp) cc_final: 0.6453 (tmm) REVERT: A 1419 GLU cc_start: 0.8245 (pp20) cc_final: 0.8019 (tt0) outliers start: 24 outliers final: 14 residues processed: 190 average time/residue: 0.0980 time to fit residues: 27.1909 Evaluate side-chains 180 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 163 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 179 GLU Chi-restraints excluded: chain A residue 205 ASP Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 236 ARG Chi-restraints excluded: chain A residue 268 SER Chi-restraints excluded: chain A residue 393 ILE Chi-restraints excluded: chain A residue 534 THR Chi-restraints excluded: chain A residue 657 ILE Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 912 VAL Chi-restraints excluded: chain A residue 1046 HIS Chi-restraints excluded: chain A residue 1164 PHE Chi-restraints excluded: chain A residue 1224 LEU Chi-restraints excluded: chain A residue 1349 LEU Chi-restraints excluded: chain A residue 1418 TYR Chi-restraints excluded: chain A residue 1436 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 19 optimal weight: 4.9990 chunk 41 optimal weight: 9.9990 chunk 71 optimal weight: 3.9990 chunk 118 optimal weight: 3.9990 chunk 125 optimal weight: 4.9990 chunk 59 optimal weight: 0.7980 chunk 6 optimal weight: 0.0020 chunk 17 optimal weight: 0.9980 chunk 82 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 119 optimal weight: 5.9990 overall best weight: 1.3592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 278 GLN A 291 HIS A 532 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.164259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.118762 restraints weight = 35153.512| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 4.98 r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3448 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3448 r_free = 0.3448 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3448 r_free = 0.3448 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3448 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.2702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11243 Z= 0.137 Angle : 0.955 32.346 15276 Z= 0.404 Chirality : 0.081 2.026 1770 Planarity : 0.005 0.058 1820 Dihedral : 17.691 178.696 2159 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.31 % Favored : 90.69 % Rotamer: Outliers : 2.73 % Allowed : 18.29 % Favored : 78.98 % 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: -1.68 (0.24), residues: 1271 helix: 0.01 (0.19), residues: 812 sheet: -3.25 (1.15), residues: 20 loop : -3.19 (0.28), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 425 TYR 0.013 0.001 TYR A 381 PHE 0.019 0.001 PHE A 623 TRP 0.019 0.001 TRP A 121 HIS 0.004 0.001 HIS A 291 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.14 (11226) covalent geometry : angle 0.94216 / 0.40 (15230) SS BOND : bond 0.00268 / 0.14 ( 5) SS BOND : angle 1.07765 / 0.86 ( 10) hydrogen bonds : bond 0.04694 / 3.42 ( 521) hydrogen bonds : angle 4.00307 / 2.85 ( 1495) link_BETA1-3 : bond 0.01623 / 0.76 ( 3) link_BETA1-3 : angle 4.53266 / 2.74 ( 9) link_BETA1-4 : bond 0.00597 / 0.30 ( 2) link_BETA1-4 : angle 1.20225 / 0.77 ( 6) link_BETA1-6 : bond 0.00191 / 0.10 ( 1) link_BETA1-6 : angle 1.96899 / 1.18 ( 3) link_NAG-ASN : bond 0.00478 / 0.29 ( 6) link_NAG-ASN : angle 3.24282 / 2.44 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2542 Ramachandran restraints generated. 1271 Oldfield, 0 Emsley, 1271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2542 Ramachandran restraints generated. 1271 Oldfield, 0 Emsley, 1271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 169 time to evaluate : 0.424 Fit side-chains revert: symmetry clash REVERT: A 159 MET cc_start: 0.7216 (ptp) cc_final: 0.6562 (tmm) REVERT: A 205 ASP cc_start: 0.9162 (OUTLIER) cc_final: 0.8910 (t0) REVERT: A 224 TYR cc_start: 0.7987 (m-80) cc_final: 0.6065 (p90) REVERT: A 236 ARG cc_start: 0.8846 (OUTLIER) cc_final: 0.8599 (ttt180) REVERT: A 613 ARG cc_start: 0.8544 (ttt90) cc_final: 0.8300 (ttt90) REVERT: A 854 LYS cc_start: 0.5485 (mmtp) cc_final: 0.4472 (ptpt) REVERT: A 905 MET cc_start: 0.7636 (tmm) cc_final: 0.7345 (tmm) REVERT: A 914 PHE cc_start: 0.8089 (t80) cc_final: 0.7472 (m-80) REVERT: A 1085 ASN cc_start: 0.8518 (t0) cc_final: 0.8152 (t0) REVERT: A 1141 MET cc_start: 0.8498 (tpp) cc_final: 0.8015 (tpt) REVERT: A 1245 ILE cc_start: 0.8703 (tp) cc_final: 0.8475 (tp) REVERT: A 1248 MET cc_start: 0.7665 (tpp) cc_final: 0.6405 (tmm) REVERT: A 1268 ARG cc_start: 0.8148 (ptm160) cc_final: 0.7719 (ttp-170) REVERT: A 1319 GLU cc_start: 0.8186 (tp30) cc_final: 0.7797 (tp30) REVERT: A 1419 GLU cc_start: 0.8226 (pp20) cc_final: 0.8024 (tt0) REVERT: A 1455 GLU cc_start: 0.7729 (mm-30) cc_final: 0.7040 (mt-10) outliers start: 31 outliers final: 18 residues processed: 190 average time/residue: 0.0965 time to fit residues: 27.2507 Evaluate side-chains 184 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 164 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 205 ASP Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 236 ARG Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 268 SER Chi-restraints excluded: chain A residue 278 GLN Chi-restraints excluded: chain A residue 393 ILE Chi-restraints excluded: chain A residue 624 TRP Chi-restraints excluded: chain A residue 657 ILE Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 897 LEU Chi-restraints excluded: chain A residue 912 VAL Chi-restraints excluded: chain A residue 938 VAL Chi-restraints excluded: chain A residue 1046 HIS Chi-restraints excluded: chain A residue 1164 PHE Chi-restraints excluded: chain A residue 1224 LEU Chi-restraints excluded: chain A residue 1349 LEU Chi-restraints excluded: chain A residue 1418 TYR Chi-restraints excluded: chain A residue 1464 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 9 optimal weight: 8.9990 chunk 110 optimal weight: 7.9990 chunk 26 optimal weight: 5.9990 chunk 28 optimal weight: 6.9990 chunk 30 optimal weight: 0.8980 chunk 35 optimal weight: 5.9990 chunk 92 optimal weight: 8.9990 chunk 44 optimal weight: 0.0870 chunk 118 optimal weight: 0.9990 chunk 36 optimal weight: 8.9990 chunk 106 optimal weight: 5.9990 overall best weight: 2.7964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 291 HIS ** A 683 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1133 GLN ** A1452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.160378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.115854 restraints weight = 24440.721| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 4.09 r_work: 0.3226 rms_B_bonded: 4.57 restraints_weight: 0.5000 r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3249 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3249 r_free = 0.3249 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3249 r_free = 0.3249 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3249 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.2663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 11243 Z= 0.186 Angle : 0.987 32.766 15276 Z= 0.425 Chirality : 0.081 2.023 1770 Planarity : 0.005 0.082 1820 Dihedral : 16.656 178.663 2156 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.02 % Favored : 89.98 % Rotamer: Outliers : 2.81 % Allowed : 18.82 % Favored : 78.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.70 (0.24), residues: 1271 helix: -0.04 (0.18), residues: 812 sheet: -3.38 (1.09), residues: 20 loop : -3.11 (0.29), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 425 TYR 0.017 0.001 TYR A 381 PHE 0.018 0.001 PHE A 684 TRP 0.016 0.001 TRP A 842 HIS 0.004 0.001 HIS A 315 Details of bonding type rmsd/Z covalent geometry : bond 0.00436 / 0.19 (11226) covalent geometry : angle 0.97399 / 0.42 (15230) SS BOND : bond 0.00264 / 0.14 ( 5) SS BOND : angle 1.28742 / 1.11 ( 10) hydrogen bonds : bond 0.05493 / 4.01 ( 521) hydrogen bonds : angle 4.15655 / 2.95 ( 1495) link_BETA1-3 : bond 0.01576 / 0.76 ( 3) link_BETA1-3 : angle 4.89411 / 2.97 ( 9) link_BETA1-4 : bond 0.00529 / 0.27 ( 2) link_BETA1-4 : angle 1.22450 / 0.78 ( 6) link_BETA1-6 : bond 0.00183 / 0.10 ( 1) link_BETA1-6 : angle 1.65741 / 0.96 ( 3) link_NAG-ASN : bond 0.00437 / 0.26 ( 6) link_NAG-ASN : angle 3.14728 / 2.36 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2542 Ramachandran restraints generated. 1271 Oldfield, 0 Emsley, 1271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2542 Ramachandran restraints generated. 1271 Oldfield, 0 Emsley, 1271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 165 time to evaluate : 0.476 Fit side-chains revert: symmetry clash REVERT: A 159 MET cc_start: 0.7190 (ptp) cc_final: 0.6237 (tmm) REVERT: A 205 ASP cc_start: 0.9192 (OUTLIER) cc_final: 0.8895 (t0) REVERT: A 224 TYR cc_start: 0.8165 (m-80) cc_final: 0.6284 (p90) REVERT: A 236 ARG cc_start: 0.8869 (OUTLIER) cc_final: 0.8437 (ttt180) REVERT: A 521 PHE cc_start: 0.7878 (t80) cc_final: 0.7627 (t80) REVERT: A 854 LYS cc_start: 0.5608 (mmtp) cc_final: 0.4380 (ptpt) REVERT: A 905 MET cc_start: 0.7608 (tmm) cc_final: 0.7260 (tmm) REVERT: A 914 PHE cc_start: 0.8380 (t80) cc_final: 0.7711 (m-80) REVERT: A 1141 MET cc_start: 0.8621 (tpp) cc_final: 0.8248 (tpt) REVERT: A 1245 ILE cc_start: 0.8693 (tp) cc_final: 0.8467 (tp) REVERT: A 1248 MET cc_start: 0.7642 (tpp) cc_final: 0.6386 (tmm) outliers start: 32 outliers final: 21 residues processed: 184 average time/residue: 0.0963 time to fit residues: 26.3095 Evaluate side-chains 183 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 160 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 205 ASP Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 236 ARG Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 268 SER Chi-restraints excluded: chain A residue 315 HIS Chi-restraints excluded: chain A residue 393 ILE Chi-restraints excluded: chain A residue 624 TRP Chi-restraints excluded: chain A residue 657 ILE Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 897 LEU Chi-restraints excluded: chain A residue 912 VAL Chi-restraints excluded: chain A residue 938 VAL Chi-restraints excluded: chain A residue 1040 SER Chi-restraints excluded: chain A residue 1046 HIS Chi-restraints excluded: chain A residue 1164 PHE Chi-restraints excluded: chain A residue 1224 LEU Chi-restraints excluded: chain A residue 1349 LEU Chi-restraints excluded: chain A residue 1418 TYR Chi-restraints excluded: chain A residue 1436 VAL Chi-restraints excluded: chain A residue 1464 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 30 optimal weight: 5.9990 chunk 84 optimal weight: 2.9990 chunk 117 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 82 optimal weight: 3.9990 chunk 6 optimal weight: 0.9990 chunk 86 optimal weight: 2.9990 chunk 22 optimal weight: 0.8980 chunk 58 optimal weight: 0.7980 chunk 43 optimal weight: 20.0000 chunk 21 optimal weight: 0.8980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 278 GLN ** A 683 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1133 GLN ** A1452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.164876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.120383 restraints weight = 23366.709| |-----------------------------------------------------------------------------| r_work (start): 0.3467 rms_B_bonded: 4.04 r_work: 0.3283 rms_B_bonded: 4.58 restraints_weight: 0.5000 r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3308 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3308 r_free = 0.3308 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3308 r_free = 0.3308 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3308 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.2955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11243 Z= 0.133 Angle : 0.924 32.093 15276 Z= 0.396 Chirality : 0.080 2.029 1770 Planarity : 0.005 0.071 1820 Dihedral : 15.947 179.352 2156 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.23 % Favored : 90.77 % Rotamer: Outliers : 2.37 % Allowed : 19.61 % Favored : 78.01 % 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 (0.24), residues: 1271 helix: 0.21 (0.19), residues: 812 sheet: -3.22 (1.14), residues: 20 loop : -3.04 (0.29), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 227 TYR 0.017 0.001 TYR A1228 PHE 0.017 0.001 PHE A 850 TRP 0.019 0.001 TRP A 715 HIS 0.003 0.001 HIS A 541 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.13 (11226) covalent geometry : angle 0.91059 / 0.39 (15230) SS BOND : bond 0.00299 / 0.15 ( 5) SS BOND : angle 1.15257 / 0.88 ( 10) hydrogen bonds : bond 0.04579 / 3.36 ( 521) hydrogen bonds : angle 3.95925 / 2.81 ( 1495) link_BETA1-3 : bond 0.01670 / 0.79 ( 3) link_BETA1-3 : angle 4.66958 / 2.82 ( 9) link_BETA1-4 : bond 0.00583 / 0.30 ( 2) link_BETA1-4 : angle 1.14825 / 0.73 ( 6) link_BETA1-6 : bond 0.00579 / 0.30 ( 1) link_BETA1-6 : angle 1.71630 / 0.99 ( 3) link_NAG-ASN : bond 0.00511 / 0.31 ( 6) link_NAG-ASN : angle 3.11894 / 2.37 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2542 Ramachandran restraints generated. 1271 Oldfield, 0 Emsley, 1271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2542 Ramachandran restraints generated. 1271 Oldfield, 0 Emsley, 1271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 163 time to evaluate : 0.379 Fit side-chains revert: symmetry clash REVERT: A 147 MET cc_start: 0.7991 (OUTLIER) cc_final: 0.7702 (mpp) REVERT: A 159 MET cc_start: 0.6977 (ptp) cc_final: 0.6076 (tmm) REVERT: A 205 ASP cc_start: 0.9202 (OUTLIER) cc_final: 0.8937 (t0) REVERT: A 213 TYR cc_start: 0.7754 (OUTLIER) cc_final: 0.6831 (t80) REVERT: A 224 TYR cc_start: 0.7935 (m-80) cc_final: 0.6589 (p90) REVERT: A 227 ARG cc_start: 0.8593 (mtm180) cc_final: 0.8288 (mtm180) REVERT: A 236 ARG cc_start: 0.8859 (OUTLIER) cc_final: 0.8481 (ttt180) REVERT: A 613 ARG cc_start: 0.8484 (ttt90) cc_final: 0.8280 (ttt90) REVERT: A 854 LYS cc_start: 0.5613 (mmtp) cc_final: 0.4431 (ptpt) REVERT: A 905 MET cc_start: 0.7579 (tmm) cc_final: 0.7280 (tmm) REVERT: A 914 PHE cc_start: 0.8285 (t80) cc_final: 0.7562 (m-80) REVERT: A 947 LEU cc_start: 0.7569 (pp) cc_final: 0.7269 (pp) REVERT: A 1088 MET cc_start: 0.8948 (tpp) cc_final: 0.8334 (mpp) REVERT: A 1141 MET cc_start: 0.8590 (tpp) cc_final: 0.8219 (tpt) REVERT: A 1245 ILE cc_start: 0.8648 (tp) cc_final: 0.8416 (tp) REVERT: A 1248 MET cc_start: 0.7552 (tpp) cc_final: 0.6333 (tmm) REVERT: A 1420 ASP cc_start: 0.8393 (t0) cc_final: 0.7921 (t0) outliers start: 27 outliers final: 19 residues processed: 180 average time/residue: 0.0996 time to fit residues: 26.3885 Evaluate side-chains 182 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 159 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 MET Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 205 ASP Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 236 ARG Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 268 SER Chi-restraints excluded: chain A residue 278 GLN Chi-restraints excluded: chain A residue 315 HIS Chi-restraints excluded: chain A residue 393 ILE Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 624 TRP Chi-restraints excluded: chain A residue 657 ILE Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 897 LEU Chi-restraints excluded: chain A residue 912 VAL Chi-restraints excluded: chain A residue 1040 SER Chi-restraints excluded: chain A residue 1046 HIS Chi-restraints excluded: chain A residue 1164 PHE Chi-restraints excluded: chain A residue 1224 LEU Chi-restraints excluded: chain A residue 1418 TYR Chi-restraints excluded: chain A residue 1436 VAL Chi-restraints excluded: chain A residue 1464 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 112 optimal weight: 6.9990 chunk 102 optimal weight: 7.9990 chunk 100 optimal weight: 10.0000 chunk 31 optimal weight: 3.9990 chunk 92 optimal weight: 8.9990 chunk 17 optimal weight: 0.7980 chunk 48 optimal weight: 0.8980 chunk 125 optimal weight: 7.9990 chunk 80 optimal weight: 5.9990 chunk 106 optimal weight: 6.9990 chunk 90 optimal weight: 4.9990 overall best weight: 3.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 291 HIS ** A 683 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.159337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.113053 restraints weight = 35662.472| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 4.96 r_work (final): 0.3375 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3374 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3374 r_free = 0.3374 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3374 r_free = 0.3374 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3374 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.2817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 11243 Z= 0.211 Angle : 0.981 32.802 15276 Z= 0.431 Chirality : 0.081 2.044 1770 Planarity : 0.005 0.063 1820 Dihedral : 15.784 179.865 2156 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.25 % Favored : 89.75 % Rotamer: Outliers : 2.20 % Allowed : 19.96 % Favored : 77.84 % 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: -1.62 (0.24), residues: 1271 helix: 0.02 (0.18), residues: 813 sheet: -3.31 (1.09), residues: 20 loop : -3.10 (0.29), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 425 TYR 0.021 0.002 TYR A1228 PHE 0.020 0.001 PHE A 684 TRP 0.017 0.001 TRP A 842 HIS 0.005 0.001 HIS A 315 Details of bonding type rmsd/Z covalent geometry : bond 0.00505 / 0.21 (11226) covalent geometry : angle 0.96751 / 0.43 (15230) SS BOND : bond 0.00227 / 0.12 ( 5) SS BOND : angle 1.24615 / 1.09 ( 10) hydrogen bonds : bond 0.05708 / 4.16 ( 521) hydrogen bonds : angle 4.16833 / 2.96 ( 1495) link_BETA1-3 : bond 0.01473 / 0.72 ( 3) link_BETA1-3 : angle 5.05315 / 3.07 ( 9) link_BETA1-4 : bond 0.00376 / 0.19 ( 2) link_BETA1-4 : angle 1.28101 / 0.81 ( 6) link_BETA1-6 : bond 0.00200 / 0.11 ( 1) link_BETA1-6 : angle 1.63657 / 0.99 ( 3) link_NAG-ASN : bond 0.00410 / 0.22 ( 6) link_NAG-ASN : angle 3.07116 / 2.31 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2542 Ramachandran restraints generated. 1271 Oldfield, 0 Emsley, 1271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2542 Ramachandran restraints generated. 1271 Oldfield, 0 Emsley, 1271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 165 time to evaluate : 0.394 Fit side-chains revert: symmetry clash REVERT: A 159 MET cc_start: 0.7139 (ptp) cc_final: 0.6508 (tmm) REVERT: A 205 ASP cc_start: 0.9215 (OUTLIER) cc_final: 0.8842 (t0) REVERT: A 224 TYR cc_start: 0.7862 (m-80) cc_final: 0.6436 (p90) REVERT: A 236 ARG cc_start: 0.8847 (OUTLIER) cc_final: 0.8349 (ttt180) REVERT: A 854 LYS cc_start: 0.5511 (mmtp) cc_final: 0.4428 (ptpt) REVERT: A 905 MET cc_start: 0.7716 (tmm) cc_final: 0.7277 (tmm) REVERT: A 914 PHE cc_start: 0.8184 (t80) cc_final: 0.7606 (m-80) REVERT: A 1141 MET cc_start: 0.8592 (tpp) cc_final: 0.8246 (tpt) REVERT: A 1245 ILE cc_start: 0.8714 (tp) cc_final: 0.8473 (tp) REVERT: A 1248 MET cc_start: 0.7651 (tpp) cc_final: 0.6361 (tmm) REVERT: A 1368 CYS cc_start: 0.4301 (OUTLIER) cc_final: 0.3881 (t) REVERT: A 1420 ASP cc_start: 0.8497 (t0) cc_final: 0.7918 (t0) outliers start: 25 outliers final: 20 residues processed: 180 average time/residue: 0.0997 time to fit residues: 26.1837 Evaluate side-chains 184 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 161 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 205 ASP Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 236 ARG Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 268 SER Chi-restraints excluded: chain A residue 315 HIS Chi-restraints excluded: chain A residue 393 ILE Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 624 TRP Chi-restraints excluded: chain A residue 657 ILE Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 897 LEU Chi-restraints excluded: chain A residue 912 VAL Chi-restraints excluded: chain A residue 938 VAL Chi-restraints excluded: chain A residue 1040 SER Chi-restraints excluded: chain A residue 1046 HIS Chi-restraints excluded: chain A residue 1164 PHE Chi-restraints excluded: chain A residue 1224 LEU Chi-restraints excluded: chain A residue 1368 CYS Chi-restraints excluded: chain A residue 1418 TYR Chi-restraints excluded: chain A residue 1464 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 36 optimal weight: 0.8980 chunk 76 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 30 optimal weight: 3.9990 chunk 2 optimal weight: 3.9990 chunk 64 optimal weight: 6.9990 chunk 84 optimal weight: 0.5980 chunk 51 optimal weight: 0.9980 chunk 120 optimal weight: 4.9990 chunk 110 optimal weight: 1.9990 chunk 89 optimal weight: 3.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 278 GLN ** A 683 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.163936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.119036 restraints weight = 27046.793| |-----------------------------------------------------------------------------| r_work (start): 0.3450 rms_B_bonded: 4.34 r_work: 0.3259 rms_B_bonded: 4.81 restraints_weight: 0.5000 r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3283 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3283 r_free = 0.3283 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3283 r_free = 0.3283 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3283 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.3066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 11243 Z= 0.137 Angle : 0.918 32.413 15276 Z= 0.396 Chirality : 0.079 2.048 1770 Planarity : 0.005 0.062 1820 Dihedral : 15.389 179.405 2156 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.38 % Favored : 90.62 % Rotamer: Outliers : 2.11 % Allowed : 20.49 % Favored : 77.40 % 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: -1.30 (0.24), residues: 1271 helix: 0.29 (0.19), residues: 813 sheet: -3.23 (1.12), residues: 20 loop : -3.00 (0.29), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 425 TYR 0.017 0.001 TYR A1228 PHE 0.016 0.001 PHE A 850 TRP 0.020 0.001 TRP A 715 HIS 0.004 0.001 HIS A 541 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.14 (11226) covalent geometry : angle 0.90476 / 0.39 (15230) SS BOND : bond 0.00319 / 0.16 ( 5) SS BOND : angle 1.12630 / 0.87 ( 10) hydrogen bonds : bond 0.04685 / 3.43 ( 521) hydrogen bonds : angle 3.91958 / 2.79 ( 1495) link_BETA1-3 : bond 0.01602 / 0.76 ( 3) link_BETA1-3 : angle 4.73442 / 2.86 ( 9) link_BETA1-4 : bond 0.00484 / 0.24 ( 2) link_BETA1-4 : angle 1.17896 / 0.74 ( 6) link_BETA1-6 : bond 0.00527 / 0.28 ( 1) link_BETA1-6 : angle 1.50048 / 0.83 ( 3) link_NAG-ASN : bond 0.00492 / 0.30 ( 6) link_NAG-ASN : angle 3.02412 / 2.30 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2542 Ramachandran restraints generated. 1271 Oldfield, 0 Emsley, 1271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2542 Ramachandran restraints generated. 1271 Oldfield, 0 Emsley, 1271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 166 time to evaluate : 0.422 Fit side-chains revert: symmetry clash REVERT: A 122 MET cc_start: 0.5011 (tmm) cc_final: 0.4435 (tmm) REVERT: A 159 MET cc_start: 0.6965 (ptp) cc_final: 0.6347 (tmm) REVERT: A 205 ASP cc_start: 0.9204 (OUTLIER) cc_final: 0.8957 (t0) REVERT: A 213 TYR cc_start: 0.7881 (OUTLIER) cc_final: 0.6990 (t80) REVERT: A 224 TYR cc_start: 0.8000 (m-80) cc_final: 0.6422 (p90) REVERT: A 613 ARG cc_start: 0.8462 (ttt90) cc_final: 0.8259 (ttt90) REVERT: A 854 LYS cc_start: 0.5653 (mmtp) cc_final: 0.4438 (ptpt) REVERT: A 905 MET cc_start: 0.7606 (tmm) cc_final: 0.7279 (tmm) REVERT: A 914 PHE cc_start: 0.8322 (t80) cc_final: 0.7597 (m-80) REVERT: A 1085 ASN cc_start: 0.8813 (t0) cc_final: 0.8565 (t0) REVERT: A 1141 MET cc_start: 0.8701 (tpp) cc_final: 0.8338 (tpt) REVERT: A 1245 ILE cc_start: 0.8664 (tp) cc_final: 0.8427 (tp) REVERT: A 1248 MET cc_start: 0.7515 (tpp) cc_final: 0.6316 (tmm) REVERT: A 1268 ARG cc_start: 0.8376 (ptm-80) cc_final: 0.7985 (ptt90) REVERT: A 1318 MET cc_start: 0.9299 (ttp) cc_final: 0.9002 (ttm) REVERT: A 1368 CYS cc_start: 0.5530 (OUTLIER) cc_final: 0.5072 (t) REVERT: A 1420 ASP cc_start: 0.8437 (t0) cc_final: 0.7899 (t0) outliers start: 24 outliers final: 19 residues processed: 182 average time/residue: 0.0975 time to fit residues: 25.9434 Evaluate side-chains 186 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 164 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 205 ASP Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 268 SER Chi-restraints excluded: chain A residue 278 GLN Chi-restraints excluded: chain A residue 315 HIS Chi-restraints excluded: chain A residue 393 ILE Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 624 TRP Chi-restraints excluded: chain A residue 657 ILE Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 897 LEU Chi-restraints excluded: chain A residue 912 VAL Chi-restraints excluded: chain A residue 1040 SER Chi-restraints excluded: chain A residue 1046 HIS Chi-restraints excluded: chain A residue 1164 PHE Chi-restraints excluded: chain A residue 1224 LEU Chi-restraints excluded: chain A residue 1368 CYS Chi-restraints excluded: chain A residue 1418 TYR Chi-restraints excluded: chain A residue 1436 VAL Chi-restraints excluded: chain A residue 1464 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 25 optimal weight: 7.9990 chunk 74 optimal weight: 0.9980 chunk 107 optimal weight: 0.6980 chunk 94 optimal weight: 4.9990 chunk 48 optimal weight: 3.9990 chunk 26 optimal weight: 3.9990 chunk 73 optimal weight: 0.1980 chunk 5 optimal weight: 0.9990 chunk 1 optimal weight: 7.9990 chunk 79 optimal weight: 0.7980 chunk 21 optimal weight: 0.0070 overall best weight: 0.5398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 278 GLN ** A 683 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.163902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.118387 restraints weight = 32171.782| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 4.76 r_work (final): 0.3442 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3442 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3442 r_free = 0.3442 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3442 r_free = 0.3442 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.3442 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.3096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.138 11243 Z= 0.179 Angle : 1.123 59.199 15276 Z= 0.557 Chirality : 0.079 2.049 1770 Planarity : 0.005 0.060 1820 Dihedral : 15.346 179.408 2152 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.38 % Favored : 90.62 % Rotamer: Outliers : 2.02 % Allowed : 20.67 % Favored : 77.31 % Cbeta Deviations : 0.08 % 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: -1.28 (0.24), residues: 1271 helix: 0.30 (0.19), residues: 813 sheet: -3.22 (1.11), residues: 20 loop : -2.99 (0.29), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 425 TYR 0.016 0.001 TYR A1228 PHE 0.016 0.001 PHE A 850 TRP 0.019 0.001 TRP A 715 HIS 0.004 0.001 HIS A 541 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.18 (11226) covalent geometry : angle 1.11345 / 0.55 (15230) SS BOND : bond 0.00331 / 0.17 ( 5) SS BOND : angle 1.11631 / 0.87 ( 10) hydrogen bonds : bond 0.04664 / 3.41 ( 521) hydrogen bonds : angle 3.91806 / 2.79 ( 1495) link_BETA1-3 : bond 0.01662 / 0.79 ( 3) link_BETA1-3 : angle 4.71959 / 2.85 ( 9) link_BETA1-4 : bond 0.00737 / 0.38 ( 2) link_BETA1-4 : angle 1.24595 / 0.79 ( 6) link_BETA1-6 : bond 0.00622 / 0.33 ( 1) link_BETA1-6 : angle 1.53859 / 0.84 ( 3) link_NAG-ASN : bond 0.00492 / 0.30 ( 6) link_NAG-ASN : angle 3.01587 / 2.30 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2542 Ramachandran restraints generated. 1271 Oldfield, 0 Emsley, 1271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2542 Ramachandran restraints generated. 1271 Oldfield, 0 Emsley, 1271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 164 time to evaluate : 0.448 Fit side-chains revert: symmetry clash REVERT: A 122 MET cc_start: 0.4435 (tmm) cc_final: 0.3926 (tmm) REVERT: A 159 MET cc_start: 0.7004 (ptp) cc_final: 0.6419 (tmm) REVERT: A 205 ASP cc_start: 0.9161 (OUTLIER) cc_final: 0.8901 (t0) REVERT: A 213 TYR cc_start: 0.8012 (OUTLIER) cc_final: 0.7044 (t80) REVERT: A 224 TYR cc_start: 0.7828 (m-80) cc_final: 0.6425 (p90) REVERT: A 613 ARG cc_start: 0.8525 (ttt90) cc_final: 0.8307 (ttt90) REVERT: A 854 LYS cc_start: 0.5486 (mmtp) cc_final: 0.4460 (ptpt) REVERT: A 905 MET cc_start: 0.7695 (tmm) cc_final: 0.7317 (tmm) REVERT: A 914 PHE cc_start: 0.8140 (t80) cc_final: 0.7511 (m-80) REVERT: A 1141 MET cc_start: 0.8622 (tpp) cc_final: 0.8197 (tpt) REVERT: A 1245 ILE cc_start: 0.8688 (tp) cc_final: 0.8445 (tp) REVERT: A 1248 MET cc_start: 0.7575 (tpp) cc_final: 0.6369 (tmm) REVERT: A 1318 MET cc_start: 0.9154 (ttp) cc_final: 0.8795 (ttm) REVERT: A 1368 CYS cc_start: 0.4339 (OUTLIER) cc_final: 0.3875 (t) REVERT: A 1420 ASP cc_start: 0.8367 (t0) cc_final: 0.7754 (t0) outliers start: 23 outliers final: 17 residues processed: 179 average time/residue: 0.0921 time to fit residues: 24.4729 Evaluate side-chains 184 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 164 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 205 ASP Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 268 SER Chi-restraints excluded: chain A residue 315 HIS Chi-restraints excluded: chain A residue 393 ILE Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 624 TRP Chi-restraints excluded: chain A residue 657 ILE Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 897 LEU Chi-restraints excluded: chain A residue 912 VAL Chi-restraints excluded: chain A residue 1040 SER Chi-restraints excluded: chain A residue 1046 HIS Chi-restraints excluded: chain A residue 1164 PHE Chi-restraints excluded: chain A residue 1224 LEU Chi-restraints excluded: chain A residue 1368 CYS Chi-restraints excluded: chain A residue 1418 TYR Chi-restraints excluded: chain A residue 1464 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 4 optimal weight: 0.1980 chunk 65 optimal weight: 0.4980 chunk 26 optimal weight: 1.9990 chunk 53 optimal weight: 0.4980 chunk 66 optimal weight: 3.9990 chunk 72 optimal weight: 0.0050 chunk 32 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 89 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 123 optimal weight: 0.5980 overall best weight: 0.3594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 683 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1452 GLN ** 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 = 0.3950 r_free = 0.3950 target = 0.163885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.118133 restraints weight = 33828.612| |-----------------------------------------------------------------------------| r_work (start): 0.3438 rms_B_bonded: 4.88 r_work (final): 0.3438 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3438 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3438 r_free = 0.3438 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3438 r_free = 0.3438 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3438 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.3087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.138 11243 Z= 0.179 Angle : 1.123 59.199 15276 Z= 0.557 Chirality : 0.079 2.049 1770 Planarity : 0.005 0.060 1820 Dihedral : 15.346 179.408 2152 Min Nonbonded Distance : 1.770 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.38 % Favored : 90.62 % Rotamer: Outliers : 1.76 % Allowed : 20.93 % Favored : 77.31 % Cbeta Deviations : 0.08 % 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: -1.28 (0.24), residues: 1271 helix: 0.30 (0.19), residues: 813 sheet: -3.22 (1.11), residues: 20 loop : -2.99 (0.29), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 425 TYR 0.016 0.001 TYR A1228 PHE 0.016 0.001 PHE A 850 TRP 0.019 0.001 TRP A 715 HIS 0.004 0.001 HIS A 541 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.18 (11226) covalent geometry : angle 1.11345 / 0.55 (15230) SS BOND : bond 0.00347 / 0.18 ( 5) SS BOND : angle 1.17554 / 0.90 ( 10) hydrogen bonds : bond 0.04664 / 3.41 ( 521) hydrogen bonds : angle 3.91806 / 2.79 ( 1495) link_BETA1-3 : bond 0.01662 / 0.79 ( 3) link_BETA1-3 : angle 4.71959 / 2.85 ( 9) link_BETA1-4 : bond 0.00737 / 0.38 ( 2) link_BETA1-4 : angle 1.24595 / 0.79 ( 6) link_BETA1-6 : bond 0.00622 / 0.33 ( 1) link_BETA1-6 : angle 1.53859 / 0.84 ( 3) link_NAG-ASN : bond 0.00492 / 0.30 ( 6) link_NAG-ASN : angle 3.01587 / 2.30 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2650.40 seconds wall clock time: 46 minutes 5.77 seconds (2765.77 seconds total)