Starting phenix.real_space_refine on Sat Jul 4 07:25:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hmb_34892/07_2026/8hmb_34892.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hmb_34892/07_2026/8hmb_34892.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8hmb_34892/07_2026/8hmb_34892.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hmb_34892/07_2026/8hmb_34892.map" model { file = "/net/cci-nas-00/data/ceres_data/8hmb_34892/07_2026/8hmb_34892.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hmb_34892/07_2026/8hmb_34892.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.073 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Ca 2 9.91 5 P 2 5.49 5 S 94 5.16 5 C 12471 2.51 5 N 3119 2.21 5 O 3459 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 44 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 19147 Number of models: 1 Model: "" Number of chains: 5 Chain: "C" Number of atoms: 1293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1293 Classifications: {'peptide': 165} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 8, 'TRANS': 156} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 10151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1253, 10151 Classifications: {'peptide': 1253} Link IDs: {'PTRANS': 40, 'TRANS': 1212} Chain breaks: 8 Chain: "E" Number of atoms: 7344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 914, 7344 Classifications: {'peptide': 914} Link IDs: {'PTRANS': 36, 'TRANS': 877} Chain breaks: 7 Chain: "D" Number of atoms: 247 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 245 Ad-hoc single atom residues: {' CA': 2} Unusual residues: {'3PE': 3, 'A1AC8': 1, 'R16': 8} Classifications: {'undetermined': 12} Link IDs: {None: 11} Chain breaks: 2 Unresolved non-hydrogen bonds: 74 Unresolved non-hydrogen angles: 81 Unresolved non-hydrogen dihedrals: 79 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'3PE:plan-1': 1, '3PE:plan-2': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Time building chain proxies: 3.24, per 1000 atoms: 0.17 Number of scatterers: 19147 At special positions: 0 Unit cell: (169.52, 115.44, 183.04, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 2 19.99 S 94 16.00 P 2 15.00 O 3459 8.00 N 3119 7.00 C 12471 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS D 298 " - pdb=" SG CYS D 326 " distance=2.03 Simple disulfide: pdb=" SG CYS D 316 " - pdb=" SG CYS D 332 " distance=2.03 Simple disulfide: pdb=" SG CYS D1078 " - pdb=" SG CYS D1089 " distance=2.03 Simple disulfide: pdb=" SG CYS D1479 " - pdb=" SG CYS D1495 " distance=2.04 Simple disulfide: pdb=" SG CYS E 303 " - pdb=" SG CYS E1044 " distance=2.03 Simple disulfide: pdb=" SG CYS E 354 " - pdb=" SG CYS E1059 " distance=2.03 Simple disulfide: pdb=" SG CYS E 904 " - pdb=" SG CYS E 974 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG E1101 " - " ASN E 92 " " NAG E1102 " - " ASN E 184 " " NAG E1103 " - " ASN E 324 " " NAG E1104 " - " ASN E 781 " " NAG E1105 " - " ASN E 468 " " NAG E1106 " - " ASN E 613 " " NAG E1107 " - " ASN E 348 " " NAG E1108 " - " ASN E 895 " Time building additional restraints: 2.26 Conformation dependent library (CDL) restraints added in 666.7 milliseconds 4584 Ramachandran restraints generated. 2292 Oldfield, 0 Emsley, 2292 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4432 Finding SS restraints... Secondary structure from input PDB file: 104 helices and 15 sheets defined 56.0% alpha, 8.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.67 Creating SS restraints... Processing helix chain 'C' and resid 240 through 256 removed outlier: 4.169A pdb=" N MET C 246 " --> pdb=" O VAL C 242 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N PHE C 253 " --> pdb=" O ALA C 249 " (cutoff:3.500A) Processing helix chain 'C' and resid 299 through 301 No H-bonds generated for 'chain 'C' and resid 299 through 301' Processing helix chain 'C' and resid 302 through 313 removed outlier: 4.279A pdb=" N ARG C 306 " --> pdb=" O SER C 302 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N ILE C 307 " --> pdb=" O GLU C 303 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N PHE C 308 " --> pdb=" O ILE C 304 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N THR C 313 " --> pdb=" O GLU C 309 " (cutoff:3.500A) Processing helix chain 'C' and resid 327 through 332 removed outlier: 3.861A pdb=" N LYS C 332 " --> pdb=" O ALA C 328 " (cutoff:3.500A) Processing helix chain 'C' and resid 348 through 355 removed outlier: 4.042A pdb=" N ARG C 352 " --> pdb=" O LYS C 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 361 through 363 No H-bonds generated for 'chain 'C' and resid 361 through 363' Processing helix chain 'C' and resid 364 through 377 removed outlier: 4.155A pdb=" N ALA C 371 " --> pdb=" O VAL C 367 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ALA C 372 " --> pdb=" O GLN C 368 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N GLN C 377 " --> pdb=" O ASP C 373 " (cutoff:3.500A) Processing helix chain 'C' and resid 379 through 383 Processing helix chain 'C' and resid 391 through 402 removed outlier: 4.171A pdb=" N GLU C 397 " --> pdb=" O GLU C 393 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ALA C 400 " --> pdb=" O CYS C 396 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ASP C 401 " --> pdb=" O GLU C 397 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N TYR C 402 " --> pdb=" O HIS C 398 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 405 No H-bonds generated for 'chain 'C' and resid 403 through 405' Processing helix chain 'D' and resid 115 through 122 removed outlier: 3.784A pdb=" N GLU D 122 " --> pdb=" O ILE D 118 " (cutoff:3.500A) Processing helix chain 'D' and resid 126 through 143 Processing helix chain 'D' and resid 153 through 180 removed outlier: 3.583A pdb=" N GLU D 160 " --> pdb=" O ASN D 156 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ARG D 161 " --> pdb=" O SER D 157 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLU D 173 " --> pdb=" O ILE D 169 " (cutoff:3.500A) Processing helix chain 'D' and resid 190 through 209 removed outlier: 4.452A pdb=" N GLY D 194 " --> pdb=" O TYR D 190 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N LEU D 198 " --> pdb=" O GLY D 194 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 241 removed outlier: 3.535A pdb=" N PHE D 239 " --> pdb=" O LEU D 236 " (cutoff:3.500A) Processing helix chain 'D' and resid 242 through 251 removed outlier: 3.715A pdb=" N ARG D 246 " --> pdb=" O LEU D 242 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LEU D 247 " --> pdb=" O ARG D 243 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N VAL D 248 " --> pdb=" O PRO D 244 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N SER D 249 " --> pdb=" O LEU D 245 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL D 251 " --> pdb=" O LEU D 247 " (cutoff:3.500A) Processing helix chain 'D' and resid 251 through 266 removed outlier: 4.139A pdb=" N VAL D 257 " --> pdb=" O SER D 253 " (cutoff:3.500A) Processing helix chain 'D' and resid 268 through 290 Processing helix chain 'D' and resid 339 through 343 removed outlier: 3.690A pdb=" N GLY D 342 " --> pdb=" O PRO D 339 " (cutoff:3.500A) Processing helix chain 'D' and resid 349 through 361 removed outlier: 3.517A pdb=" N LEU D 354 " --> pdb=" O ALA D 350 " (cutoff:3.500A) Processing helix chain 'D' and resid 366 through 377 removed outlier: 3.677A pdb=" N VAL D 372 " --> pdb=" O VAL D 368 " (cutoff:3.500A) Processing helix chain 'D' and resid 380 through 393 removed outlier: 3.912A pdb=" N TYR D 384 " --> pdb=" O TRP D 380 " (cutoff:3.500A) Processing helix chain 'D' and resid 394 through 415 removed outlier: 3.688A pdb=" N VAL D 400 " --> pdb=" O VAL D 396 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLU D 413 " --> pdb=" O SER D 409 " (cutoff:3.500A) Processing helix chain 'D' and resid 419 through 446 removed outlier: 3.764A pdb=" N LYS D 435 " --> pdb=" O GLU D 431 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N TRP D 440 " --> pdb=" O GLY D 436 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ASP D 446 " --> pdb=" O THR D 442 " (cutoff:3.500A) Processing helix chain 'D' and resid 513 through 523 removed outlier: 4.307A pdb=" N ALA D 519 " --> pdb=" O ARG D 515 " (cutoff:3.500A) Processing helix chain 'D' and resid 523 through 543 removed outlier: 3.607A pdb=" N VAL D 534 " --> pdb=" O VAL D 530 " (cutoff:3.500A) Processing helix chain 'D' and resid 549 through 578 removed outlier: 3.509A pdb=" N THR D 553 " --> pdb=" O PRO D 549 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLU D 554 " --> pdb=" O ASN D 550 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU D 563 " --> pdb=" O ALA D 559 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LYS D 574 " --> pdb=" O GLU D 570 " (cutoff:3.500A) Processing helix chain 'D' and resid 579 through 584 Processing helix chain 'D' and resid 586 through 609 Processing helix chain 'D' and resid 612 through 626 removed outlier: 4.041A pdb=" N ARG D 620 " --> pdb=" O ILE D 616 " (cutoff:3.500A) Processing helix chain 'D' and resid 627 through 630 Processing helix chain 'D' and resid 635 through 647 Processing helix chain 'D' and resid 647 through 674 removed outlier: 3.542A pdb=" N SER D 653 " --> pdb=" O ARG D 649 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLY D 669 " --> pdb=" O PHE D 665 " (cutoff:3.500A) Processing helix chain 'D' and resid 691 through 705 removed outlier: 3.571A pdb=" N THR D 698 " --> pdb=" O GLN D 694 " (cutoff:3.500A) Processing helix chain 'D' and resid 707 through 719 removed outlier: 3.554A pdb=" N GLY D 715 " --> pdb=" O VAL D 711 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N TYR D 719 " --> pdb=" O GLY D 715 " (cutoff:3.500A) Processing helix chain 'D' and resid 729 through 755 removed outlier: 4.062A pdb=" N PHE D 733 " --> pdb=" O VAL D 729 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N PHE D 737 " --> pdb=" O PHE D 733 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ASN D 741 " --> pdb=" O PHE D 737 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ILE D 743 " --> pdb=" O CYS D 739 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ALA D 752 " --> pdb=" O PHE D 748 " (cutoff:3.500A) Processing helix chain 'D' and resid 760 through 778 removed outlier: 4.239A pdb=" N GLU D 768 " --> pdb=" O SER D 764 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLU D 769 " --> pdb=" O ALA D 765 " (cutoff:3.500A) Processing helix chain 'D' and resid 901 through 906 Processing helix chain 'D' and resid 906 through 919 removed outlier: 4.267A pdb=" N LEU D 912 " --> pdb=" O PHE D 908 " (cutoff:3.500A) Processing helix chain 'D' and resid 927 through 971 removed outlier: 3.697A pdb=" N HIS D 931 " --> pdb=" O SER D 927 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ILE D 932 " --> pdb=" O PHE D 928 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLU D 967 " --> pdb=" O ILE D 943 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ILE D 968 " --> pdb=" O PHE D 964 " (cutoff:3.500A) Processing helix chain 'D' and resid 979 through 981 No H-bonds generated for 'chain 'D' and resid 979 through 981' Processing helix chain 'D' and resid 982 through 987 removed outlier: 4.128A pdb=" N ASN D 987 " --> pdb=" O SER D 983 " (cutoff:3.500A) Processing helix chain 'D' and resid 987 through 1010 removed outlier: 4.009A pdb=" N ILE D 991 " --> pdb=" O ASN D 987 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N PHE D1004 " --> pdb=" O SER D1000 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N SER D1008 " --> pdb=" O PHE D1004 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N SER D1009 " --> pdb=" O GLY D1005 " (cutoff:3.500A) Processing helix chain 'D' and resid 1013 through 1021 removed outlier: 4.119A pdb=" N VAL D1019 " --> pdb=" O LYS D1015 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ARG D1021 " --> pdb=" O LEU D1017 " (cutoff:3.500A) Processing helix chain 'D' and resid 1022 through 1025 Proline residue: D1025 - end of helix No H-bonds generated for 'chain 'D' and resid 1022 through 1025' Processing helix chain 'D' and resid 1026 through 1032 removed outlier: 4.158A pdb=" N ASN D1030 " --> pdb=" O LEU D1026 " (cutoff:3.500A) Processing helix chain 'D' and resid 1032 through 1071 removed outlier: 3.854A pdb=" N HIS D1037 " --> pdb=" O LYS D1033 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N PHE D1043 " --> pdb=" O VAL D1039 " (cutoff:3.500A) removed outlier: 5.115A pdb=" N ASN D1051 " --> pdb=" O ARG D1047 " (cutoff:3.500A) removed outlier: 5.895A pdb=" N ILE D1052 " --> pdb=" O THR D1048 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N VAL D1053 " --> pdb=" O ILE D1049 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N PHE D1061 " --> pdb=" O THR D1057 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N MET D1062 " --> pdb=" O LEU D1058 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N PHE D1063 " --> pdb=" O LEU D1059 " (cutoff:3.500A) Processing helix chain 'D' and resid 1098 through 1100 No H-bonds generated for 'chain 'D' and resid 1098 through 1100' Processing helix chain 'D' and resid 1120 through 1133 removed outlier: 3.574A pdb=" N VAL D1131 " --> pdb=" O ALA D1127 " (cutoff:3.500A) Processing helix chain 'D' and resid 1136 through 1142 Processing helix chain 'D' and resid 1162 through 1173 removed outlier: 3.565A pdb=" N PHE D1166 " --> pdb=" O ILE D1162 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ILE D1170 " --> pdb=" O PHE D1166 " (cutoff:3.500A) Processing helix chain 'D' and resid 1178 through 1194 removed outlier: 3.912A pdb=" N VAL D1182 " --> pdb=" O MET D1178 " (cutoff:3.500A) Processing helix chain 'D' and resid 1195 through 1197 No H-bonds generated for 'chain 'D' and resid 1195 through 1197' Processing helix chain 'D' and resid 1203 through 1212 removed outlier: 3.506A pdb=" N ARG D1207 " --> pdb=" O ASP D1203 " (cutoff:3.500A) Processing helix chain 'D' and resid 1213 through 1215 No H-bonds generated for 'chain 'D' and resid 1213 through 1215' Processing helix chain 'D' and resid 1230 through 1238 Processing helix chain 'D' and resid 1238 through 1258 removed outlier: 3.646A pdb=" N GLU D1242 " --> pdb=" O SER D1238 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU D1244 " --> pdb=" O TYR D1240 " (cutoff:3.500A) Processing helix chain 'D' and resid 1264 through 1293 removed outlier: 3.518A pdb=" N ILE D1269 " --> pdb=" O CYS D1265 " (cutoff:3.500A) Processing helix chain 'D' and resid 1294 through 1299 Processing helix chain 'D' and resid 1301 through 1321 Processing helix chain 'D' and resid 1374 through 1376 No H-bonds generated for 'chain 'D' and resid 1374 through 1376' Processing helix chain 'D' and resid 1377 through 1383 removed outlier: 4.317A pdb=" N VAL D1381 " --> pdb=" O ARG D1377 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N MET D1382 " --> pdb=" O LEU D1378 " (cutoff:3.500A) Processing helix chain 'D' and resid 1383 through 1389 removed outlier: 3.899A pdb=" N LEU D1387 " --> pdb=" O ARG D1383 " (cutoff:3.500A) Processing helix chain 'D' and resid 1391 through 1407 removed outlier: 3.539A pdb=" N ARG D1395 " --> pdb=" O GLY D1391 " (cutoff:3.500A) Processing helix chain 'D' and resid 1410 through 1431 removed outlier: 3.712A pdb=" N ILE D1415 " --> pdb=" O VAL D1411 " (cutoff:3.500A) Processing helix chain 'D' and resid 1449 through 1462 Processing helix chain 'D' and resid 1465 through 1473 removed outlier: 3.517A pdb=" N ILE D1469 " --> pdb=" O ALA D1465 " (cutoff:3.500A) Processing helix chain 'D' and resid 1499 through 1526 removed outlier: 3.721A pdb=" N ILE D1516 " --> pdb=" O ALA D1512 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ASN D1526 " --> pdb=" O VAL D1522 " (cutoff:3.500A) Processing helix chain 'D' and resid 1526 through 1531 removed outlier: 3.605A pdb=" N THR D1531 " --> pdb=" O PHE D1527 " (cutoff:3.500A) Processing helix chain 'D' and resid 1538 through 1552 Processing helix chain 'D' and resid 1585 through 1593 Processing helix chain 'D' and resid 1608 through 1619 removed outlier: 3.637A pdb=" N LEU D1618 " --> pdb=" O VAL D1614 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ARG D1619 " --> pdb=" O ARG D1615 " (cutoff:3.500A) Processing helix chain 'D' and resid 1625 through 1638 Processing helix chain 'E' and resid 29 through 53 removed outlier: 3.748A pdb=" N GLY E 53 " --> pdb=" O LYS E 49 " (cutoff:3.500A) Processing helix chain 'E' and resid 53 through 64 removed outlier: 4.121A pdb=" N ASP E 59 " --> pdb=" O ASN E 55 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N ILE E 60 " --> pdb=" O GLN E 56 " (cutoff:3.500A) Processing helix chain 'E' and resid 76 through 107 removed outlier: 3.667A pdb=" N ASP E 85 " --> pdb=" O ILE E 81 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLU E 87 " --> pdb=" O ALA E 83 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N SER E 94 " --> pdb=" O LEU E 90 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLU E 103 " --> pdb=" O ARG E 99 " (cutoff:3.500A) Processing helix chain 'E' and resid 176 through 186 removed outlier: 3.836A pdb=" N GLU E 182 " --> pdb=" O ILE E 178 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N THR E 186 " --> pdb=" O GLU E 182 " (cutoff:3.500A) Processing helix chain 'E' and resid 189 through 200 removed outlier: 3.760A pdb=" N LYS E 195 " --> pdb=" O GLU E 191 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ARG E 197 " --> pdb=" O PHE E 193 " (cutoff:3.500A) Processing helix chain 'E' and resid 237 through 240 Processing helix chain 'E' and resid 241 through 246 Processing helix chain 'E' and resid 261 through 265 removed outlier: 3.505A pdb=" N VAL E 264 " --> pdb=" O SER E 261 " (cutoff:3.500A) Processing helix chain 'E' and resid 266 through 278 removed outlier: 3.712A pdb=" N LYS E 270 " --> pdb=" O GLY E 266 " (cutoff:3.500A) Processing helix chain 'E' and resid 279 through 283 removed outlier: 3.775A pdb=" N LEU E 283 " --> pdb=" O LEU E 280 " (cutoff:3.500A) Processing helix chain 'E' and resid 311 through 323 removed outlier: 3.932A pdb=" N LYS E 316 " --> pdb=" O VAL E 312 " (cutoff:3.500A) Processing helix chain 'E' and resid 332 through 344 removed outlier: 3.812A pdb=" N PHE E 339 " --> pdb=" O LYS E 335 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ALA E 340 " --> pdb=" O GLY E 336 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N GLU E 342 " --> pdb=" O SER E 338 " (cutoff:3.500A) Processing helix chain 'E' and resid 371 through 376 Processing helix chain 'E' and resid 396 through 406 Processing helix chain 'E' and resid 419 through 424 removed outlier: 3.973A pdb=" N GLN E 424 " --> pdb=" O ARG E 420 " (cutoff:3.500A) Processing helix chain 'E' and resid 426 through 431 Processing helix chain 'E' and resid 431 through 436 removed outlier: 3.511A pdb=" N LEU E 436 " --> pdb=" O ARG E 432 " (cutoff:3.500A) Processing helix chain 'E' and resid 494 through 498 Processing helix chain 'E' and resid 560 through 565 removed outlier: 3.671A pdb=" N GLU E 565 " --> pdb=" O PHE E 561 " (cutoff:3.500A) Processing helix chain 'E' and resid 570 through 580 removed outlier: 3.729A pdb=" N ASP E 580 " --> pdb=" O ASN E 576 " (cutoff:3.500A) Processing helix chain 'E' and resid 639 through 648 removed outlier: 3.568A pdb=" N GLU E 646 " --> pdb=" O ALA E 642 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N LEU E 648 " --> pdb=" O TYR E 644 " (cutoff:3.500A) Processing helix chain 'E' and resid 649 through 651 No H-bonds generated for 'chain 'E' and resid 649 through 651' Processing helix chain 'E' and resid 652 through 657 Processing helix chain 'E' and resid 675 through 690 removed outlier: 3.659A pdb=" N PHE E 679 " --> pdb=" O ASN E 675 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ASN E 684 " --> pdb=" O LEU E 680 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N GLU E 685 " --> pdb=" O LEU E 681 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N PHE E 686 " --> pdb=" O ASN E 682 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LYS E 690 " --> pdb=" O PHE E 686 " (cutoff:3.500A) Processing helix chain 'E' and resid 699 through 723 removed outlier: 3.715A pdb=" N LEU E 706 " --> pdb=" O ILE E 702 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU E 707 " --> pdb=" O ASN E 703 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU E 715 " --> pdb=" O PHE E 711 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N TRP E 720 " --> pdb=" O VAL E 716 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N SER E 721 " --> pdb=" O GLN E 717 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N LYS E 722 " --> pdb=" O ASN E 718 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLN E 723 " --> pdb=" O TYR E 719 " (cutoff:3.500A) Processing helix chain 'E' and resid 747 through 752 Processing helix chain 'E' and resid 757 through 760 Processing helix chain 'E' and resid 761 through 770 removed outlier: 3.578A pdb=" N ASN E 770 " --> pdb=" O ARG E 766 " (cutoff:3.500A) Processing helix chain 'E' and resid 817 through 827 removed outlier: 3.517A pdb=" N GLU E 823 " --> pdb=" O ASN E 819 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ASN E 824 " --> pdb=" O SER E 820 " (cutoff:3.500A) Processing helix chain 'E' and resid 879 through 888 removed outlier: 3.531A pdb=" N MET E 883 " --> pdb=" O ASP E 879 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N HIS E 885 " --> pdb=" O SER E 881 " (cutoff:3.500A) Processing helix chain 'E' and resid 1042 through 1047 removed outlier: 3.715A pdb=" N VAL E1047 " --> pdb=" O PRO E1043 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 263 through 266 removed outlier: 6.240A pdb=" N SER C 263 " --> pdb=" O VAL C 318 " (cutoff:3.500A) removed outlier: 7.699A pdb=" N ASP C 320 " --> pdb=" O SER C 263 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N THR C 265 " --> pdb=" O ASP C 320 " (cutoff:3.500A) removed outlier: 5.488A pdb=" N VAL C 230 " --> pdb=" O LEU C 319 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N VAL C 340 " --> pdb=" O PRO C 229 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N VAL C 231 " --> pdb=" O VAL C 340 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'D' and resid 297 through 300 Processing sheet with id=AA3, first strand: chain 'D' and resid 1077 through 1078 Processing sheet with id=AA4, first strand: chain 'D' and resid 1092 through 1096 Processing sheet with id=AA5, first strand: chain 'E' and resid 70 through 72 Processing sheet with id=AA6, first strand: chain 'E' and resid 125 through 126 removed outlier: 6.494A pdb=" N TYR E 125 " --> pdb=" O VAL E 166 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 150 through 152 removed outlier: 3.704A pdb=" N ARG E 157 " --> pdb=" O ASP E 152 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 206 through 210 removed outlier: 3.540A pdb=" N VAL E 487 " --> pdb=" O GLY E 209 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N GLY E 486 " --> pdb=" O VAL E 466 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 206 through 210 removed outlier: 3.540A pdb=" N VAL E 487 " --> pdb=" O GLY E 209 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N GLY E 486 " --> pdb=" O VAL E 466 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 298 through 300 removed outlier: 6.294A pdb=" N ILE E 256 " --> pdb=" O ALA E 292 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N PHE E 294 " --> pdb=" O ILE E 256 " (cutoff:3.500A) removed outlier: 7.367A pdb=" N VAL E 258 " --> pdb=" O PHE E 294 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N LEU E 257 " --> pdb=" O PHE E 361 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N LEU E 360 " --> pdb=" O PHE E 387 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N VAL E 389 " --> pdb=" O LEU E 360 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N THR E 362 " --> pdb=" O VAL E 389 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N THR E 386 " --> pdb=" O TYR E 411 " (cutoff:3.500A) removed outlier: 7.703A pdb=" N ILE E 413 " --> pdb=" O THR E 386 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N SER E 388 " --> pdb=" O ILE E 413 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 521 through 522 removed outlier: 3.645A pdb=" N ILE E 515 " --> pdb=" O SER E 618 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N TRP E 609 " --> pdb=" O GLY E 584 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 741 through 743 removed outlier: 3.987A pdb=" N MET E 793 " --> pdb=" O THR E 776 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N THR E 776 " --> pdb=" O MET E 793 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 800 through 801 Processing sheet with id=AB5, first strand: chain 'E' and resid 858 through 862 removed outlier: 6.336A pdb=" N LEU E 859 " --> pdb=" O ASP E 854 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N ASP E 854 " --> pdb=" O LEU E 859 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N MET E 861 " --> pdb=" O ILE E 852 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N PHE E1003 " --> pdb=" O GLY E 992 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 893 through 903 removed outlier: 5.173A pdb=" N PHE E 894 " --> pdb=" O PHE E 982 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N PHE E 982 " --> pdb=" O PHE E 894 " (cutoff:3.500A) removed outlier: 5.794A pdb=" N LYS E 896 " --> pdb=" O GLN E 980 " (cutoff:3.500A) removed outlier: 7.836A pdb=" N GLN E 980 " --> pdb=" O LYS E 896 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N TYR E 898 " --> pdb=" O GLN E 978 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N GLN E 978 " --> pdb=" O TYR E 898 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N TYR E 900 " --> pdb=" O THR E 976 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N THR E 976 " --> pdb=" O TYR E 900 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N SER E 902 " --> pdb=" O CYS E 974 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N GLN E1036 " --> pdb=" O GLU E 977 " (cutoff:3.500A) 868 hydrogen bonds defined for protein. 2514 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.57 Time building geometry restraints manager: 2.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 3081 1.30 - 1.43: 5137 1.43 - 1.56: 11178 1.56 - 1.69: 7 1.69 - 1.81: 142 Bond restraints: 19545 Sorted by residual: bond pdb=" CA VAL E 612 " pdb=" C VAL E 612 " ideal model delta sigma weight residual 1.525 1.445 0.080 1.10e-02 8.26e+03 5.23e+01 bond pdb=" C14 A1AC8 D2311 " pdb=" N07 A1AC8 D2311 " ideal model delta sigma weight residual 1.450 1.310 0.140 2.00e-02 2.50e+03 4.91e+01 bond pdb=" C21 3PE D2312 " pdb=" O21 3PE D2312 " ideal model delta sigma weight residual 1.316 1.455 -0.139 2.00e-02 2.50e+03 4.83e+01 bond pdb=" C15 A1AC8 D2311 " pdb=" N07 A1AC8 D2311 " ideal model delta sigma weight residual 1.455 1.318 0.137 2.00e-02 2.50e+03 4.67e+01 bond pdb=" C12 A1AC8 D2311 " pdb=" N07 A1AC8 D2311 " ideal model delta sigma weight residual 1.446 1.313 0.133 2.00e-02 2.50e+03 4.40e+01 ... (remaining 19540 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.67: 26318 4.67 - 9.34: 91 9.34 - 14.00: 6 14.00 - 18.67: 0 18.67 - 23.34: 1 Bond angle restraints: 26416 Sorted by residual: angle pdb=" O12 3PE D2303 " pdb=" P 3PE D2303 " pdb=" O14 3PE D2303 " ideal model delta sigma weight residual 123.79 100.45 23.34 3.00e+00 1.11e-01 6.05e+01 angle pdb=" N ASN D1051 " pdb=" CA ASN D1051 " pdb=" C ASN D1051 " ideal model delta sigma weight residual 111.33 118.46 -7.13 1.21e+00 6.83e-01 3.47e+01 angle pdb=" N VAL E 612 " pdb=" CA VAL E 612 " pdb=" C VAL E 612 " ideal model delta sigma weight residual 106.88 98.56 8.32 1.52e+00 4.33e-01 3.00e+01 angle pdb=" CA PRO E 611 " pdb=" C PRO E 611 " pdb=" O PRO E 611 " ideal model delta sigma weight residual 122.08 116.29 5.79 1.28e+00 6.10e-01 2.04e+01 angle pdb=" CA PRO E 611 " pdb=" C PRO E 611 " pdb=" N VAL E 612 " ideal model delta sigma weight residual 114.82 120.89 -6.07 1.35e+00 5.49e-01 2.02e+01 ... (remaining 26411 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.25: 10652 19.25 - 38.50: 1005 38.50 - 57.75: 136 57.75 - 77.00: 29 77.00 - 96.24: 23 Dihedral angle restraints: 11845 sinusoidal: 5007 harmonic: 6838 Sorted by residual: dihedral pdb=" CB CYS E 354 " pdb=" SG CYS E 354 " pdb=" SG CYS E1059 " pdb=" CB CYS E1059 " ideal model delta sinusoidal sigma weight residual -86.00 -174.06 88.06 1 1.00e+01 1.00e-02 9.27e+01 dihedral pdb=" CB CYS D 298 " pdb=" SG CYS D 298 " pdb=" SG CYS D 326 " pdb=" CB CYS D 326 " ideal model delta sinusoidal sigma weight residual 93.00 167.03 -74.03 1 1.00e+01 1.00e-02 6.96e+01 dihedral pdb=" CB CYS E 303 " pdb=" SG CYS E 303 " pdb=" SG CYS E1044 " pdb=" CB CYS E1044 " ideal model delta sinusoidal sigma weight residual 93.00 164.02 -71.02 1 1.00e+01 1.00e-02 6.48e+01 ... (remaining 11842 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.139: 2970 0.139 - 0.279: 25 0.279 - 0.418: 2 0.418 - 0.557: 0 0.557 - 0.696: 1 Chirality restraints: 2998 Sorted by residual: chirality pdb=" C1 NAG E1105 " pdb=" ND2 ASN E 468 " pdb=" C2 NAG E1105 " pdb=" O5 NAG E1105 " both_signs ideal model delta sigma weight residual False -2.40 -1.70 -0.70 2.00e-01 2.50e+01 1.21e+01 chirality pdb=" C1 NAG E1102 " pdb=" ND2 ASN E 184 " pdb=" C2 NAG E1102 " pdb=" O5 NAG E1102 " both_signs ideal model delta sigma weight residual False -2.40 -2.01 -0.39 2.00e-01 2.50e+01 3.87e+00 chirality pdb=" CA ASN D1051 " pdb=" N ASN D1051 " pdb=" C ASN D1051 " pdb=" CB ASN D1051 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.88e+00 ... (remaining 2995 not shown) Planarity restraints: 3315 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG E1108 " -0.044 2.00e-02 2.50e+03 3.65e-02 1.66e+01 pdb=" C7 NAG E1108 " 0.012 2.00e-02 2.50e+03 pdb=" C8 NAG E1108 " -0.034 2.00e-02 2.50e+03 pdb=" N2 NAG E1108 " 0.058 2.00e-02 2.50e+03 pdb=" O7 NAG E1108 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG E1107 " -0.044 2.00e-02 2.50e+03 3.64e-02 1.65e+01 pdb=" C7 NAG E1107 " 0.012 2.00e-02 2.50e+03 pdb=" C8 NAG E1107 " -0.034 2.00e-02 2.50e+03 pdb=" N2 NAG E1107 " 0.058 2.00e-02 2.50e+03 pdb=" O7 NAG E1107 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE D1181 " 0.031 2.00e-02 2.50e+03 2.54e-02 1.13e+01 pdb=" CG PHE D1181 " -0.054 2.00e-02 2.50e+03 pdb=" CD1 PHE D1181 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 PHE D1181 " 0.011 2.00e-02 2.50e+03 pdb=" CE1 PHE D1181 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE D1181 " -0.009 2.00e-02 2.50e+03 pdb=" CZ PHE D1181 " 0.020 2.00e-02 2.50e+03 ... (remaining 3312 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 2428 2.74 - 3.28: 20195 3.28 - 3.82: 30315 3.82 - 4.36: 37173 4.36 - 4.90: 62756 Nonbonded interactions: 152867 Sorted by model distance: nonbonded pdb=" O LEU C 310 " pdb=" OG1 THR C 313 " model vdw 2.200 3.040 nonbonded pdb=" O PHE D 628 " pdb=" O ILE D 630 " model vdw 2.202 3.040 nonbonded pdb=" O ASP E 854 " pdb=" OH TYR E 892 " model vdw 2.207 3.040 nonbonded pdb=" O ALA C 274 " pdb=" NZ LYS C 332 " model vdw 2.209 3.120 nonbonded pdb=" OD2 ASP D1437 " pdb=" NH1 ARG D1443 " model vdw 2.210 3.120 ... (remaining 152862 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.110 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: 0.060 Set scattering table: 0.060 Process input model: 15.350 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:0.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 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 : 0.008 0.140 19560 Z= 0.376 Angle : 0.865 23.341 26454 Z= 0.447 Chirality : 0.052 0.696 2998 Planarity : 0.005 0.059 3307 Dihedral : 15.147 96.244 7392 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 13.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.07 % Favored : 91.93 % Rotamer: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % 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: -2.30 (0.17), residues: 2292 helix: -0.99 (0.15), residues: 1130 sheet: -1.96 (0.36), residues: 189 loop : -1.97 (0.20), residues: 973 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG D1217 TYR 0.023 0.002 TYR D 633 PHE 0.054 0.002 PHE D1181 TRP 0.028 0.002 TRP D 634 HIS 0.005 0.001 HIS E 885 Details of bonding type rmsd/Z covalent geometry : bond 0.00825 / 0.38 (19545) covalent geometry : angle 0.85683 / 0.45 (26416) SS BOND : bond 0.00267 / 0.14 ( 7) SS BOND : angle 2.53583 / 1.56 ( 14) hydrogen bonds : bond 0.19661 / 12.84 ( 858) hydrogen bonds : angle 7.63514 / 5.47 ( 2514) link_NAG-ASN : bond 0.00767 / 0.33 ( 8) link_NAG-ASN : angle 3.61065 / 2.88 ( 24) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4584 Ramachandran restraints generated. 2292 Oldfield, 0 Emsley, 2292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4584 Ramachandran restraints generated. 2292 Oldfield, 0 Emsley, 2292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 2070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 296 time to evaluate : 0.718 Fit side-chains revert: symmetry clash REVERT: C 308 PHE cc_start: 0.6399 (m-80) cc_final: 0.6006 (m-80) REVERT: C 339 ILE cc_start: 0.6068 (mm) cc_final: 0.5829 (mm) REVERT: D 439 ASP cc_start: 0.7671 (m-30) cc_final: 0.7328 (m-30) REVERT: D 1227 GLN cc_start: 0.7272 (tp40) cc_final: 0.6974 (pp30) REVERT: E 234 ASP cc_start: 0.7724 (t0) cc_final: 0.7492 (t0) REVERT: E 295 ASN cc_start: 0.8553 (p0) cc_final: 0.8305 (p0) REVERT: E 668 ASN cc_start: 0.8166 (p0) cc_final: 0.7061 (p0) REVERT: E 864 HIS cc_start: 0.6900 (t-90) cc_final: 0.5953 (m90) REVERT: E 1017 MET cc_start: 0.5983 (pmm) cc_final: 0.5635 (pmm) outliers start: 0 outliers final: 0 residues processed: 296 average time/residue: 0.1206 time to fit residues: 55.8737 Evaluate side-chains 242 residues out of total 2070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 242 time to evaluate : 0.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 216 optimal weight: 0.0670 chunk 98 optimal weight: 0.0770 chunk 194 optimal weight: 0.5980 chunk 227 optimal weight: 0.9980 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 0.5980 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 0.9980 chunk 200 optimal weight: 2.9990 overall best weight: 0.4676 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.160848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.116621 restraints weight = 28608.804| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 2.66 r_work: 0.3224 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.3082 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.1375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 19560 Z= 0.133 Angle : 0.637 9.728 26454 Z= 0.324 Chirality : 0.043 0.225 2998 Planarity : 0.004 0.044 3307 Dihedral : 9.407 87.095 2906 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 0.63 % Allowed : 8.67 % Favored : 90.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.54 (0.18), residues: 2292 helix: -0.23 (0.15), residues: 1205 sheet: -1.44 (0.36), residues: 200 loop : -1.96 (0.21), residues: 887 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 257 TYR 0.015 0.001 TYR D 742 PHE 0.018 0.001 PHE E1003 TRP 0.016 0.001 TRP D 336 HIS 0.004 0.001 HIS C 398 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 (19545) covalent geometry : angle 0.63380 / 0.32 (26416) SS BOND : bond 0.00170 / 0.10 ( 7) SS BOND : angle 1.12042 / 0.72 ( 14) hydrogen bonds : bond 0.04469 / 3.11 ( 858) hydrogen bonds : angle 4.93960 / 3.51 ( 2514) link_NAG-ASN : bond 0.00532 / 0.27 ( 8) link_NAG-ASN : angle 2.21517 / 1.67 ( 24) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4584 Ramachandran restraints generated. 2292 Oldfield, 0 Emsley, 2292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4584 Ramachandran restraints generated. 2292 Oldfield, 0 Emsley, 2292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 2070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 312 time to evaluate : 0.555 Fit side-chains revert: symmetry clash REVERT: C 308 PHE cc_start: 0.6435 (m-80) cc_final: 0.6133 (m-80) REVERT: D 234 LYS cc_start: 0.8577 (mptt) cc_final: 0.8013 (tppt) REVERT: D 265 MET cc_start: 0.7397 (tmm) cc_final: 0.7156 (tmm) REVERT: D 330 THR cc_start: 0.7693 (p) cc_final: 0.7452 (p) REVERT: D 439 ASP cc_start: 0.7824 (m-30) cc_final: 0.7449 (m-30) REVERT: D 1098 ASP cc_start: 0.8153 (m-30) cc_final: 0.7733 (t0) REVERT: D 1161 GLU cc_start: 0.7915 (mp0) cc_final: 0.7644 (pm20) REVERT: D 1222 TYR cc_start: 0.6583 (t80) cc_final: 0.6358 (t80) REVERT: D 1258 MET cc_start: 0.8450 (mpp) cc_final: 0.7946 (mpp) REVERT: D 1293 PHE cc_start: 0.7454 (p90) cc_final: 0.6970 (p90) REVERT: E 234 ASP cc_start: 0.8110 (t0) cc_final: 0.7813 (t0) REVERT: E 469 ILE cc_start: 0.8648 (OUTLIER) cc_final: 0.8393 (pp) REVERT: E 516 ASP cc_start: 0.8750 (m-30) cc_final: 0.8515 (m-30) REVERT: E 536 ILE cc_start: 0.8798 (OUTLIER) cc_final: 0.8161 (pt) REVERT: E 716 VAL cc_start: 0.8060 (OUTLIER) cc_final: 0.7820 (p) REVERT: E 864 HIS cc_start: 0.7048 (t-90) cc_final: 0.5945 (m90) REVERT: E 1017 MET cc_start: 0.6283 (pmm) cc_final: 0.5899 (pmm) outliers start: 13 outliers final: 7 residues processed: 318 average time/residue: 0.1174 time to fit residues: 58.6230 Evaluate side-chains 269 residues out of total 2070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 259 time to evaluate : 0.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 637 LEU Chi-restraints excluded: chain D residue 910 ILE Chi-restraints excluded: chain D residue 917 LEU Chi-restraints excluded: chain D residue 970 LEU Chi-restraints excluded: chain D residue 1046 ILE Chi-restraints excluded: chain D residue 1248 LEU Chi-restraints excluded: chain E residue 469 ILE Chi-restraints excluded: chain E residue 536 ILE Chi-restraints excluded: chain E residue 716 VAL Chi-restraints excluded: chain E residue 1002 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 18 optimal weight: 5.9990 chunk 119 optimal weight: 0.9990 chunk 218 optimal weight: 3.9990 chunk 210 optimal weight: 2.9990 chunk 42 optimal weight: 0.7980 chunk 205 optimal weight: 6.9990 chunk 61 optimal weight: 2.9990 chunk 215 optimal weight: 1.9990 chunk 123 optimal weight: 0.0270 chunk 66 optimal weight: 1.9990 chunk 207 optimal weight: 1.9990 overall best weight: 1.1644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.159815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.116106 restraints weight = 28897.517| |-----------------------------------------------------------------------------| r_work (start): 0.3451 rms_B_bonded: 2.82 r_work: 0.3199 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.3058 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.1677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 19560 Z= 0.156 Angle : 0.604 9.806 26454 Z= 0.309 Chirality : 0.043 0.186 2998 Planarity : 0.004 0.046 3307 Dihedral : 9.036 86.476 2906 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 1.79 % Allowed : 12.64 % Favored : 85.57 % 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: -1.25 (0.18), residues: 2292 helix: -0.04 (0.15), residues: 1203 sheet: -1.19 (0.38), residues: 184 loop : -1.77 (0.21), residues: 905 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D1571 TYR 0.014 0.001 TYR E 512 PHE 0.013 0.001 PHE E 513 TRP 0.015 0.001 TRP E 185 HIS 0.005 0.001 HIS D1148 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.16 (19545) covalent geometry : angle 0.60081 / 0.31 (26416) SS BOND : bond 0.00192 / 0.10 ( 7) SS BOND : angle 1.07826 / 0.70 ( 14) hydrogen bonds : bond 0.03961 / 2.76 ( 858) hydrogen bonds : angle 4.61677 / 3.27 ( 2514) link_NAG-ASN : bond 0.00295 / 0.15 ( 8) link_NAG-ASN : angle 1.99872 / 1.51 ( 24) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4584 Ramachandran restraints generated. 2292 Oldfield, 0 Emsley, 2292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4584 Ramachandran restraints generated. 2292 Oldfield, 0 Emsley, 2292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 2070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 284 time to evaluate : 0.643 Fit side-chains revert: symmetry clash REVERT: C 233 VAL cc_start: 0.7651 (m) cc_final: 0.7371 (p) REVERT: C 257 ARG cc_start: 0.8654 (ptp-110) cc_final: 0.7799 (ptp90) REVERT: C 374 LYS cc_start: 0.7537 (tmtt) cc_final: 0.7144 (ptmt) REVERT: D 234 LYS cc_start: 0.8484 (mptt) cc_final: 0.7993 (mmmm) REVERT: D 265 MET cc_start: 0.7457 (tmm) cc_final: 0.7186 (tmm) REVERT: D 330 THR cc_start: 0.7833 (p) cc_final: 0.7613 (p) REVERT: D 348 ASN cc_start: 0.8737 (t0) cc_final: 0.8437 (m110) REVERT: D 1178 MET cc_start: 0.8695 (tpp) cc_final: 0.8480 (tpp) REVERT: D 1222 TYR cc_start: 0.6757 (t80) cc_final: 0.6460 (t80) REVERT: D 1227 GLN cc_start: 0.6983 (tp40) cc_final: 0.6689 (tm-30) REVERT: D 1258 MET cc_start: 0.8423 (mpp) cc_final: 0.7835 (mpp) REVERT: D 1285 GLU cc_start: 0.7660 (tt0) cc_final: 0.7416 (tt0) REVERT: D 1293 PHE cc_start: 0.7388 (p90) cc_final: 0.6822 (p90) REVERT: E 234 ASP cc_start: 0.8189 (t0) cc_final: 0.7917 (t0) REVERT: E 469 ILE cc_start: 0.8641 (OUTLIER) cc_final: 0.8336 (pp) REVERT: E 686 PHE cc_start: 0.7647 (m-80) cc_final: 0.7446 (t80) REVERT: E 708 ASP cc_start: 0.8657 (OUTLIER) cc_final: 0.8379 (t0) REVERT: E 716 VAL cc_start: 0.7977 (OUTLIER) cc_final: 0.7764 (p) REVERT: E 719 TYR cc_start: 0.7725 (m-80) cc_final: 0.7515 (m-10) REVERT: E 744 TYR cc_start: 0.7224 (t80) cc_final: 0.7002 (t80) REVERT: E 864 HIS cc_start: 0.6974 (t-90) cc_final: 0.5841 (m90) REVERT: E 1017 MET cc_start: 0.6568 (pmm) cc_final: 0.6241 (pmm) REVERT: E 1045 ASP cc_start: 0.8971 (t0) cc_final: 0.8523 (t0) outliers start: 37 outliers final: 20 residues processed: 301 average time/residue: 0.1115 time to fit residues: 53.3930 Evaluate side-chains 284 residues out of total 2070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 261 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 265 THR Chi-restraints excluded: chain C residue 320 ASP Chi-restraints excluded: chain D residue 353 MET Chi-restraints excluded: chain D residue 360 ILE Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 683 GLN Chi-restraints excluded: chain D residue 910 ILE Chi-restraints excluded: chain D residue 917 LEU Chi-restraints excluded: chain D residue 935 TYR Chi-restraints excluded: chain D residue 970 LEU Chi-restraints excluded: chain D residue 1042 VAL Chi-restraints excluded: chain D residue 1046 ILE Chi-restraints excluded: chain D residue 1248 LEU Chi-restraints excluded: chain E residue 469 ILE Chi-restraints excluded: chain E residue 661 ILE Chi-restraints excluded: chain E residue 708 ASP Chi-restraints excluded: chain E residue 716 VAL Chi-restraints excluded: chain E residue 768 LEU Chi-restraints excluded: chain E residue 903 VAL Chi-restraints excluded: chain E residue 1002 ILE Chi-restraints excluded: chain E residue 1046 MET Chi-restraints excluded: chain E residue 1058 VAL Chi-restraints excluded: chain E residue 1065 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 213 optimal weight: 9.9990 chunk 227 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 30 optimal weight: 0.8980 chunk 15 optimal weight: 10.0000 chunk 106 optimal weight: 0.9980 chunk 180 optimal weight: 0.0570 chunk 219 optimal weight: 3.9990 chunk 201 optimal weight: 3.9990 chunk 57 optimal weight: 4.9990 chunk 135 optimal weight: 6.9990 overall best weight: 1.3902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.159332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.115496 restraints weight = 28945.715| |-----------------------------------------------------------------------------| r_work (start): 0.3443 rms_B_bonded: 2.82 r_work: 0.3188 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.1903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 19560 Z= 0.165 Angle : 0.602 9.792 26454 Z= 0.305 Chirality : 0.043 0.195 2998 Planarity : 0.004 0.049 3307 Dihedral : 8.819 86.318 2906 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 2.57 % Allowed : 14.67 % Favored : 82.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.09 (0.18), residues: 2292 helix: 0.11 (0.15), residues: 1195 sheet: -1.21 (0.36), residues: 189 loop : -1.67 (0.21), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D1571 TYR 0.014 0.001 TYR E 512 PHE 0.023 0.001 PHE E1003 TRP 0.015 0.001 TRP E 185 HIS 0.006 0.001 HIS D1148 Details of bonding type rmsd/Z covalent geometry : bond 0.00392 / 0.17 (19545) covalent geometry : angle 0.59956 / 0.30 (26416) SS BOND : bond 0.00195 / 0.10 ( 7) SS BOND : angle 1.02238 / 0.66 ( 14) hydrogen bonds : bond 0.03719 / 2.61 ( 858) hydrogen bonds : angle 4.48170 / 3.17 ( 2514) link_NAG-ASN : bond 0.00337 / 0.17 ( 8) link_NAG-ASN : angle 1.87001 / 1.36 ( 24) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4584 Ramachandran restraints generated. 2292 Oldfield, 0 Emsley, 2292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4584 Ramachandran restraints generated. 2292 Oldfield, 0 Emsley, 2292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 2070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 282 time to evaluate : 0.687 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 234 LYS cc_start: 0.8472 (mptt) cc_final: 0.7982 (mmmm) REVERT: D 265 MET cc_start: 0.7502 (tmm) cc_final: 0.7204 (tmm) REVERT: D 288 GLU cc_start: 0.8431 (mm-30) cc_final: 0.8205 (mm-30) REVERT: D 330 THR cc_start: 0.7836 (p) cc_final: 0.7588 (p) REVERT: D 348 ASN cc_start: 0.8496 (t0) cc_final: 0.8263 (m110) REVERT: D 1162 ILE cc_start: 0.8977 (tp) cc_final: 0.8764 (tp) REVERT: D 1222 TYR cc_start: 0.7016 (t80) cc_final: 0.6703 (t80) REVERT: D 1227 GLN cc_start: 0.6996 (tp40) cc_final: 0.6709 (tm-30) REVERT: D 1258 MET cc_start: 0.8202 (OUTLIER) cc_final: 0.7643 (mpp) REVERT: D 1293 PHE cc_start: 0.7407 (p90) cc_final: 0.6812 (p90) REVERT: E 234 ASP cc_start: 0.8048 (t0) cc_final: 0.7848 (t0) REVERT: E 344 LEU cc_start: 0.9135 (OUTLIER) cc_final: 0.8711 (mt) REVERT: E 469 ILE cc_start: 0.8645 (OUTLIER) cc_final: 0.8354 (pp) REVERT: E 536 ILE cc_start: 0.8817 (OUTLIER) cc_final: 0.8142 (pt) REVERT: E 631 ILE cc_start: 0.8742 (mt) cc_final: 0.8426 (tp) REVERT: E 686 PHE cc_start: 0.7929 (m-80) cc_final: 0.7712 (t80) REVERT: E 708 ASP cc_start: 0.8611 (t0) cc_final: 0.8316 (t0) REVERT: E 716 VAL cc_start: 0.7912 (OUTLIER) cc_final: 0.7689 (p) REVERT: E 719 TYR cc_start: 0.7625 (m-80) cc_final: 0.7294 (m-10) REVERT: E 744 TYR cc_start: 0.7155 (t80) cc_final: 0.6894 (t80) REVERT: E 864 HIS cc_start: 0.7068 (t-90) cc_final: 0.5959 (m90) REVERT: E 1045 ASP cc_start: 0.8863 (t0) cc_final: 0.8375 (t0) outliers start: 53 outliers final: 26 residues processed: 314 average time/residue: 0.1075 time to fit residues: 54.4210 Evaluate side-chains 292 residues out of total 2070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 261 time to evaluate : 0.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 256 HIS Chi-restraints excluded: chain C residue 265 THR Chi-restraints excluded: chain C residue 320 ASP Chi-restraints excluded: chain D residue 121 VAL Chi-restraints excluded: chain D residue 129 ILE Chi-restraints excluded: chain D residue 353 MET Chi-restraints excluded: chain D residue 360 ILE Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 624 LEU Chi-restraints excluded: chain D residue 910 ILE Chi-restraints excluded: chain D residue 917 LEU Chi-restraints excluded: chain D residue 935 TYR Chi-restraints excluded: chain D residue 970 LEU Chi-restraints excluded: chain D residue 1042 VAL Chi-restraints excluded: chain D residue 1046 ILE Chi-restraints excluded: chain D residue 1248 LEU Chi-restraints excluded: chain D residue 1258 MET Chi-restraints excluded: chain D residue 1652 VAL Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 150 ILE Chi-restraints excluded: chain E residue 344 LEU Chi-restraints excluded: chain E residue 469 ILE Chi-restraints excluded: chain E residue 536 ILE Chi-restraints excluded: chain E residue 661 ILE Chi-restraints excluded: chain E residue 716 VAL Chi-restraints excluded: chain E residue 768 LEU Chi-restraints excluded: chain E residue 903 VAL Chi-restraints excluded: chain E residue 1002 ILE Chi-restraints excluded: chain E residue 1046 MET Chi-restraints excluded: chain E residue 1058 VAL Chi-restraints excluded: chain E residue 1065 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 75 optimal weight: 0.7980 chunk 34 optimal weight: 6.9990 chunk 88 optimal weight: 1.9990 chunk 174 optimal weight: 2.9990 chunk 229 optimal weight: 0.7980 chunk 26 optimal weight: 2.9990 chunk 152 optimal weight: 0.9990 chunk 103 optimal weight: 0.0060 chunk 109 optimal weight: 1.9990 chunk 79 optimal weight: 9.9990 chunk 194 optimal weight: 3.9990 overall best weight: 0.9200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.160781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.117125 restraints weight = 28799.647| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 2.83 r_work: 0.3218 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3078 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.2161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 19560 Z= 0.131 Angle : 0.576 9.731 26454 Z= 0.290 Chirality : 0.042 0.185 2998 Planarity : 0.004 0.049 3307 Dihedral : 8.503 82.989 2906 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 2.47 % Allowed : 16.27 % Favored : 81.26 % 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: -0.94 (0.18), residues: 2292 helix: 0.24 (0.15), residues: 1197 sheet: -1.35 (0.37), residues: 176 loop : -1.57 (0.21), residues: 919 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D1571 TYR 0.013 0.001 TYR E 512 PHE 0.012 0.001 PHE E 513 TRP 0.016 0.001 TRP E 821 HIS 0.006 0.001 HIS D1148 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.13 (19545) covalent geometry : angle 0.57345 / 0.29 (26416) SS BOND : bond 0.00176 / 0.09 ( 7) SS BOND : angle 0.92094 / 0.61 ( 14) hydrogen bonds : bond 0.03453 / 2.43 ( 858) hydrogen bonds : angle 4.32828 / 3.05 ( 2514) link_NAG-ASN : bond 0.00193 / 0.09 ( 8) link_NAG-ASN : angle 1.82277 / 1.30 ( 24) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4584 Ramachandran restraints generated. 2292 Oldfield, 0 Emsley, 2292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4584 Ramachandran restraints generated. 2292 Oldfield, 0 Emsley, 2292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 2070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 279 time to evaluate : 0.631 Fit side-chains revert: symmetry clash REVERT: C 233 VAL cc_start: 0.7565 (m) cc_final: 0.7267 (p) REVERT: C 248 LYS cc_start: 0.8442 (mttp) cc_final: 0.8232 (mttp) REVERT: C 257 ARG cc_start: 0.8432 (ptm160) cc_final: 0.7722 (ptt180) REVERT: C 374 LYS cc_start: 0.7407 (ptmt) cc_final: 0.7025 (ptmt) REVERT: C 386 ILE cc_start: 0.8533 (mm) cc_final: 0.7779 (pt) REVERT: D 234 LYS cc_start: 0.8469 (mptt) cc_final: 0.7981 (mmmm) REVERT: D 265 MET cc_start: 0.7481 (tmm) cc_final: 0.7214 (tmm) REVERT: D 330 THR cc_start: 0.7774 (p) cc_final: 0.7490 (p) REVERT: D 348 ASN cc_start: 0.8662 (t0) cc_final: 0.8374 (m110) REVERT: D 771 GLU cc_start: 0.8037 (OUTLIER) cc_final: 0.7776 (tm-30) REVERT: D 1162 ILE cc_start: 0.9087 (tp) cc_final: 0.8855 (tp) REVERT: D 1222 TYR cc_start: 0.7068 (t80) cc_final: 0.6736 (t80) REVERT: D 1227 GLN cc_start: 0.7122 (tp40) cc_final: 0.6808 (tm-30) REVERT: D 1258 MET cc_start: 0.8427 (OUTLIER) cc_final: 0.7869 (mpp) REVERT: D 1293 PHE cc_start: 0.7366 (p90) cc_final: 0.6650 (p90) REVERT: D 1382 MET cc_start: 0.8748 (mmm) cc_final: 0.8468 (mmm) REVERT: D 1482 GLU cc_start: 0.8006 (mp0) cc_final: 0.7783 (mp0) REVERT: E 234 ASP cc_start: 0.8249 (t0) cc_final: 0.7960 (t0) REVERT: E 469 ILE cc_start: 0.8755 (OUTLIER) cc_final: 0.8448 (pp) REVERT: E 536 ILE cc_start: 0.8822 (OUTLIER) cc_final: 0.8198 (pt) REVERT: E 631 ILE cc_start: 0.8744 (mt) cc_final: 0.8459 (tp) REVERT: E 682 ASN cc_start: 0.9034 (m110) cc_final: 0.8593 (m110) REVERT: E 708 ASP cc_start: 0.8655 (OUTLIER) cc_final: 0.8318 (t0) REVERT: E 719 TYR cc_start: 0.7797 (m-80) cc_final: 0.7448 (m-10) REVERT: E 744 TYR cc_start: 0.7113 (t80) cc_final: 0.6783 (t80) REVERT: E 864 HIS cc_start: 0.6976 (t-90) cc_final: 0.5964 (m90) REVERT: E 1017 MET cc_start: 0.6562 (OUTLIER) cc_final: 0.6245 (mpp) REVERT: E 1045 ASP cc_start: 0.8963 (t0) cc_final: 0.8531 (t0) outliers start: 51 outliers final: 31 residues processed: 307 average time/residue: 0.1220 time to fit residues: 59.3246 Evaluate side-chains 293 residues out of total 2070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 256 time to evaluate : 0.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 256 HIS Chi-restraints excluded: chain C residue 265 THR Chi-restraints excluded: chain C residue 320 ASP Chi-restraints excluded: chain D residue 121 VAL Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain D residue 248 VAL Chi-restraints excluded: chain D residue 353 MET Chi-restraints excluded: chain D residue 360 ILE Chi-restraints excluded: chain D residue 439 ASP Chi-restraints excluded: chain D residue 530 VAL Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 545 HIS Chi-restraints excluded: chain D residue 624 LEU Chi-restraints excluded: chain D residue 637 LEU Chi-restraints excluded: chain D residue 771 GLU Chi-restraints excluded: chain D residue 910 ILE Chi-restraints excluded: chain D residue 917 LEU Chi-restraints excluded: chain D residue 935 TYR Chi-restraints excluded: chain D residue 970 LEU Chi-restraints excluded: chain D residue 1046 ILE Chi-restraints excluded: chain D residue 1248 LEU Chi-restraints excluded: chain D residue 1258 MET Chi-restraints excluded: chain D residue 1290 LEU Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 150 ILE Chi-restraints excluded: chain E residue 389 VAL Chi-restraints excluded: chain E residue 469 ILE Chi-restraints excluded: chain E residue 516 ASP Chi-restraints excluded: chain E residue 536 ILE Chi-restraints excluded: chain E residue 622 VAL Chi-restraints excluded: chain E residue 708 ASP Chi-restraints excluded: chain E residue 734 VAL Chi-restraints excluded: chain E residue 768 LEU Chi-restraints excluded: chain E residue 903 VAL Chi-restraints excluded: chain E residue 1002 ILE Chi-restraints excluded: chain E residue 1017 MET Chi-restraints excluded: chain E residue 1058 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 121 optimal weight: 1.9990 chunk 175 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 76 optimal weight: 0.9990 chunk 167 optimal weight: 0.0270 chunk 168 optimal weight: 0.0470 chunk 108 optimal weight: 6.9990 chunk 117 optimal weight: 5.9990 chunk 52 optimal weight: 1.9990 chunk 106 optimal weight: 5.9990 chunk 49 optimal weight: 0.9980 overall best weight: 0.8140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.162211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.117298 restraints weight = 28461.030| |-----------------------------------------------------------------------------| r_work (start): 0.3467 rms_B_bonded: 2.64 r_work: 0.3231 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.3091 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.2376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 19560 Z= 0.126 Angle : 0.569 9.642 26454 Z= 0.285 Chirality : 0.042 0.192 2998 Planarity : 0.004 0.048 3307 Dihedral : 8.351 80.853 2906 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 2.86 % Allowed : 16.46 % Favored : 80.68 % 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: -0.76 (0.18), residues: 2292 helix: 0.40 (0.15), residues: 1197 sheet: -1.26 (0.37), residues: 176 loop : -1.51 (0.21), residues: 919 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D1217 TYR 0.015 0.001 TYR E 644 PHE 0.027 0.001 PHE E1003 TRP 0.014 0.001 TRP E 36 HIS 0.008 0.001 HIS D1148 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 (19545) covalent geometry : angle 0.56657 / 0.28 (26416) SS BOND : bond 0.00164 / 0.08 ( 7) SS BOND : angle 0.85989 / 0.57 ( 14) hydrogen bonds : bond 0.03315 / 2.33 ( 858) hydrogen bonds : angle 4.22285 / 2.98 ( 2514) link_NAG-ASN : bond 0.00252 / 0.13 ( 8) link_NAG-ASN : angle 1.72469 / 1.23 ( 24) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4584 Ramachandran restraints generated. 2292 Oldfield, 0 Emsley, 2292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4584 Ramachandran restraints generated. 2292 Oldfield, 0 Emsley, 2292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 2070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 288 time to evaluate : 0.736 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 233 VAL cc_start: 0.7558 (m) cc_final: 0.7275 (p) REVERT: C 248 LYS cc_start: 0.8466 (mttp) cc_final: 0.8242 (mttp) REVERT: C 257 ARG cc_start: 0.8412 (ptm160) cc_final: 0.7673 (ptt180) REVERT: C 374 LYS cc_start: 0.7409 (ptmt) cc_final: 0.7034 (ptmt) REVERT: C 386 ILE cc_start: 0.8492 (mm) cc_final: 0.7729 (pt) REVERT: D 234 LYS cc_start: 0.8443 (mptt) cc_final: 0.7960 (mmmm) REVERT: D 265 MET cc_start: 0.7669 (tmm) cc_final: 0.7389 (tmm) REVERT: D 330 THR cc_start: 0.7784 (p) cc_final: 0.7461 (p) REVERT: D 348 ASN cc_start: 0.8614 (t0) cc_final: 0.8353 (m110) REVERT: D 771 GLU cc_start: 0.8184 (OUTLIER) cc_final: 0.7907 (tm-30) REVERT: D 970 LEU cc_start: 0.7933 (OUTLIER) cc_final: 0.7200 (mt) REVERT: D 1098 ASP cc_start: 0.8008 (m-30) cc_final: 0.7607 (t0) REVERT: D 1222 TYR cc_start: 0.7262 (t80) cc_final: 0.6891 (t80) REVERT: D 1227 GLN cc_start: 0.7063 (tp40) cc_final: 0.6814 (tm-30) REVERT: D 1258 MET cc_start: 0.8515 (OUTLIER) cc_final: 0.7935 (mpp) REVERT: D 1293 PHE cc_start: 0.7386 (p90) cc_final: 0.6702 (p90) REVERT: D 1382 MET cc_start: 0.8827 (mmm) cc_final: 0.8581 (mmm) REVERT: D 1474 MET cc_start: 0.8710 (mmt) cc_final: 0.8287 (mmt) REVERT: D 1482 GLU cc_start: 0.7987 (mp0) cc_final: 0.7763 (mp0) REVERT: E 234 ASP cc_start: 0.8249 (t0) cc_final: 0.7992 (t0) REVERT: E 469 ILE cc_start: 0.8776 (OUTLIER) cc_final: 0.8489 (pp) REVERT: E 536 ILE cc_start: 0.8809 (OUTLIER) cc_final: 0.8149 (pt) REVERT: E 631 ILE cc_start: 0.8737 (mt) cc_final: 0.8481 (tp) REVERT: E 682 ASN cc_start: 0.9037 (m110) cc_final: 0.8639 (m110) REVERT: E 708 ASP cc_start: 0.8676 (t0) cc_final: 0.8337 (t0) REVERT: E 719 TYR cc_start: 0.7807 (m-80) cc_final: 0.7473 (m-10) REVERT: E 744 TYR cc_start: 0.7129 (t80) cc_final: 0.6913 (t80) REVERT: E 864 HIS cc_start: 0.7106 (t-90) cc_final: 0.6054 (m90) REVERT: E 985 ASN cc_start: 0.7577 (m110) cc_final: 0.7309 (m110) REVERT: E 1017 MET cc_start: 0.6568 (OUTLIER) cc_final: 0.6334 (mpp) REVERT: E 1045 ASP cc_start: 0.8945 (t0) cc_final: 0.8504 (t0) outliers start: 59 outliers final: 40 residues processed: 325 average time/residue: 0.1184 time to fit residues: 61.6083 Evaluate side-chains 313 residues out of total 2070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 267 time to evaluate : 0.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 256 HIS Chi-restraints excluded: chain C residue 265 THR Chi-restraints excluded: chain C residue 320 ASP Chi-restraints excluded: chain D residue 121 VAL Chi-restraints excluded: chain D residue 129 ILE Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain D residue 248 VAL Chi-restraints excluded: chain D residue 251 VAL Chi-restraints excluded: chain D residue 353 MET Chi-restraints excluded: chain D residue 360 ILE Chi-restraints excluded: chain D residue 439 ASP Chi-restraints excluded: chain D residue 530 VAL Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 545 HIS Chi-restraints excluded: chain D residue 572 LEU Chi-restraints excluded: chain D residue 624 LEU Chi-restraints excluded: chain D residue 637 LEU Chi-restraints excluded: chain D residue 771 GLU Chi-restraints excluded: chain D residue 910 ILE Chi-restraints excluded: chain D residue 917 LEU Chi-restraints excluded: chain D residue 935 TYR Chi-restraints excluded: chain D residue 970 LEU Chi-restraints excluded: chain D residue 1042 VAL Chi-restraints excluded: chain D residue 1046 ILE Chi-restraints excluded: chain D residue 1180 ILE Chi-restraints excluded: chain D residue 1248 LEU Chi-restraints excluded: chain D residue 1255 CYS Chi-restraints excluded: chain D residue 1258 MET Chi-restraints excluded: chain D residue 1290 LEU Chi-restraints excluded: chain D residue 1652 VAL Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 150 ILE Chi-restraints excluded: chain E residue 343 GLN Chi-restraints excluded: chain E residue 389 VAL Chi-restraints excluded: chain E residue 469 ILE Chi-restraints excluded: chain E residue 516 ASP Chi-restraints excluded: chain E residue 536 ILE Chi-restraints excluded: chain E residue 622 VAL Chi-restraints excluded: chain E residue 661 ILE Chi-restraints excluded: chain E residue 734 VAL Chi-restraints excluded: chain E residue 768 LEU Chi-restraints excluded: chain E residue 811 VAL Chi-restraints excluded: chain E residue 903 VAL Chi-restraints excluded: chain E residue 1002 ILE Chi-restraints excluded: chain E residue 1017 MET Chi-restraints excluded: chain E residue 1058 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 36 optimal weight: 6.9990 chunk 142 optimal weight: 0.8980 chunk 215 optimal weight: 0.9980 chunk 149 optimal weight: 0.1980 chunk 33 optimal weight: 10.0000 chunk 230 optimal weight: 0.0040 chunk 11 optimal weight: 10.0000 chunk 108 optimal weight: 6.9990 chunk 9 optimal weight: 0.0010 chunk 192 optimal weight: 3.9990 chunk 216 optimal weight: 0.7980 overall best weight: 0.3798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.162665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.118514 restraints weight = 28866.218| |-----------------------------------------------------------------------------| r_work (start): 0.3502 rms_B_bonded: 2.83 r_work: 0.3280 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.2673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 19560 Z= 0.106 Angle : 0.562 11.347 26454 Z= 0.280 Chirality : 0.041 0.176 2998 Planarity : 0.003 0.048 3307 Dihedral : 8.116 79.579 2906 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 2.57 % Allowed : 17.38 % Favored : 80.05 % 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: -0.58 (0.18), residues: 2292 helix: 0.56 (0.15), residues: 1201 sheet: -1.11 (0.38), residues: 176 loop : -1.47 (0.21), residues: 915 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D1571 TYR 0.013 0.001 TYR D 742 PHE 0.015 0.001 PHE D1004 TRP 0.020 0.001 TRP E 821 HIS 0.009 0.001 HIS D1148 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.11 (19545) covalent geometry : angle 0.55940 / 0.28 (26416) SS BOND : bond 0.00151 / 0.08 ( 7) SS BOND : angle 1.54451 / 1.06 ( 14) hydrogen bonds : bond 0.03158 / 2.22 ( 858) hydrogen bonds : angle 4.10004 / 2.89 ( 2514) link_NAG-ASN : bond 0.00207 / 0.10 ( 8) link_NAG-ASN : angle 1.49412 / 1.08 ( 24) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4584 Ramachandran restraints generated. 2292 Oldfield, 0 Emsley, 2292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4584 Ramachandran restraints generated. 2292 Oldfield, 0 Emsley, 2292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 2070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 294 time to evaluate : 0.650 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 257 ARG cc_start: 0.8398 (ptm160) cc_final: 0.7575 (ptp90) REVERT: C 374 LYS cc_start: 0.7411 (ptmt) cc_final: 0.7041 (ptmt) REVERT: C 386 ILE cc_start: 0.8497 (mm) cc_final: 0.7755 (pt) REVERT: D 234 LYS cc_start: 0.8374 (mptt) cc_final: 0.7893 (mmmm) REVERT: D 265 MET cc_start: 0.7642 (tmm) cc_final: 0.7155 (tmm) REVERT: D 348 ASN cc_start: 0.8278 (t0) cc_final: 0.8051 (m110) REVERT: D 626 ARG cc_start: 0.8408 (ttp-170) cc_final: 0.8165 (ttp-170) REVERT: D 937 ASP cc_start: 0.7985 (t0) cc_final: 0.7757 (t0) REVERT: D 970 LEU cc_start: 0.7999 (OUTLIER) cc_final: 0.7231 (mt) REVERT: D 1222 TYR cc_start: 0.7261 (t80) cc_final: 0.6909 (t80) REVERT: D 1258 MET cc_start: 0.8308 (OUTLIER) cc_final: 0.7744 (mpp) REVERT: D 1293 PHE cc_start: 0.7354 (p90) cc_final: 0.6773 (p90) REVERT: D 1382 MET cc_start: 0.8758 (mmm) cc_final: 0.8554 (mmm) REVERT: D 1474 MET cc_start: 0.8539 (mmt) cc_final: 0.8229 (mmt) REVERT: D 1482 GLU cc_start: 0.7917 (mp0) cc_final: 0.7707 (mp0) REVERT: E 469 ILE cc_start: 0.8751 (OUTLIER) cc_final: 0.8471 (pp) REVERT: E 536 ILE cc_start: 0.8753 (OUTLIER) cc_final: 0.8067 (pt) REVERT: E 682 ASN cc_start: 0.8957 (m110) cc_final: 0.8650 (m110) REVERT: E 708 ASP cc_start: 0.8510 (OUTLIER) cc_final: 0.8217 (t0) REVERT: E 719 TYR cc_start: 0.7621 (m-80) cc_final: 0.7309 (m-10) REVERT: E 864 HIS cc_start: 0.7145 (t-90) cc_final: 0.6237 (m90) REVERT: E 977 GLU cc_start: 0.8194 (tt0) cc_final: 0.7969 (tt0) REVERT: E 1045 ASP cc_start: 0.8812 (t0) cc_final: 0.8352 (t0) outliers start: 53 outliers final: 34 residues processed: 330 average time/residue: 0.1182 time to fit residues: 61.8869 Evaluate side-chains 306 residues out of total 2070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 267 time to evaluate : 0.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 256 HIS Chi-restraints excluded: chain C residue 265 THR Chi-restraints excluded: chain C residue 320 ASP Chi-restraints excluded: chain D residue 129 ILE Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain D residue 248 VAL Chi-restraints excluded: chain D residue 251 VAL Chi-restraints excluded: chain D residue 360 ILE Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 545 HIS Chi-restraints excluded: chain D residue 624 LEU Chi-restraints excluded: chain D residue 633 TYR Chi-restraints excluded: chain D residue 637 LEU Chi-restraints excluded: chain D residue 762 LEU Chi-restraints excluded: chain D residue 910 ILE Chi-restraints excluded: chain D residue 917 LEU Chi-restraints excluded: chain D residue 935 TYR Chi-restraints excluded: chain D residue 970 LEU Chi-restraints excluded: chain D residue 1180 ILE Chi-restraints excluded: chain D residue 1248 LEU Chi-restraints excluded: chain D residue 1255 CYS Chi-restraints excluded: chain D residue 1258 MET Chi-restraints excluded: chain D residue 1290 LEU Chi-restraints excluded: chain D residue 1552 TYR Chi-restraints excluded: chain D residue 1652 VAL Chi-restraints excluded: chain E residue 183 LEU Chi-restraints excluded: chain E residue 389 VAL Chi-restraints excluded: chain E residue 469 ILE Chi-restraints excluded: chain E residue 516 ASP Chi-restraints excluded: chain E residue 536 ILE Chi-restraints excluded: chain E residue 622 VAL Chi-restraints excluded: chain E residue 661 ILE Chi-restraints excluded: chain E residue 708 ASP Chi-restraints excluded: chain E residue 734 VAL Chi-restraints excluded: chain E residue 768 LEU Chi-restraints excluded: chain E residue 811 VAL Chi-restraints excluded: chain E residue 903 VAL Chi-restraints excluded: chain E residue 1002 ILE Chi-restraints excluded: chain E residue 1058 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 171 optimal weight: 0.9990 chunk 143 optimal weight: 9.9990 chunk 182 optimal weight: 0.8980 chunk 67 optimal weight: 0.9990 chunk 213 optimal weight: 0.7980 chunk 125 optimal weight: 0.7980 chunk 20 optimal weight: 2.9990 chunk 105 optimal weight: 0.0670 chunk 24 optimal weight: 2.9990 chunk 154 optimal weight: 1.9990 chunk 166 optimal weight: 0.9990 overall best weight: 0.7120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.160820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.117762 restraints weight = 28453.973| |-----------------------------------------------------------------------------| r_work (start): 0.3488 rms_B_bonded: 2.75 r_work: 0.3266 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.2778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 19560 Z= 0.121 Angle : 0.586 12.626 26454 Z= 0.290 Chirality : 0.042 0.233 2998 Planarity : 0.003 0.048 3307 Dihedral : 8.083 80.154 2906 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 2.18 % Allowed : 18.60 % Favored : 79.23 % 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: -0.49 (0.18), residues: 2292 helix: 0.63 (0.15), residues: 1197 sheet: -1.01 (0.38), residues: 179 loop : -1.44 (0.21), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D1571 TYR 0.016 0.001 TYR E 666 PHE 0.030 0.001 PHE E1003 TRP 0.017 0.001 TRP E 821 HIS 0.011 0.001 HIS D1148 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.12 (19545) covalent geometry : angle 0.58293 / 0.29 (26416) SS BOND : bond 0.00156 / 0.08 ( 7) SS BOND : angle 1.36430 / 0.94 ( 14) hydrogen bonds : bond 0.03209 / 2.23 ( 858) hydrogen bonds : angle 4.12807 / 2.90 ( 2514) link_NAG-ASN : bond 0.00341 / 0.18 ( 8) link_NAG-ASN : angle 1.75115 / 1.19 ( 24) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4584 Ramachandran restraints generated. 2292 Oldfield, 0 Emsley, 2292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4584 Ramachandran restraints generated. 2292 Oldfield, 0 Emsley, 2292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 2070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 277 time to evaluate : 0.578 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 257 ARG cc_start: 0.8398 (ptm160) cc_final: 0.7582 (ptp90) REVERT: C 374 LYS cc_start: 0.7403 (ptmt) cc_final: 0.6920 (ptmt) REVERT: C 386 ILE cc_start: 0.8517 (mm) cc_final: 0.7787 (pt) REVERT: D 234 LYS cc_start: 0.8339 (mptt) cc_final: 0.7850 (mmmm) REVERT: D 265 MET cc_start: 0.7632 (tmm) cc_final: 0.7159 (tmm) REVERT: D 348 ASN cc_start: 0.8308 (t0) cc_final: 0.8104 (m110) REVERT: D 626 ARG cc_start: 0.8379 (ttp-170) cc_final: 0.8154 (ttp-170) REVERT: D 937 ASP cc_start: 0.7989 (t0) cc_final: 0.7763 (t0) REVERT: D 970 LEU cc_start: 0.7957 (OUTLIER) cc_final: 0.7200 (mt) REVERT: D 1222 TYR cc_start: 0.7369 (t80) cc_final: 0.7101 (t80) REVERT: D 1258 MET cc_start: 0.8328 (OUTLIER) cc_final: 0.7760 (mpp) REVERT: D 1293 PHE cc_start: 0.7328 (p90) cc_final: 0.6697 (p90) REVERT: D 1382 MET cc_start: 0.8776 (mmm) cc_final: 0.8559 (mmm) REVERT: D 1474 MET cc_start: 0.8584 (mmt) cc_final: 0.8243 (mmt) REVERT: D 1482 GLU cc_start: 0.7885 (mp0) cc_final: 0.7667 (mp0) REVERT: E 469 ILE cc_start: 0.8772 (OUTLIER) cc_final: 0.8497 (pp) REVERT: E 536 ILE cc_start: 0.8750 (OUTLIER) cc_final: 0.8064 (pt) REVERT: E 682 ASN cc_start: 0.8946 (m110) cc_final: 0.8643 (m110) REVERT: E 708 ASP cc_start: 0.8587 (OUTLIER) cc_final: 0.8229 (t0) REVERT: E 864 HIS cc_start: 0.7136 (t-90) cc_final: 0.6243 (m90) REVERT: E 977 GLU cc_start: 0.8234 (tt0) cc_final: 0.8015 (tt0) REVERT: E 1045 ASP cc_start: 0.8842 (t0) cc_final: 0.8392 (t0) outliers start: 45 outliers final: 37 residues processed: 306 average time/residue: 0.1184 time to fit residues: 57.4520 Evaluate side-chains 308 residues out of total 2070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 266 time to evaluate : 0.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 256 HIS Chi-restraints excluded: chain C residue 265 THR Chi-restraints excluded: chain C residue 320 ASP Chi-restraints excluded: chain D residue 121 VAL Chi-restraints excluded: chain D residue 129 ILE Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain D residue 248 VAL Chi-restraints excluded: chain D residue 251 VAL Chi-restraints excluded: chain D residue 353 MET Chi-restraints excluded: chain D residue 360 ILE Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 572 LEU Chi-restraints excluded: chain D residue 624 LEU Chi-restraints excluded: chain D residue 633 TYR Chi-restraints excluded: chain D residue 637 LEU Chi-restraints excluded: chain D residue 762 LEU Chi-restraints excluded: chain D residue 910 ILE Chi-restraints excluded: chain D residue 917 LEU Chi-restraints excluded: chain D residue 935 TYR Chi-restraints excluded: chain D residue 970 LEU Chi-restraints excluded: chain D residue 1095 THR Chi-restraints excluded: chain D residue 1248 LEU Chi-restraints excluded: chain D residue 1255 CYS Chi-restraints excluded: chain D residue 1258 MET Chi-restraints excluded: chain D residue 1290 LEU Chi-restraints excluded: chain D residue 1552 TYR Chi-restraints excluded: chain D residue 1652 VAL Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 183 LEU Chi-restraints excluded: chain E residue 389 VAL Chi-restraints excluded: chain E residue 469 ILE Chi-restraints excluded: chain E residue 516 ASP Chi-restraints excluded: chain E residue 536 ILE Chi-restraints excluded: chain E residue 622 VAL Chi-restraints excluded: chain E residue 661 ILE Chi-restraints excluded: chain E residue 708 ASP Chi-restraints excluded: chain E residue 734 VAL Chi-restraints excluded: chain E residue 768 LEU Chi-restraints excluded: chain E residue 811 VAL Chi-restraints excluded: chain E residue 903 VAL Chi-restraints excluded: chain E residue 1002 ILE Chi-restraints excluded: chain E residue 1058 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 203 optimal weight: 0.7980 chunk 44 optimal weight: 0.0570 chunk 22 optimal weight: 9.9990 chunk 52 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 78 optimal weight: 10.0000 chunk 61 optimal weight: 4.9990 chunk 167 optimal weight: 0.6980 chunk 101 optimal weight: 0.5980 chunk 192 optimal weight: 3.9990 chunk 27 optimal weight: 0.6980 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.162857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.118695 restraints weight = 28790.101| |-----------------------------------------------------------------------------| r_work (start): 0.3507 rms_B_bonded: 2.81 r_work: 0.3287 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3146 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.2922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 19560 Z= 0.114 Angle : 0.584 14.091 26454 Z= 0.290 Chirality : 0.042 0.193 2998 Planarity : 0.004 0.049 3307 Dihedral : 8.084 79.790 2906 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 2.18 % Allowed : 18.98 % Favored : 78.84 % 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: -0.36 (0.18), residues: 2292 helix: 0.75 (0.15), residues: 1195 sheet: -0.92 (0.38), residues: 178 loop : -1.38 (0.21), residues: 919 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D1571 TYR 0.019 0.001 TYR E 666 PHE 0.021 0.001 PHE E 686 TRP 0.022 0.001 TRP E 821 HIS 0.011 0.001 HIS D1148 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.11 (19545) covalent geometry : angle 0.58152 / 0.29 (26416) SS BOND : bond 0.00143 / 0.07 ( 7) SS BOND : angle 1.14761 / 0.79 ( 14) hydrogen bonds : bond 0.03152 / 2.20 ( 858) hydrogen bonds : angle 4.10128 / 2.88 ( 2514) link_NAG-ASN : bond 0.00208 / 0.10 ( 8) link_NAG-ASN : angle 1.52345 / 1.07 ( 24) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4584 Ramachandran restraints generated. 2292 Oldfield, 0 Emsley, 2292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4584 Ramachandran restraints generated. 2292 Oldfield, 0 Emsley, 2292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 2070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 278 time to evaluate : 0.736 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 257 ARG cc_start: 0.8364 (ptm160) cc_final: 0.7541 (ptp90) REVERT: C 374 LYS cc_start: 0.7329 (ptmt) cc_final: 0.6978 (ptmt) REVERT: C 386 ILE cc_start: 0.8519 (mm) cc_final: 0.7793 (pt) REVERT: D 234 LYS cc_start: 0.8346 (mptt) cc_final: 0.7858 (mmmm) REVERT: D 265 MET cc_start: 0.7669 (tmm) cc_final: 0.7231 (tmm) REVERT: D 348 ASN cc_start: 0.8431 (t0) cc_final: 0.8214 (m110) REVERT: D 937 ASP cc_start: 0.8118 (t0) cc_final: 0.7824 (t0) REVERT: D 970 LEU cc_start: 0.8092 (OUTLIER) cc_final: 0.7403 (mt) REVERT: D 1222 TYR cc_start: 0.7424 (t80) cc_final: 0.7184 (t80) REVERT: D 1258 MET cc_start: 0.8563 (OUTLIER) cc_final: 0.8004 (mpp) REVERT: D 1293 PHE cc_start: 0.7191 (p90) cc_final: 0.6553 (p90) REVERT: D 1482 GLU cc_start: 0.7987 (mp0) cc_final: 0.7748 (mp0) REVERT: E 469 ILE cc_start: 0.8836 (OUTLIER) cc_final: 0.8568 (pp) REVERT: E 682 ASN cc_start: 0.8973 (m110) cc_final: 0.8685 (m110) REVERT: E 708 ASP cc_start: 0.8657 (OUTLIER) cc_final: 0.8307 (t0) REVERT: E 864 HIS cc_start: 0.7278 (t-90) cc_final: 0.6329 (m90) REVERT: E 977 GLU cc_start: 0.8453 (tt0) cc_final: 0.8250 (tt0) REVERT: E 1045 ASP cc_start: 0.8966 (t0) cc_final: 0.8552 (t0) outliers start: 45 outliers final: 38 residues processed: 307 average time/residue: 0.1108 time to fit residues: 54.1691 Evaluate side-chains 307 residues out of total 2070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 265 time to evaluate : 0.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 256 HIS Chi-restraints excluded: chain C residue 265 THR Chi-restraints excluded: chain C residue 320 ASP Chi-restraints excluded: chain D residue 121 VAL Chi-restraints excluded: chain D residue 129 ILE Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain D residue 353 MET Chi-restraints excluded: chain D residue 360 ILE Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 545 HIS Chi-restraints excluded: chain D residue 572 LEU Chi-restraints excluded: chain D residue 624 LEU Chi-restraints excluded: chain D residue 633 TYR Chi-restraints excluded: chain D residue 637 LEU Chi-restraints excluded: chain D residue 762 LEU Chi-restraints excluded: chain D residue 910 ILE Chi-restraints excluded: chain D residue 917 LEU Chi-restraints excluded: chain D residue 935 TYR Chi-restraints excluded: chain D residue 970 LEU Chi-restraints excluded: chain D residue 1095 THR Chi-restraints excluded: chain D residue 1160 VAL Chi-restraints excluded: chain D residue 1180 ILE Chi-restraints excluded: chain D residue 1248 LEU Chi-restraints excluded: chain D residue 1255 CYS Chi-restraints excluded: chain D residue 1258 MET Chi-restraints excluded: chain D residue 1290 LEU Chi-restraints excluded: chain D residue 1552 TYR Chi-restraints excluded: chain D residue 1652 VAL Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 183 LEU Chi-restraints excluded: chain E residue 389 VAL Chi-restraints excluded: chain E residue 469 ILE Chi-restraints excluded: chain E residue 516 ASP Chi-restraints excluded: chain E residue 622 VAL Chi-restraints excluded: chain E residue 661 ILE Chi-restraints excluded: chain E residue 708 ASP Chi-restraints excluded: chain E residue 734 VAL Chi-restraints excluded: chain E residue 768 LEU Chi-restraints excluded: chain E residue 811 VAL Chi-restraints excluded: chain E residue 903 VAL Chi-restraints excluded: chain E residue 1002 ILE Chi-restraints excluded: chain E residue 1058 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 146 optimal weight: 4.9990 chunk 36 optimal weight: 6.9990 chunk 69 optimal weight: 0.6980 chunk 3 optimal weight: 3.9990 chunk 142 optimal weight: 2.9990 chunk 110 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 75 optimal weight: 0.7980 chunk 111 optimal weight: 0.7980 chunk 163 optimal weight: 2.9990 chunk 102 optimal weight: 0.8980 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.159610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.116269 restraints weight = 28455.239| |-----------------------------------------------------------------------------| r_work (start): 0.3470 rms_B_bonded: 2.66 r_work: 0.3249 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3111 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.2856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 19560 Z= 0.153 Angle : 0.615 13.829 26454 Z= 0.304 Chirality : 0.043 0.190 2998 Planarity : 0.004 0.054 3307 Dihedral : 8.232 82.522 2906 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 2.13 % Allowed : 19.13 % Favored : 78.74 % 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: -0.39 (0.18), residues: 2292 helix: 0.68 (0.15), residues: 1200 sheet: -0.63 (0.39), residues: 177 loop : -1.42 (0.21), residues: 915 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D1590 TYR 0.023 0.001 TYR E 666 PHE 0.029 0.001 PHE E1003 TRP 0.027 0.001 TRP E 821 HIS 0.012 0.001 HIS D1148 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.15 (19545) covalent geometry : angle 0.61280 / 0.30 (26416) SS BOND : bond 0.00166 / 0.08 ( 7) SS BOND : angle 1.21941 / 0.82 ( 14) hydrogen bonds : bond 0.03318 / 2.30 ( 858) hydrogen bonds : angle 4.18845 / 2.95 ( 2514) link_NAG-ASN : bond 0.00200 / 0.10 ( 8) link_NAG-ASN : angle 1.70754 / 1.20 ( 24) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4584 Ramachandran restraints generated. 2292 Oldfield, 0 Emsley, 2292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4584 Ramachandran restraints generated. 2292 Oldfield, 0 Emsley, 2292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 2070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 263 time to evaluate : 0.684 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 257 ARG cc_start: 0.8369 (ptm160) cc_final: 0.7549 (ptp90) REVERT: C 374 LYS cc_start: 0.7360 (ptmt) cc_final: 0.7020 (ptmt) REVERT: C 386 ILE cc_start: 0.8587 (mm) cc_final: 0.7885 (pt) REVERT: D 234 LYS cc_start: 0.8349 (mptt) cc_final: 0.7886 (mmmm) REVERT: D 265 MET cc_start: 0.7718 (tmm) cc_final: 0.7252 (tmm) REVERT: D 937 ASP cc_start: 0.8133 (t0) cc_final: 0.7875 (t0) REVERT: D 970 LEU cc_start: 0.7855 (OUTLIER) cc_final: 0.7148 (mt) REVERT: D 1222 TYR cc_start: 0.7450 (t80) cc_final: 0.7198 (t80) REVERT: D 1258 MET cc_start: 0.8571 (OUTLIER) cc_final: 0.8002 (mpp) REVERT: D 1293 PHE cc_start: 0.7213 (p90) cc_final: 0.6584 (p90) REVERT: E 469 ILE cc_start: 0.8841 (OUTLIER) cc_final: 0.8588 (pp) REVERT: E 682 ASN cc_start: 0.8991 (m110) cc_final: 0.8685 (m110) REVERT: E 708 ASP cc_start: 0.8663 (OUTLIER) cc_final: 0.8320 (t0) REVERT: E 821 TRP cc_start: 0.8870 (t60) cc_final: 0.8401 (t60) REVERT: E 864 HIS cc_start: 0.7211 (t-90) cc_final: 0.6251 (m90) REVERT: E 977 GLU cc_start: 0.8494 (tt0) cc_final: 0.8270 (tt0) REVERT: E 1045 ASP cc_start: 0.8960 (t0) cc_final: 0.8538 (t0) outliers start: 44 outliers final: 36 residues processed: 291 average time/residue: 0.1155 time to fit residues: 53.6147 Evaluate side-chains 294 residues out of total 2070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 254 time to evaluate : 0.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 256 HIS Chi-restraints excluded: chain C residue 265 THR Chi-restraints excluded: chain C residue 320 ASP Chi-restraints excluded: chain D residue 121 VAL Chi-restraints excluded: chain D residue 129 ILE Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain D residue 248 VAL Chi-restraints excluded: chain D residue 353 MET Chi-restraints excluded: chain D residue 360 ILE Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 545 HIS Chi-restraints excluded: chain D residue 572 LEU Chi-restraints excluded: chain D residue 624 LEU Chi-restraints excluded: chain D residue 633 TYR Chi-restraints excluded: chain D residue 637 LEU Chi-restraints excluded: chain D residue 762 LEU Chi-restraints excluded: chain D residue 910 ILE Chi-restraints excluded: chain D residue 917 LEU Chi-restraints excluded: chain D residue 935 TYR Chi-restraints excluded: chain D residue 970 LEU Chi-restraints excluded: chain D residue 1095 THR Chi-restraints excluded: chain D residue 1160 VAL Chi-restraints excluded: chain D residue 1180 ILE Chi-restraints excluded: chain D residue 1248 LEU Chi-restraints excluded: chain D residue 1255 CYS Chi-restraints excluded: chain D residue 1258 MET Chi-restraints excluded: chain D residue 1290 LEU Chi-restraints excluded: chain D residue 1652 VAL Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 389 VAL Chi-restraints excluded: chain E residue 469 ILE Chi-restraints excluded: chain E residue 516 ASP Chi-restraints excluded: chain E residue 622 VAL Chi-restraints excluded: chain E residue 661 ILE Chi-restraints excluded: chain E residue 708 ASP Chi-restraints excluded: chain E residue 734 VAL Chi-restraints excluded: chain E residue 768 LEU Chi-restraints excluded: chain E residue 811 VAL Chi-restraints excluded: chain E residue 903 VAL Chi-restraints excluded: chain E residue 1058 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 50 optimal weight: 0.7980 chunk 151 optimal weight: 4.9990 chunk 227 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 181 optimal weight: 0.1980 chunk 94 optimal weight: 1.9990 chunk 3 optimal weight: 0.3980 chunk 220 optimal weight: 0.7980 chunk 229 optimal weight: 4.9990 chunk 68 optimal weight: 1.9990 chunk 37 optimal weight: 0.3980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.162246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.119807 restraints weight = 28371.794| |-----------------------------------------------------------------------------| r_work (start): 0.3531 rms_B_bonded: 2.59 r_work: 0.3303 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3167 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.3046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 19560 Z= 0.113 Angle : 0.592 14.479 26454 Z= 0.292 Chirality : 0.042 0.175 2998 Planarity : 0.004 0.060 3307 Dihedral : 8.051 89.239 2906 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 2.28 % Allowed : 19.37 % Favored : 78.35 % 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: -0.26 (0.18), residues: 2292 helix: 0.79 (0.15), residues: 1200 sheet: -0.64 (0.38), residues: 183 loop : -1.36 (0.21), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D1571 TYR 0.016 0.001 TYR E 666 PHE 0.020 0.001 PHE E 686 TRP 0.025 0.001 TRP E 821 HIS 0.012 0.001 HIS D1148 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.11 (19545) covalent geometry : angle 0.59021 / 0.29 (26416) SS BOND : bond 0.00152 / 0.08 ( 7) SS BOND : angle 1.01271 / 0.71 ( 14) hydrogen bonds : bond 0.03091 / 2.15 ( 858) hydrogen bonds : angle 4.05697 / 2.87 ( 2514) link_NAG-ASN : bond 0.00228 / 0.11 ( 8) link_NAG-ASN : angle 1.44602 / 1.03 ( 24) Origin is already at (0, 0, 0), no shifts will be applied Model does not fit in PDB format. =============================================================================== Job complete usr+sys time: 5277.00 seconds wall clock time: 90 minutes 15.99 seconds (5415.99 seconds total)