Starting phenix.real_space_refine on Mon May 4 07:06:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hmb_34892/05_2026/8hmb_34892.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hmb_34892/05_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 { model { file = "/net/cci-nas-00/data/ceres_data/8hmb_34892/05_2026/8hmb_34892.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hmb_34892/05_2026/8hmb_34892.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8hmb_34892/05_2026/8hmb_34892.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hmb_34892/05_2026/8hmb_34892.map" } 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): 0.15s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/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, 247 Unusual residues: {' CA': 2, '3PE': 3, 'A1AC8': 1, 'R16': 8} Classifications: {'undetermined': 14} Link IDs: {None: 13} 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: 4.47, per 1000 atoms: 0.23 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: 1.71 Conformation dependent library (CDL) restraints added in 810.3 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: 0.68 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: 3.51 Time building geometry restraints manager: 2.16 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: 2.220 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: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 18.170 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 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 covalent geometry : bond 0.00825 (19545) covalent geometry : angle 0.85683 (26416) SS BOND : bond 0.00267 ( 7) SS BOND : angle 2.53583 ( 14) hydrogen bonds : bond 0.19661 ( 858) hydrogen bonds : angle 7.63514 ( 2514) link_NAG-ASN : bond 0.00767 ( 8) link_NAG-ASN : angle 3.61065 ( 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 : 0.760 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: 0.1417 time to fit residues: 65.3254 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 : 0.711 ------------------------------------------------------------------------------- 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... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.161626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.116904 restraints weight = 28293.492| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 2.61 r_work: 0.3222 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.3084 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.1347 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= 0.137 Angle : 0.642 9.740 26454 Z= 0.328 Chirality : 0.043 0.191 2998 Planarity : 0.004 0.045 3307 Dihedral : 9.443 86.581 2906 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 0.68 % Allowed : 8.67 % Favored : 90.65 % 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: -1.56 (0.17), residues: 2292 helix: -0.23 (0.15), residues: 1200 sheet: -1.45 (0.36), residues: 200 loop : -1.96 (0.21), residues: 892 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 0.019 0.001 PHE E1003 TRP 0.016 0.001 TRP E 821 HIS 0.004 0.001 HIS E1004 Details of bonding type rmsd covalent geometry : bond 0.00299 (19545) covalent geometry : angle 0.63770 (26416) SS BOND : bond 0.00162 ( 7) SS BOND : angle 1.10629 ( 14) hydrogen bonds : bond 0.04378 ( 858) hydrogen bonds : angle 4.94689 ( 2514) link_NAG-ASN : bond 0.00522 ( 8) link_NAG-ASN : angle 2.32838 ( 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 314 residues out of total 2070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 300 time to evaluate : 0.705 Fit side-chains revert: symmetry clash REVERT: C 308 PHE cc_start: 0.6435 (m-80) cc_final: 0.6135 (m-80) REVERT: C 339 ILE cc_start: 0.5909 (mm) cc_final: 0.5671 (mm) REVERT: D 234 LYS cc_start: 0.8584 (mptt) cc_final: 0.8014 (tppt) REVERT: D 265 MET cc_start: 0.7414 (tmm) cc_final: 0.7169 (tmm) REVERT: D 330 THR cc_start: 0.7732 (p) cc_final: 0.7488 (p) REVERT: D 439 ASP cc_start: 0.7818 (m-30) cc_final: 0.7444 (m-30) REVERT: D 1098 ASP cc_start: 0.8122 (m-30) cc_final: 0.7696 (t0) REVERT: D 1161 GLU cc_start: 0.7911 (mp0) cc_final: 0.7642 (pm20) REVERT: D 1222 TYR cc_start: 0.6617 (t80) cc_final: 0.6400 (t80) REVERT: D 1258 MET cc_start: 0.8478 (mpp) cc_final: 0.7937 (mpp) REVERT: D 1293 PHE cc_start: 0.7453 (p90) cc_final: 0.6961 (p90) REVERT: E 234 ASP cc_start: 0.8096 (t0) cc_final: 0.7804 (t0) REVERT: E 469 ILE cc_start: 0.8646 (OUTLIER) cc_final: 0.8394 (pp) REVERT: E 536 ILE cc_start: 0.8799 (OUTLIER) cc_final: 0.8163 (pt) REVERT: E 716 VAL cc_start: 0.8113 (OUTLIER) cc_final: 0.7870 (p) REVERT: E 864 HIS cc_start: 0.7072 (t-90) cc_final: 0.5963 (m90) REVERT: E 883 MET cc_start: 0.8246 (tpp) cc_final: 0.7995 (tpt) REVERT: E 1017 MET cc_start: 0.6284 (pmm) cc_final: 0.5914 (pmm) outliers start: 14 outliers final: 8 residues processed: 306 average time/residue: 0.1409 time to fit residues: 67.5311 Evaluate side-chains 278 residues out of total 2070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 267 time to evaluate : 0.525 ------------------------------------------------------------------------------- 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 903 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: 0.9980 chunk 218 optimal weight: 5.9990 chunk 210 optimal weight: 2.9990 chunk 42 optimal weight: 0.9980 chunk 205 optimal weight: 6.9990 chunk 61 optimal weight: 0.9990 chunk 215 optimal weight: 2.9990 chunk 123 optimal weight: 0.0870 chunk 66 optimal weight: 1.9990 chunk 207 optimal weight: 3.9990 overall best weight: 1.0162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.160981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.115932 restraints weight = 28540.728| |-----------------------------------------------------------------------------| r_work (start): 0.3444 rms_B_bonded: 2.66 r_work: 0.3202 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.1652 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= 0.146 Angle : 0.600 9.802 26454 Z= 0.306 Chirality : 0.042 0.184 2998 Planarity : 0.004 0.046 3307 Dihedral : 9.049 85.991 2906 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 1.74 % Allowed : 12.15 % Favored : 86.10 % 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: -1.26 (0.18), residues: 2292 helix: -0.02 (0.15), residues: 1199 sheet: -1.22 (0.38), residues: 184 loop : -1.78 (0.21), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D1571 TYR 0.013 0.001 TYR E 512 PHE 0.013 0.001 PHE C 383 TRP 0.014 0.001 TRP E 185 HIS 0.005 0.001 HIS D1148 Details of bonding type rmsd covalent geometry : bond 0.00340 (19545) covalent geometry : angle 0.59649 (26416) SS BOND : bond 0.00186 ( 7) SS BOND : angle 1.04560 ( 14) hydrogen bonds : bond 0.03961 ( 858) hydrogen bonds : angle 4.63281 ( 2514) link_NAG-ASN : bond 0.00215 ( 8) link_NAG-ASN : angle 2.00002 ( 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 329 residues out of total 2070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 293 time to evaluate : 0.548 Fit side-chains revert: symmetry clash REVERT: C 233 VAL cc_start: 0.7611 (m) cc_final: 0.7331 (p) REVERT: C 257 ARG cc_start: 0.8663 (ptp-110) cc_final: 0.7812 (ptp90) REVERT: D 234 LYS cc_start: 0.8465 (mptt) cc_final: 0.7965 (mmmm) REVERT: D 265 MET cc_start: 0.7464 (tmm) cc_final: 0.7170 (tmm) REVERT: D 330 THR cc_start: 0.7794 (p) cc_final: 0.7559 (p) REVERT: D 348 ASN cc_start: 0.8543 (t0) cc_final: 0.8273 (m110) REVERT: D 1098 ASP cc_start: 0.7850 (m-30) cc_final: 0.7534 (t0) REVERT: D 1222 TYR cc_start: 0.6769 (t80) cc_final: 0.6480 (t80) REVERT: D 1227 GLN cc_start: 0.6939 (tp40) cc_final: 0.6676 (tm-30) REVERT: D 1230 TYR cc_start: 0.6832 (t80) cc_final: 0.6499 (t80) REVERT: D 1258 MET cc_start: 0.8235 (mpp) cc_final: 0.7658 (mpp) REVERT: D 1285 GLU cc_start: 0.7672 (tt0) cc_final: 0.7342 (tt0) REVERT: D 1293 PHE cc_start: 0.7424 (p90) cc_final: 0.6907 (p90) REVERT: E 469 ILE cc_start: 0.8598 (OUTLIER) cc_final: 0.8288 (pp) REVERT: E 686 PHE cc_start: 0.7576 (m-80) cc_final: 0.7343 (t80) REVERT: E 708 ASP cc_start: 0.8558 (OUTLIER) cc_final: 0.8263 (t0) REVERT: E 716 VAL cc_start: 0.7957 (OUTLIER) cc_final: 0.7745 (p) REVERT: E 719 TYR cc_start: 0.7592 (m-80) cc_final: 0.7391 (m-10) REVERT: E 744 TYR cc_start: 0.7193 (t80) cc_final: 0.6992 (t80) REVERT: E 864 HIS cc_start: 0.7009 (t-90) cc_final: 0.5925 (m90) REVERT: E 1017 MET cc_start: 0.6349 (pmm) cc_final: 0.6058 (pmm) REVERT: E 1045 ASP cc_start: 0.8838 (t0) cc_final: 0.8347 (t0) outliers start: 36 outliers final: 20 residues processed: 309 average time/residue: 0.1315 time to fit residues: 64.2764 Evaluate side-chains 286 residues out of total 2070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 263 time to evaluate : 0.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 265 THR 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 670 MET 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 516 ASP 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 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: 10.0000 chunk 227 optimal weight: 2.9990 chunk 29 optimal weight: 0.5980 chunk 30 optimal weight: 0.6980 chunk 15 optimal weight: 6.9990 chunk 106 optimal weight: 2.9990 chunk 180 optimal weight: 1.9990 chunk 219 optimal weight: 5.9990 chunk 201 optimal weight: 3.9990 chunk 57 optimal weight: 0.7980 chunk 135 optimal weight: 9.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.158207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.114589 restraints weight = 28623.528| |-----------------------------------------------------------------------------| r_work (start): 0.3437 rms_B_bonded: 2.56 r_work: 0.3194 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3055 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.1863 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= 0.168 Angle : 0.608 9.805 26454 Z= 0.308 Chirality : 0.043 0.194 2998 Planarity : 0.004 0.049 3307 Dihedral : 8.826 84.010 2906 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 2.18 % Allowed : 14.43 % Favored : 83.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.10 (0.18), residues: 2292 helix: 0.10 (0.15), residues: 1196 sheet: -1.20 (0.37), residues: 189 loop : -1.68 (0.21), residues: 907 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D1571 TYR 0.015 0.001 TYR E 512 PHE 0.022 0.001 PHE E1003 TRP 0.016 0.001 TRP E 185 HIS 0.005 0.001 HIS D1148 Details of bonding type rmsd covalent geometry : bond 0.00399 (19545) covalent geometry : angle 0.60469 (26416) SS BOND : bond 0.00200 ( 7) SS BOND : angle 1.03918 ( 14) hydrogen bonds : bond 0.03773 ( 858) hydrogen bonds : angle 4.49840 ( 2514) link_NAG-ASN : bond 0.00262 ( 8) link_NAG-ASN : angle 1.98614 ( 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 321 residues out of total 2070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 276 time to evaluate : 0.748 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 257 ARG cc_start: 0.8568 (ptp-110) cc_final: 0.7764 (ptp90) REVERT: C 374 LYS cc_start: 0.7669 (tmtt) cc_final: 0.7215 (ptmt) REVERT: D 234 LYS cc_start: 0.8487 (mptt) cc_final: 0.8000 (mmmm) REVERT: D 265 MET cc_start: 0.7550 (tmm) cc_final: 0.7270 (tmm) REVERT: D 288 GLU cc_start: 0.8604 (mm-30) cc_final: 0.8373 (mm-30) REVERT: D 330 THR cc_start: 0.7887 (p) cc_final: 0.7638 (p) REVERT: D 348 ASN cc_start: 0.8692 (t0) cc_final: 0.8412 (m110) REVERT: D 1222 TYR cc_start: 0.7051 (t80) cc_final: 0.6736 (t80) REVERT: D 1227 GLN cc_start: 0.7058 (tp40) cc_final: 0.6743 (tm-30) REVERT: D 1258 MET cc_start: 0.8432 (OUTLIER) cc_final: 0.7895 (mpp) REVERT: D 1293 PHE cc_start: 0.7417 (p90) cc_final: 0.6853 (p90) REVERT: D 1482 GLU cc_start: 0.8091 (mp0) cc_final: 0.7849 (mp0) REVERT: D 1524 MET cc_start: 0.9235 (mmm) cc_final: 0.9005 (mmm) REVERT: E 344 LEU cc_start: 0.9254 (OUTLIER) cc_final: 0.8806 (mt) REVERT: E 469 ILE cc_start: 0.8692 (OUTLIER) cc_final: 0.8397 (pp) REVERT: E 536 ILE cc_start: 0.8824 (OUTLIER) cc_final: 0.8148 (pt) REVERT: E 686 PHE cc_start: 0.7918 (m-80) cc_final: 0.7687 (t80) REVERT: E 708 ASP cc_start: 0.8727 (t0) cc_final: 0.8442 (t0) REVERT: E 716 VAL cc_start: 0.7963 (OUTLIER) cc_final: 0.7743 (p) REVERT: E 719 TYR cc_start: 0.7772 (m-80) cc_final: 0.7444 (m-10) REVERT: E 744 TYR cc_start: 0.7230 (t80) cc_final: 0.6955 (t80) REVERT: E 864 HIS cc_start: 0.7032 (t-90) cc_final: 0.5894 (m90) REVERT: E 883 MET cc_start: 0.8277 (tpp) cc_final: 0.8020 (tpt) REVERT: E 1045 ASP cc_start: 0.8970 (t0) cc_final: 0.8527 (t0) outliers start: 45 outliers final: 24 residues processed: 304 average time/residue: 0.1328 time to fit residues: 64.3264 Evaluate side-chains 287 residues out of total 2070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 258 time to evaluate : 0.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 256 HIS Chi-restraints excluded: chain C residue 265 THR Chi-restraints excluded: chain D residue 121 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 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: 0.9990 chunk 34 optimal weight: 6.9990 chunk 88 optimal weight: 0.9980 chunk 174 optimal weight: 0.7980 chunk 229 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 152 optimal weight: 0.2980 chunk 103 optimal weight: 5.9990 chunk 109 optimal weight: 0.7980 chunk 79 optimal weight: 9.9990 chunk 194 optimal weight: 5.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.161189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.116912 restraints weight = 28846.382| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 2.66 r_work: 0.3225 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.3085 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.2155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 19560 Z= 0.124 Angle : 0.572 9.729 26454 Z= 0.289 Chirality : 0.042 0.197 2998 Planarity : 0.004 0.049 3307 Dihedral : 8.505 83.026 2906 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 2.42 % Allowed : 16.03 % Favored : 81.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.93 (0.18), residues: 2292 helix: 0.26 (0.15), residues: 1199 sheet: -1.35 (0.38), residues: 176 loop : -1.59 (0.21), residues: 917 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D1571 TYR 0.013 0.001 TYR E 512 PHE 0.012 0.001 PHE D1308 TRP 0.015 0.001 TRP E 185 HIS 0.006 0.000 HIS D1148 Details of bonding type rmsd covalent geometry : bond 0.00287 (19545) covalent geometry : angle 0.56982 (26416) SS BOND : bond 0.00168 ( 7) SS BOND : angle 0.88589 ( 14) hydrogen bonds : bond 0.03440 ( 858) hydrogen bonds : angle 4.32411 ( 2514) link_NAG-ASN : bond 0.00215 ( 8) link_NAG-ASN : angle 1.83627 ( 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 325 residues out of total 2070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 275 time to evaluate : 0.746 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 233 VAL cc_start: 0.7533 (m) cc_final: 0.7242 (p) REVERT: C 257 ARG cc_start: 0.8664 (ptp-110) cc_final: 0.7827 (ptp90) REVERT: C 374 LYS cc_start: 0.7627 (tmtt) cc_final: 0.7233 (ptmt) REVERT: C 386 ILE cc_start: 0.8551 (mm) cc_final: 0.7794 (pt) REVERT: D 234 LYS cc_start: 0.8471 (mptt) cc_final: 0.7990 (mmmm) REVERT: D 265 MET cc_start: 0.7538 (tmm) cc_final: 0.7269 (tmm) REVERT: D 330 THR cc_start: 0.7796 (p) cc_final: 0.7511 (p) REVERT: D 348 ASN cc_start: 0.8641 (t0) cc_final: 0.8377 (m110) REVERT: D 771 GLU cc_start: 0.7973 (OUTLIER) cc_final: 0.7741 (tm-30) REVERT: D 970 LEU cc_start: 0.7862 (OUTLIER) cc_final: 0.7129 (mt) REVERT: D 1222 TYR cc_start: 0.7163 (t80) cc_final: 0.6786 (t80) REVERT: D 1227 GLN cc_start: 0.7143 (tp40) cc_final: 0.6821 (tm-30) REVERT: D 1258 MET cc_start: 0.8450 (OUTLIER) cc_final: 0.7923 (mpp) REVERT: D 1293 PHE cc_start: 0.7385 (p90) cc_final: 0.6676 (p90) REVERT: D 1482 GLU cc_start: 0.8017 (mp0) cc_final: 0.7795 (mp0) REVERT: E 344 LEU cc_start: 0.9206 (OUTLIER) cc_final: 0.8759 (mt) REVERT: E 469 ILE cc_start: 0.8747 (OUTLIER) cc_final: 0.8426 (pp) REVERT: E 536 ILE cc_start: 0.8816 (OUTLIER) cc_final: 0.8182 (pt) REVERT: E 631 ILE cc_start: 0.8753 (mt) cc_final: 0.8483 (tp) REVERT: E 682 ASN cc_start: 0.9043 (m110) cc_final: 0.8609 (m110) REVERT: E 708 ASP cc_start: 0.8664 (OUTLIER) cc_final: 0.8321 (t0) REVERT: E 719 TYR cc_start: 0.7796 (m-80) cc_final: 0.7456 (m-10) REVERT: E 744 TYR cc_start: 0.7206 (t80) cc_final: 0.6869 (t80) REVERT: E 864 HIS cc_start: 0.6999 (t-90) cc_final: 0.5966 (m90) REVERT: E 1017 MET cc_start: 0.6553 (OUTLIER) cc_final: 0.6177 (mpp) REVERT: E 1045 ASP cc_start: 0.8962 (t0) cc_final: 0.8527 (t0) outliers start: 50 outliers final: 27 residues processed: 303 average time/residue: 0.1353 time to fit residues: 65.0200 Evaluate side-chains 293 residues out of total 2070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 258 time to evaluate : 0.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 256 HIS Chi-restraints excluded: chain C residue 265 THR 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 439 ASP 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 670 MET 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 150 ILE Chi-restraints excluded: chain E residue 344 LEU Chi-restraints excluded: chain E residue 389 VAL Chi-restraints excluded: chain E residue 469 ILE 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: 2.9990 chunk 91 optimal weight: 3.9990 chunk 76 optimal weight: 0.8980 chunk 167 optimal weight: 1.9990 chunk 168 optimal weight: 1.9990 chunk 108 optimal weight: 7.9990 chunk 117 optimal weight: 2.9990 chunk 52 optimal weight: 0.9980 chunk 106 optimal weight: 3.9990 chunk 49 optimal weight: 0.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.159510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.115272 restraints weight = 28841.679| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 2.69 r_work: 0.3198 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.3058 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.2215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 19560 Z= 0.163 Angle : 0.596 9.708 26454 Z= 0.299 Chirality : 0.043 0.191 2998 Planarity : 0.004 0.048 3307 Dihedral : 8.552 83.185 2906 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 2.62 % Allowed : 16.66 % Favored : 80.73 % 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: -0.84 (0.18), residues: 2292 helix: 0.33 (0.15), residues: 1198 sheet: -1.25 (0.37), residues: 182 loop : -1.55 (0.21), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D1571 TYR 0.015 0.001 TYR E 512 PHE 0.014 0.001 PHE D1507 TRP 0.016 0.001 TRP E 821 HIS 0.009 0.001 HIS D1148 Details of bonding type rmsd covalent geometry : bond 0.00390 (19545) covalent geometry : angle 0.59301 (26416) SS BOND : bond 0.00191 ( 7) SS BOND : angle 0.98177 ( 14) hydrogen bonds : bond 0.03524 ( 858) hydrogen bonds : angle 4.31704 ( 2514) link_NAG-ASN : bond 0.00241 ( 8) link_NAG-ASN : angle 1.96160 ( 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 326 residues out of total 2070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 272 time to evaluate : 0.745 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 233 VAL cc_start: 0.7601 (m) cc_final: 0.7309 (p) REVERT: C 257 ARG cc_start: 0.8639 (ptp-110) cc_final: 0.7899 (ptt180) REVERT: C 386 ILE cc_start: 0.8586 (mm) cc_final: 0.7830 (pt) REVERT: D 234 LYS cc_start: 0.8466 (mptt) cc_final: 0.7976 (mmmm) REVERT: D 265 MET cc_start: 0.7563 (tmm) cc_final: 0.7279 (tmm) REVERT: D 330 THR cc_start: 0.7826 (p) cc_final: 0.7513 (p) REVERT: D 348 ASN cc_start: 0.8671 (t0) cc_final: 0.8412 (m110) REVERT: D 771 GLU cc_start: 0.8090 (OUTLIER) cc_final: 0.7842 (tm-30) REVERT: D 970 LEU cc_start: 0.7934 (OUTLIER) cc_final: 0.7208 (mt) REVERT: D 1222 TYR cc_start: 0.7135 (t80) cc_final: 0.6825 (t80) REVERT: D 1227 GLN cc_start: 0.7150 (tp40) cc_final: 0.6874 (tm-30) REVERT: D 1258 MET cc_start: 0.8532 (OUTLIER) cc_final: 0.7934 (mpp) REVERT: D 1293 PHE cc_start: 0.7363 (p90) cc_final: 0.6628 (p90) REVERT: D 1482 GLU cc_start: 0.8010 (mp0) cc_final: 0.7784 (mp0) REVERT: E 59 ASP cc_start: 0.8758 (p0) cc_final: 0.8548 (p0) REVERT: E 469 ILE cc_start: 0.8757 (OUTLIER) cc_final: 0.8450 (pp) REVERT: E 631 ILE cc_start: 0.8753 (mt) cc_final: 0.8479 (tp) REVERT: E 682 ASN cc_start: 0.9058 (m110) cc_final: 0.8608 (m110) REVERT: E 708 ASP cc_start: 0.8686 (OUTLIER) cc_final: 0.8368 (t0) REVERT: E 719 TYR cc_start: 0.7845 (m-80) cc_final: 0.7508 (m-10) REVERT: E 744 TYR cc_start: 0.7220 (t80) cc_final: 0.6973 (t80) REVERT: E 864 HIS cc_start: 0.7052 (t-90) cc_final: 0.6045 (m90) REVERT: E 985 ASN cc_start: 0.7485 (m110) cc_final: 0.7163 (m110) REVERT: E 1017 MET cc_start: 0.6615 (OUTLIER) cc_final: 0.6354 (mpp) REVERT: E 1045 ASP cc_start: 0.8966 (t0) cc_final: 0.8548 (t0) outliers start: 54 outliers final: 37 residues processed: 306 average time/residue: 0.1349 time to fit residues: 65.0866 Evaluate side-chains 296 residues out of total 2070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 253 time to evaluate : 0.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 256 HIS Chi-restraints excluded: chain C residue 265 THR 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 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 70 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 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 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: 0.9980 chunk 142 optimal weight: 0.7980 chunk 215 optimal weight: 4.9990 chunk 149 optimal weight: 0.0970 chunk 33 optimal weight: 5.9990 chunk 230 optimal weight: 0.0060 chunk 11 optimal weight: 3.9990 chunk 108 optimal weight: 6.9990 chunk 9 optimal weight: 0.9990 chunk 192 optimal weight: 0.6980 chunk 216 optimal weight: 0.8980 overall best weight: 0.4994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.161159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.116901 restraints weight = 28817.801| |-----------------------------------------------------------------------------| r_work (start): 0.3480 rms_B_bonded: 2.76 r_work: 0.3257 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3117 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.2496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 19560 Z= 0.113 Angle : 0.573 10.126 26454 Z= 0.286 Chirality : 0.041 0.180 2998 Planarity : 0.004 0.049 3307 Dihedral : 8.304 81.539 2906 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 2.42 % Allowed : 17.24 % Favored : 80.34 % 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: -0.69 (0.18), residues: 2292 helix: 0.46 (0.15), residues: 1202 sheet: -1.16 (0.38), residues: 176 loop : -1.51 (0.21), residues: 914 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D1217 TYR 0.013 0.001 TYR E 644 PHE 0.015 0.001 PHE D1004 TRP 0.019 0.001 TRP E 821 HIS 0.010 0.000 HIS D1148 Details of bonding type rmsd covalent geometry : bond 0.00259 (19545) covalent geometry : angle 0.56986 (26416) SS BOND : bond 0.00363 ( 7) SS BOND : angle 1.56997 ( 14) hydrogen bonds : bond 0.03258 ( 858) hydrogen bonds : angle 4.18920 ( 2514) link_NAG-ASN : bond 0.00194 ( 8) link_NAG-ASN : angle 1.61035 ( 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 338 residues out of total 2070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 288 time to evaluate : 0.861 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 257 ARG cc_start: 0.8628 (ptp-110) cc_final: 0.7815 (ptp90) REVERT: C 374 LYS cc_start: 0.7461 (ptmt) cc_final: 0.7065 (ptmt) REVERT: C 386 ILE cc_start: 0.8555 (mm) cc_final: 0.7795 (pt) REVERT: D 234 LYS cc_start: 0.8434 (mptt) cc_final: 0.7946 (mmmm) REVERT: D 265 MET cc_start: 0.7700 (tmm) cc_final: 0.7430 (tmm) REVERT: D 330 THR cc_start: 0.7802 (p) cc_final: 0.7462 (p) REVERT: D 348 ASN cc_start: 0.8562 (t0) cc_final: 0.8289 (m110) REVERT: D 656 LEU cc_start: 0.7666 (OUTLIER) cc_final: 0.7463 (tt) REVERT: D 771 GLU cc_start: 0.8213 (OUTLIER) cc_final: 0.7938 (tm-30) REVERT: D 937 ASP cc_start: 0.7958 (t0) cc_final: 0.7722 (t0) REVERT: D 970 LEU cc_start: 0.7925 (OUTLIER) cc_final: 0.7164 (mt) REVERT: D 1033 LYS cc_start: 0.7630 (mttp) cc_final: 0.7429 (tttt) REVERT: D 1222 TYR cc_start: 0.7199 (t80) cc_final: 0.6830 (t80) REVERT: D 1227 GLN cc_start: 0.7138 (tp40) cc_final: 0.6847 (tm-30) REVERT: D 1258 MET cc_start: 0.8557 (OUTLIER) cc_final: 0.7992 (mpp) REVERT: D 1293 PHE cc_start: 0.7375 (p90) cc_final: 0.6713 (p90) REVERT: D 1474 MET cc_start: 0.8673 (mmt) cc_final: 0.8315 (mmt) REVERT: D 1482 GLU cc_start: 0.7967 (mp0) cc_final: 0.7739 (mp0) REVERT: D 1547 ARG cc_start: 0.8338 (ptt180) cc_final: 0.8051 (ptt90) REVERT: E 469 ILE cc_start: 0.8796 (OUTLIER) cc_final: 0.8492 (pp) REVERT: E 536 ILE cc_start: 0.8787 (OUTLIER) cc_final: 0.8107 (pt) REVERT: E 631 ILE cc_start: 0.8740 (mt) cc_final: 0.8491 (tp) REVERT: E 682 ASN cc_start: 0.9013 (m110) cc_final: 0.8638 (m110) REVERT: E 708 ASP cc_start: 0.8651 (OUTLIER) cc_final: 0.8349 (t0) REVERT: E 719 TYR cc_start: 0.7777 (m-80) cc_final: 0.7455 (m-10) REVERT: E 744 TYR cc_start: 0.7099 (t80) cc_final: 0.6863 (t80) REVERT: E 864 HIS cc_start: 0.7145 (t-90) cc_final: 0.6172 (m90) REVERT: E 883 MET cc_start: 0.8293 (tpt) cc_final: 0.7965 (tpp) REVERT: E 1045 ASP cc_start: 0.8965 (t0) cc_final: 0.8530 (t0) outliers start: 50 outliers final: 33 residues processed: 322 average time/residue: 0.1362 time to fit residues: 69.4283 Evaluate side-chains 304 residues out of total 2070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 264 time to evaluate : 0.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 256 HIS Chi-restraints excluded: chain C residue 265 THR 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 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 656 LEU Chi-restraints excluded: chain D residue 762 LEU Chi-restraints excluded: chain D residue 771 GLU 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 1652 VAL Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 150 ILE Chi-restraints excluded: chain E residue 183 LEU Chi-restraints excluded: chain E residue 469 ILE 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: 3.9990 chunk 143 optimal weight: 10.0000 chunk 182 optimal weight: 3.9990 chunk 67 optimal weight: 0.8980 chunk 213 optimal weight: 10.0000 chunk 125 optimal weight: 0.5980 chunk 20 optimal weight: 2.9990 chunk 105 optimal weight: 10.0000 chunk 24 optimal weight: 1.9990 chunk 154 optimal weight: 1.9990 chunk 166 optimal weight: 0.0670 overall best weight: 1.1122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.159953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.115185 restraints weight = 28951.375| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 2.74 r_work: 0.3231 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.3090 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.2532 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= 0.145 Angle : 0.597 11.417 26454 Z= 0.297 Chirality : 0.042 0.186 2998 Planarity : 0.004 0.049 3307 Dihedral : 8.334 82.397 2906 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 2.52 % Allowed : 17.92 % Favored : 79.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.63 (0.18), residues: 2292 helix: 0.51 (0.15), residues: 1201 sheet: -1.05 (0.38), residues: 175 loop : -1.49 (0.21), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D1217 TYR 0.026 0.001 TYR E 666 PHE 0.031 0.001 PHE E 686 TRP 0.017 0.001 TRP E 821 HIS 0.011 0.001 HIS D1148 Details of bonding type rmsd covalent geometry : bond 0.00346 (19545) covalent geometry : angle 0.59372 (26416) SS BOND : bond 0.00171 ( 7) SS BOND : angle 1.44890 ( 14) hydrogen bonds : bond 0.03363 ( 858) hydrogen bonds : angle 4.20803 ( 2514) link_NAG-ASN : bond 0.00241 ( 8) link_NAG-ASN : angle 1.89253 ( 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 323 residues out of total 2070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 271 time to evaluate : 0.721 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 257 ARG cc_start: 0.8607 (ptp-110) cc_final: 0.7727 (ptp90) REVERT: C 308 PHE cc_start: 0.6558 (m-80) cc_final: 0.6284 (m-80) REVERT: C 374 LYS cc_start: 0.7450 (ptmt) cc_final: 0.7055 (ptmt) REVERT: C 386 ILE cc_start: 0.8599 (mm) cc_final: 0.7904 (pt) REVERT: D 234 LYS cc_start: 0.8424 (mptt) cc_final: 0.7935 (mmmm) REVERT: D 265 MET cc_start: 0.7665 (tmm) cc_final: 0.7387 (tmm) REVERT: D 348 ASN cc_start: 0.8632 (t0) cc_final: 0.8373 (m110) REVERT: D 571 MET cc_start: 0.6995 (ttp) cc_final: 0.6753 (ttt) REVERT: D 656 LEU cc_start: 0.7672 (OUTLIER) cc_final: 0.7445 (tt) REVERT: D 937 ASP cc_start: 0.7977 (t0) cc_final: 0.7712 (t0) REVERT: D 970 LEU cc_start: 0.7889 (OUTLIER) cc_final: 0.7133 (mt) REVERT: D 1033 LYS cc_start: 0.7616 (mttp) cc_final: 0.7405 (tttt) REVERT: D 1222 TYR cc_start: 0.7284 (t80) cc_final: 0.6907 (t80) REVERT: D 1227 GLN cc_start: 0.7334 (tp40) cc_final: 0.7017 (tm-30) REVERT: D 1258 MET cc_start: 0.8563 (OUTLIER) cc_final: 0.7984 (mpp) REVERT: D 1293 PHE cc_start: 0.7302 (p90) cc_final: 0.6667 (p90) REVERT: D 1482 GLU cc_start: 0.7958 (mp0) cc_final: 0.7692 (mp0) REVERT: E 469 ILE cc_start: 0.8739 (OUTLIER) cc_final: 0.8442 (pp) REVERT: E 631 ILE cc_start: 0.8689 (mt) cc_final: 0.8466 (tp) REVERT: E 682 ASN cc_start: 0.9000 (m110) cc_final: 0.8668 (m110) REVERT: E 708 ASP cc_start: 0.8736 (OUTLIER) cc_final: 0.8372 (t0) REVERT: E 719 TYR cc_start: 0.7816 (m-80) cc_final: 0.7480 (m-10) REVERT: E 744 TYR cc_start: 0.7109 (t80) cc_final: 0.6873 (t80) REVERT: E 864 HIS cc_start: 0.7132 (t-90) cc_final: 0.6162 (m90) REVERT: E 883 MET cc_start: 0.8284 (tpt) cc_final: 0.7980 (tpp) REVERT: E 1045 ASP cc_start: 0.8964 (t0) cc_final: 0.8547 (t0) outliers start: 52 outliers final: 41 residues processed: 306 average time/residue: 0.1352 time to fit residues: 65.4897 Evaluate side-chains 307 residues out of total 2070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 261 time to evaluate : 0.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 256 HIS Chi-restraints excluded: chain C residue 265 THR 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 167 LEU 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 656 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 1046 ILE Chi-restraints excluded: chain D residue 1095 THR 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 183 LEU Chi-restraints excluded: chain E residue 389 VAL Chi-restraints excluded: chain E residue 469 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 Chi-restraints excluded: chain E residue 1065 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 203 optimal weight: 2.9990 chunk 44 optimal weight: 0.4980 chunk 22 optimal weight: 9.9990 chunk 52 optimal weight: 0.9990 chunk 48 optimal weight: 10.0000 chunk 78 optimal weight: 9.9990 chunk 61 optimal weight: 3.9990 chunk 167 optimal weight: 0.0020 chunk 101 optimal weight: 0.9980 chunk 192 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 overall best weight: 0.6790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.161375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.116982 restraints weight = 28763.795| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 2.75 r_work: 0.3260 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3120 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.2704 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= 0.120 Angle : 0.586 11.199 26454 Z= 0.293 Chirality : 0.042 0.181 2998 Planarity : 0.004 0.049 3307 Dihedral : 8.169 80.649 2906 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 2.03 % Allowed : 18.64 % Favored : 79.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.51 (0.18), residues: 2292 helix: 0.62 (0.15), residues: 1202 sheet: -0.89 (0.39), residues: 169 loop : -1.49 (0.21), residues: 921 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 626 TYR 0.015 0.001 TYR E 666 PHE 0.021 0.001 PHE E 686 TRP 0.023 0.001 TRP E 821 HIS 0.012 0.001 HIS D1148 Details of bonding type rmsd covalent geometry : bond 0.00280 (19545) covalent geometry : angle 0.58413 (26416) SS BOND : bond 0.00160 ( 7) SS BOND : angle 1.18357 ( 14) hydrogen bonds : bond 0.03254 ( 858) hydrogen bonds : angle 4.14083 ( 2514) link_NAG-ASN : bond 0.00205 ( 8) link_NAG-ASN : angle 1.61047 ( 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 316 residues out of total 2070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 274 time to evaluate : 0.779 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 257 ARG cc_start: 0.8589 (ptp-110) cc_final: 0.7796 (ptp90) REVERT: C 369 MET cc_start: 0.7636 (mtm) cc_final: 0.7431 (mpp) REVERT: C 374 LYS cc_start: 0.7367 (ptmt) cc_final: 0.7033 (ptmt) REVERT: C 386 ILE cc_start: 0.8610 (mm) cc_final: 0.7906 (pt) REVERT: D 234 LYS cc_start: 0.8375 (mptt) cc_final: 0.7888 (mmmm) REVERT: D 265 MET cc_start: 0.7627 (tmm) cc_final: 0.7165 (tmm) REVERT: D 348 ASN cc_start: 0.8568 (t0) cc_final: 0.8323 (m110) REVERT: D 656 LEU cc_start: 0.7644 (OUTLIER) cc_final: 0.7421 (tt) REVERT: D 937 ASP cc_start: 0.8072 (t0) cc_final: 0.7795 (t0) REVERT: D 970 LEU cc_start: 0.7883 (OUTLIER) cc_final: 0.7115 (mt) REVERT: D 1033 LYS cc_start: 0.7596 (mttp) cc_final: 0.7389 (tttt) REVERT: D 1222 TYR cc_start: 0.7330 (t80) cc_final: 0.7017 (t80) REVERT: D 1227 GLN cc_start: 0.7270 (tp40) cc_final: 0.6980 (tm-30) REVERT: D 1258 MET cc_start: 0.8560 (OUTLIER) cc_final: 0.7954 (mpp) REVERT: D 1293 PHE cc_start: 0.7273 (p90) cc_final: 0.6659 (p90) REVERT: D 1474 MET cc_start: 0.8612 (mmt) cc_final: 0.8302 (mmt) REVERT: D 1482 GLU cc_start: 0.8017 (mp0) cc_final: 0.7760 (mp0) REVERT: E 469 ILE cc_start: 0.8746 (OUTLIER) cc_final: 0.8461 (pp) REVERT: E 631 ILE cc_start: 0.8683 (mt) cc_final: 0.8466 (tp) REVERT: E 682 ASN cc_start: 0.8972 (m110) cc_final: 0.8660 (m110) REVERT: E 708 ASP cc_start: 0.8714 (OUTLIER) cc_final: 0.8370 (t0) REVERT: E 744 TYR cc_start: 0.7087 (t80) cc_final: 0.6857 (t80) REVERT: E 864 HIS cc_start: 0.7120 (t-90) cc_final: 0.6217 (m90) REVERT: E 883 MET cc_start: 0.8234 (tpt) cc_final: 0.7916 (tpp) REVERT: E 1045 ASP cc_start: 0.8958 (t0) cc_final: 0.8523 (t0) outliers start: 42 outliers final: 35 residues processed: 301 average time/residue: 0.1324 time to fit residues: 63.5956 Evaluate side-chains 304 residues out of total 2070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 264 time to evaluate : 0.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 256 HIS Chi-restraints excluded: chain C residue 265 THR 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 167 LEU 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 656 LEU Chi-restraints excluded: chain D residue 762 LEU 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 1652 VAL Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 150 ILE 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 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 146 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 69 optimal weight: 0.7980 chunk 3 optimal weight: 0.7980 chunk 142 optimal weight: 0.9990 chunk 110 optimal weight: 2.9990 chunk 28 optimal weight: 4.9990 chunk 75 optimal weight: 0.0040 chunk 111 optimal weight: 1.9990 chunk 163 optimal weight: 1.9990 chunk 102 optimal weight: 0.9980 overall best weight: 0.7194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.161629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.117140 restraints weight = 28886.929| |-----------------------------------------------------------------------------| r_work (start): 0.3485 rms_B_bonded: 2.81 r_work: 0.3262 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3122 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.2804 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= 0.122 Angle : 0.594 10.874 26454 Z= 0.293 Chirality : 0.042 0.301 2998 Planarity : 0.004 0.049 3307 Dihedral : 8.147 82.333 2906 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 2.03 % Allowed : 18.89 % Favored : 79.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.44 (0.18), residues: 2292 helix: 0.68 (0.15), residues: 1204 sheet: -0.84 (0.39), residues: 169 loop : -1.46 (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 0.030 0.001 PHE E1003 TRP 0.020 0.001 TRP E 821 HIS 0.011 0.001 HIS D1148 Details of bonding type rmsd covalent geometry : bond 0.00284 (19545) covalent geometry : angle 0.59129 (26416) SS BOND : bond 0.00143 ( 7) SS BOND : angle 1.14542 ( 14) hydrogen bonds : bond 0.03200 ( 858) hydrogen bonds : angle 4.11396 ( 2514) link_NAG-ASN : bond 0.00206 ( 8) link_NAG-ASN : angle 1.67948 ( 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 318 residues out of total 2070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 276 time to evaluate : 0.755 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 257 ARG cc_start: 0.8582 (ptp-110) cc_final: 0.7719 (ptp90) REVERT: C 326 HIS cc_start: 0.6515 (t-90) cc_final: 0.6312 (t-90) REVERT: C 374 LYS cc_start: 0.7348 (ptmt) cc_final: 0.6845 (ptmt) REVERT: D 234 LYS cc_start: 0.8363 (mptt) cc_final: 0.7862 (mmmm) REVERT: D 265 MET cc_start: 0.7617 (tmm) cc_final: 0.7175 (tmm) REVERT: D 348 ASN cc_start: 0.8492 (t0) cc_final: 0.8274 (m110) REVERT: D 937 ASP cc_start: 0.8130 (t0) cc_final: 0.7889 (t0) REVERT: D 970 LEU cc_start: 0.7837 (OUTLIER) cc_final: 0.7084 (mt) REVERT: D 1222 TYR cc_start: 0.7406 (t80) cc_final: 0.7192 (t80) REVERT: D 1227 GLN cc_start: 0.7273 (tp40) cc_final: 0.7049 (tm-30) REVERT: D 1258 MET cc_start: 0.8576 (OUTLIER) cc_final: 0.7966 (mpp) REVERT: D 1293 PHE cc_start: 0.7158 (p90) cc_final: 0.6522 (p90) REVERT: D 1474 MET cc_start: 0.8583 (mmt) cc_final: 0.8270 (mmt) REVERT: D 1482 GLU cc_start: 0.7994 (mp0) cc_final: 0.7749 (mp0) REVERT: D 1524 MET cc_start: 0.9052 (mmm) cc_final: 0.8846 (mmm) REVERT: E 469 ILE cc_start: 0.8798 (OUTLIER) cc_final: 0.8529 (pp) REVERT: E 631 ILE cc_start: 0.8670 (mt) cc_final: 0.8469 (tp) REVERT: E 682 ASN cc_start: 0.8970 (m110) cc_final: 0.8665 (m110) REVERT: E 708 ASP cc_start: 0.8676 (t0) cc_final: 0.8318 (t0) REVERT: E 744 TYR cc_start: 0.7089 (t80) cc_final: 0.6874 (t80) REVERT: E 864 HIS cc_start: 0.7183 (t-90) cc_final: 0.6236 (m90) REVERT: E 977 GLU cc_start: 0.8465 (tt0) cc_final: 0.8220 (tt0) REVERT: E 1045 ASP cc_start: 0.8972 (t0) cc_final: 0.8550 (t0) outliers start: 42 outliers final: 38 residues processed: 301 average time/residue: 0.1319 time to fit residues: 63.4233 Evaluate side-chains 300 residues out of total 2070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 259 time to evaluate : 0.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 256 HIS Chi-restraints excluded: chain C residue 265 THR 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 167 LEU Chi-restraints excluded: chain D residue 239 PHE Chi-restraints excluded: chain D residue 248 VAL Chi-restraints excluded: chain D residue 251 VAL Chi-restraints excluded: chain D residue 330 THR 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 762 LEU 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 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 1552 TYR 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 183 LEU Chi-restraints excluded: chain E residue 389 VAL Chi-restraints excluded: chain E residue 469 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 1058 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 50 optimal weight: 1.9990 chunk 151 optimal weight: 2.9990 chunk 227 optimal weight: 0.6980 chunk 28 optimal weight: 3.9990 chunk 181 optimal weight: 0.0010 chunk 94 optimal weight: 0.9980 chunk 3 optimal weight: 2.9990 chunk 220 optimal weight: 4.9990 chunk 229 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 37 optimal weight: 0.5980 overall best weight: 0.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.161129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.116632 restraints weight = 28744.632| |-----------------------------------------------------------------------------| r_work (start): 0.3480 rms_B_bonded: 2.78 r_work: 0.3254 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.3113 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.2868 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= 0.128 Angle : 0.602 11.858 26454 Z= 0.296 Chirality : 0.042 0.241 2998 Planarity : 0.004 0.059 3307 Dihedral : 8.185 87.242 2906 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 2.03 % Allowed : 19.32 % Favored : 78.64 % 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: -0.44 (0.18), residues: 2292 helix: 0.67 (0.15), residues: 1206 sheet: -0.78 (0.39), residues: 169 loop : -1.45 (0.21), residues: 917 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D1571 TYR 0.024 0.001 TYR E 666 PHE 0.022 0.001 PHE E 686 TRP 0.032 0.001 TRP E 821 HIS 0.011 0.001 HIS D1148 Details of bonding type rmsd covalent geometry : bond 0.00302 (19545) covalent geometry : angle 0.59973 (26416) SS BOND : bond 0.00154 ( 7) SS BOND : angle 1.10249 ( 14) hydrogen bonds : bond 0.03224 ( 858) hydrogen bonds : angle 4.10943 ( 2514) link_NAG-ASN : bond 0.00210 ( 8) link_NAG-ASN : angle 1.56044 ( 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: 6436.85 seconds wall clock time: 109 minutes 52.06 seconds (6592.06 seconds total)