Starting phenix.real_space_refine on Tue Nov 18 04:09:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6bhu_7099/11_2025/6bhu_7099.cif Found real_map, /net/cci-nas-00/data/ceres_data/6bhu_7099/11_2025/6bhu_7099.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.14 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6bhu_7099/11_2025/6bhu_7099.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6bhu_7099/11_2025/6bhu_7099.map" model { file = "/net/cci-nas-00/data/ceres_data/6bhu_7099/11_2025/6bhu_7099.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6bhu_7099/11_2025/6bhu_7099.cif" } resolution = 3.14 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= 0.008 sd= 0.236 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 47 5.16 5 C 6616 2.51 5 N 1727 2.21 5 O 1875 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10273 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 10125 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1328, 10125 Classifications: {'peptide': 1328} Incomplete info: {'truncation_to_alanine': 120} Link IDs: {'PTRANS': 44, 'TRANS': 1283} Chain breaks: 8 Unresolved non-hydrogen bonds: 240 Unresolved non-hydrogen angles: 360 Unresolved non-hydrogen dihedrals: 120 Planarities with less than four sites: {'UNK:plan-1': 120} Unresolved non-hydrogen planarities: 120 Chain: "A" Number of atoms: 148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 148 Unusual residues: {' MG': 2, 'ATP': 2, 'CLR': 3} Classifications: {'undetermined': 7} Link IDs: {None: 6} Time building chain proxies: 2.66, per 1000 atoms: 0.26 Number of scatterers: 10273 At special positions: 0 Unit cell: (144.609, 98.857, 97.223, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 47 16.00 P 6 15.00 Mg 2 11.99 O 1875 8.00 N 1727 7.00 C 6616 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 Time building additional restraints: 0.87 Conformation dependent library (CDL) restraints added in 379.5 milliseconds 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2518 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 5 sheets defined 77.6% alpha, 6.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.40 Creating SS restraints... Processing helix chain 'A' and resid 30 through 40 Processing helix chain 'A' and resid 42 through 50 Processing helix chain 'A' and resid 76 through 99 Processing helix chain 'A' and resid 106 through 130 removed outlier: 3.520A pdb=" N UNK A 130 " --> pdb=" O UNK A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 152 removed outlier: 3.519A pdb=" N UNK A 148 " --> pdb=" O UNK A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 158 removed outlier: 4.215A pdb=" N UNK A 157 " --> pdb=" O UNK A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 194 removed outlier: 3.625A pdb=" N UNK A 194 " --> pdb=" O UNK A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 221 Processing helix chain 'A' and resid 224 through 234 removed outlier: 3.563A pdb=" N MET A 228 " --> pdb=" O ILE A 224 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLN A 230 " --> pdb=" O GLY A 226 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ARG A 233 " --> pdb=" O VAL A 229 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLN A 234 " --> pdb=" O GLN A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 241 removed outlier: 3.569A pdb=" N ASP A 240 " --> pdb=" O GLU A 237 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N LEU A 241 " --> pdb=" O SER A 238 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 237 through 241' Processing helix chain 'A' and resid 249 through 268 Proline residue: A 255 - end of helix removed outlier: 3.954A pdb=" N SER A 268 " --> pdb=" O GLU A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 320 Processing helix chain 'A' and resid 321 through 326 Processing helix chain 'A' and resid 327 through 355 Proline residue: A 343 - end of helix removed outlier: 3.629A pdb=" N ASN A 354 " --> pdb=" O ILE A 350 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ASP A 355 " --> pdb=" O ASN A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 360 through 408 removed outlier: 4.228A pdb=" N TYR A 364 " --> pdb=" O GLU A 360 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LEU A 408 " --> pdb=" O TYR A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 418 removed outlier: 3.762A pdb=" N SER A 417 " --> pdb=" O ALA A 413 " (cutoff:3.500A) Processing helix chain 'A' and resid 419 through 441 removed outlier: 3.550A pdb=" N ILE A 423 " --> pdb=" O THR A 419 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ASP A 430 " --> pdb=" O LEU A 426 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N ALA A 431 " --> pdb=" O MET A 427 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N GLN A 432 " --> pdb=" O SER A 428 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N THR A 439 " --> pdb=" O MET A 435 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N TYR A 440 " --> pdb=" O ASP A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 442 through 462 removed outlier: 3.733A pdb=" N SER A 446 " --> pdb=" O ASN A 442 " (cutoff:3.500A) Proline residue: A 448 - end of helix removed outlier: 3.534A pdb=" N LEU A 458 " --> pdb=" O ALA A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 510 removed outlier: 3.692A pdb=" N MET A 473 " --> pdb=" O GLY A 469 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL A 474 " --> pdb=" O VAL A 470 " (cutoff:3.500A) Proline residue: A 478 - end of helix removed outlier: 3.781A pdb=" N THR A 489 " --> pdb=" O MET A 485 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLU A 507 " --> pdb=" O LYS A 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 511 through 519 removed outlier: 3.726A pdb=" N LEU A 515 " --> pdb=" O GLY A 511 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 555 Processing helix chain 'A' and resid 555 through 571 removed outlier: 3.874A pdb=" N LEU A 559 " --> pdb=" O CYS A 555 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N VAL A 567 " --> pdb=" O SER A 563 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N TYR A 568 " --> pdb=" O THR A 564 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N VAL A 569 " --> pdb=" O PHE A 565 " (cutoff:3.500A) Processing helix chain 'A' and resid 579 through 590 removed outlier: 3.655A pdb=" N PHE A 583 " --> pdb=" O ALA A 579 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N VAL A 584 " --> pdb=" O GLN A 580 " (cutoff:3.500A) Processing helix chain 'A' and resid 592 through 598 removed outlier: 4.071A pdb=" N LEU A 596 " --> pdb=" O LEU A 592 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ILE A 598 " --> pdb=" O PHE A 594 " (cutoff:3.500A) Processing helix chain 'A' and resid 598 through 621 removed outlier: 3.591A pdb=" N VAL A 602 " --> pdb=" O ILE A 598 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N SER A 612 " --> pdb=" O GLN A 608 " (cutoff:3.500A) Processing helix chain 'A' and resid 626 through 630 removed outlier: 3.847A pdb=" N SER A 629 " --> pdb=" O ASP A 626 " (cutoff:3.500A) Processing helix chain 'A' and resid 683 through 691 Processing helix chain 'A' and resid 721 through 728 Processing helix chain 'A' and resid 733 through 744 Processing helix chain 'A' and resid 746 through 753 removed outlier: 3.738A pdb=" N LEU A 753 " --> pdb=" O ASP A 749 " (cutoff:3.500A) Processing helix chain 'A' and resid 769 through 785 removed outlier: 3.700A pdb=" N ALA A 781 " --> pdb=" O SER A 777 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ASP A 785 " --> pdb=" O ALA A 781 " (cutoff:3.500A) Processing helix chain 'A' and resid 799 through 810 Processing helix chain 'A' and resid 831 through 835 Processing helix chain 'A' and resid 851 through 859 removed outlier: 3.816A pdb=" N ASP A 859 " --> pdb=" O LEU A 855 " (cutoff:3.500A) Processing helix chain 'A' and resid 860 through 866 Processing helix chain 'A' and resid 958 through 970 removed outlier: 3.956A pdb=" N TYR A 962 " --> pdb=" O LYS A 958 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ILE A 969 " --> pdb=" O TYR A 965 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLY A 970 " --> pdb=" O MET A 966 " (cutoff:3.500A) Processing helix chain 'A' and resid 970 through 1000 removed outlier: 3.559A pdb=" N SER A 974 " --> pdb=" O GLY A 970 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASN A 992 " --> pdb=" O SER A 988 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N ASP A1000 " --> pdb=" O SER A 996 " (cutoff:3.500A) Processing helix chain 'A' and resid 1007 through 1058 removed outlier: 3.577A pdb=" N THR A1011 " --> pdb=" O THR A1007 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N GLN A1012 " --> pdb=" O GLN A1008 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N SER A1016 " --> pdb=" O GLN A1012 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N VAL A1017 " --> pdb=" O VAL A1013 " (cutoff:3.500A) Processing helix chain 'A' and resid 1059 through 1066 removed outlier: 3.924A pdb=" N PHE A1063 " --> pdb=" O PRO A1059 " (cutoff:3.500A) Processing helix chain 'A' and resid 1067 through 1110 removed outlier: 3.846A pdb=" N LEU A1071 " --> pdb=" O PRO A1067 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ARG A1074 " --> pdb=" O ASN A1070 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N GLU A1078 " --> pdb=" O ARG A1074 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N LEU A1079 " --> pdb=" O PHE A1075 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N ILE A1086 " --> pdb=" O VAL A1082 " (cutoff:3.500A) Proline residue: A1087 - end of helix Processing helix chain 'A' and resid 1117 through 1147 removed outlier: 3.611A pdb=" N LEU A1121 " --> pdb=" O ILE A1117 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N TYR A1125 " --> pdb=" O LEU A1121 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N PHE A1127 " --> pdb=" O LEU A1123 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ALA A1134 " --> pdb=" O ARG A1130 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N SER A1135 " --> pdb=" O PHE A1131 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N GLN A1138 " --> pdb=" O ALA A1134 " (cutoff:3.500A) Processing helix chain 'A' and resid 1147 through 1160 removed outlier: 3.652A pdb=" N PHE A1154 " --> pdb=" O VAL A1150 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LEU A1159 " --> pdb=" O ASN A1155 " (cutoff:3.500A) Processing helix chain 'A' and resid 1160 through 1168 Processing helix chain 'A' and resid 1169 through 1220 removed outlier: 3.685A pdb=" N PHE A1173 " --> pdb=" O GLU A1169 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLU A1183 " --> pdb=" O LEU A1179 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ASN A1184 " --> pdb=" O LYS A1180 " (cutoff:3.500A) Proline residue: A1190 - end of helix Processing helix chain 'A' and resid 1225 through 1257 removed outlier: 3.575A pdb=" N VAL A1229 " --> pdb=" O SER A1225 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLY A1230 " --> pdb=" O ALA A1226 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N LEU A1231 " --> pdb=" O GLY A1227 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N VAL A1233 " --> pdb=" O VAL A1229 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N SER A1234 " --> pdb=" O GLY A1230 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N TYR A1235 " --> pdb=" O LEU A1231 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N SER A1236 " --> pdb=" O SER A1232 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU A1237 " --> pdb=" O VAL A1233 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N GLN A1238 " --> pdb=" O SER A1234 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N THR A1240 " --> pdb=" O SER A1236 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL A1247 " --> pdb=" O LEU A1243 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ARG A1248 " --> pdb=" O ASN A1244 " (cutoff:3.500A) Processing helix chain 'A' and resid 1257 through 1264 Processing helix chain 'A' and resid 1265 through 1267 No H-bonds generated for 'chain 'A' and resid 1265 through 1267' Processing helix chain 'A' and resid 1332 through 1340 removed outlier: 3.643A pdb=" N THR A1336 " --> pdb=" O LYS A1332 " (cutoff:3.500A) Processing helix chain 'A' and resid 1361 through 1367 removed outlier: 3.649A pdb=" N PHE A1367 " --> pdb=" O HIS A1363 " (cutoff:3.500A) Processing helix chain 'A' and resid 1383 through 1388 removed outlier: 3.552A pdb=" N LEU A1387 " --> pdb=" O LEU A1383 " (cutoff:3.500A) Processing helix chain 'A' and resid 1394 through 1405 removed outlier: 3.891A pdb=" N VAL A1398 " --> pdb=" O SER A1394 " (cutoff:3.500A) Processing helix chain 'A' and resid 1407 through 1414 Processing helix chain 'A' and resid 1430 through 1446 removed outlier: 3.635A pdb=" N LEU A1436 " --> pdb=" O GLY A1432 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ARG A1445 " --> pdb=" O ARG A1441 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LYS A1446 " --> pdb=" O ALA A1442 " (cutoff:3.500A) Processing helix chain 'A' and resid 1460 through 1475 removed outlier: 3.855A pdb=" N ASP A1465 " --> pdb=" O LEU A1461 " (cutoff:3.500A) Processing helix chain 'A' and resid 1486 through 1491 Processing helix chain 'A' and resid 1509 through 1517 removed outlier: 3.934A pdb=" N ARG A1517 " --> pdb=" O LEU A1513 " (cutoff:3.500A) Processing helix chain 'A' and resid 1518 through 1528 Processing sheet with id=AA1, first strand: chain 'A' and resid 664 through 669 removed outlier: 5.740A pdb=" N ILE A 664 " --> pdb=" O ASN A 648 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ILE A 644 " --> pdb=" O VAL A 704 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N VAL A 704 " --> pdb=" O ILE A 644 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N VAL A 646 " --> pdb=" O VAL A 702 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N VAL A 702 " --> pdb=" O VAL A 646 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N ASN A 648 " --> pdb=" O GLY A 700 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N THR A 650 " --> pdb=" O VAL A 698 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 708 through 711 removed outlier: 6.591A pdb=" N ALA A 709 " --> pdb=" O LEU A 790 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N TYR A 789 " --> pdb=" O LEU A 823 " (cutoff:3.500A) removed outlier: 7.873A pdb=" N VAL A 825 " --> pdb=" O TYR A 789 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N LEU A 791 " --> pdb=" O VAL A 825 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N VAL A 837 " --> pdb=" O LEU A 673 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N VAL A 840 " --> pdb=" O SER A 847 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1315 through 1316 removed outlier: 4.182A pdb=" N TYR A1297 " --> pdb=" O GLU A1347 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N GLU A1347 " --> pdb=" O TYR A1297 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1370 through 1372 removed outlier: 6.271A pdb=" N GLY A1323 " --> pdb=" O ILE A1497 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N LEU A1499 " --> pdb=" O GLY A1323 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N VAL A1325 " --> pdb=" O LEU A1499 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1381 through 1382 645 hydrogen bonds defined for protein. 1887 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.93 Time building geometry restraints manager: 1.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1738 1.33 - 1.45: 2600 1.45 - 1.57: 6048 1.57 - 1.69: 10 1.69 - 1.81: 79 Bond restraints: 10475 Sorted by residual: bond pdb=" C4 ATP A1602 " pdb=" C5 ATP A1602 " ideal model delta sigma weight residual 1.388 1.473 -0.085 1.00e-02 1.00e+04 7.20e+01 bond pdb=" C4 ATP A1601 " pdb=" C5 ATP A1601 " ideal model delta sigma weight residual 1.388 1.473 -0.085 1.00e-02 1.00e+04 7.17e+01 bond pdb=" C5 ATP A1601 " pdb=" C6 ATP A1601 " ideal model delta sigma weight residual 1.409 1.485 -0.076 1.00e-02 1.00e+04 5.72e+01 bond pdb=" C5 ATP A1602 " pdb=" C6 ATP A1602 " ideal model delta sigma weight residual 1.409 1.481 -0.072 1.00e-02 1.00e+04 5.25e+01 bond pdb=" C8 ATP A1601 " pdb=" N7 ATP A1601 " ideal model delta sigma weight residual 1.310 1.358 -0.048 1.00e-02 1.00e+04 2.34e+01 ... (remaining 10470 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.69: 14113 3.69 - 7.38: 131 7.38 - 11.07: 10 11.07 - 14.77: 0 14.77 - 18.46: 4 Bond angle restraints: 14258 Sorted by residual: angle pdb=" PB ATP A1602 " pdb=" O3B ATP A1602 " pdb=" PG ATP A1602 " ideal model delta sigma weight residual 139.87 121.41 18.46 1.00e+00 1.00e+00 3.41e+02 angle pdb=" PB ATP A1601 " pdb=" O3B ATP A1601 " pdb=" PG ATP A1601 " ideal model delta sigma weight residual 139.87 121.57 18.30 1.00e+00 1.00e+00 3.35e+02 angle pdb=" PA ATP A1602 " pdb=" O3A ATP A1602 " pdb=" PB ATP A1602 " ideal model delta sigma weight residual 136.83 121.48 15.35 1.00e+00 1.00e+00 2.36e+02 angle pdb=" PA ATP A1601 " pdb=" O3A ATP A1601 " pdb=" PB ATP A1601 " ideal model delta sigma weight residual 136.83 121.79 15.04 1.00e+00 1.00e+00 2.26e+02 angle pdb=" C5 ATP A1602 " pdb=" C4 ATP A1602 " pdb=" N3 ATP A1602 " ideal model delta sigma weight residual 126.80 118.41 8.39 1.00e+00 1.00e+00 7.03e+01 ... (remaining 14253 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.96: 5950 16.96 - 33.91: 394 33.91 - 50.87: 85 50.87 - 67.82: 14 67.82 - 84.77: 6 Dihedral angle restraints: 6449 sinusoidal: 2574 harmonic: 3875 Sorted by residual: dihedral pdb=" CA TYR A 318 " pdb=" C TYR A 318 " pdb=" N LYS A 319 " pdb=" CA LYS A 319 " ideal model delta harmonic sigma weight residual 180.00 154.27 25.73 0 5.00e+00 4.00e-02 2.65e+01 dihedral pdb=" CA ALA A1110 " pdb=" C ALA A1110 " pdb=" N THR A1111 " pdb=" CA THR A1111 " ideal model delta harmonic sigma weight residual 180.00 -159.78 -20.22 0 5.00e+00 4.00e-02 1.64e+01 dihedral pdb=" C ARG A1486 " pdb=" N ARG A1486 " pdb=" CA ARG A1486 " pdb=" CB ARG A1486 " ideal model delta harmonic sigma weight residual -122.60 -112.59 -10.01 0 2.50e+00 1.60e-01 1.60e+01 ... (remaining 6446 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 1438 0.083 - 0.167: 217 0.167 - 0.250: 31 0.250 - 0.334: 4 0.334 - 0.417: 1 Chirality restraints: 1691 Sorted by residual: chirality pdb=" CA CYS A 682 " pdb=" N CYS A 682 " pdb=" C CYS A 682 " pdb=" CB CYS A 682 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.42 2.00e-01 2.50e+01 4.35e+00 chirality pdb=" CA ILE A1483 " pdb=" N ILE A1483 " pdb=" C ILE A1483 " pdb=" CB ILE A1483 " both_signs ideal model delta sigma weight residual False 2.43 2.77 -0.33 2.00e-01 2.50e+01 2.78e+00 chirality pdb=" CA LEU A1487 " pdb=" N LEU A1487 " pdb=" C LEU A1487 " pdb=" CB LEU A1487 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.61e+00 ... (remaining 1688 not shown) Planarity restraints: 1766 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL A 825 " 0.013 2.00e-02 2.50e+03 2.61e-02 6.82e+00 pdb=" C VAL A 825 " -0.045 2.00e-02 2.50e+03 pdb=" O VAL A 825 " 0.017 2.00e-02 2.50e+03 pdb=" N THR A 826 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A1486 " 0.009 2.00e-02 2.50e+03 1.81e-02 3.27e+00 pdb=" C ARG A1486 " -0.031 2.00e-02 2.50e+03 pdb=" O ARG A1486 " 0.012 2.00e-02 2.50e+03 pdb=" N LEU A1487 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 824 " -0.008 2.00e-02 2.50e+03 1.78e-02 3.17e+00 pdb=" C LEU A 824 " 0.031 2.00e-02 2.50e+03 pdb=" O LEU A 824 " -0.012 2.00e-02 2.50e+03 pdb=" N VAL A 825 " -0.010 2.00e-02 2.50e+03 ... (remaining 1763 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 15 2.51 - 3.11: 6631 3.11 - 3.71: 15455 3.71 - 4.30: 20868 4.30 - 4.90: 35631 Nonbonded interactions: 78600 Sorted by model distance: nonbonded pdb=" OG SER A1333 " pdb="MG MG A1604 " model vdw 1.915 2.170 nonbonded pdb=" O1G ATP A1601 " pdb="MG MG A1603 " model vdw 1.988 2.170 nonbonded pdb=" O1B ATP A1601 " pdb="MG MG A1603 " model vdw 2.000 2.170 nonbonded pdb=" OE1 GLN A 713 " pdb="MG MG A1603 " model vdw 2.003 2.170 nonbonded pdb=" OG SER A 685 " pdb="MG MG A1603 " model vdw 2.017 2.170 ... (remaining 78595 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.470 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: 0.250 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.280 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6694 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 0.085 10475 Z= 0.602 Angle : 1.220 18.457 14258 Z= 0.862 Chirality : 0.062 0.417 1691 Planarity : 0.004 0.042 1766 Dihedral : 12.533 84.775 3931 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 0.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % 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: -1.76 (0.21), residues: 1200 helix: -0.39 (0.16), residues: 715 sheet: -1.21 (0.52), residues: 74 loop : -2.45 (0.25), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A1137 TYR 0.020 0.002 TYR A1032 PHE 0.012 0.002 PHE A1063 TRP 0.012 0.001 TRP A 520 HIS 0.006 0.001 HIS A 382 Details of bonding type rmsd covalent geometry : bond 0.00822 (10475) covalent geometry : angle 1.21978 (14258) hydrogen bonds : bond 0.21543 ( 645) hydrogen bonds : angle 7.52659 ( 1887) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 243 time to evaluate : 0.378 Fit side-chains revert: symmetry clash REVERT: A 219 ILE cc_start: 0.8251 (tt) cc_final: 0.8039 (tt) REVERT: A 237 GLU cc_start: 0.7673 (tp30) cc_final: 0.7052 (tt0) REVERT: A 239 THR cc_start: 0.7639 (m) cc_final: 0.7390 (p) REVERT: A 246 LYS cc_start: 0.7523 (mtmt) cc_final: 0.7023 (mmtt) REVERT: A 251 GLU cc_start: 0.8340 (tt0) cc_final: 0.7951 (tp30) REVERT: A 473 MET cc_start: 0.7092 (mtm) cc_final: 0.6836 (mtm) REVERT: A 576 ILE cc_start: 0.8121 (mm) cc_final: 0.7830 (mm) REVERT: A 641 THR cc_start: 0.8021 (p) cc_final: 0.7776 (t) REVERT: A 694 GLU cc_start: 0.7783 (mm-30) cc_final: 0.7172 (mm-30) REVERT: A 696 ASP cc_start: 0.8116 (t70) cc_final: 0.7662 (t0) REVERT: A 864 GLU cc_start: 0.8627 (tt0) cc_final: 0.8211 (mm-30) REVERT: A 946 LEU cc_start: 0.6795 (tp) cc_final: 0.6588 (tp) REVERT: A 993 TYR cc_start: 0.7574 (t80) cc_final: 0.6683 (t80) REVERT: A 1027 ILE cc_start: 0.8173 (mm) cc_final: 0.7918 (mp) REVERT: A 1245 TRP cc_start: 0.7185 (m100) cc_final: 0.6674 (m-10) REVERT: A 1248 ARG cc_start: 0.6464 (mtp-110) cc_final: 0.6137 (mtp85) REVERT: A 1252 GLU cc_start: 0.6828 (mm-30) cc_final: 0.6520 (mm-30) REVERT: A 1280 MET cc_start: 0.9096 (mtm) cc_final: 0.8771 (mtp) REVERT: A 1284 LYS cc_start: 0.8973 (mttt) cc_final: 0.8736 (ptmm) REVERT: A 1303 GLU cc_start: 0.8584 (mt-10) cc_final: 0.8262 (tp30) REVERT: A 1355 ILE cc_start: 0.8037 (mm) cc_final: 0.7811 (tt) REVERT: A 1513 LEU cc_start: 0.8025 (mt) cc_final: 0.7793 (mp) outliers start: 0 outliers final: 0 residues processed: 243 average time/residue: 0.1041 time to fit residues: 35.5963 Evaluate side-chains 145 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 145 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 98 optimal weight: 0.7980 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 0.8980 chunk 55 optimal weight: 4.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 432 GLN A 956 GLN A1392 GLN A1454 GLN A1485 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.132652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.105416 restraints weight = 17517.892| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 2.64 r_work: 0.3276 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.2482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 10475 Z= 0.163 Angle : 0.568 9.933 14258 Z= 0.299 Chirality : 0.040 0.166 1691 Planarity : 0.004 0.065 1766 Dihedral : 7.944 89.156 1676 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 2.09 % Allowed : 9.21 % Favored : 88.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.42 (0.24), residues: 1200 helix: 1.62 (0.19), residues: 723 sheet: -1.41 (0.49), residues: 86 loop : -1.94 (0.28), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 633 TYR 0.023 0.002 TYR A1032 PHE 0.018 0.001 PHE A 551 TRP 0.011 0.001 TRP A 223 HIS 0.007 0.001 HIS A 985 Details of bonding type rmsd covalent geometry : bond 0.00357 (10475) covalent geometry : angle 0.56849 (14258) hydrogen bonds : bond 0.06370 ( 645) hydrogen bonds : angle 4.52992 ( 1887) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 171 time to evaluate : 0.409 Fit side-chains revert: symmetry clash REVERT: A 219 ILE cc_start: 0.8836 (tt) cc_final: 0.8571 (tt) REVERT: A 237 GLU cc_start: 0.8279 (tp30) cc_final: 0.7759 (tt0) REVERT: A 246 LYS cc_start: 0.8302 (mtmt) cc_final: 0.7766 (mmtt) REVERT: A 339 MET cc_start: 0.8428 (ttp) cc_final: 0.8218 (ttp) REVERT: A 696 ASP cc_start: 0.8540 (t70) cc_final: 0.8201 (t0) REVERT: A 849 MET cc_start: 0.9229 (mtp) cc_final: 0.8953 (mtm) REVERT: A 1027 ILE cc_start: 0.8866 (mm) cc_final: 0.8651 (mm) REVERT: A 1245 TRP cc_start: 0.8051 (m100) cc_final: 0.7709 (m-10) REVERT: A 1353 ASP cc_start: 0.8256 (OUTLIER) cc_final: 0.8012 (m-30) REVERT: A 1447 THR cc_start: 0.7878 (OUTLIER) cc_final: 0.7618 (t) outliers start: 22 outliers final: 13 residues processed: 184 average time/residue: 0.0931 time to fit residues: 25.2144 Evaluate side-chains 144 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 129 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 340 PHE Chi-restraints excluded: chain A residue 444 ILE Chi-restraints excluded: chain A residue 496 LYS Chi-restraints excluded: chain A residue 761 ILE Chi-restraints excluded: chain A residue 837 VAL Chi-restraints excluded: chain A residue 954 THR Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 971 LEU Chi-restraints excluded: chain A residue 1104 CYS Chi-restraints excluded: chain A residue 1325 VAL Chi-restraints excluded: chain A residue 1353 ASP Chi-restraints excluded: chain A residue 1447 THR Chi-restraints excluded: chain A residue 1487 LEU Chi-restraints excluded: chain A residue 1490 ILE Chi-restraints excluded: chain A residue 1503 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 89 optimal weight: 3.9990 chunk 0 optimal weight: 9.9990 chunk 81 optimal weight: 0.7980 chunk 84 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 chunk 49 optimal weight: 0.6980 chunk 23 optimal weight: 5.9990 chunk 97 optimal weight: 0.7980 chunk 10 optimal weight: 10.0000 chunk 99 optimal weight: 0.6980 chunk 73 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 425 ASN A 533 GLN A 725 ASN A 956 GLN A1048 HIS A1184 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.132870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.106185 restraints weight = 17696.312| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 2.65 r_work: 0.3284 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.3179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10475 Z= 0.132 Angle : 0.510 6.973 14258 Z= 0.264 Chirality : 0.037 0.159 1691 Planarity : 0.004 0.058 1766 Dihedral : 7.309 82.297 1676 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.94 % Allowed : 10.92 % Favored : 86.13 % 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: 1.05 (0.24), residues: 1200 helix: 2.18 (0.19), residues: 725 sheet: -1.13 (0.49), residues: 87 loop : -1.84 (0.28), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 633 TYR 0.021 0.001 TYR A1032 PHE 0.020 0.001 PHE A 340 TRP 0.013 0.001 TRP A 459 HIS 0.008 0.001 HIS A 985 Details of bonding type rmsd covalent geometry : bond 0.00284 (10475) covalent geometry : angle 0.50991 (14258) hydrogen bonds : bond 0.05375 ( 645) hydrogen bonds : angle 4.07147 ( 1887) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 145 time to evaluate : 0.416 Fit side-chains REVERT: A 219 ILE cc_start: 0.8815 (tt) cc_final: 0.8530 (tt) REVERT: A 237 GLU cc_start: 0.8263 (tp30) cc_final: 0.7809 (tt0) REVERT: A 246 LYS cc_start: 0.8327 (mtmt) cc_final: 0.7786 (mmtt) REVERT: A 338 MET cc_start: 0.8900 (mmp) cc_final: 0.8612 (mmt) REVERT: A 340 PHE cc_start: 0.8446 (OUTLIER) cc_final: 0.8087 (t80) REVERT: A 369 LEU cc_start: 0.8681 (OUTLIER) cc_final: 0.8462 (mp) REVERT: A 466 VAL cc_start: 0.6939 (OUTLIER) cc_final: 0.6692 (t) REVERT: A 591 ILE cc_start: 0.8242 (tt) cc_final: 0.7772 (mm) REVERT: A 656 ASN cc_start: 0.8730 (m-40) cc_final: 0.8176 (t0) REVERT: A 696 ASP cc_start: 0.8378 (t70) cc_final: 0.8027 (t0) REVERT: A 849 MET cc_start: 0.9169 (mtp) cc_final: 0.8932 (mtm) REVERT: A 964 ASP cc_start: 0.7730 (m-30) cc_final: 0.7321 (m-30) REVERT: A 1013 VAL cc_start: 0.8341 (t) cc_final: 0.8133 (p) REVERT: A 1245 TRP cc_start: 0.7901 (m100) cc_final: 0.7488 (m-10) REVERT: A 1278 GLN cc_start: 0.8567 (tp40) cc_final: 0.8240 (tp40) REVERT: A 1447 THR cc_start: 0.8010 (OUTLIER) cc_final: 0.7732 (t) outliers start: 31 outliers final: 16 residues processed: 161 average time/residue: 0.0884 time to fit residues: 21.2968 Evaluate side-chains 149 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 129 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 340 PHE Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 444 ILE Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 496 LYS Chi-restraints excluded: chain A residue 761 ILE Chi-restraints excluded: chain A residue 820 LYS Chi-restraints excluded: chain A residue 837 VAL Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 966 MET Chi-restraints excluded: chain A residue 971 LEU Chi-restraints excluded: chain A residue 982 LEU Chi-restraints excluded: chain A residue 1079 LEU Chi-restraints excluded: chain A residue 1104 CYS Chi-restraints excluded: chain A residue 1243 LEU Chi-restraints excluded: chain A residue 1325 VAL Chi-restraints excluded: chain A residue 1363 HIS Chi-restraints excluded: chain A residue 1447 THR Chi-restraints excluded: chain A residue 1487 LEU Chi-restraints excluded: chain A residue 1503 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 58 optimal weight: 2.9990 chunk 83 optimal weight: 0.7980 chunk 10 optimal weight: 10.0000 chunk 95 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 chunk 54 optimal weight: 0.0030 chunk 86 optimal weight: 0.9990 chunk 125 optimal weight: 1.9990 chunk 84 optimal weight: 0.9990 chunk 0 optimal weight: 9.9990 chunk 37 optimal weight: 0.9990 overall best weight: 0.7194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 425 ASN A 956 GLN A1256 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.132732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.105858 restraints weight = 17746.239| |-----------------------------------------------------------------------------| r_work (start): 0.3391 rms_B_bonded: 2.68 r_work: 0.3271 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.3527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 10475 Z= 0.122 Angle : 0.489 6.638 14258 Z= 0.252 Chirality : 0.037 0.153 1691 Planarity : 0.004 0.054 1766 Dihedral : 6.630 75.736 1676 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 3.42 % Allowed : 12.25 % Favored : 84.33 % 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: 1.36 (0.24), residues: 1200 helix: 2.39 (0.19), residues: 728 sheet: -0.97 (0.50), residues: 82 loop : -1.68 (0.28), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A1147 TYR 0.021 0.001 TYR A1032 PHE 0.015 0.001 PHE A 340 TRP 0.015 0.001 TRP A 459 HIS 0.006 0.001 HIS A 985 Details of bonding type rmsd covalent geometry : bond 0.00260 (10475) covalent geometry : angle 0.48859 (14258) hydrogen bonds : bond 0.04956 ( 645) hydrogen bonds : angle 3.91004 ( 1887) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 135 time to evaluate : 0.458 Fit side-chains REVERT: A 219 ILE cc_start: 0.8826 (tt) cc_final: 0.8524 (tt) REVERT: A 237 GLU cc_start: 0.8244 (tp30) cc_final: 0.7712 (tt0) REVERT: A 246 LYS cc_start: 0.8378 (mtmt) cc_final: 0.7817 (mmtt) REVERT: A 338 MET cc_start: 0.8854 (mmp) cc_final: 0.8598 (mmt) REVERT: A 369 LEU cc_start: 0.8651 (OUTLIER) cc_final: 0.8442 (mp) REVERT: A 515 LEU cc_start: 0.8709 (OUTLIER) cc_final: 0.8375 (mp) REVERT: A 591 ILE cc_start: 0.8189 (tt) cc_final: 0.7683 (mm) REVERT: A 696 ASP cc_start: 0.8525 (t70) cc_final: 0.8218 (t0) REVERT: A 849 MET cc_start: 0.9161 (mtp) cc_final: 0.8938 (mtm) REVERT: A 964 ASP cc_start: 0.7730 (m-30) cc_final: 0.7326 (m-30) REVERT: A 1013 VAL cc_start: 0.8291 (t) cc_final: 0.8069 (p) REVERT: A 1245 TRP cc_start: 0.7861 (m100) cc_final: 0.7543 (m-10) REVERT: A 1278 GLN cc_start: 0.8596 (tp40) cc_final: 0.8314 (tp40) REVERT: A 1393 TYR cc_start: 0.7815 (OUTLIER) cc_final: 0.6994 (p90) REVERT: A 1447 THR cc_start: 0.8230 (OUTLIER) cc_final: 0.8012 (t) outliers start: 36 outliers final: 21 residues processed: 155 average time/residue: 0.0895 time to fit residues: 20.7706 Evaluate side-chains 149 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 124 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 TRP Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 444 ILE Chi-restraints excluded: chain A residue 496 LYS Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain A residue 761 ILE Chi-restraints excluded: chain A residue 820 LYS Chi-restraints excluded: chain A residue 837 VAL Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 966 MET Chi-restraints excluded: chain A residue 982 LEU Chi-restraints excluded: chain A residue 1015 LEU Chi-restraints excluded: chain A residue 1079 LEU Chi-restraints excluded: chain A residue 1104 CYS Chi-restraints excluded: chain A residue 1105 ILE Chi-restraints excluded: chain A residue 1243 LEU Chi-restraints excluded: chain A residue 1325 VAL Chi-restraints excluded: chain A residue 1363 HIS Chi-restraints excluded: chain A residue 1375 ASP Chi-restraints excluded: chain A residue 1393 TYR Chi-restraints excluded: chain A residue 1429 LEU Chi-restraints excluded: chain A residue 1447 THR Chi-restraints excluded: chain A residue 1487 LEU Chi-restraints excluded: chain A residue 1503 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 18 optimal weight: 2.9990 chunk 0 optimal weight: 9.9990 chunk 60 optimal weight: 2.9990 chunk 111 optimal weight: 2.9990 chunk 101 optimal weight: 1.9990 chunk 80 optimal weight: 0.0770 chunk 3 optimal weight: 20.0000 chunk 55 optimal weight: 0.0970 chunk 90 optimal weight: 1.9990 chunk 129 optimal weight: 3.9990 chunk 11 optimal weight: 9.9990 overall best weight: 1.4342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 597 ASN A 827 HIS A 956 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.129015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.102052 restraints weight = 17756.460| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 2.63 r_work: 0.3211 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.3738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 10475 Z= 0.168 Angle : 0.548 7.467 14258 Z= 0.279 Chirality : 0.039 0.156 1691 Planarity : 0.004 0.051 1766 Dihedral : 6.457 75.014 1676 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 3.32 % Allowed : 13.68 % Favored : 83.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.30 (0.24), residues: 1200 helix: 2.30 (0.19), residues: 727 sheet: -0.88 (0.49), residues: 82 loop : -1.64 (0.28), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1065 TYR 0.018 0.001 TYR A1032 PHE 0.021 0.002 PHE A 340 TRP 0.017 0.001 TRP A 459 HIS 0.005 0.001 HIS A 985 Details of bonding type rmsd covalent geometry : bond 0.00396 (10475) covalent geometry : angle 0.54771 (14258) hydrogen bonds : bond 0.05644 ( 645) hydrogen bonds : angle 4.05476 ( 1887) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 139 time to evaluate : 0.314 Fit side-chains revert: symmetry clash REVERT: A 219 ILE cc_start: 0.8822 (tt) cc_final: 0.8493 (tt) REVERT: A 237 GLU cc_start: 0.8261 (tp30) cc_final: 0.7685 (mt-10) REVERT: A 246 LYS cc_start: 0.8353 (mtmt) cc_final: 0.7795 (mmtt) REVERT: A 338 MET cc_start: 0.8801 (mmp) cc_final: 0.8502 (mmt) REVERT: A 369 LEU cc_start: 0.8703 (OUTLIER) cc_final: 0.8454 (mp) REVERT: A 515 LEU cc_start: 0.8732 (OUTLIER) cc_final: 0.8428 (mp) REVERT: A 656 ASN cc_start: 0.8849 (m-40) cc_final: 0.8206 (t0) REVERT: A 964 ASP cc_start: 0.7856 (m-30) cc_final: 0.7483 (m-30) REVERT: A 1013 VAL cc_start: 0.8348 (t) cc_final: 0.8143 (p) REVERT: A 1245 TRP cc_start: 0.7911 (m100) cc_final: 0.7598 (m-10) REVERT: A 1278 GLN cc_start: 0.8613 (tp40) cc_final: 0.8331 (tp40) REVERT: A 1393 TYR cc_start: 0.8072 (OUTLIER) cc_final: 0.7277 (p90) outliers start: 35 outliers final: 22 residues processed: 161 average time/residue: 0.0897 time to fit residues: 21.5866 Evaluate side-chains 148 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 123 time to evaluate : 0.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 444 ILE Chi-restraints excluded: chain A residue 496 LYS Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 761 ILE Chi-restraints excluded: chain A residue 837 VAL Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 966 MET Chi-restraints excluded: chain A residue 982 LEU Chi-restraints excluded: chain A residue 1015 LEU Chi-restraints excluded: chain A residue 1029 VAL Chi-restraints excluded: chain A residue 1079 LEU Chi-restraints excluded: chain A residue 1100 VAL Chi-restraints excluded: chain A residue 1104 CYS Chi-restraints excluded: chain A residue 1105 ILE Chi-restraints excluded: chain A residue 1109 LEU Chi-restraints excluded: chain A residue 1142 LEU Chi-restraints excluded: chain A residue 1325 VAL Chi-restraints excluded: chain A residue 1363 HIS Chi-restraints excluded: chain A residue 1375 ASP Chi-restraints excluded: chain A residue 1393 TYR Chi-restraints excluded: chain A residue 1429 LEU Chi-restraints excluded: chain A residue 1487 LEU Chi-restraints excluded: chain A residue 1503 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 54 optimal weight: 3.9990 chunk 128 optimal weight: 0.9980 chunk 77 optimal weight: 0.9980 chunk 53 optimal weight: 3.9990 chunk 93 optimal weight: 0.8980 chunk 88 optimal weight: 0.8980 chunk 9 optimal weight: 10.0000 chunk 87 optimal weight: 0.9980 chunk 95 optimal weight: 0.8980 chunk 15 optimal weight: 4.9990 chunk 84 optimal weight: 1.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 382 HIS A 956 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.130982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.104160 restraints weight = 17691.131| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 2.63 r_work: 0.3251 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.3929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10475 Z= 0.131 Angle : 0.509 8.529 14258 Z= 0.259 Chirality : 0.037 0.150 1691 Planarity : 0.004 0.050 1766 Dihedral : 6.254 72.265 1676 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 3.04 % Allowed : 13.87 % Favored : 83.10 % 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: 1.55 (0.24), residues: 1200 helix: 2.49 (0.19), residues: 729 sheet: -0.71 (0.49), residues: 81 loop : -1.56 (0.28), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 593 TYR 0.020 0.001 TYR A1032 PHE 0.018 0.001 PHE A1030 TRP 0.017 0.001 TRP A 459 HIS 0.006 0.001 HIS A 985 Details of bonding type rmsd covalent geometry : bond 0.00293 (10475) covalent geometry : angle 0.50909 (14258) hydrogen bonds : bond 0.05051 ( 645) hydrogen bonds : angle 3.85819 ( 1887) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 135 time to evaluate : 0.400 Fit side-chains revert: symmetry clash REVERT: A 219 ILE cc_start: 0.8818 (tt) cc_final: 0.8489 (tt) REVERT: A 237 GLU cc_start: 0.8248 (tp30) cc_final: 0.7675 (mt-10) REVERT: A 246 LYS cc_start: 0.8313 (mtmt) cc_final: 0.7767 (mmtt) REVERT: A 338 MET cc_start: 0.8817 (mmp) cc_final: 0.8547 (mmt) REVERT: A 369 LEU cc_start: 0.8672 (OUTLIER) cc_final: 0.8455 (mp) REVERT: A 515 LEU cc_start: 0.8704 (OUTLIER) cc_final: 0.8392 (mp) REVERT: A 568 TYR cc_start: 0.8139 (t80) cc_final: 0.7934 (t80) REVERT: A 591 ILE cc_start: 0.8131 (tt) cc_final: 0.7736 (mm) REVERT: A 656 ASN cc_start: 0.8838 (m-40) cc_final: 0.8347 (m-40) REVERT: A 964 ASP cc_start: 0.7810 (m-30) cc_final: 0.7442 (m-30) REVERT: A 1013 VAL cc_start: 0.8344 (t) cc_final: 0.8119 (p) REVERT: A 1245 TRP cc_start: 0.7867 (m100) cc_final: 0.7580 (m-10) REVERT: A 1278 GLN cc_start: 0.8586 (tp40) cc_final: 0.8355 (tp40) REVERT: A 1393 TYR cc_start: 0.8072 (OUTLIER) cc_final: 0.7270 (p90) outliers start: 32 outliers final: 25 residues processed: 155 average time/residue: 0.0932 time to fit residues: 21.5490 Evaluate side-chains 157 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 129 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 TRP Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 444 ILE Chi-restraints excluded: chain A residue 496 LYS Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 761 ILE Chi-restraints excluded: chain A residue 820 LYS Chi-restraints excluded: chain A residue 837 VAL Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 966 MET Chi-restraints excluded: chain A residue 971 LEU Chi-restraints excluded: chain A residue 982 LEU Chi-restraints excluded: chain A residue 1015 LEU Chi-restraints excluded: chain A residue 1034 MET Chi-restraints excluded: chain A residue 1079 LEU Chi-restraints excluded: chain A residue 1100 VAL Chi-restraints excluded: chain A residue 1104 CYS Chi-restraints excluded: chain A residue 1105 ILE Chi-restraints excluded: chain A residue 1123 LEU Chi-restraints excluded: chain A residue 1142 LEU Chi-restraints excluded: chain A residue 1325 VAL Chi-restraints excluded: chain A residue 1363 HIS Chi-restraints excluded: chain A residue 1375 ASP Chi-restraints excluded: chain A residue 1393 TYR Chi-restraints excluded: chain A residue 1429 LEU Chi-restraints excluded: chain A residue 1487 LEU Chi-restraints excluded: chain A residue 1503 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 131 optimal weight: 1.9990 chunk 62 optimal weight: 4.9990 chunk 110 optimal weight: 0.9990 chunk 53 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 12 optimal weight: 9.9990 chunk 46 optimal weight: 0.6980 chunk 97 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 106 optimal weight: 0.7980 overall best weight: 1.2986 ------------------------------------------------------------------------------- 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 = 0.3704 r_free = 0.3704 target = 0.129167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.102036 restraints weight = 17582.891| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 2.63 r_work: 0.3206 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.4035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 10475 Z= 0.157 Angle : 0.537 10.430 14258 Z= 0.272 Chirality : 0.038 0.152 1691 Planarity : 0.004 0.051 1766 Dihedral : 6.263 72.971 1676 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 3.13 % Allowed : 14.72 % Favored : 82.15 % 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: 1.49 (0.24), residues: 1200 helix: 2.41 (0.19), residues: 728 sheet: -0.65 (0.49), residues: 81 loop : -1.51 (0.28), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 593 TYR 0.020 0.001 TYR A1032 PHE 0.016 0.001 PHE A1030 TRP 0.019 0.001 TRP A 459 HIS 0.005 0.001 HIS A 985 Details of bonding type rmsd covalent geometry : bond 0.00371 (10475) covalent geometry : angle 0.53721 (14258) hydrogen bonds : bond 0.05359 ( 645) hydrogen bonds : angle 3.93338 ( 1887) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 128 time to evaluate : 0.327 Fit side-chains revert: symmetry clash REVERT: A 219 ILE cc_start: 0.8828 (tt) cc_final: 0.8496 (tt) REVERT: A 237 GLU cc_start: 0.8243 (tp30) cc_final: 0.7670 (mt-10) REVERT: A 246 LYS cc_start: 0.8361 (mtmt) cc_final: 0.7807 (mmtt) REVERT: A 338 MET cc_start: 0.8775 (mmp) cc_final: 0.8544 (mmt) REVERT: A 369 LEU cc_start: 0.8678 (OUTLIER) cc_final: 0.8461 (mp) REVERT: A 515 LEU cc_start: 0.8702 (OUTLIER) cc_final: 0.8409 (mp) REVERT: A 591 ILE cc_start: 0.8152 (tt) cc_final: 0.7796 (mm) REVERT: A 656 ASN cc_start: 0.8869 (m-40) cc_final: 0.8375 (m-40) REVERT: A 964 ASP cc_start: 0.7853 (m-30) cc_final: 0.7481 (m-30) REVERT: A 1013 VAL cc_start: 0.8347 (t) cc_final: 0.8121 (p) REVERT: A 1245 TRP cc_start: 0.7868 (m100) cc_final: 0.7577 (m-10) REVERT: A 1278 GLN cc_start: 0.8615 (tp40) cc_final: 0.8390 (tp40) REVERT: A 1393 TYR cc_start: 0.8221 (OUTLIER) cc_final: 0.7423 (p90) outliers start: 33 outliers final: 28 residues processed: 146 average time/residue: 0.0927 time to fit residues: 20.4028 Evaluate side-chains 159 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 128 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 444 ILE Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 496 LYS Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 552 THR Chi-restraints excluded: chain A residue 761 ILE Chi-restraints excluded: chain A residue 820 LYS Chi-restraints excluded: chain A residue 837 VAL Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 966 MET Chi-restraints excluded: chain A residue 971 LEU Chi-restraints excluded: chain A residue 982 LEU Chi-restraints excluded: chain A residue 989 LEU Chi-restraints excluded: chain A residue 1015 LEU Chi-restraints excluded: chain A residue 1034 MET Chi-restraints excluded: chain A residue 1079 LEU Chi-restraints excluded: chain A residue 1100 VAL Chi-restraints excluded: chain A residue 1104 CYS Chi-restraints excluded: chain A residue 1109 LEU Chi-restraints excluded: chain A residue 1123 LEU Chi-restraints excluded: chain A residue 1142 LEU Chi-restraints excluded: chain A residue 1325 VAL Chi-restraints excluded: chain A residue 1363 HIS Chi-restraints excluded: chain A residue 1375 ASP Chi-restraints excluded: chain A residue 1393 TYR Chi-restraints excluded: chain A residue 1429 LEU Chi-restraints excluded: chain A residue 1487 LEU Chi-restraints excluded: chain A residue 1496 VAL Chi-restraints excluded: chain A residue 1503 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 0 optimal weight: 9.9990 chunk 13 optimal weight: 0.9980 chunk 126 optimal weight: 0.9980 chunk 131 optimal weight: 0.9980 chunk 99 optimal weight: 0.7980 chunk 86 optimal weight: 0.7980 chunk 113 optimal weight: 0.7980 chunk 37 optimal weight: 3.9990 chunk 82 optimal weight: 0.6980 chunk 81 optimal weight: 0.6980 chunk 83 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 956 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.131309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.104153 restraints weight = 17663.455| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 2.66 r_work: 0.3265 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.4155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 10475 Z= 0.122 Angle : 0.505 11.344 14258 Z= 0.255 Chirality : 0.036 0.150 1691 Planarity : 0.004 0.050 1766 Dihedral : 6.156 73.150 1676 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 3.42 % Allowed : 14.81 % Favored : 81.77 % 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: 1.69 (0.25), residues: 1200 helix: 2.56 (0.19), residues: 729 sheet: -0.50 (0.50), residues: 80 loop : -1.44 (0.29), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 593 TYR 0.020 0.001 TYR A1032 PHE 0.020 0.001 PHE A1030 TRP 0.018 0.001 TRP A 459 HIS 0.005 0.001 HIS A 985 Details of bonding type rmsd covalent geometry : bond 0.00271 (10475) covalent geometry : angle 0.50521 (14258) hydrogen bonds : bond 0.04816 ( 645) hydrogen bonds : angle 3.77731 ( 1887) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 135 time to evaluate : 0.338 Fit side-chains revert: symmetry clash REVERT: A 219 ILE cc_start: 0.8813 (tt) cc_final: 0.8485 (tt) REVERT: A 237 GLU cc_start: 0.8236 (tp30) cc_final: 0.7649 (mt-10) REVERT: A 246 LYS cc_start: 0.8328 (mtmt) cc_final: 0.7782 (mmtt) REVERT: A 338 MET cc_start: 0.8734 (mmp) cc_final: 0.8528 (mmt) REVERT: A 515 LEU cc_start: 0.8670 (OUTLIER) cc_final: 0.8378 (mp) REVERT: A 591 ILE cc_start: 0.8192 (tt) cc_final: 0.7806 (mm) REVERT: A 656 ASN cc_start: 0.8865 (m-40) cc_final: 0.8373 (m-40) REVERT: A 964 ASP cc_start: 0.7752 (m-30) cc_final: 0.7367 (m-30) REVERT: A 1013 VAL cc_start: 0.8302 (t) cc_final: 0.8058 (p) REVERT: A 1176 GLN cc_start: 0.8424 (OUTLIER) cc_final: 0.8173 (mt0) REVERT: A 1245 TRP cc_start: 0.7825 (m100) cc_final: 0.7568 (m-10) REVERT: A 1278 GLN cc_start: 0.8606 (tp40) cc_final: 0.8389 (tp40) REVERT: A 1393 TYR cc_start: 0.8198 (OUTLIER) cc_final: 0.7392 (p90) outliers start: 36 outliers final: 29 residues processed: 154 average time/residue: 0.0894 time to fit residues: 20.6412 Evaluate side-chains 163 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 131 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 TRP Chi-restraints excluded: chain A residue 444 ILE Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 496 LYS Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 552 THR Chi-restraints excluded: chain A residue 761 ILE Chi-restraints excluded: chain A residue 820 LYS Chi-restraints excluded: chain A residue 837 VAL Chi-restraints excluded: chain A residue 841 MET Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 966 MET Chi-restraints excluded: chain A residue 971 LEU Chi-restraints excluded: chain A residue 982 LEU Chi-restraints excluded: chain A residue 989 LEU Chi-restraints excluded: chain A residue 1015 LEU Chi-restraints excluded: chain A residue 1034 MET Chi-restraints excluded: chain A residue 1079 LEU Chi-restraints excluded: chain A residue 1100 VAL Chi-restraints excluded: chain A residue 1104 CYS Chi-restraints excluded: chain A residue 1109 LEU Chi-restraints excluded: chain A residue 1123 LEU Chi-restraints excluded: chain A residue 1142 LEU Chi-restraints excluded: chain A residue 1176 GLN Chi-restraints excluded: chain A residue 1325 VAL Chi-restraints excluded: chain A residue 1363 HIS Chi-restraints excluded: chain A residue 1375 ASP Chi-restraints excluded: chain A residue 1393 TYR Chi-restraints excluded: chain A residue 1429 LEU Chi-restraints excluded: chain A residue 1487 LEU Chi-restraints excluded: chain A residue 1496 VAL Chi-restraints excluded: chain A residue 1503 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 107 optimal weight: 4.9990 chunk 104 optimal weight: 0.7980 chunk 94 optimal weight: 0.7980 chunk 23 optimal weight: 1.9990 chunk 79 optimal weight: 4.9990 chunk 131 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 70 optimal weight: 0.4980 chunk 115 optimal weight: 0.9980 chunk 10 optimal weight: 10.0000 chunk 89 optimal weight: 1.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- 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 = 0.3706 r_free = 0.3706 target = 0.129725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.102542 restraints weight = 17618.879| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 2.73 r_work: 0.3219 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.4225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 10475 Z= 0.138 Angle : 0.530 12.029 14258 Z= 0.266 Chirality : 0.037 0.152 1691 Planarity : 0.004 0.051 1766 Dihedral : 6.149 72.847 1676 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 3.61 % Allowed : 14.81 % Favored : 81.58 % 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: 1.66 (0.24), residues: 1200 helix: 2.52 (0.19), residues: 729 sheet: -0.49 (0.50), residues: 80 loop : -1.39 (0.29), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 593 TYR 0.020 0.001 TYR A1032 PHE 0.017 0.001 PHE A1030 TRP 0.020 0.001 TRP A 459 HIS 0.005 0.001 HIS A 985 Details of bonding type rmsd covalent geometry : bond 0.00321 (10475) covalent geometry : angle 0.53007 (14258) hydrogen bonds : bond 0.05002 ( 645) hydrogen bonds : angle 3.81472 ( 1887) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 133 time to evaluate : 0.402 Fit side-chains revert: symmetry clash REVERT: A 219 ILE cc_start: 0.8637 (tt) cc_final: 0.8315 (tt) REVERT: A 237 GLU cc_start: 0.8143 (tp30) cc_final: 0.7469 (mt-10) REVERT: A 246 LYS cc_start: 0.8211 (mtmt) cc_final: 0.7631 (mmtt) REVERT: A 338 MET cc_start: 0.8689 (mmp) cc_final: 0.8408 (mmm) REVERT: A 515 LEU cc_start: 0.8392 (OUTLIER) cc_final: 0.8121 (mp) REVERT: A 656 ASN cc_start: 0.8966 (m-40) cc_final: 0.8569 (m-40) REVERT: A 964 ASP cc_start: 0.7724 (m-30) cc_final: 0.7338 (m-30) REVERT: A 1013 VAL cc_start: 0.8239 (t) cc_final: 0.8003 (p) REVERT: A 1176 GLN cc_start: 0.8287 (OUTLIER) cc_final: 0.8042 (mt0) REVERT: A 1245 TRP cc_start: 0.7737 (m100) cc_final: 0.7441 (m-10) REVERT: A 1278 GLN cc_start: 0.8658 (tp40) cc_final: 0.8445 (tp40) REVERT: A 1393 TYR cc_start: 0.8258 (OUTLIER) cc_final: 0.7548 (p90) outliers start: 38 outliers final: 29 residues processed: 154 average time/residue: 0.0878 time to fit residues: 20.4901 Evaluate side-chains 164 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 132 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 444 ILE Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 496 LYS Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 552 THR Chi-restraints excluded: chain A residue 761 ILE Chi-restraints excluded: chain A residue 820 LYS Chi-restraints excluded: chain A residue 837 VAL Chi-restraints excluded: chain A residue 841 MET Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 966 MET Chi-restraints excluded: chain A residue 971 LEU Chi-restraints excluded: chain A residue 982 LEU Chi-restraints excluded: chain A residue 989 LEU Chi-restraints excluded: chain A residue 1015 LEU Chi-restraints excluded: chain A residue 1034 MET Chi-restraints excluded: chain A residue 1079 LEU Chi-restraints excluded: chain A residue 1100 VAL Chi-restraints excluded: chain A residue 1104 CYS Chi-restraints excluded: chain A residue 1109 LEU Chi-restraints excluded: chain A residue 1123 LEU Chi-restraints excluded: chain A residue 1142 LEU Chi-restraints excluded: chain A residue 1161 VAL Chi-restraints excluded: chain A residue 1176 GLN Chi-restraints excluded: chain A residue 1325 VAL Chi-restraints excluded: chain A residue 1363 HIS Chi-restraints excluded: chain A residue 1375 ASP Chi-restraints excluded: chain A residue 1393 TYR Chi-restraints excluded: chain A residue 1429 LEU Chi-restraints excluded: chain A residue 1487 LEU Chi-restraints excluded: chain A residue 1496 VAL Chi-restraints excluded: chain A residue 1503 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 28 optimal weight: 0.8980 chunk 57 optimal weight: 0.9980 chunk 109 optimal weight: 5.9990 chunk 68 optimal weight: 0.9990 chunk 34 optimal weight: 0.3980 chunk 99 optimal weight: 1.9990 chunk 81 optimal weight: 0.9990 chunk 67 optimal weight: 0.1980 chunk 85 optimal weight: 5.9990 chunk 7 optimal weight: 9.9990 chunk 41 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3728 r_free = 0.3728 target = 0.131541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.104814 restraints weight = 17392.377| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 2.63 r_work: 0.3256 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.4342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 10475 Z= 0.119 Angle : 0.517 12.821 14258 Z= 0.258 Chirality : 0.036 0.151 1691 Planarity : 0.004 0.051 1766 Dihedral : 6.062 73.144 1676 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.94 % Allowed : 15.48 % Favored : 81.58 % 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: 1.79 (0.25), residues: 1200 helix: 2.63 (0.19), residues: 729 sheet: -0.39 (0.52), residues: 79 loop : -1.38 (0.29), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1221 TYR 0.021 0.001 TYR A1032 PHE 0.020 0.001 PHE A1030 TRP 0.018 0.001 TRP A 459 HIS 0.005 0.001 HIS A 985 Details of bonding type rmsd covalent geometry : bond 0.00265 (10475) covalent geometry : angle 0.51748 (14258) hydrogen bonds : bond 0.04595 ( 645) hydrogen bonds : angle 3.70048 ( 1887) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 145 time to evaluate : 0.440 Fit side-chains REVERT: A 219 ILE cc_start: 0.8742 (tt) cc_final: 0.8414 (tt) REVERT: A 246 LYS cc_start: 0.8216 (mtmt) cc_final: 0.7657 (mmtt) REVERT: A 319 LYS cc_start: 0.7045 (mmmm) cc_final: 0.6839 (mmmm) REVERT: A 338 MET cc_start: 0.8696 (mmp) cc_final: 0.8470 (mmt) REVERT: A 515 LEU cc_start: 0.8513 (OUTLIER) cc_final: 0.8233 (mp) REVERT: A 591 ILE cc_start: 0.8186 (tt) cc_final: 0.7843 (mm) REVERT: A 656 ASN cc_start: 0.8939 (m-40) cc_final: 0.8546 (m-40) REVERT: A 960 SER cc_start: 0.7630 (p) cc_final: 0.6948 (t) REVERT: A 964 ASP cc_start: 0.7704 (m-30) cc_final: 0.7207 (m-30) REVERT: A 1013 VAL cc_start: 0.8295 (t) cc_final: 0.8048 (p) REVERT: A 1176 GLN cc_start: 0.8372 (OUTLIER) cc_final: 0.8122 (mt0) REVERT: A 1203 GLU cc_start: 0.8302 (tt0) cc_final: 0.8061 (tt0) REVERT: A 1245 TRP cc_start: 0.7741 (m100) cc_final: 0.7463 (m-10) REVERT: A 1393 TYR cc_start: 0.8148 (OUTLIER) cc_final: 0.7414 (p90) outliers start: 31 outliers final: 27 residues processed: 162 average time/residue: 0.0863 time to fit residues: 21.0039 Evaluate side-chains 169 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 139 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 TRP Chi-restraints excluded: chain A residue 444 ILE Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 496 LYS Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 552 THR Chi-restraints excluded: chain A residue 761 ILE Chi-restraints excluded: chain A residue 820 LYS Chi-restraints excluded: chain A residue 837 VAL Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 966 MET Chi-restraints excluded: chain A residue 971 LEU Chi-restraints excluded: chain A residue 982 LEU Chi-restraints excluded: chain A residue 989 LEU Chi-restraints excluded: chain A residue 1015 LEU Chi-restraints excluded: chain A residue 1034 MET Chi-restraints excluded: chain A residue 1079 LEU Chi-restraints excluded: chain A residue 1104 CYS Chi-restraints excluded: chain A residue 1109 LEU Chi-restraints excluded: chain A residue 1123 LEU Chi-restraints excluded: chain A residue 1142 LEU Chi-restraints excluded: chain A residue 1161 VAL Chi-restraints excluded: chain A residue 1176 GLN Chi-restraints excluded: chain A residue 1325 VAL Chi-restraints excluded: chain A residue 1363 HIS Chi-restraints excluded: chain A residue 1393 TYR Chi-restraints excluded: chain A residue 1429 LEU Chi-restraints excluded: chain A residue 1487 LEU Chi-restraints excluded: chain A residue 1496 VAL Chi-restraints excluded: chain A residue 1503 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 33 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 63 optimal weight: 0.4980 chunk 64 optimal weight: 0.5980 chunk 129 optimal weight: 0.9990 chunk 128 optimal weight: 0.7980 chunk 44 optimal weight: 0.9990 chunk 27 optimal weight: 0.5980 chunk 34 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.3729 r_free = 0.3729 target = 0.131702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.104610 restraints weight = 17687.819| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 2.74 r_work: 0.3246 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.4412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 10475 Z= 0.118 Angle : 0.529 13.131 14258 Z= 0.263 Chirality : 0.036 0.151 1691 Planarity : 0.004 0.052 1766 Dihedral : 6.023 73.163 1676 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 2.75 % Allowed : 16.62 % Favored : 80.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.82 (0.24), residues: 1200 helix: 2.62 (0.19), residues: 730 sheet: -0.36 (0.52), residues: 79 loop : -1.30 (0.29), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 593 TYR 0.020 0.001 TYR A1032 PHE 0.019 0.001 PHE A 365 TRP 0.015 0.001 TRP A 459 HIS 0.005 0.001 HIS A 985 Details of bonding type rmsd covalent geometry : bond 0.00263 (10475) covalent geometry : angle 0.52923 (14258) hydrogen bonds : bond 0.04542 ( 645) hydrogen bonds : angle 3.68995 ( 1887) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2557.10 seconds wall clock time: 44 minutes 35.15 seconds (2675.15 seconds total)