Starting phenix.real_space_refine on Fri Sep 11 16:06:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6uy0_20945/09_2026/6uy0_20945.cif Found real_map, /net/cci-nas-00/data/ceres_data/6uy0_20945/09_2026/6uy0_20945.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.23 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6uy0_20945/09_2026/6uy0_20945.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6uy0_20945/09_2026/6uy0_20945.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6uy0_20945/09_2026/6uy0_20945.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6uy0_20945/09_2026/6uy0_20945.cif" model { file = "/net/cci-nas-00/data/ceres_data/6uy0_20945/09_2026/6uy0_20945.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6uy0_20945/09_2026/6uy0_20945.cif" } resolution = 3.23 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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 5 5.49 5 Mg 2 5.21 5 S 47 5.16 5 C 6266 2.51 5 N 1607 2.21 5 O 1757 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 33 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9684 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 9540 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1210, 9540 Classifications: {'peptide': 1210} Link IDs: {'PTRANS': 44, 'TRANS': 1165} Chain breaks: 3 Chain: "A" Number of atoms: 144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 144 Unusual residues: {' MG': 2, 'ADP': 1, 'ATP': 1, 'CLR': 3} Classifications: {'undetermined': 7} Link IDs: {None: 6} Time building chain proxies: 2.02, per 1000 atoms: 0.21 Number of scatterers: 9684 At special positions: 0 Unit cell: (143.17, 98.88, 83.43, 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 5 15.00 Mg 2 11.99 O 1757 8.00 N 1607 7.00 C 6266 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: 0.62 Conformation dependent library (CDL) restraints added in 274.0 milliseconds 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2282 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 5 sheets defined 68.1% alpha, 7.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.33 Creating SS restraints... Processing helix chain 'A' and resid 214 through 221 removed outlier: 3.714A pdb=" N THR A 220 " --> pdb=" O LEU A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 234 Processing helix chain 'A' and resid 245 through 248 Processing helix chain 'A' and resid 249 through 268 Proline residue: A 255 - end of helix removed outlier: 3.539A pdb=" N LYS A 267 " --> pdb=" O LYS A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 326 Processing helix chain 'A' and resid 326 through 355 removed outlier: 3.763A pdb=" N LEU A 330 " --> pdb=" O LEU A 326 " (cutoff:3.500A) Proline residue: A 343 - end of helix removed outlier: 3.660A pdb=" N ASN A 354 " --> pdb=" O ILE A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 408 removed outlier: 3.948A pdb=" N GLY A 363 " --> pdb=" O PRO A 359 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N TYR A 364 " --> pdb=" O GLU A 360 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N PHE A 365 " --> pdb=" O TRP A 361 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N TYR A 366 " --> pdb=" O GLN A 362 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N THR A 367 " --> pdb=" O GLY A 363 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LEU A 408 " --> pdb=" O TYR A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 418 removed outlier: 3.591A pdb=" N SER A 417 " --> pdb=" O ALA A 413 " (cutoff:3.500A) Processing helix chain 'A' and resid 419 through 441 removed outlier: 3.819A pdb=" N ASP A 430 " --> pdb=" O LEU A 426 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N ALA A 431 " --> pdb=" O MET A 427 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLN A 432 " --> pdb=" O SER A 428 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N THR A 439 " --> pdb=" O MET A 435 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N TYR A 440 " --> pdb=" O ASP A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 442 through 462 removed outlier: 3.763A pdb=" N SER A 446 " --> pdb=" O ASN A 442 " (cutoff:3.500A) Proline residue: A 448 - end of helix removed outlier: 3.593A pdb=" N LEU A 457 " --> pdb=" O LEU A 453 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 511 removed outlier: 3.573A pdb=" N VAL A 477 " --> pdb=" O MET A 473 " (cutoff:3.500A) Proline residue: A 478 - end of helix removed outlier: 3.783A pdb=" N THR A 489 " --> pdb=" O MET A 485 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N TYR A 490 " --> pdb=" O LYS A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 511 through 519 Processing helix chain 'A' and resid 520 through 555 removed outlier: 3.696A pdb=" N CYS A 555 " --> pdb=" O PHE A 551 " (cutoff:3.500A) Processing helix chain 'A' and resid 555 through 572 removed outlier: 3.552A pdb=" N LEU A 559 " --> pdb=" O CYS A 555 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N VAL A 567 " --> pdb=" O SER A 563 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N TYR A 568 " --> pdb=" O THR A 564 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N VAL A 569 " --> pdb=" O PHE A 565 " (cutoff:3.500A) Processing helix chain 'A' and resid 580 through 590 removed outlier: 3.867A pdb=" N VAL A 584 " --> pdb=" O GLN A 580 " (cutoff:3.500A) Processing helix chain 'A' and resid 592 through 597 removed outlier: 4.006A pdb=" N LEU A 596 " --> pdb=" O LEU A 592 " (cutoff:3.500A) Processing helix chain 'A' and resid 598 through 621 removed outlier: 3.609A pdb=" N VAL A 602 " --> pdb=" O ILE A 598 " (cutoff:3.500A) Processing helix chain 'A' and resid 626 through 630 removed outlier: 3.594A pdb=" N SER A 629 " --> pdb=" O ASP A 626 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ILE A 630 " --> pdb=" O PRO A 627 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 626 through 630' Processing helix chain 'A' and resid 683 through 692 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 Processing helix chain 'A' and resid 769 through 785 removed outlier: 3.636A pdb=" N ALA A 781 " --> pdb=" O SER A 777 " (cutoff:3.500A) removed outlier: 3.680A 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 858 Processing helix chain 'A' and resid 860 through 870 removed outlier: 3.578A pdb=" N GLU A 864 " --> pdb=" O GLY A 860 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N THR A 868 " --> pdb=" O GLU A 864 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N TYR A 869 " --> pdb=" O PHE A 865 " (cutoff:3.500A) Processing helix chain 'A' and resid 958 through 970 removed outlier: 4.017A pdb=" N TYR A 962 " --> pdb=" O LYS A 958 " (cutoff:3.500A) Processing helix chain 'A' and resid 970 through 1000 removed outlier: 3.539A pdb=" N SER A 974 " --> pdb=" O GLY A 970 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N ASP A1000 " --> pdb=" O SER A 996 " (cutoff:3.500A) Processing helix chain 'A' and resid 1009 through 1058 removed outlier: 3.988A pdb=" N SER A1016 " --> pdb=" O GLN A1012 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N VAL A1017 " --> pdb=" O VAL A1013 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N SER A1037 " --> pdb=" O SER A1033 " (cutoff:3.500A) Processing helix chain 'A' and resid 1059 through 1066 removed outlier: 3.927A pdb=" N PHE A1063 " --> pdb=" O PRO A1059 " (cutoff:3.500A) Processing helix chain 'A' and resid 1067 through 1111 removed outlier: 3.805A pdb=" N LEU A1071 " --> pdb=" O PRO A1067 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ARG A1074 " --> pdb=" O ASN A1070 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N GLU A1078 " --> pdb=" O ARG A1074 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N LEU A1079 " --> pdb=" O PHE A1075 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N ILE A1086 " --> pdb=" O VAL A1082 " (cutoff:3.500A) Proline residue: A1087 - end of helix removed outlier: 3.568A pdb=" N ILE A1106 " --> pdb=" O GLY A1102 " (cutoff:3.500A) Processing helix chain 'A' and resid 1112 through 1115 removed outlier: 3.787A pdb=" N ALA A1115 " --> pdb=" O PRO A1112 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1112 through 1115' Processing helix chain 'A' and resid 1117 through 1147 removed outlier: 3.536A pdb=" N TYR A1125 " --> pdb=" O LEU A1121 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ALA A1134 " --> pdb=" O ARG A1130 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N SER A1135 " --> pdb=" O PHE A1131 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N GLN A1138 " --> pdb=" O ALA A1134 " (cutoff:3.500A) Processing helix chain 'A' and resid 1147 through 1160 removed outlier: 3.748A pdb=" N TYR A1151 " --> pdb=" O ARG A1147 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LEU A1159 " --> pdb=" O ASN A1155 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLY A1160 " --> pdb=" O GLU A1156 " (cutoff:3.500A) Processing helix chain 'A' and resid 1160 through 1168 Processing helix chain 'A' and resid 1169 through 1220 removed outlier: 3.778A pdb=" N GLU A1183 " --> pdb=" O LEU A1179 " (cutoff:3.500A) removed outlier: 3.887A 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: 3.688A pdb=" N GLY A1230 " --> pdb=" O ALA A1226 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N LEU A1231 " --> pdb=" O GLY A1227 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N SER A1232 " --> pdb=" O LEU A1228 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N VAL A1233 " --> pdb=" O VAL A1229 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N SER A1234 " --> pdb=" O GLY A1230 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N TYR A1235 " --> pdb=" O LEU A1231 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N GLN A1238 " --> pdb=" O SER A1234 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N THR A1240 " --> pdb=" O SER A1236 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ARG A1248 " --> pdb=" O ASN A1244 " (cutoff:3.500A) Processing helix chain 'A' and resid 1257 through 1265 removed outlier: 3.556A pdb=" N GLU A1265 " --> pdb=" O GLU A1261 " (cutoff:3.500A) Processing helix chain 'A' and resid 1332 through 1340 removed outlier: 3.587A pdb=" N THR A1336 " --> pdb=" O LYS A1332 " (cutoff:3.500A) Processing helix chain 'A' and resid 1361 through 1367 Processing helix chain 'A' and resid 1383 through 1388 removed outlier: 3.548A pdb=" N LEU A1387 " --> pdb=" O LEU A1383 " (cutoff:3.500A) Processing helix chain 'A' and resid 1394 through 1405 removed outlier: 3.584A pdb=" N VAL A1398 " --> pdb=" O SER A1394 " (cutoff:3.500A) Processing helix chain 'A' and resid 1407 through 1413 Processing helix chain 'A' and resid 1430 through 1446 removed outlier: 3.596A 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: 3.734A pdb=" N LYS A1446 " --> pdb=" O ALA A1442 " (cutoff:3.500A) Processing helix chain 'A' and resid 1460 through 1475 Processing helix chain 'A' and resid 1486 through 1490 Processing helix chain 'A' and resid 1509 through 1517 removed outlier: 3.644A pdb=" N ARG A1517 " --> pdb=" O LEU A1513 " (cutoff:3.500A) Processing helix chain 'A' and resid 1519 through 1528 Processing sheet with id=AA1, first strand: chain 'A' and resid 661 through 669 removed outlier: 7.244A pdb=" N HIS A 662 " --> pdb=" O THR A 650 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N THR A 650 " --> pdb=" O HIS A 662 " (cutoff:3.500A) removed outlier: 5.750A pdb=" N ILE A 664 " --> pdb=" O ASN A 648 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N ILE A 644 " --> pdb=" O VAL A 704 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N VAL A 704 " --> pdb=" O ILE A 644 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N VAL A 646 " --> pdb=" O VAL A 702 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N VAL A 702 " --> pdb=" O VAL A 646 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N ASN A 648 " --> pdb=" O GLY A 700 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N GLY A 700 " --> pdb=" O ASN A 648 " (cutoff:3.500A) removed outlier: 6.788A 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: 6.565A pdb=" N ALA A 709 " --> pdb=" O LEU A 790 " (cutoff:3.500A) removed outlier: 7.653A pdb=" N ASP A 792 " --> pdb=" O ALA A 709 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N VAL A 711 " --> pdb=" O ASP A 792 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N TYR A 789 " --> pdb=" O LEU A 823 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N VAL A 825 " --> pdb=" O TYR A 789 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N LEU A 791 " --> pdb=" O VAL A 825 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N VAL A 674 " --> pdb=" O LEU A 824 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N LEU A 673 " --> pdb=" O VAL A 837 " (cutoff:3.500A) removed outlier: 8.233A pdb=" N ILE A 839 " --> pdb=" O LEU A 673 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ALA A 675 " --> pdb=" O ILE A 839 " (cutoff:3.500A) removed outlier: 7.855A pdb=" N MET A 841 " --> pdb=" O ALA A 675 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N VAL A 677 " --> pdb=" O MET A 841 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLU A 848 " --> pdb=" O VAL A 840 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N SER A 842 " --> pdb=" O ILE A 846 " (cutoff:3.500A) removed outlier: 5.815A pdb=" N ILE A 846 " --> pdb=" O SER A 842 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1309 through 1316 removed outlier: 6.432A pdb=" N LYS A1310 " --> pdb=" O GLY A1298 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N GLY A1298 " --> pdb=" O LYS A1310 " (cutoff:3.500A) removed outlier: 5.148A pdb=" N ILE A1312 " --> pdb=" O ASP A1296 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N VAL A1314 " --> pdb=" O PHE A1294 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N TYR A1297 " --> pdb=" O GLU A1347 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N GLU A1347 " --> pdb=" O TYR A1297 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1369 through 1372 removed outlier: 3.584A pdb=" N ARG A1495 " --> pdb=" O LYS A1321 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1381 through 1382 572 hydrogen bonds defined for protein. 1692 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: 1.75 Time building geometry restraints manager: 0.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 1820 1.34 - 1.46: 2296 1.46 - 1.58: 5689 1.58 - 1.70: 8 1.70 - 1.82: 79 Bond restraints: 9892 Sorted by residual: bond pdb=" C4 ATP A1601 " pdb=" C5 ATP A1601 " ideal model delta sigma weight residual 1.388 1.465 -0.077 1.00e-02 1.00e+04 5.91e+01 bond pdb=" C5 ATP A1601 " pdb=" C6 ATP A1601 " ideal model delta sigma weight residual 1.409 1.477 -0.068 1.00e-02 1.00e+04 4.61e+01 bond pdb=" C8 ATP A1601 " pdb=" N7 ATP A1601 " ideal model delta sigma weight residual 1.310 1.356 -0.046 1.00e-02 1.00e+04 2.12e+01 bond pdb=" N VAL A 668 " pdb=" CA VAL A 668 " ideal model delta sigma weight residual 1.456 1.496 -0.040 8.70e-03 1.32e+04 2.11e+01 bond pdb=" N VAL A 711 " pdb=" CA VAL A 711 " ideal model delta sigma weight residual 1.456 1.494 -0.038 8.60e-03 1.35e+04 1.96e+01 ... (remaining 9887 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.78: 9056 1.78 - 3.56: 3570 3.56 - 5.34: 776 5.34 - 7.12: 41 7.12 - 8.90: 7 Bond angle restraints: 13450 Sorted by residual: angle pdb=" C5 ATP A1601 " pdb=" C4 ATP A1601 " pdb=" N3 ATP A1601 " ideal model delta sigma weight residual 126.80 118.75 8.05 1.00e+00 1.00e+00 6.48e+01 angle pdb=" PB ATP A1601 " pdb=" O3B ATP A1601 " pdb=" PG ATP A1601 " ideal model delta sigma weight residual 139.87 131.94 7.93 1.00e+00 1.00e+00 6.30e+01 angle pdb=" PA ATP A1601 " pdb=" O3A ATP A1601 " pdb=" PB ATP A1601 " ideal model delta sigma weight residual 136.83 129.85 6.98 1.00e+00 1.00e+00 4.87e+01 angle pdb=" N3 ATP A1601 " pdb=" C4 ATP A1601 " pdb=" N9 ATP A1601 " ideal model delta sigma weight residual 127.04 134.79 -7.75 1.15e+00 7.59e-01 4.56e+01 angle pdb=" CA GLY A 762 " pdb=" C GLY A 762 " pdb=" O GLY A 762 " ideal model delta sigma weight residual 122.23 117.85 4.38 6.90e-01 2.10e+00 4.03e+01 ... (remaining 13445 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.50: 5487 21.50 - 43.01: 343 43.01 - 64.51: 41 64.51 - 86.02: 5 86.02 - 107.52: 2 Dihedral angle restraints: 5878 sinusoidal: 2351 harmonic: 3527 Sorted by residual: dihedral pdb=" O1B ADP A1602 " pdb=" O3A ADP A1602 " pdb=" PB ADP A1602 " pdb=" PA ADP A1602 " ideal model delta sinusoidal sigma weight residual -60.00 -167.52 107.52 1 2.00e+01 2.50e-03 3.12e+01 dihedral pdb=" C5' ADP A1602 " pdb=" O5' ADP A1602 " pdb=" PA ADP A1602 " pdb=" O2A ADP A1602 " ideal model delta sinusoidal sigma weight residual -60.00 -163.32 103.32 1 2.00e+01 2.50e-03 2.95e+01 dihedral pdb=" CA ASN A 575 " pdb=" C ASN A 575 " pdb=" N ILE A 576 " pdb=" CA ILE A 576 " ideal model delta harmonic sigma weight residual -180.00 -157.68 -22.32 0 5.00e+00 4.00e-02 1.99e+01 ... (remaining 5875 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 559 0.045 - 0.090: 515 0.090 - 0.134: 365 0.134 - 0.179: 114 0.179 - 0.224: 21 Chirality restraints: 1574 Sorted by residual: 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 2.66 -0.22 2.00e-01 2.50e+01 1.26e+00 chirality pdb=" CA PRO A1119 " pdb=" N PRO A1119 " pdb=" C PRO A1119 " pdb=" CB PRO A1119 " both_signs ideal model delta sigma weight residual False 2.72 2.50 0.22 2.00e-01 2.50e+01 1.20e+00 chirality pdb=" CA VAL A1451 " pdb=" N VAL A1451 " pdb=" C VAL A1451 " pdb=" CB VAL A1451 " both_signs ideal model delta sigma weight residual False 2.44 2.66 -0.22 2.00e-01 2.50e+01 1.17e+00 ... (remaining 1571 not shown) Planarity restraints: 1654 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 869 " -0.021 2.00e-02 2.50e+03 1.11e-02 2.47e+00 pdb=" CG TYR A 869 " 0.021 2.00e-02 2.50e+03 pdb=" CD1 TYR A 869 " 0.003 2.00e-02 2.50e+03 pdb=" CD2 TYR A 869 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR A 869 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR A 869 " 0.000 2.00e-02 2.50e+03 pdb=" CZ TYR A 869 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR A 869 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A1481 " 0.006 2.00e-02 2.50e+03 1.27e-02 1.62e+00 pdb=" C LEU A1481 " -0.022 2.00e-02 2.50e+03 pdb=" O LEU A1481 " 0.008 2.00e-02 2.50e+03 pdb=" N THR A1482 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A1277 " -0.006 2.00e-02 2.50e+03 1.26e-02 1.59e+00 pdb=" C ILE A1277 " 0.022 2.00e-02 2.50e+03 pdb=" O ILE A1277 " -0.008 2.00e-02 2.50e+03 pdb=" N GLN A1278 " -0.008 2.00e-02 2.50e+03 ... (remaining 1651 not shown) Histogram of nonbonded interaction distances: 1.86 - 2.47: 9 2.47 - 3.08: 5508 3.08 - 3.68: 14748 3.68 - 4.29: 19551 4.29 - 4.90: 35672 Nonbonded interactions: 75488 Sorted by model distance: nonbonded pdb=" OG SER A1333 " pdb="MG MG A1604 " model vdw 1.861 2.170 nonbonded pdb=" OG SER A 685 " pdb="MG MG A1603 " model vdw 1.863 2.170 nonbonded pdb=" O1G ATP A1601 " pdb="MG MG A1603 " model vdw 1.912 2.170 nonbonded pdb=" O2B ADP A1602 " pdb="MG MG A1604 " model vdw 1.982 2.170 nonbonded pdb=" O1B ATP A1601 " pdb="MG MG A1603 " model vdw 2.028 2.170 ... (remaining 75483 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.180 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 9.680 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6661 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 : 0.014 0.077 9892 Z= 1.077 Angle : 1.845 8.902 13450 Z= 1.415 Chirality : 0.083 0.224 1574 Planarity : 0.003 0.013 1654 Dihedral : 13.824 107.522 3596 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 1.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.56 (0.19), residues: 1202 helix: -1.20 (0.16), residues: 716 sheet: -1.37 (0.52), residues: 76 loop : -2.44 (0.25), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 775 TYR 0.021 0.002 TYR A 869 PHE 0.018 0.002 PHE A1379 TRP 0.018 0.002 TRP A 963 HIS 0.007 0.001 HIS A 382 Details of bonding type rmsd/Z covalent geometry : bond 0.01373 / 1.08 ( 9892) covalent geometry : angle 1.84534 / 1.41 (13450) hydrogen bonds : bond 0.22235 / 14.45 ( 572) hydrogen bonds : angle 7.28801 / 5.31 ( 1692) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 184 time to evaluate : 0.383 Fit side-chains revert: symmetry clash REVERT: A 230 GLN cc_start: 0.7213 (tt0) cc_final: 0.6612 (tp40) REVERT: A 234 GLN cc_start: 0.6526 (mp10) cc_final: 0.6196 (pp30) REVERT: A 361 TRP cc_start: 0.7268 (p-90) cc_final: 0.6908 (p-90) REVERT: A 648 ASN cc_start: 0.7215 (t0) cc_final: 0.6837 (m-40) REVERT: A 670 GLU cc_start: 0.7866 (mt-10) cc_final: 0.7509 (tp30) REVERT: A 679 GLN cc_start: 0.7154 (mm110) cc_final: 0.6709 (mm-40) REVERT: A 733 GLN cc_start: 0.5598 (mp10) cc_final: 0.5224 (mt0) REVERT: A 796 SER cc_start: 0.8245 (t) cc_final: 0.7885 (p) REVERT: A 835 MET cc_start: 0.7563 (mmt) cc_final: 0.7199 (mmt) REVERT: A 851 SER cc_start: 0.6608 (m) cc_final: 0.6387 (t) REVERT: A 864 GLU cc_start: 0.7789 (tt0) cc_final: 0.7488 (tp30) REVERT: A 966 MET cc_start: 0.7429 (mmm) cc_final: 0.7186 (mmt) REVERT: A 993 TYR cc_start: 0.6223 (t80) cc_final: 0.5467 (t80) REVERT: A 1057 ARG cc_start: 0.6949 (tpt-90) cc_final: 0.6686 (mmm160) REVERT: A 1088 GLN cc_start: 0.6431 (tt0) cc_final: 0.6191 (tt0) REVERT: A 1123 LEU cc_start: 0.6189 (tp) cc_final: 0.5941 (mp) REVERT: A 1280 MET cc_start: 0.6847 (mtm) cc_final: 0.6604 (mtm) REVERT: A 1375 ASP cc_start: 0.6861 (p0) cc_final: 0.6554 (p0) REVERT: A 1396 GLU cc_start: 0.7675 (mp0) cc_final: 0.6900 (pt0) REVERT: A 1417 LYS cc_start: 0.7543 (mptt) cc_final: 0.7158 (mmmt) REVERT: A 1465 ASP cc_start: 0.7282 (t70) cc_final: 0.7070 (t0) outliers start: 0 outliers final: 0 residues processed: 184 average time/residue: 0.1086 time to fit residues: 27.5598 Evaluate side-chains 128 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 128 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 108 optimal weight: 0.9990 chunk 49 optimal weight: 0.6980 chunk 97 optimal weight: 1.9990 chunk 113 optimal weight: 0.9990 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.0870 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 117 optimal weight: 1.9990 overall best weight: 0.7360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 725 ASN A1356 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.122708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.100686 restraints weight = 12852.960| |-----------------------------------------------------------------------------| r_work (start): 0.3078 rms_B_bonded: 1.49 r_work: 0.2977 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2855 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.1776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 9892 Z= 0.148 Angle : 0.579 7.164 13450 Z= 0.301 Chirality : 0.040 0.182 1574 Planarity : 0.004 0.037 1654 Dihedral : 7.150 99.353 1342 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.42 % Allowed : 7.12 % Favored : 91.46 % 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: 0.41 (0.23), residues: 1202 helix: 1.38 (0.18), residues: 757 sheet: -0.83 (0.54), residues: 77 loop : -1.86 (0.28), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1495 TYR 0.024 0.001 TYR A1032 PHE 0.010 0.001 PHE A 524 TRP 0.016 0.001 TRP A 520 HIS 0.007 0.001 HIS A 382 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.15 ( 9892) covalent geometry : angle 0.57949 / 0.30 (13450) hydrogen bonds : bond 0.06068 / 3.96 ( 572) hydrogen bonds : angle 4.32618 / 3.18 ( 1692) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 134 time to evaluate : 0.364 Fit side-chains REVERT: A 623 GLU cc_start: 0.8524 (mm-30) cc_final: 0.8229 (tt0) REVERT: A 648 ASN cc_start: 0.8178 (t0) cc_final: 0.7811 (t0) REVERT: A 742 GLU cc_start: 0.8060 (tm-30) cc_final: 0.7728 (pt0) REVERT: A 835 MET cc_start: 0.8820 (mmt) cc_final: 0.8260 (mmt) REVERT: A 836 ASP cc_start: 0.7897 (m-30) cc_final: 0.7553 (t0) REVERT: A 1123 LEU cc_start: 0.7898 (tp) cc_final: 0.7126 (mp) REVERT: A 1238 GLN cc_start: 0.7457 (mt0) cc_final: 0.7120 (mm110) REVERT: A 1375 ASP cc_start: 0.7373 (p0) cc_final: 0.6920 (p0) REVERT: A 1393 TYR cc_start: 0.6920 (OUTLIER) cc_final: 0.6092 (p90) REVERT: A 1417 LYS cc_start: 0.8493 (mptt) cc_final: 0.8220 (mmmt) REVERT: A 1465 ASP cc_start: 0.8144 (t70) cc_final: 0.7830 (t0) outliers start: 15 outliers final: 8 residues processed: 141 average time/residue: 0.0933 time to fit residues: 18.9940 Evaluate side-chains 124 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 115 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 351 ASN Chi-restraints excluded: chain A residue 452 ILE Chi-restraints excluded: chain A residue 838 ILE Chi-restraints excluded: chain A residue 954 THR Chi-restraints excluded: chain A residue 989 LEU Chi-restraints excluded: chain A residue 997 LEU Chi-restraints excluded: chain A residue 1393 TYR Chi-restraints excluded: chain A residue 1429 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 117 optimal weight: 3.9990 chunk 3 optimal weight: 0.0020 chunk 120 optimal weight: 0.7980 chunk 64 optimal weight: 0.3980 chunk 98 optimal weight: 4.9990 chunk 114 optimal weight: 0.7980 chunk 77 optimal weight: 0.6980 chunk 0 optimal weight: 4.9990 chunk 73 optimal weight: 0.9990 chunk 49 optimal weight: 4.9990 chunk 30 optimal weight: 1.9990 overall best weight: 0.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 234 GLN A 450 GLN A1010 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.127695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.106150 restraints weight = 12600.056| |-----------------------------------------------------------------------------| r_work (start): 0.3101 rms_B_bonded: 1.44 r_work: 0.3003 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2885 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.2271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9892 Z= 0.120 Angle : 0.508 7.421 13450 Z= 0.259 Chirality : 0.038 0.143 1574 Planarity : 0.004 0.050 1654 Dihedral : 6.834 95.142 1342 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.42 % Allowed : 10.34 % Favored : 88.24 % 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: 1.37 (0.24), residues: 1202 helix: 2.19 (0.18), residues: 764 sheet: -0.64 (0.54), residues: 77 loop : -1.63 (0.29), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 233 TYR 0.023 0.001 TYR A1032 PHE 0.009 0.001 PHE A 524 TRP 0.010 0.001 TRP A 520 HIS 0.006 0.001 HIS A 382 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.12 ( 9892) covalent geometry : angle 0.50803 / 0.26 (13450) hydrogen bonds : bond 0.05175 / 3.38 ( 572) hydrogen bonds : angle 3.81619 / 2.81 ( 1692) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 125 time to evaluate : 0.355 Fit side-chains REVERT: A 623 GLU cc_start: 0.8570 (mm-30) cc_final: 0.8298 (tt0) REVERT: A 648 ASN cc_start: 0.8132 (t0) cc_final: 0.7615 (t0) REVERT: A 738 LYS cc_start: 0.8354 (ttmt) cc_final: 0.6947 (pttp) REVERT: A 742 GLU cc_start: 0.8054 (tm-30) cc_final: 0.7820 (pt0) REVERT: A 796 SER cc_start: 0.9052 (t) cc_final: 0.8803 (p) REVERT: A 835 MET cc_start: 0.8833 (mmt) cc_final: 0.8320 (mmt) REVERT: A 836 ASP cc_start: 0.7913 (m-30) cc_final: 0.7604 (t0) REVERT: A 1034 MET cc_start: 0.8373 (tpp) cc_final: 0.8131 (mmm) REVERT: A 1278 GLN cc_start: 0.7919 (pp30) cc_final: 0.7412 (pp30) REVERT: A 1393 TYR cc_start: 0.6822 (OUTLIER) cc_final: 0.6065 (p90) REVERT: A 1465 ASP cc_start: 0.8218 (t70) cc_final: 0.7957 (t0) outliers start: 15 outliers final: 11 residues processed: 134 average time/residue: 0.0918 time to fit residues: 17.8586 Evaluate side-chains 124 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 112 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 265 CYS Chi-restraints excluded: chain A residue 327 MET Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 351 ASN Chi-restraints excluded: chain A residue 452 ILE Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 838 ILE Chi-restraints excluded: chain A residue 943 THR Chi-restraints excluded: chain A residue 995 LEU Chi-restraints excluded: chain A residue 997 LEU Chi-restraints excluded: chain A residue 1393 TYR Chi-restraints excluded: chain A residue 1429 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 8 optimal weight: 0.6980 chunk 72 optimal weight: 0.8980 chunk 110 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 chunk 4 optimal weight: 0.0770 chunk 7 optimal weight: 0.9990 chunk 13 optimal weight: 0.9980 chunk 5 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 overall best weight: 0.7338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.123062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.101357 restraints weight = 12799.443| |-----------------------------------------------------------------------------| r_work (start): 0.3084 rms_B_bonded: 1.47 r_work: 0.2985 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.2862 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.2862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.2496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9892 Z= 0.127 Angle : 0.505 7.343 13450 Z= 0.256 Chirality : 0.038 0.135 1574 Planarity : 0.004 0.057 1654 Dihedral : 6.767 94.734 1342 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.52 % Allowed : 11.67 % Favored : 86.81 % 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: 1.51 (0.24), residues: 1202 helix: 2.26 (0.18), residues: 772 sheet: -0.46 (0.55), residues: 77 loop : -1.61 (0.30), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 655 TYR 0.021 0.001 TYR A1032 PHE 0.011 0.001 PHE A 524 TRP 0.009 0.001 TRP A1197 HIS 0.006 0.001 HIS A 382 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.13 ( 9892) covalent geometry : angle 0.50540 / 0.26 (13450) hydrogen bonds : bond 0.05093 / 3.34 ( 572) hydrogen bonds : angle 3.68452 / 2.72 ( 1692) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 116 time to evaluate : 0.359 Fit side-chains REVERT: A 623 GLU cc_start: 0.8437 (mm-30) cc_final: 0.8230 (tt0) REVERT: A 648 ASN cc_start: 0.8149 (t0) cc_final: 0.7692 (t0) REVERT: A 733 GLN cc_start: 0.7417 (mp10) cc_final: 0.7213 (mt0) REVERT: A 738 LYS cc_start: 0.8305 (ttmt) cc_final: 0.6873 (pttp) REVERT: A 742 GLU cc_start: 0.8014 (tm-30) cc_final: 0.7726 (pt0) REVERT: A 796 SER cc_start: 0.9067 (t) cc_final: 0.8838 (p) REVERT: A 835 MET cc_start: 0.8810 (mmt) cc_final: 0.8313 (mmt) REVERT: A 836 ASP cc_start: 0.7884 (m-30) cc_final: 0.7574 (t0) REVERT: A 1278 GLN cc_start: 0.7986 (pp30) cc_final: 0.7547 (pp30) REVERT: A 1393 TYR cc_start: 0.6757 (OUTLIER) cc_final: 0.6019 (p90) REVERT: A 1465 ASP cc_start: 0.8253 (t70) cc_final: 0.8017 (t0) outliers start: 16 outliers final: 11 residues processed: 127 average time/residue: 0.0905 time to fit residues: 16.9293 Evaluate side-chains 119 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 107 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 327 MET Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 351 ASN Chi-restraints excluded: chain A residue 452 ILE Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 838 ILE Chi-restraints excluded: chain A residue 943 THR Chi-restraints excluded: chain A residue 995 LEU Chi-restraints excluded: chain A residue 1240 THR Chi-restraints excluded: chain A residue 1357 ILE Chi-restraints excluded: chain A residue 1393 TYR Chi-restraints excluded: chain A residue 1429 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 77 optimal weight: 0.9990 chunk 78 optimal weight: 0.9990 chunk 94 optimal weight: 3.9990 chunk 118 optimal weight: 2.9990 chunk 83 optimal weight: 0.9990 chunk 34 optimal weight: 0.5980 chunk 116 optimal weight: 4.9990 chunk 7 optimal weight: 0.2980 chunk 68 optimal weight: 0.0010 chunk 32 optimal weight: 0.0040 chunk 10 optimal weight: 0.7980 overall best weight: 0.3398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.126375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.104447 restraints weight = 12692.777| |-----------------------------------------------------------------------------| r_work (start): 0.3132 rms_B_bonded: 1.51 r_work: 0.3032 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2910 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.2745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 9892 Z= 0.104 Angle : 0.472 7.247 13450 Z= 0.240 Chirality : 0.037 0.188 1574 Planarity : 0.004 0.061 1654 Dihedral : 6.640 94.628 1342 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.23 % Allowed : 12.24 % Favored : 86.53 % 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: 1.89 (0.24), residues: 1202 helix: 2.56 (0.19), residues: 766 sheet: -0.34 (0.58), residues: 76 loop : -1.39 (0.29), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1248 TYR 0.020 0.001 TYR A1032 PHE 0.008 0.001 PHE A 666 TRP 0.009 0.001 TRP A1197 HIS 0.005 0.001 HIS A 382 Details of bonding type rmsd/Z covalent geometry : bond 0.00214 / 0.10 ( 9892) covalent geometry : angle 0.47231 / 0.24 (13450) hydrogen bonds : bond 0.04357 / 2.86 ( 572) hydrogen bonds : angle 3.51579 / 2.59 ( 1692) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 114 time to evaluate : 0.392 Fit side-chains REVERT: A 623 GLU cc_start: 0.8450 (mm-30) cc_final: 0.8197 (tt0) REVERT: A 648 ASN cc_start: 0.8094 (t0) cc_final: 0.7812 (m-40) REVERT: A 738 LYS cc_start: 0.8269 (ttmt) cc_final: 0.6834 (pttp) REVERT: A 742 GLU cc_start: 0.7940 (tm-30) cc_final: 0.7694 (pt0) REVERT: A 835 MET cc_start: 0.8747 (mmt) cc_final: 0.8437 (mmp) REVERT: A 836 ASP cc_start: 0.7895 (m-30) cc_final: 0.7641 (t0) REVERT: A 1034 MET cc_start: 0.8357 (tpp) cc_final: 0.8134 (mmm) REVERT: A 1380 SER cc_start: 0.9040 (t) cc_final: 0.8820 (p) REVERT: A 1393 TYR cc_start: 0.6673 (OUTLIER) cc_final: 0.5981 (p90) REVERT: A 1465 ASP cc_start: 0.8181 (t70) cc_final: 0.7935 (t0) outliers start: 13 outliers final: 9 residues processed: 124 average time/residue: 0.0838 time to fit residues: 15.3151 Evaluate side-chains 115 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 105 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 327 MET Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 422 GLU Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 838 ILE Chi-restraints excluded: chain A residue 954 THR Chi-restraints excluded: chain A residue 995 LEU Chi-restraints excluded: chain A residue 1337 LEU Chi-restraints excluded: chain A residue 1393 TYR Chi-restraints excluded: chain A residue 1429 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 88 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 96 optimal weight: 3.9990 chunk 109 optimal weight: 0.0570 chunk 1 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 74 optimal weight: 0.5980 chunk 19 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 80 optimal weight: 0.7980 overall best weight: 0.8902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 412 ASN A1515 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.123870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.099716 restraints weight = 12683.682| |-----------------------------------------------------------------------------| r_work (start): 0.3057 rms_B_bonded: 1.80 r_work: 0.2944 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2812 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.2796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9892 Z= 0.137 Angle : 0.512 7.229 13450 Z= 0.260 Chirality : 0.039 0.166 1574 Planarity : 0.004 0.062 1654 Dihedral : 6.666 93.097 1342 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.90 % Allowed : 13.28 % Favored : 84.82 % 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: 1.74 (0.24), residues: 1202 helix: 2.39 (0.18), residues: 767 sheet: -0.29 (0.58), residues: 76 loop : -1.36 (0.30), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1302 TYR 0.021 0.001 TYR A1032 PHE 0.012 0.001 PHE A 524 TRP 0.006 0.001 TRP A1197 HIS 0.012 0.001 HIS A 382 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.14 ( 9892) covalent geometry : angle 0.51204 / 0.26 (13450) hydrogen bonds : bond 0.05057 / 3.33 ( 572) hydrogen bonds : angle 3.57923 / 2.63 ( 1692) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 112 time to evaluate : 0.394 Fit side-chains REVERT: A 623 GLU cc_start: 0.8495 (mm-30) cc_final: 0.8141 (tt0) REVERT: A 648 ASN cc_start: 0.8024 (t0) cc_final: 0.7708 (m-40) REVERT: A 738 LYS cc_start: 0.8227 (ttmt) cc_final: 0.6795 (pttp) REVERT: A 742 GLU cc_start: 0.7963 (tm-30) cc_final: 0.7580 (pt0) REVERT: A 824 LEU cc_start: 0.8580 (OUTLIER) cc_final: 0.8313 (pp) REVERT: A 835 MET cc_start: 0.8732 (mmt) cc_final: 0.8434 (mmp) REVERT: A 836 ASP cc_start: 0.7934 (m-30) cc_final: 0.7503 (t0) REVERT: A 1130 ARG cc_start: 0.7998 (OUTLIER) cc_final: 0.7791 (mmp-170) REVERT: A 1293 GLU cc_start: 0.8007 (tt0) cc_final: 0.7777 (tt0) REVERT: A 1302 ARG cc_start: 0.7832 (mtm180) cc_final: 0.7611 (mtp-110) REVERT: A 1393 TYR cc_start: 0.6748 (OUTLIER) cc_final: 0.6057 (p90) REVERT: A 1465 ASP cc_start: 0.8261 (t70) cc_final: 0.8030 (t0) outliers start: 20 outliers final: 16 residues processed: 126 average time/residue: 0.0969 time to fit residues: 17.6712 Evaluate side-chains 129 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 110 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 327 MET Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 351 ASN Chi-restraints excluded: chain A residue 452 ILE Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 476 MET Chi-restraints excluded: chain A residue 824 LEU Chi-restraints excluded: chain A residue 838 ILE Chi-restraints excluded: chain A residue 954 THR Chi-restraints excluded: chain A residue 995 LEU Chi-restraints excluded: chain A residue 1130 ARG Chi-restraints excluded: chain A residue 1240 THR Chi-restraints excluded: chain A residue 1278 GLN Chi-restraints excluded: chain A residue 1284 LYS Chi-restraints excluded: chain A residue 1337 LEU Chi-restraints excluded: chain A residue 1357 ILE Chi-restraints excluded: chain A residue 1393 TYR Chi-restraints excluded: chain A residue 1429 LEU Chi-restraints excluded: chain A residue 1481 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 53 optimal weight: 4.9990 chunk 15 optimal weight: 0.9990 chunk 112 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 57 optimal weight: 0.9980 chunk 104 optimal weight: 0.2980 chunk 51 optimal weight: 0.6980 chunk 46 optimal weight: 0.7980 chunk 92 optimal weight: 0.6980 chunk 18 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.124745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.100696 restraints weight = 12579.012| |-----------------------------------------------------------------------------| r_work (start): 0.3064 rms_B_bonded: 1.79 r_work: 0.2951 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2820 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.2915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9892 Z= 0.121 Angle : 0.493 7.157 13450 Z= 0.250 Chirality : 0.038 0.156 1574 Planarity : 0.004 0.061 1654 Dihedral : 6.533 89.078 1342 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 1.71 % Allowed : 13.57 % Favored : 84.72 % 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: 1.81 (0.24), residues: 1202 helix: 2.44 (0.18), residues: 768 sheet: -0.28 (0.59), residues: 76 loop : -1.34 (0.30), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A1221 TYR 0.020 0.001 TYR A1032 PHE 0.010 0.001 PHE A 524 TRP 0.009 0.001 TRP A1197 HIS 0.010 0.001 HIS A 382 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 ( 9892) covalent geometry : angle 0.49343 / 0.25 (13450) hydrogen bonds : bond 0.04795 / 3.15 ( 572) hydrogen bonds : angle 3.51872 / 2.59 ( 1692) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 111 time to evaluate : 0.384 Fit side-chains REVERT: A 623 GLU cc_start: 0.8476 (mm-30) cc_final: 0.8147 (tt0) REVERT: A 648 ASN cc_start: 0.8018 (t0) cc_final: 0.7700 (m-40) REVERT: A 738 LYS cc_start: 0.8197 (ttmt) cc_final: 0.6830 (pttp) REVERT: A 742 GLU cc_start: 0.7944 (tm-30) cc_final: 0.7610 (pt0) REVERT: A 824 LEU cc_start: 0.8531 (OUTLIER) cc_final: 0.8261 (pp) REVERT: A 835 MET cc_start: 0.8712 (mmt) cc_final: 0.8292 (mmt) REVERT: A 836 ASP cc_start: 0.7968 (m-30) cc_final: 0.7557 (t0) REVERT: A 1034 MET cc_start: 0.8336 (tpp) cc_final: 0.8106 (mmm) REVERT: A 1130 ARG cc_start: 0.7984 (OUTLIER) cc_final: 0.7781 (mmp-170) REVERT: A 1293 GLU cc_start: 0.7958 (tt0) cc_final: 0.7724 (tt0) REVERT: A 1393 TYR cc_start: 0.6772 (OUTLIER) cc_final: 0.5954 (p90) REVERT: A 1465 ASP cc_start: 0.8236 (t70) cc_final: 0.8005 (t0) outliers start: 18 outliers final: 13 residues processed: 123 average time/residue: 0.1044 time to fit residues: 18.3823 Evaluate side-chains 123 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 107 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 327 MET Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 351 ASN Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 824 LEU Chi-restraints excluded: chain A residue 838 ILE Chi-restraints excluded: chain A residue 954 THR Chi-restraints excluded: chain A residue 995 LEU Chi-restraints excluded: chain A residue 1130 ARG Chi-restraints excluded: chain A residue 1240 THR Chi-restraints excluded: chain A residue 1278 GLN Chi-restraints excluded: chain A residue 1284 LYS Chi-restraints excluded: chain A residue 1357 ILE Chi-restraints excluded: chain A residue 1393 TYR Chi-restraints excluded: chain A residue 1429 LEU Chi-restraints excluded: chain A residue 1481 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 10 optimal weight: 1.9990 chunk 89 optimal weight: 0.8980 chunk 101 optimal weight: 0.7980 chunk 61 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 91 optimal weight: 0.8980 chunk 4 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 chunk 94 optimal weight: 2.9990 chunk 68 optimal weight: 5.9990 chunk 79 optimal weight: 0.9980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1485 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.122267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.098162 restraints weight = 12687.749| |-----------------------------------------------------------------------------| r_work (start): 0.3025 rms_B_bonded: 1.79 r_work: 0.2911 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2779 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.2936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9892 Z= 0.156 Angle : 0.531 7.237 13450 Z= 0.270 Chirality : 0.039 0.167 1574 Planarity : 0.004 0.062 1654 Dihedral : 6.550 85.077 1342 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.99 % Allowed : 13.76 % Favored : 84.25 % 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: 1.59 (0.24), residues: 1202 helix: 2.26 (0.18), residues: 767 sheet: -0.28 (0.57), residues: 77 loop : -1.41 (0.30), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1074 TYR 0.021 0.001 TYR A1032 PHE 0.012 0.001 PHE A 524 TRP 0.008 0.001 TRP A1197 HIS 0.012 0.001 HIS A 382 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.16 ( 9892) covalent geometry : angle 0.53093 / 0.27 (13450) hydrogen bonds : bond 0.05409 / 3.55 ( 572) hydrogen bonds : angle 3.63582 / 2.67 ( 1692) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 108 time to evaluate : 0.363 Fit side-chains REVERT: A 623 GLU cc_start: 0.8483 (mm-30) cc_final: 0.8150 (tt0) REVERT: A 648 ASN cc_start: 0.8043 (t0) cc_final: 0.7713 (m-40) REVERT: A 738 LYS cc_start: 0.8242 (ttmt) cc_final: 0.6840 (pttp) REVERT: A 742 GLU cc_start: 0.7972 (tm-30) cc_final: 0.7577 (pt0) REVERT: A 824 LEU cc_start: 0.8581 (OUTLIER) cc_final: 0.8314 (pp) REVERT: A 835 MET cc_start: 0.8785 (mmt) cc_final: 0.8330 (mmt) REVERT: A 836 ASP cc_start: 0.8010 (m-30) cc_final: 0.7576 (t0) REVERT: A 1130 ARG cc_start: 0.8018 (OUTLIER) cc_final: 0.7807 (mmp-170) REVERT: A 1393 TYR cc_start: 0.6927 (OUTLIER) cc_final: 0.5981 (p90) REVERT: A 1396 GLU cc_start: 0.8227 (mm-30) cc_final: 0.7753 (pt0) REVERT: A 1465 ASP cc_start: 0.8289 (t70) cc_final: 0.8050 (t0) outliers start: 21 outliers final: 16 residues processed: 121 average time/residue: 0.1014 time to fit residues: 17.5452 Evaluate side-chains 126 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 107 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 327 MET Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 351 ASN Chi-restraints excluded: chain A residue 452 ILE Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 476 MET Chi-restraints excluded: chain A residue 824 LEU Chi-restraints excluded: chain A residue 838 ILE Chi-restraints excluded: chain A residue 954 THR Chi-restraints excluded: chain A residue 995 LEU Chi-restraints excluded: chain A residue 1130 ARG Chi-restraints excluded: chain A residue 1240 THR Chi-restraints excluded: chain A residue 1278 GLN Chi-restraints excluded: chain A residue 1284 LYS Chi-restraints excluded: chain A residue 1355 ILE Chi-restraints excluded: chain A residue 1357 ILE Chi-restraints excluded: chain A residue 1393 TYR Chi-restraints excluded: chain A residue 1429 LEU Chi-restraints excluded: chain A residue 1481 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 83 optimal weight: 1.9990 chunk 82 optimal weight: 0.9990 chunk 94 optimal weight: 0.6980 chunk 104 optimal weight: 0.9980 chunk 97 optimal weight: 5.9990 chunk 110 optimal weight: 4.9990 chunk 108 optimal weight: 4.9990 chunk 39 optimal weight: 0.9980 chunk 114 optimal weight: 0.8980 chunk 1 optimal weight: 0.0020 chunk 36 optimal weight: 1.9990 overall best weight: 0.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1515 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.123970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.102059 restraints weight = 12622.922| |-----------------------------------------------------------------------------| r_work (start): 0.3074 rms_B_bonded: 1.50 r_work: 0.2974 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.2854 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.2854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.3035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9892 Z= 0.125 Angle : 0.501 6.897 13450 Z= 0.255 Chirality : 0.038 0.155 1574 Planarity : 0.004 0.061 1654 Dihedral : 6.406 84.517 1342 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.71 % Allowed : 13.95 % Favored : 84.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.71 (0.24), residues: 1202 helix: 2.37 (0.18), residues: 767 sheet: -0.20 (0.59), residues: 76 loop : -1.40 (0.30), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 233 TYR 0.020 0.001 TYR A1032 PHE 0.010 0.001 PHE A 524 TRP 0.010 0.001 TRP A1197 HIS 0.010 0.001 HIS A 382 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.13 ( 9892) covalent geometry : angle 0.50082 / 0.25 (13450) hydrogen bonds : bond 0.04934 / 3.24 ( 572) hydrogen bonds : angle 3.57425 / 2.62 ( 1692) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 110 time to evaluate : 0.403 Fit side-chains REVERT: A 623 GLU cc_start: 0.8393 (mm-30) cc_final: 0.8182 (tt0) REVERT: A 648 ASN cc_start: 0.8090 (t0) cc_final: 0.7784 (m-40) REVERT: A 738 LYS cc_start: 0.8263 (ttmt) cc_final: 0.6871 (pttp) REVERT: A 742 GLU cc_start: 0.7997 (tm-30) cc_final: 0.7690 (pt0) REVERT: A 824 LEU cc_start: 0.8547 (OUTLIER) cc_final: 0.8278 (pp) REVERT: A 835 MET cc_start: 0.8837 (mmt) cc_final: 0.8380 (mmt) REVERT: A 836 ASP cc_start: 0.7946 (m-30) cc_final: 0.7603 (t0) REVERT: A 1130 ARG cc_start: 0.8029 (OUTLIER) cc_final: 0.7811 (mmp-170) REVERT: A 1393 TYR cc_start: 0.6894 (OUTLIER) cc_final: 0.5973 (p90) REVERT: A 1396 GLU cc_start: 0.8182 (mm-30) cc_final: 0.7768 (pt0) REVERT: A 1465 ASP cc_start: 0.8271 (t70) cc_final: 0.8030 (t0) outliers start: 18 outliers final: 12 residues processed: 121 average time/residue: 0.1008 time to fit residues: 17.5587 Evaluate side-chains 122 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 107 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 327 MET Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 351 ASN Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 824 LEU Chi-restraints excluded: chain A residue 838 ILE Chi-restraints excluded: chain A residue 954 THR Chi-restraints excluded: chain A residue 995 LEU Chi-restraints excluded: chain A residue 1130 ARG Chi-restraints excluded: chain A residue 1240 THR Chi-restraints excluded: chain A residue 1278 GLN Chi-restraints excluded: chain A residue 1357 ILE Chi-restraints excluded: chain A residue 1393 TYR Chi-restraints excluded: chain A residue 1429 LEU Chi-restraints excluded: chain A residue 1481 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 34 optimal weight: 0.6980 chunk 51 optimal weight: 0.0170 chunk 87 optimal weight: 0.5980 chunk 8 optimal weight: 1.9990 chunk 70 optimal weight: 0.9990 chunk 49 optimal weight: 0.6980 chunk 11 optimal weight: 0.0170 chunk 54 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 75 optimal weight: 0.0270 chunk 53 optimal weight: 2.9990 overall best weight: 0.2714 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1515 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.127338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.105731 restraints weight = 12526.112| |-----------------------------------------------------------------------------| r_work (start): 0.3143 rms_B_bonded: 1.48 r_work: 0.3048 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.2929 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.3253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 9892 Z= 0.101 Angle : 0.473 6.289 13450 Z= 0.240 Chirality : 0.037 0.142 1574 Planarity : 0.004 0.061 1654 Dihedral : 6.095 89.564 1342 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.42 % Allowed : 14.33 % Favored : 84.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.08 (0.25), residues: 1202 helix: 2.67 (0.19), residues: 762 sheet: -0.07 (0.60), residues: 75 loop : -1.22 (0.30), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 233 TYR 0.019 0.001 TYR A1032 PHE 0.008 0.001 PHE A1030 TRP 0.011 0.001 TRP A1197 HIS 0.007 0.001 HIS A 382 Details of bonding type rmsd/Z covalent geometry : bond 0.00207 / 0.10 ( 9892) covalent geometry : angle 0.47304 / 0.24 (13450) hydrogen bonds : bond 0.04106 / 2.70 ( 572) hydrogen bonds : angle 3.43624 / 2.52 ( 1692) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 115 time to evaluate : 0.377 Fit side-chains REVERT: A 648 ASN cc_start: 0.8041 (t0) cc_final: 0.7769 (m-40) REVERT: A 738 LYS cc_start: 0.8289 (ttmt) cc_final: 0.7156 (pttp) REVERT: A 824 LEU cc_start: 0.8391 (OUTLIER) cc_final: 0.8111 (pp) REVERT: A 835 MET cc_start: 0.8783 (mmt) cc_final: 0.8327 (mmt) REVERT: A 966 MET cc_start: 0.8139 (mmt) cc_final: 0.7549 (mmt) REVERT: A 1034 MET cc_start: 0.8359 (tpp) cc_final: 0.8143 (mmm) REVERT: A 1130 ARG cc_start: 0.7927 (OUTLIER) cc_final: 0.7725 (mmp-170) REVERT: A 1393 TYR cc_start: 0.6789 (OUTLIER) cc_final: 0.5895 (p90) REVERT: A 1465 ASP cc_start: 0.8230 (t70) cc_final: 0.8000 (t0) outliers start: 15 outliers final: 11 residues processed: 126 average time/residue: 0.0947 time to fit residues: 16.8266 Evaluate side-chains 119 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 105 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 327 MET Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 824 LEU Chi-restraints excluded: chain A residue 838 ILE Chi-restraints excluded: chain A residue 954 THR Chi-restraints excluded: chain A residue 995 LEU Chi-restraints excluded: chain A residue 1130 ARG Chi-restraints excluded: chain A residue 1240 THR Chi-restraints excluded: chain A residue 1278 GLN Chi-restraints excluded: chain A residue 1357 ILE Chi-restraints excluded: chain A residue 1393 TYR Chi-restraints excluded: chain A residue 1429 LEU Chi-restraints excluded: chain A residue 1481 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 15 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 chunk 106 optimal weight: 3.9990 chunk 91 optimal weight: 3.9990 chunk 16 optimal weight: 0.6980 chunk 27 optimal weight: 0.5980 chunk 57 optimal weight: 3.9990 chunk 79 optimal weight: 5.9990 chunk 46 optimal weight: 0.9980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1515 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.121872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.099932 restraints weight = 12756.446| |-----------------------------------------------------------------------------| r_work (start): 0.3061 rms_B_bonded: 1.50 r_work: 0.2963 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.2844 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.3178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9892 Z= 0.145 Angle : 0.526 6.998 13450 Z= 0.264 Chirality : 0.039 0.158 1574 Planarity : 0.004 0.061 1654 Dihedral : 6.047 85.333 1342 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.33 % Allowed : 15.09 % Favored : 83.59 % 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 (0.24), residues: 1202 helix: 2.42 (0.18), residues: 767 sheet: -0.08 (0.58), residues: 76 loop : -1.36 (0.30), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 655 TYR 0.021 0.001 TYR A1032 PHE 0.012 0.001 PHE A 524 TRP 0.008 0.001 TRP A1286 HIS 0.011 0.001 HIS A 382 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.15 ( 9892) covalent geometry : angle 0.52561 / 0.26 (13450) hydrogen bonds : bond 0.05057 / 3.32 ( 572) hydrogen bonds : angle 3.58595 / 2.63 ( 1692) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2405.63 seconds wall clock time: 41 minutes 57.38 seconds (2517.38 seconds total)