Starting phenix.real_space_refine on Sat Aug 23 09:00:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hw2_35049/08_2025/8hw2_35049.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hw2_35049/08_2025/8hw2_35049.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.65 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8hw2_35049/08_2025/8hw2_35049.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hw2_35049/08_2025/8hw2_35049.map" model { file = "/net/cci-nas-00/data/ceres_data/8hw2_35049/08_2025/8hw2_35049.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hw2_35049/08_2025/8hw2_35049.cif" } resolution = 3.65 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= 0.003 sd= 0.059 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: 4 Type Number sf(0) Gaussians S 57 5.16 5 C 7063 2.51 5 N 1812 2.21 5 O 1921 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 55 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10853 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 10789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1375, 10789 Classifications: {'peptide': 1375} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 61, 'TRANS': 1313} Chain breaks: 2 Chain: "A" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 64 Unusual residues: {'U38': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 2.56, per 1000 atoms: 0.24 Number of scatterers: 10853 At special positions: 0 Unit cell: (78.11, 109.14, 149.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 57 16.00 O 1921 8.00 N 1812 7.00 C 7063 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.00 Conformation dependent library (CDL) restraints added in 463.8 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2738 Ramachandran restraints generated. 1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2580 Finding SS restraints... Secondary structure from input PDB file: 77 helices and 5 sheets defined 63.7% alpha, 7.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.49 Creating SS restraints... Processing helix chain 'A' and resid 34 through 38 removed outlier: 4.392A pdb=" N LEU A 37 " --> pdb=" O ASN A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 39 through 59 removed outlier: 3.716A pdb=" N ILE A 43 " --> pdb=" O TRP A 39 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N TYR A 44 " --> pdb=" O VAL A 40 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N TRP A 46 " --> pdb=" O CYS A 42 " (cutoff:3.500A) Proline residue: A 50 - end of helix removed outlier: 4.167A pdb=" N TYR A 55 " --> pdb=" O CYS A 51 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LEU A 56 " --> pdb=" O TYR A 52 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N HIS A 59 " --> pdb=" O TYR A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 94 removed outlier: 3.658A pdb=" N LYS A 71 " --> pdb=" O SER A 67 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLY A 77 " --> pdb=" O LYS A 73 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LEU A 88 " --> pdb=" O SER A 84 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLY A 94 " --> pdb=" O TYR A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 106 removed outlier: 4.218A pdb=" N PHE A 106 " --> pdb=" O PRO A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 127 removed outlier: 3.697A pdb=" N VAL A 114 " --> pdb=" O LEU A 110 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N LEU A 117 " --> pdb=" O GLY A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 156 removed outlier: 3.800A pdb=" N VAL A 150 " --> pdb=" O VAL A 146 " (cutoff:3.500A) Proline residue: A 151 - end of helix Processing helix chain 'A' and resid 167 through 189 Processing helix chain 'A' and resid 220 through 222 No H-bonds generated for 'chain 'A' and resid 220 through 222' Processing helix chain 'A' and resid 223 through 228 Processing helix chain 'A' and resid 236 through 240 Processing helix chain 'A' and resid 252 through 263 Processing helix chain 'A' and resid 298 through 305 removed outlier: 3.761A pdb=" N ALA A 302 " --> pdb=" O SER A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 311 removed outlier: 5.766A pdb=" N SER A 309 " --> pdb=" O THR A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 326 removed outlier: 3.915A pdb=" N PHE A 326 " --> pdb=" O ASP A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 340 removed outlier: 4.350A pdb=" N SER A 333 " --> pdb=" O PRO A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 362 removed outlier: 4.013A pdb=" N GLY A 349 " --> pdb=" O PRO A 345 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU A 358 " --> pdb=" O GLY A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 386 removed outlier: 3.789A pdb=" N THR A 377 " --> pdb=" O TYR A 373 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLY A 378 " --> pdb=" O ILE A 374 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N MET A 386 " --> pdb=" O ARG A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 394 removed outlier: 3.911A pdb=" N ARG A 391 " --> pdb=" O GLY A 387 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LYS A 392 " --> pdb=" O VAL A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 404 removed outlier: 3.584A pdb=" N LYS A 401 " --> pdb=" O THR A 397 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N SER A 404 " --> pdb=" O VAL A 400 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 412 Processing helix chain 'A' and resid 423 through 428 removed outlier: 3.881A pdb=" N ASN A 428 " --> pdb=" O ALA A 424 " (cutoff:3.500A) Processing helix chain 'A' and resid 428 through 436 removed outlier: 3.960A pdb=" N SER A 432 " --> pdb=" O ASN A 428 " (cutoff:3.500A) Proline residue: A 434 - end of helix Processing helix chain 'A' and resid 440 through 448 removed outlier: 3.696A pdb=" N LEU A 444 " --> pdb=" O ALA A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 472 removed outlier: 3.667A pdb=" N MET A 459 " --> pdb=" O GLY A 455 " (cutoff:3.500A) Proline residue: A 464 - end of helix removed outlier: 4.649A pdb=" N VAL A 469 " --> pdb=" O LEU A 465 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ALA A 470 " --> pdb=" O ASN A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 477 Processing helix chain 'A' and resid 481 through 496 Processing helix chain 'A' and resid 497 through 504 removed outlier: 3.704A pdb=" N TYR A 504 " --> pdb=" O VAL A 500 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 526 removed outlier: 3.700A pdb=" N PHE A 510 " --> pdb=" O TRP A 506 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N ILE A 517 " --> pdb=" O GLN A 513 " (cutoff:3.500A) Processing helix chain 'A' and resid 527 through 528 No H-bonds generated for 'chain 'A' and resid 527 through 528' Processing helix chain 'A' and resid 529 through 533 removed outlier: 3.583A pdb=" N THR A 533 " --> pdb=" O TYR A 530 " (cutoff:3.500A) Processing helix chain 'A' and resid 534 through 556 removed outlier: 3.693A pdb=" N THR A 538 " --> pdb=" O THR A 534 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N TRP A 539 " --> pdb=" O THR A 535 " (cutoff:3.500A) Proline residue: A 543 - end of helix Processing helix chain 'A' and resid 564 through 579 removed outlier: 4.909A pdb=" N VAL A 570 " --> pdb=" O GLU A 566 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ASN A 576 " --> pdb=" O VAL A 572 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ILE A 577 " --> pdb=" O SER A 573 " (cutoff:3.500A) Processing helix chain 'A' and resid 579 through 584 removed outlier: 3.584A pdb=" N ASN A 583 " --> pdb=" O ARG A 579 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N MET A 584 " --> pdb=" O LEU A 580 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 579 through 584' Processing helix chain 'A' and resid 584 through 606 removed outlier: 3.575A pdb=" N LEU A 588 " --> pdb=" O MET A 584 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N THR A 593 " --> pdb=" O ILE A 589 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N SER A 598 " --> pdb=" O GLN A 594 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ARG A 601 " --> pdb=" O VAL A 597 " (cutoff:3.500A) Processing helix chain 'A' and resid 666 through 675 removed outlier: 4.142A pdb=" N VAL A 671 " --> pdb=" O LYS A 667 " (cutoff:3.500A) removed outlier: 5.091A pdb=" N SER A 672 " --> pdb=" O SER A 668 " (cutoff:3.500A) Processing helix chain 'A' and resid 704 through 711 Processing helix chain 'A' and resid 716 through 727 Processing helix chain 'A' and resid 729 through 734 Processing helix chain 'A' and resid 738 through 742 Processing helix chain 'A' and resid 752 through 767 removed outlier: 4.285A pdb=" N ARG A 758 " --> pdb=" O GLY A 754 " (cutoff:3.500A) Processing helix chain 'A' and resid 782 through 793 removed outlier: 3.975A pdb=" N HIS A 788 " --> pdb=" O HIS A 784 " (cutoff:3.500A) Processing helix chain 'A' and resid 834 through 842 removed outlier: 3.952A pdb=" N ARG A 841 " --> pdb=" O ALA A 837 " (cutoff:3.500A) Processing helix chain 'A' and resid 843 through 852 removed outlier: 3.871A pdb=" N ASN A 847 " --> pdb=" O GLY A 843 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N PHE A 848 " --> pdb=" O SER A 844 " (cutoff:3.500A) Processing helix chain 'A' and resid 955 through 967 removed outlier: 4.363A pdb=" N PHE A 959 " --> pdb=" O GLU A 955 " (cutoff:3.500A) Processing helix chain 'A' and resid 967 through 972 Processing helix chain 'A' and resid 974 through 997 Processing helix chain 'A' and resid 998 through 1001 removed outlier: 3.762A pdb=" N ALA A1001 " --> pdb=" O ASP A 998 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 998 through 1001' Processing helix chain 'A' and resid 1004 through 1006 No H-bonds generated for 'chain 'A' and resid 1004 through 1006' Processing helix chain 'A' and resid 1007 through 1020 removed outlier: 4.083A pdb=" N LEU A1012 " --> pdb=" O THR A1008 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N GLY A1013 " --> pdb=" O SER A1009 " (cutoff:3.500A) Processing helix chain 'A' and resid 1026 through 1053 removed outlier: 3.895A pdb=" N ALA A1032 " --> pdb=" O LEU A1028 " (cutoff:3.500A) Processing helix chain 'A' and resid 1056 through 1063 removed outlier: 4.019A pdb=" N PHE A1060 " --> pdb=" O PRO A1056 " (cutoff:3.500A) Processing helix chain 'A' and resid 1065 through 1071 removed outlier: 3.713A pdb=" N CYS A1071 " --> pdb=" O ARG A1067 " (cutoff:3.500A) Processing helix chain 'A' and resid 1076 through 1082 Processing helix chain 'A' and resid 1083 through 1108 removed outlier: 3.729A pdb=" N PHE A1095 " --> pdb=" O LEU A1091 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N THR A1100 " --> pdb=" O ASN A1096 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N MET A1105 " --> pdb=" O LEU A1101 " (cutoff:3.500A) Processing helix chain 'A' and resid 1116 through 1151 removed outlier: 4.592A pdb=" N TYR A1122 " --> pdb=" O LEU A1118 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ARG A1134 " --> pdb=" O ALA A1130 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N SER A1143 " --> pdb=" O LEU A1139 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N SER A1145 " --> pdb=" O SER A1141 " (cutoff:3.500A) Proline residue: A1146 - end of helix Processing helix chain 'A' and resid 1157 through 1162 Processing helix chain 'A' and resid 1167 through 1169 No H-bonds generated for 'chain 'A' and resid 1167 through 1169' Processing helix chain 'A' and resid 1170 through 1183 removed outlier: 3.877A pdb=" N THR A1176 " --> pdb=" O ILE A1172 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ASN A1181 " --> pdb=" O LYS A1177 " (cutoff:3.500A) Processing helix chain 'A' and resid 1185 through 1190 removed outlier: 3.640A pdb=" N ILE A1189 " --> pdb=" O CYS A1185 " (cutoff:3.500A) Processing helix chain 'A' and resid 1201 through 1217 removed outlier: 4.436A pdb=" N VAL A1207 " --> pdb=" O GLY A1203 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N PHE A1213 " --> pdb=" O PHE A1209 " (cutoff:3.500A) Processing helix chain 'A' and resid 1218 through 1221 Processing helix chain 'A' and resid 1222 through 1232 Processing helix chain 'A' and resid 1235 through 1240 removed outlier: 3.624A pdb=" N ALA A1239 " --> pdb=" O GLN A1235 " (cutoff:3.500A) Processing helix chain 'A' and resid 1249 through 1253 Processing helix chain 'A' and resid 1254 through 1263 Processing helix chain 'A' and resid 1274 through 1278 Processing helix chain 'A' and resid 1328 through 1337 removed outlier: 3.505A pdb=" N MET A1332 " --> pdb=" O GLY A1328 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N PHE A1337 " --> pdb=" O THR A1333 " (cutoff:3.500A) Processing helix chain 'A' and resid 1358 through 1365 removed outlier: 3.735A pdb=" N GLN A1365 " --> pdb=" O ASP A1361 " (cutoff:3.500A) Processing helix chain 'A' and resid 1379 through 1385 removed outlier: 3.625A pdb=" N ASN A1383 " --> pdb=" O THR A1379 " (cutoff:3.500A) Processing helix chain 'A' and resid 1391 through 1402 Processing helix chain 'A' and resid 1404 through 1411 Processing helix chain 'A' and resid 1413 through 1417 Processing helix chain 'A' and resid 1420 through 1424 removed outlier: 3.630A pdb=" N GLU A1424 " --> pdb=" O GLU A1421 " (cutoff:3.500A) Processing helix chain 'A' and resid 1427 through 1443 removed outlier: 3.731A pdb=" N ARG A1442 " --> pdb=" O ARG A1438 " (cutoff:3.500A) Processing helix chain 'A' and resid 1457 through 1472 removed outlier: 3.959A pdb=" N LEU A1463 " --> pdb=" O GLU A1459 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N PHE A1472 " --> pdb=" O ILE A1468 " (cutoff:3.500A) Processing helix chain 'A' and resid 1506 through 1514 removed outlier: 3.775A pdb=" N ALA A1512 " --> pdb=" O ALA A1508 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ARG A1514 " --> pdb=" O LEU A1510 " (cutoff:3.500A) Processing helix chain 'A' and resid 1515 through 1524 Processing sheet with id=AA1, first strand: chain 'A' and resid 642 through 647 removed outlier: 5.492A pdb=" N HIS A 645 " --> pdb=" O PHE A 634 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N PHE A 634 " --> pdb=" O HIS A 645 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 642 through 647 removed outlier: 5.492A pdb=" N HIS A 645 " --> pdb=" O PHE A 634 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N PHE A 634 " --> pdb=" O HIS A 645 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N THR A 628 " --> pdb=" O HIS A 686 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N GLY A 632 " --> pdb=" O GLU A 682 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N GLU A 682 " --> pdb=" O GLY A 632 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N PHE A 634 " --> pdb=" O LYS A 680 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N LYS A 680 " --> pdb=" O PHE A 634 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 692 through 694 removed outlier: 6.032A pdb=" N PHE A 772 " --> pdb=" O VAL A 806 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N VAL A 808 " --> pdb=" O PHE A 772 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N LEU A 774 " --> pdb=" O VAL A 808 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N VAL A 657 " --> pdb=" O LEU A 807 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL A 823 " --> pdb=" O GLU A 831 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N GLU A 831 " --> pdb=" O VAL A 823 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N ALA A 825 " --> pdb=" O VAL A 829 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N VAL A 829 " --> pdb=" O ALA A 825 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1304 through 1309 removed outlier: 3.624A pdb=" N ASP A1308 " --> pdb=" O TYR A1294 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N TYR A1294 " --> pdb=" O ASP A1308 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N PHE A1291 " --> pdb=" O ARG A1348 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N ARG A1348 " --> pdb=" O PHE A1291 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N ASN A1293 " --> pdb=" O GLU A1346 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N GLU A1346 " --> pdb=" O ASN A1293 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N ARG A1297 " --> pdb=" O ALA A1342 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N ALA A1342 " --> pdb=" O ARG A1297 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1368 through 1369 removed outlier: 3.823A pdb=" N ILE A1369 " --> pdb=" O VAL A1448 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ILE A1480 " --> pdb=" O LEU A1449 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N GLY A1320 " --> pdb=" O LEU A1494 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N LEU A1496 " --> pdb=" O GLY A1320 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N VAL A1322 " --> pdb=" O LEU A1496 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N VAL A1493 " --> pdb=" O PHE A1504 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N PHE A1504 " --> pdb=" O VAL A1493 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N VAL A1495 " --> pdb=" O ALA A1502 " (cutoff:3.500A) 514 hydrogen bonds defined for protein. 1476 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: 1.99 Time building geometry restraints manager: 1.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1711 1.32 - 1.44: 2999 1.44 - 1.57: 6300 1.57 - 1.69: 12 1.69 - 1.82: 91 Bond restraints: 11113 Sorted by residual: bond pdb=" C10 U38 A1602 " pdb=" C11 U38 A1602 " ideal model delta sigma weight residual 1.389 1.604 -0.215 2.00e-02 2.50e+03 1.16e+02 bond pdb=" C10 U38 A1601 " pdb=" C11 U38 A1601 " ideal model delta sigma weight residual 1.389 1.603 -0.214 2.00e-02 2.50e+03 1.14e+02 bond pdb=" C23 U38 A1602 " pdb=" C7 U38 A1602 " ideal model delta sigma weight residual 1.391 1.603 -0.212 2.00e-02 2.50e+03 1.13e+02 bond pdb=" C23 U38 A1601 " pdb=" C7 U38 A1601 " ideal model delta sigma weight residual 1.391 1.602 -0.211 2.00e-02 2.50e+03 1.12e+02 bond pdb=" C8 U38 A1601 " pdb=" C9 U38 A1601 " ideal model delta sigma weight residual 1.390 1.196 0.194 2.00e-02 2.50e+03 9.45e+01 ... (remaining 11108 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.43: 14795 2.43 - 4.86: 270 4.86 - 7.29: 50 7.29 - 9.72: 10 9.72 - 12.14: 3 Bond angle restraints: 15128 Sorted by residual: angle pdb=" N VAL A1026 " pdb=" CA VAL A1026 " pdb=" C VAL A1026 " ideal model delta sigma weight residual 113.71 107.72 5.99 9.50e-01 1.11e+00 3.98e+01 angle pdb=" N VAL A 114 " pdb=" CA VAL A 114 " pdb=" C VAL A 114 " ideal model delta sigma weight residual 112.96 107.58 5.38 1.00e+00 1.00e+00 2.89e+01 angle pdb=" C PHE A 420 " pdb=" N MET A 421 " pdb=" CA MET A 421 " ideal model delta sigma weight residual 121.54 131.38 -9.84 1.91e+00 2.74e-01 2.65e+01 angle pdb=" N VAL A1199 " pdb=" CA VAL A1199 " pdb=" C VAL A1199 " ideal model delta sigma weight residual 111.62 108.22 3.40 7.90e-01 1.60e+00 1.85e+01 angle pdb=" C20 U38 A1601 " pdb=" C21 U38 A1601 " pdb=" C22 U38 A1601 " ideal model delta sigma weight residual 112.77 124.91 -12.14 3.00e+00 1.11e-01 1.64e+01 ... (remaining 15123 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.42: 6258 24.42 - 48.85: 378 48.85 - 73.27: 36 73.27 - 97.69: 11 97.69 - 122.12: 5 Dihedral angle restraints: 6688 sinusoidal: 2694 harmonic: 3994 Sorted by residual: dihedral pdb=" CD ARG A1245 " pdb=" NE ARG A1245 " pdb=" CZ ARG A1245 " pdb=" NH1 ARG A1245 " ideal model delta sinusoidal sigma weight residual 0.00 -66.78 66.78 1 1.00e+01 1.00e-02 5.81e+01 dihedral pdb=" CA TRP A1283 " pdb=" C TRP A1283 " pdb=" N PRO A1284 " pdb=" CA PRO A1284 " ideal model delta harmonic sigma weight residual 180.00 147.73 32.27 0 5.00e+00 4.00e-02 4.16e+01 dihedral pdb=" CA PHE A 196 " pdb=" C PHE A 196 " pdb=" N PHE A 197 " pdb=" CA PHE A 197 " ideal model delta harmonic sigma weight residual 180.00 -154.37 -25.63 0 5.00e+00 4.00e-02 2.63e+01 ... (remaining 6685 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.102: 1697 0.102 - 0.204: 63 0.204 - 0.306: 3 0.306 - 0.409: 2 0.409 - 0.511: 3 Chirality restraints: 1768 Sorted by residual: chirality pdb=" C15 U38 A1601 " pdb=" C14 U38 A1601 " pdb=" C16 U38 A1601 " pdb=" C19 U38 A1601 " both_signs ideal model delta sigma weight residual False 2.38 2.89 -0.51 2.00e-01 2.50e+01 6.52e+00 chirality pdb=" C22 U38 A1602 " pdb=" C14 U38 A1602 " pdb=" C21 U38 A1602 " pdb=" C23 U38 A1602 " both_signs ideal model delta sigma weight residual False 2.47 2.92 -0.45 2.00e-01 2.50e+01 5.06e+00 chirality pdb=" C22 U38 A1601 " pdb=" C14 U38 A1601 " pdb=" C21 U38 A1601 " pdb=" C23 U38 A1601 " both_signs ideal model delta sigma weight residual False 2.47 2.92 -0.45 2.00e-01 2.50e+01 5.02e+00 ... (remaining 1765 not shown) Planarity restraints: 1883 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A1245 " -1.007 9.50e-02 1.11e+02 4.51e-01 1.23e+02 pdb=" NE ARG A1245 " 0.060 2.00e-02 2.50e+03 pdb=" CZ ARG A1245 " 0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG A1245 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG A1245 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TRP A1283 " -0.065 5.00e-02 4.00e+02 9.87e-02 1.56e+01 pdb=" N PRO A1284 " 0.171 5.00e-02 4.00e+02 pdb=" CA PRO A1284 " -0.052 5.00e-02 4.00e+02 pdb=" CD PRO A1284 " -0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A 205 " -0.031 5.00e-02 4.00e+02 4.72e-02 3.56e+00 pdb=" N PRO A 206 " 0.082 5.00e-02 4.00e+02 pdb=" CA PRO A 206 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 206 " -0.026 5.00e-02 4.00e+02 ... (remaining 1880 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 381 2.70 - 3.25: 12029 3.25 - 3.80: 17578 3.80 - 4.35: 22027 4.35 - 4.90: 34946 Nonbonded interactions: 86961 Sorted by model distance: nonbonded pdb=" OG SER A 364 " pdb=" OE1 GLU A1200 " model vdw 2.154 3.040 nonbonded pdb=" OD1 ASP A 416 " pdb=" OG SER A 598 " model vdw 2.184 3.040 nonbonded pdb=" OG1 THR A 383 " pdb=" OE1 GLN A1182 " model vdw 2.184 3.040 nonbonded pdb=" O SER A 844 " pdb=" ND2 ASN A 847 " model vdw 2.188 3.120 nonbonded pdb=" O HIS A1050 " pdb=" NH1 ARG A1054 " model vdw 2.196 3.120 ... (remaining 86956 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.080 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: 0.000 Extract box with map and model: 0.120 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.620 Find NCS groups from input model: 0.030 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:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.679 11115 Z= 0.871 Angle : 0.850 12.144 15128 Z= 0.440 Chirality : 0.052 0.511 1768 Planarity : 0.012 0.451 1883 Dihedral : 15.684 122.116 4108 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 14.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.16 % Favored : 92.84 % Rotamer: Outliers : 0.09 % Allowed : 0.17 % Favored : 99.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.67 % 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 aren not related in a simple way. whole: -2.33 (0.22), residues: 1369 helix: -1.37 (0.18), residues: 812 sheet: -0.87 (0.62), residues: 76 loop : -1.68 (0.28), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A1144 TYR 0.017 0.002 TYR A 90 PHE 0.028 0.002 PHE A 89 TRP 0.013 0.001 TRP A 431 HIS 0.004 0.001 HIS A 177 Details of bonding type rmsd covalent geometry : bond 0.00761 (11113) covalent geometry : angle 0.84990 (15128) hydrogen bonds : bond 0.17817 ( 512) hydrogen bonds : angle 7.32454 ( 1476) Misc. bond : bond 0.58600 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2738 Ramachandran restraints generated. 1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2738 Ramachandran restraints generated. 1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 194 time to evaluate : 0.444 Fit side-chains revert: symmetry clash REVERT: A 459 MET cc_start: 0.7916 (mmt) cc_final: 0.7295 (mmt) REVERT: A 493 GLU cc_start: 0.7999 (tm-30) cc_final: 0.7706 (tm-30) REVERT: A 496 ASN cc_start: 0.8682 (m-40) cc_final: 0.8352 (m-40) REVERT: A 504 TYR cc_start: 0.8447 (p90) cc_final: 0.7900 (p90) REVERT: A 540 MET cc_start: 0.8023 (mmm) cc_final: 0.7004 (mmm) REVERT: A 820 PHE cc_start: 0.7268 (t80) cc_final: 0.6325 (t80) REVERT: A 835 TYR cc_start: 0.7405 (t80) cc_final: 0.7157 (t80) REVERT: A 1294 TYR cc_start: 0.7911 (t80) cc_final: 0.7053 (t80) REVERT: A 1472 PHE cc_start: 0.7862 (m-80) cc_final: 0.7625 (m-80) outliers start: 1 outliers final: 1 residues processed: 194 average time/residue: 0.0895 time to fit residues: 26.0826 Evaluate side-chains 146 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 145 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1245 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 98 optimal weight: 0.8980 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 0.4980 chunk 122 optimal weight: 0.4980 chunk 91 optimal weight: 1.9990 chunk 55 optimal weight: 0.0370 overall best weight: 0.5058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 428 ASN A1165 ASN A1430 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.153063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.107654 restraints weight = 18365.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.107960 restraints weight = 11231.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.108165 restraints weight = 7950.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.109102 restraints weight = 7394.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.109278 restraints weight = 6520.837| |-----------------------------------------------------------------------------| r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.1296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11115 Z= 0.147 Angle : 0.738 10.633 15128 Z= 0.371 Chirality : 0.045 0.185 1768 Planarity : 0.005 0.097 1883 Dihedral : 8.758 101.371 1623 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 1.11 % Allowed : 11.48 % Favored : 87.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.67 % 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 aren not related in a simple way. whole: -2.03 (0.22), residues: 1369 helix: -1.01 (0.18), residues: 840 sheet: -0.63 (0.66), residues: 71 loop : -1.86 (0.29), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1144 TYR 0.012 0.001 TYR A 90 PHE 0.028 0.002 PHE A1111 TRP 0.016 0.001 TRP A1242 HIS 0.006 0.001 HIS A1050 Details of bonding type rmsd covalent geometry : bond 0.00306 (11113) covalent geometry : angle 0.73761 (15128) hydrogen bonds : bond 0.04863 ( 512) hydrogen bonds : angle 5.27995 ( 1476) Misc. bond : bond 0.00677 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2738 Ramachandran restraints generated. 1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2738 Ramachandran restraints generated. 1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 172 time to evaluate : 0.454 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 155 LYS cc_start: 0.8230 (pttm) cc_final: 0.7819 (tptt) REVERT: A 171 PHE cc_start: 0.8010 (t80) cc_final: 0.7662 (t80) REVERT: A 493 GLU cc_start: 0.8072 (tm-30) cc_final: 0.7688 (tm-30) REVERT: A 496 ASN cc_start: 0.8814 (m-40) cc_final: 0.8544 (m-40) REVERT: A 504 TYR cc_start: 0.8375 (p90) cc_final: 0.7821 (p90) REVERT: A 687 MET cc_start: 0.7303 (mmp) cc_final: 0.7037 (mmp) REVERT: A 1094 PHE cc_start: 0.8638 (t80) cc_final: 0.8191 (t80) REVERT: A 1105 MET cc_start: 0.8193 (mmm) cc_final: 0.7946 (mmm) REVERT: A 1294 TYR cc_start: 0.7485 (t80) cc_final: 0.7258 (t80) REVERT: A 1449 LEU cc_start: 0.9018 (tt) cc_final: 0.8327 (mp) REVERT: A 1472 PHE cc_start: 0.7801 (m-80) cc_final: 0.7577 (m-80) outliers start: 13 outliers final: 7 residues processed: 176 average time/residue: 0.0897 time to fit residues: 24.1259 Evaluate side-chains 161 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 154 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 314 SER Chi-restraints excluded: chain A residue 1098 ILE Chi-restraints excluded: chain A residue 1112 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 135 optimal weight: 3.9990 chunk 107 optimal weight: 2.9990 chunk 4 optimal weight: 6.9990 chunk 81 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 chunk 102 optimal weight: 0.9980 chunk 134 optimal weight: 8.9990 chunk 76 optimal weight: 6.9990 chunk 9 optimal weight: 8.9990 chunk 82 optimal weight: 2.9990 chunk 3 optimal weight: 6.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1165 ASN A1312 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.147719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.102905 restraints weight = 18762.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.101866 restraints weight = 11655.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.102085 restraints weight = 8893.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.102940 restraints weight = 7936.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.103187 restraints weight = 7002.442| |-----------------------------------------------------------------------------| r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.1648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 11115 Z= 0.283 Angle : 0.791 9.168 15128 Z= 0.398 Chirality : 0.048 0.186 1768 Planarity : 0.005 0.094 1883 Dihedral : 7.414 106.800 1619 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.33 % Favored : 91.67 % Rotamer: Outliers : 2.81 % Allowed : 16.24 % Favored : 80.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.67 % 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 aren not related in a simple way. whole: -2.11 (0.22), residues: 1369 helix: -1.03 (0.18), residues: 843 sheet: -0.71 (0.65), residues: 71 loop : -1.99 (0.28), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1278 TYR 0.020 0.002 TYR A 835 PHE 0.026 0.002 PHE A 820 TRP 0.018 0.002 TRP A 960 HIS 0.008 0.001 HIS A1050 Details of bonding type rmsd covalent geometry : bond 0.00648 (11113) covalent geometry : angle 0.79109 (15128) hydrogen bonds : bond 0.04547 ( 512) hydrogen bonds : angle 5.10482 ( 1476) Misc. bond : bond 0.00185 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2738 Ramachandran restraints generated. 1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2738 Ramachandran restraints generated. 1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 161 time to evaluate : 0.433 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 155 LYS cc_start: 0.8298 (pttm) cc_final: 0.7829 (tptt) REVERT: A 171 PHE cc_start: 0.8047 (t80) cc_final: 0.7766 (t80) REVERT: A 496 ASN cc_start: 0.8866 (m-40) cc_final: 0.8630 (m-40) REVERT: A 504 TYR cc_start: 0.8623 (p90) cc_final: 0.7893 (p90) REVERT: A 1105 MET cc_start: 0.8374 (mmm) cc_final: 0.8130 (mmm) REVERT: A 1110 LEU cc_start: 0.8287 (OUTLIER) cc_final: 0.8041 (tt) REVERT: A 1195 LEU cc_start: 0.8629 (OUTLIER) cc_final: 0.8197 (tp) REVERT: A 1232 TYR cc_start: 0.8485 (OUTLIER) cc_final: 0.7747 (m-10) REVERT: A 1449 LEU cc_start: 0.9102 (tt) cc_final: 0.8339 (mt) REVERT: A 1472 PHE cc_start: 0.7939 (m-80) cc_final: 0.7647 (m-80) outliers start: 33 outliers final: 20 residues processed: 178 average time/residue: 0.0809 time to fit residues: 22.4017 Evaluate side-chains 170 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 147 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 82 CYS Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 314 SER Chi-restraints excluded: chain A residue 339 ILE Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 421 MET Chi-restraints excluded: chain A residue 544 PHE Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 606 LEU Chi-restraints excluded: chain A residue 767 SER Chi-restraints excluded: chain A residue 1008 THR Chi-restraints excluded: chain A residue 1098 ILE Chi-restraints excluded: chain A residue 1110 LEU Chi-restraints excluded: chain A residue 1112 THR Chi-restraints excluded: chain A residue 1120 VAL Chi-restraints excluded: chain A residue 1142 VAL Chi-restraints excluded: chain A residue 1165 ASN Chi-restraints excluded: chain A residue 1195 LEU Chi-restraints excluded: chain A residue 1232 TYR Chi-restraints excluded: chain A residue 1371 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 114 optimal weight: 10.0000 chunk 7 optimal weight: 5.9990 chunk 57 optimal weight: 9.9990 chunk 119 optimal weight: 0.3980 chunk 39 optimal weight: 0.5980 chunk 40 optimal weight: 0.9980 chunk 95 optimal weight: 0.2980 chunk 118 optimal weight: 0.7980 chunk 46 optimal weight: 0.8980 chunk 10 optimal weight: 7.9990 chunk 105 optimal weight: 0.9980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 997 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1165 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.152614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.106724 restraints weight = 18600.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.105982 restraints weight = 10595.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.107458 restraints weight = 7724.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.107983 restraints weight = 6576.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.108295 restraints weight = 5743.517| |-----------------------------------------------------------------------------| r_work (final): 0.3436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.1883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11115 Z= 0.131 Angle : 0.714 10.787 15128 Z= 0.347 Chirality : 0.044 0.171 1768 Planarity : 0.005 0.097 1883 Dihedral : 6.864 114.121 1619 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.87 % Favored : 93.13 % Rotamer: Outliers : 2.81 % Allowed : 19.64 % Favored : 77.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.67 % 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 aren not related in a simple way. whole: -1.78 (0.23), residues: 1369 helix: -0.79 (0.18), residues: 841 sheet: -0.52 (0.66), residues: 71 loop : -1.81 (0.28), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1278 TYR 0.014 0.001 TYR A1294 PHE 0.022 0.001 PHE A 820 TRP 0.013 0.001 TRP A 960 HIS 0.007 0.001 HIS A1050 Details of bonding type rmsd covalent geometry : bond 0.00282 (11113) covalent geometry : angle 0.71423 (15128) hydrogen bonds : bond 0.03909 ( 512) hydrogen bonds : angle 4.68368 ( 1476) Misc. bond : bond 0.00674 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2738 Ramachandran restraints generated. 1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2738 Ramachandran restraints generated. 1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 172 time to evaluate : 0.419 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 MET cc_start: 0.6296 (ttt) cc_final: 0.6008 (ttp) REVERT: A 155 LYS cc_start: 0.8291 (pttm) cc_final: 0.7857 (tptt) REVERT: A 171 PHE cc_start: 0.8110 (t80) cc_final: 0.7867 (t80) REVERT: A 421 MET cc_start: 0.8232 (OUTLIER) cc_final: 0.7979 (ptm) REVERT: A 496 ASN cc_start: 0.8897 (m-40) cc_final: 0.8666 (m-40) REVERT: A 504 TYR cc_start: 0.8519 (p90) cc_final: 0.7824 (p90) REVERT: A 551 LEU cc_start: 0.9515 (OUTLIER) cc_final: 0.9288 (mm) REVERT: A 679 GLU cc_start: 0.7821 (OUTLIER) cc_final: 0.7539 (pm20) REVERT: A 832 MET cc_start: 0.7967 (tmm) cc_final: 0.7735 (tmm) REVERT: A 1094 PHE cc_start: 0.8736 (t80) cc_final: 0.8273 (t80) REVERT: A 1110 LEU cc_start: 0.8108 (OUTLIER) cc_final: 0.7866 (tt) REVERT: A 1195 LEU cc_start: 0.8466 (OUTLIER) cc_final: 0.8002 (tp) REVERT: A 1232 TYR cc_start: 0.8359 (OUTLIER) cc_final: 0.7610 (m-10) REVERT: A 1449 LEU cc_start: 0.9092 (tt) cc_final: 0.8461 (mt) REVERT: A 1472 PHE cc_start: 0.7900 (m-80) cc_final: 0.7606 (m-80) outliers start: 33 outliers final: 18 residues processed: 193 average time/residue: 0.0814 time to fit residues: 24.0991 Evaluate side-chains 175 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 151 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 82 CYS Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 314 SER Chi-restraints excluded: chain A residue 339 ILE Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 421 MET Chi-restraints excluded: chain A residue 544 PHE Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 592 LEU Chi-restraints excluded: chain A residue 602 ILE Chi-restraints excluded: chain A residue 606 LEU Chi-restraints excluded: chain A residue 679 GLU Chi-restraints excluded: chain A residue 1098 ILE Chi-restraints excluded: chain A residue 1110 LEU Chi-restraints excluded: chain A residue 1112 THR Chi-restraints excluded: chain A residue 1195 LEU Chi-restraints excluded: chain A residue 1232 TYR Chi-restraints excluded: chain A residue 1336 LEU Chi-restraints excluded: chain A residue 1371 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 118 optimal weight: 0.9990 chunk 126 optimal weight: 3.9990 chunk 107 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 113 optimal weight: 0.2980 chunk 28 optimal weight: 0.0980 chunk 103 optimal weight: 0.0980 chunk 60 optimal weight: 9.9990 chunk 39 optimal weight: 0.4980 chunk 8 optimal weight: 0.9990 overall best weight: 0.3982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 560 ASN ** A 997 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1051 ASN A1165 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.154576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.108730 restraints weight = 18156.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.109023 restraints weight = 10858.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.109258 restraints weight = 8200.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.110191 restraints weight = 7254.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.110339 restraints weight = 6245.907| |-----------------------------------------------------------------------------| r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.2166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11115 Z= 0.123 Angle : 0.690 10.246 15128 Z= 0.338 Chirality : 0.043 0.178 1768 Planarity : 0.005 0.095 1883 Dihedral : 6.581 119.849 1619 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.79 % Favored : 93.21 % Rotamer: Outliers : 3.32 % Allowed : 21.51 % Favored : 75.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.67 % 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 aren not related in a simple way. whole: -1.64 (0.23), residues: 1369 helix: -0.66 (0.18), residues: 850 sheet: -0.27 (0.66), residues: 70 loop : -1.82 (0.29), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 474 TYR 0.012 0.001 TYR A 90 PHE 0.018 0.001 PHE A 544 TRP 0.010 0.001 TRP A 241 HIS 0.006 0.001 HIS A1050 Details of bonding type rmsd covalent geometry : bond 0.00264 (11113) covalent geometry : angle 0.69007 (15128) hydrogen bonds : bond 0.03610 ( 512) hydrogen bonds : angle 4.48662 ( 1476) Misc. bond : bond 0.00115 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2738 Ramachandran restraints generated. 1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2738 Ramachandran restraints generated. 1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 182 time to evaluate : 0.412 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 LEU cc_start: 0.8589 (tt) cc_final: 0.8181 (mm) REVERT: A 155 LYS cc_start: 0.8201 (pttm) cc_final: 0.7791 (tptt) REVERT: A 171 PHE cc_start: 0.8100 (t80) cc_final: 0.7882 (t80) REVERT: A 247 ASP cc_start: 0.7698 (t0) cc_final: 0.7460 (t0) REVERT: A 421 MET cc_start: 0.8129 (OUTLIER) cc_final: 0.7857 (ptm) REVERT: A 496 ASN cc_start: 0.8860 (m-40) cc_final: 0.8376 (m-40) REVERT: A 504 TYR cc_start: 0.8428 (p90) cc_final: 0.7792 (p90) REVERT: A 551 LEU cc_start: 0.9487 (OUTLIER) cc_final: 0.9233 (mm) REVERT: A 572 VAL cc_start: 0.9145 (OUTLIER) cc_final: 0.8932 (p) REVERT: A 679 GLU cc_start: 0.7851 (OUTLIER) cc_final: 0.7578 (pm20) REVERT: A 832 MET cc_start: 0.8066 (tmm) cc_final: 0.7814 (tmm) REVERT: A 1094 PHE cc_start: 0.8737 (t80) cc_final: 0.8299 (t80) REVERT: A 1110 LEU cc_start: 0.7966 (OUTLIER) cc_final: 0.7754 (tt) REVERT: A 1145 SER cc_start: 0.9062 (m) cc_final: 0.8790 (p) REVERT: A 1195 LEU cc_start: 0.8444 (OUTLIER) cc_final: 0.8020 (tp) REVERT: A 1232 TYR cc_start: 0.8345 (OUTLIER) cc_final: 0.7470 (m-10) REVERT: A 1449 LEU cc_start: 0.8991 (tt) cc_final: 0.8392 (mt) outliers start: 39 outliers final: 14 residues processed: 204 average time/residue: 0.0855 time to fit residues: 26.6380 Evaluate side-chains 181 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 160 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 314 SER Chi-restraints excluded: chain A residue 339 ILE Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 421 MET Chi-restraints excluded: chain A residue 544 PHE Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 572 VAL Chi-restraints excluded: chain A residue 592 LEU Chi-restraints excluded: chain A residue 606 LEU Chi-restraints excluded: chain A residue 679 GLU Chi-restraints excluded: chain A residue 1098 ILE Chi-restraints excluded: chain A residue 1110 LEU Chi-restraints excluded: chain A residue 1195 LEU Chi-restraints excluded: chain A residue 1232 TYR Chi-restraints excluded: chain A residue 1249 ASP Chi-restraints excluded: chain A residue 1336 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 123 optimal weight: 0.7980 chunk 78 optimal weight: 5.9990 chunk 117 optimal weight: 0.3980 chunk 73 optimal weight: 1.9990 chunk 101 optimal weight: 2.9990 chunk 53 optimal weight: 0.8980 chunk 81 optimal weight: 2.9990 chunk 63 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 66 optimal weight: 7.9990 chunk 11 optimal weight: 1.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 997 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1165 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.152597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.106544 restraints weight = 18438.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.105668 restraints weight = 10598.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.107049 restraints weight = 8094.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.107876 restraints weight = 6752.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.107746 restraints weight = 6099.578| |-----------------------------------------------------------------------------| r_work (final): 0.3429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.2300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 11115 Z= 0.155 Angle : 0.700 11.655 15128 Z= 0.342 Chirality : 0.044 0.162 1768 Planarity : 0.005 0.093 1883 Dihedral : 6.624 121.279 1619 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.23 % Favored : 92.77 % Rotamer: Outliers : 3.74 % Allowed : 22.45 % Favored : 73.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.67 % 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 aren not related in a simple way. whole: -1.59 (0.23), residues: 1369 helix: -0.62 (0.18), residues: 844 sheet: -0.42 (0.65), residues: 71 loop : -1.79 (0.29), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1144 TYR 0.015 0.001 TYR A1294 PHE 0.019 0.001 PHE A 544 TRP 0.011 0.001 TRP A 991 HIS 0.006 0.001 HIS A1050 Details of bonding type rmsd covalent geometry : bond 0.00351 (11113) covalent geometry : angle 0.70034 (15128) hydrogen bonds : bond 0.03633 ( 512) hydrogen bonds : angle 4.45777 ( 1476) Misc. bond : bond 0.00111 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2738 Ramachandran restraints generated. 1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2738 Ramachandran restraints generated. 1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 170 time to evaluate : 0.329 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 155 LYS cc_start: 0.8227 (pttm) cc_final: 0.7816 (tptt) REVERT: A 171 PHE cc_start: 0.8116 (t80) cc_final: 0.7869 (t80) REVERT: A 421 MET cc_start: 0.8227 (OUTLIER) cc_final: 0.7973 (ptm) REVERT: A 496 ASN cc_start: 0.8833 (m-40) cc_final: 0.8468 (m110) REVERT: A 504 TYR cc_start: 0.8509 (p90) cc_final: 0.7641 (p90) REVERT: A 551 LEU cc_start: 0.9538 (OUTLIER) cc_final: 0.9286 (mm) REVERT: A 678 MET cc_start: 0.8123 (tpt) cc_final: 0.7733 (tpt) REVERT: A 1110 LEU cc_start: 0.8031 (OUTLIER) cc_final: 0.7801 (tt) REVERT: A 1145 SER cc_start: 0.9054 (m) cc_final: 0.8777 (p) REVERT: A 1182 GLN cc_start: 0.8709 (mt0) cc_final: 0.8452 (mt0) REVERT: A 1195 LEU cc_start: 0.8568 (OUTLIER) cc_final: 0.8105 (tp) REVERT: A 1232 TYR cc_start: 0.8390 (OUTLIER) cc_final: 0.7603 (m-10) REVERT: A 1449 LEU cc_start: 0.9009 (tt) cc_final: 0.8413 (mt) outliers start: 44 outliers final: 23 residues processed: 198 average time/residue: 0.0860 time to fit residues: 25.8866 Evaluate side-chains 189 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 161 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 82 CYS Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 89 PHE Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 314 SER Chi-restraints excluded: chain A residue 339 ILE Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 421 MET Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 544 PHE Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 592 LEU Chi-restraints excluded: chain A residue 602 ILE Chi-restraints excluded: chain A residue 606 LEU Chi-restraints excluded: chain A residue 1098 ILE Chi-restraints excluded: chain A residue 1110 LEU Chi-restraints excluded: chain A residue 1195 LEU Chi-restraints excluded: chain A residue 1232 TYR Chi-restraints excluded: chain A residue 1249 ASP Chi-restraints excluded: chain A residue 1336 LEU Chi-restraints excluded: chain A residue 1371 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 61 optimal weight: 0.7980 chunk 107 optimal weight: 5.9990 chunk 41 optimal weight: 1.9990 chunk 127 optimal weight: 6.9990 chunk 82 optimal weight: 0.0000 chunk 110 optimal weight: 0.8980 chunk 102 optimal weight: 0.5980 chunk 9 optimal weight: 0.9980 chunk 54 optimal weight: 0.9990 chunk 122 optimal weight: 0.8980 chunk 101 optimal weight: 3.9990 overall best weight: 0.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 997 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1165 ASN A1314 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.152427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.105983 restraints weight = 18921.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.105621 restraints weight = 11532.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.105614 restraints weight = 8613.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.106726 restraints weight = 7429.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.107005 restraints weight = 6534.664| |-----------------------------------------------------------------------------| r_work (final): 0.3456 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.2468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 11115 Z= 0.127 Angle : 0.705 12.086 15128 Z= 0.337 Chirality : 0.043 0.163 1768 Planarity : 0.004 0.094 1883 Dihedral : 6.478 123.189 1619 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 3.15 % Allowed : 23.98 % Favored : 72.87 % 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 aren not related in a simple way. whole: -1.44 (0.23), residues: 1369 helix: -0.51 (0.18), residues: 844 sheet: -0.41 (0.65), residues: 71 loop : -1.69 (0.29), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1144 TYR 0.011 0.001 TYR A 231 PHE 0.018 0.001 PHE A 544 TRP 0.010 0.001 TRP A 241 HIS 0.007 0.001 HIS A1050 Details of bonding type rmsd covalent geometry : bond 0.00281 (11113) covalent geometry : angle 0.70521 (15128) hydrogen bonds : bond 0.03489 ( 512) hydrogen bonds : angle 4.32863 ( 1476) Misc. bond : bond 0.00092 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2738 Ramachandran restraints generated. 1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2738 Ramachandran restraints generated. 1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 173 time to evaluate : 0.405 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 LEU cc_start: 0.8569 (tt) cc_final: 0.8154 (mm) REVERT: A 155 LYS cc_start: 0.8257 (pttm) cc_final: 0.7894 (tptt) REVERT: A 165 ILE cc_start: 0.7913 (OUTLIER) cc_final: 0.7619 (tt) REVERT: A 171 PHE cc_start: 0.8101 (t80) cc_final: 0.7888 (t80) REVERT: A 421 MET cc_start: 0.8143 (OUTLIER) cc_final: 0.7849 (ptm) REVERT: A 474 ARG cc_start: 0.7857 (mmp80) cc_final: 0.7560 (mtm180) REVERT: A 496 ASN cc_start: 0.8918 (m-40) cc_final: 0.8521 (m110) REVERT: A 504 TYR cc_start: 0.8325 (p90) cc_final: 0.7544 (p90) REVERT: A 551 LEU cc_start: 0.9509 (OUTLIER) cc_final: 0.9260 (mm) REVERT: A 678 MET cc_start: 0.8153 (tpt) cc_final: 0.7699 (tpt) REVERT: A 1094 PHE cc_start: 0.8811 (t80) cc_final: 0.8353 (t80) REVERT: A 1110 LEU cc_start: 0.8037 (OUTLIER) cc_final: 0.7816 (tt) REVERT: A 1145 SER cc_start: 0.8995 (m) cc_final: 0.8708 (p) REVERT: A 1195 LEU cc_start: 0.8447 (OUTLIER) cc_final: 0.8034 (tp) REVERT: A 1232 TYR cc_start: 0.8372 (OUTLIER) cc_final: 0.7598 (m-10) REVERT: A 1449 LEU cc_start: 0.8970 (tt) cc_final: 0.8442 (pp) outliers start: 37 outliers final: 22 residues processed: 196 average time/residue: 0.0864 time to fit residues: 25.5890 Evaluate side-chains 193 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 165 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 89 PHE Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 314 SER Chi-restraints excluded: chain A residue 339 ILE Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 421 MET Chi-restraints excluded: chain A residue 544 PHE Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 592 LEU Chi-restraints excluded: chain A residue 602 ILE Chi-restraints excluded: chain A residue 606 LEU Chi-restraints excluded: chain A residue 1098 ILE Chi-restraints excluded: chain A residue 1110 LEU Chi-restraints excluded: chain A residue 1195 LEU Chi-restraints excluded: chain A residue 1232 TYR Chi-restraints excluded: chain A residue 1249 ASP Chi-restraints excluded: chain A residue 1336 LEU Chi-restraints excluded: chain A residue 1371 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 16 optimal weight: 0.0010 chunk 131 optimal weight: 3.9990 chunk 103 optimal weight: 1.9990 chunk 90 optimal weight: 0.9980 chunk 31 optimal weight: 0.6980 chunk 85 optimal weight: 5.9990 chunk 93 optimal weight: 0.8980 chunk 99 optimal weight: 4.9990 chunk 126 optimal weight: 0.7980 chunk 49 optimal weight: 0.9980 chunk 61 optimal weight: 0.4980 overall best weight: 0.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 560 ASN ** A 997 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.153734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.113257 restraints weight = 18506.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.114102 restraints weight = 12118.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.114641 restraints weight = 9652.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.115238 restraints weight = 7121.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.116693 restraints weight = 6195.520| |-----------------------------------------------------------------------------| r_work (final): 0.3585 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 moved from start: 0.2645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 11115 Z= 0.124 Angle : 0.701 12.514 15128 Z= 0.334 Chirality : 0.043 0.174 1768 Planarity : 0.004 0.093 1883 Dihedral : 6.417 125.162 1619 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 2.98 % Allowed : 24.49 % Favored : 72.53 % 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 aren not related in a simple way. whole: -1.28 (0.23), residues: 1369 helix: -0.39 (0.18), residues: 842 sheet: -0.36 (0.64), residues: 71 loop : -1.61 (0.29), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1054 TYR 0.017 0.001 TYR A1294 PHE 0.018 0.001 PHE A 544 TRP 0.010 0.001 TRP A 241 HIS 0.006 0.001 HIS A1050 Details of bonding type rmsd covalent geometry : bond 0.00276 (11113) covalent geometry : angle 0.70076 (15128) hydrogen bonds : bond 0.03362 ( 512) hydrogen bonds : angle 4.25221 ( 1476) Misc. bond : bond 0.00090 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2738 Ramachandran restraints generated. 1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2738 Ramachandran restraints generated. 1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 172 time to evaluate : 0.423 Fit side-chains revert: symmetry clash REVERT: A 37 LEU cc_start: 0.8577 (tt) cc_final: 0.8120 (mm) REVERT: A 155 LYS cc_start: 0.8226 (pttm) cc_final: 0.7811 (tptt) REVERT: A 171 PHE cc_start: 0.8147 (t80) cc_final: 0.7909 (t80) REVERT: A 410 VAL cc_start: 0.8760 (OUTLIER) cc_final: 0.8489 (p) REVERT: A 421 MET cc_start: 0.8057 (OUTLIER) cc_final: 0.7775 (ptm) REVERT: A 496 ASN cc_start: 0.8845 (m-40) cc_final: 0.8437 (m110) REVERT: A 504 TYR cc_start: 0.8206 (p90) cc_final: 0.7504 (p90) REVERT: A 551 LEU cc_start: 0.9505 (OUTLIER) cc_final: 0.9263 (mm) REVERT: A 678 MET cc_start: 0.8151 (tpt) cc_final: 0.7779 (tpt) REVERT: A 1094 PHE cc_start: 0.8844 (t80) cc_final: 0.8386 (t80) REVERT: A 1145 SER cc_start: 0.8961 (m) cc_final: 0.8640 (p) REVERT: A 1195 LEU cc_start: 0.8360 (OUTLIER) cc_final: 0.7964 (tp) REVERT: A 1232 TYR cc_start: 0.8372 (OUTLIER) cc_final: 0.7542 (m-10) REVERT: A 1340 LEU cc_start: 0.9037 (mt) cc_final: 0.8833 (mt) REVERT: A 1449 LEU cc_start: 0.8899 (tt) cc_final: 0.8440 (pp) outliers start: 35 outliers final: 21 residues processed: 191 average time/residue: 0.0791 time to fit residues: 23.5668 Evaluate side-chains 184 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 158 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 82 CYS Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 89 PHE Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 140 PHE Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 314 SER Chi-restraints excluded: chain A residue 339 ILE Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 421 MET Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 544 PHE Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 592 LEU Chi-restraints excluded: chain A residue 602 ILE Chi-restraints excluded: chain A residue 606 LEU Chi-restraints excluded: chain A residue 1098 ILE Chi-restraints excluded: chain A residue 1112 THR Chi-restraints excluded: chain A residue 1195 LEU Chi-restraints excluded: chain A residue 1232 TYR Chi-restraints excluded: chain A residue 1249 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 13 optimal weight: 9.9990 chunk 79 optimal weight: 10.0000 chunk 130 optimal weight: 3.9990 chunk 98 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 27 optimal weight: 0.7980 chunk 91 optimal weight: 1.9990 chunk 122 optimal weight: 0.9990 chunk 126 optimal weight: 0.5980 chunk 109 optimal weight: 6.9990 chunk 41 optimal weight: 3.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 997 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.154004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.108971 restraints weight = 18097.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.107509 restraints weight = 10105.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.108821 restraints weight = 7746.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.109523 restraints weight = 6502.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.109744 restraints weight = 5635.995| |-----------------------------------------------------------------------------| r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.2708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11115 Z= 0.146 Angle : 0.722 12.524 15128 Z= 0.344 Chirality : 0.044 0.170 1768 Planarity : 0.005 0.091 1883 Dihedral : 6.497 127.070 1619 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.87 % Favored : 93.13 % Rotamer: Outliers : 2.81 % Allowed : 25.34 % Favored : 71.85 % 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 aren not related in a simple way. whole: -1.24 (0.23), residues: 1369 helix: -0.34 (0.18), residues: 841 sheet: -0.68 (0.60), residues: 78 loop : -1.58 (0.30), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1144 TYR 0.012 0.001 TYR A 231 PHE 0.018 0.001 PHE A 544 TRP 0.025 0.001 TRP A 431 HIS 0.006 0.001 HIS A1050 Details of bonding type rmsd covalent geometry : bond 0.00335 (11113) covalent geometry : angle 0.72239 (15128) hydrogen bonds : bond 0.03464 ( 512) hydrogen bonds : angle 4.26878 ( 1476) Misc. bond : bond 0.00089 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2738 Ramachandran restraints generated. 1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2738 Ramachandran restraints generated. 1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 158 time to evaluate : 0.290 Fit side-chains revert: symmetry clash REVERT: A 37 LEU cc_start: 0.8570 (tt) cc_final: 0.8092 (mm) REVERT: A 74 MET cc_start: 0.6059 (ttp) cc_final: 0.4840 (mmt) REVERT: A 155 LYS cc_start: 0.8349 (pttm) cc_final: 0.7895 (tptt) REVERT: A 165 ILE cc_start: 0.7871 (OUTLIER) cc_final: 0.7567 (tt) REVERT: A 171 PHE cc_start: 0.8144 (t80) cc_final: 0.7901 (t80) REVERT: A 410 VAL cc_start: 0.8760 (OUTLIER) cc_final: 0.8507 (p) REVERT: A 421 MET cc_start: 0.8197 (OUTLIER) cc_final: 0.7943 (ptm) REVERT: A 474 ARG cc_start: 0.7893 (mmp80) cc_final: 0.7660 (mtm180) REVERT: A 493 GLU cc_start: 0.8462 (tm-30) cc_final: 0.8156 (tm-30) REVERT: A 496 ASN cc_start: 0.8869 (m-40) cc_final: 0.8463 (m110) REVERT: A 504 TYR cc_start: 0.8274 (p90) cc_final: 0.7474 (p90) REVERT: A 551 LEU cc_start: 0.9523 (OUTLIER) cc_final: 0.9280 (mm) REVERT: A 678 MET cc_start: 0.8209 (tpt) cc_final: 0.7680 (tpt) REVERT: A 832 MET cc_start: 0.7975 (tmm) cc_final: 0.7547 (tmm) REVERT: A 1145 SER cc_start: 0.8965 (m) cc_final: 0.8620 (p) REVERT: A 1195 LEU cc_start: 0.8498 (OUTLIER) cc_final: 0.8095 (tp) REVERT: A 1232 TYR cc_start: 0.8381 (OUTLIER) cc_final: 0.7631 (m-10) REVERT: A 1449 LEU cc_start: 0.8916 (tt) cc_final: 0.8409 (pp) outliers start: 33 outliers final: 22 residues processed: 176 average time/residue: 0.0751 time to fit residues: 20.8560 Evaluate side-chains 184 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 156 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 82 CYS Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 89 PHE Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 140 PHE Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 314 SER Chi-restraints excluded: chain A residue 339 ILE Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 421 MET Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 544 PHE Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 592 LEU Chi-restraints excluded: chain A residue 602 ILE Chi-restraints excluded: chain A residue 606 LEU Chi-restraints excluded: chain A residue 1098 ILE Chi-restraints excluded: chain A residue 1112 THR Chi-restraints excluded: chain A residue 1175 ASP Chi-restraints excluded: chain A residue 1195 LEU Chi-restraints excluded: chain A residue 1232 TYR Chi-restraints excluded: chain A residue 1249 ASP Chi-restraints excluded: chain A residue 1371 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 10 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 38 optimal weight: 0.0370 chunk 6 optimal weight: 0.7980 chunk 41 optimal weight: 1.9990 chunk 102 optimal weight: 0.7980 chunk 62 optimal weight: 0.9990 chunk 84 optimal weight: 2.9990 chunk 54 optimal weight: 0.9990 chunk 12 optimal weight: 0.3980 chunk 134 optimal weight: 5.9990 overall best weight: 0.6060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 250 GLN A 560 ASN ** A 997 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.155192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.109876 restraints weight = 18191.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.109027 restraints weight = 10429.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.110315 restraints weight = 7582.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.111249 restraints weight = 6521.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.111734 restraints weight = 5773.867| |-----------------------------------------------------------------------------| r_work (final): 0.3499 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.2864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11115 Z= 0.125 Angle : 0.716 12.748 15128 Z= 0.337 Chirality : 0.043 0.169 1768 Planarity : 0.005 0.091 1883 Dihedral : 6.404 129.142 1619 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 2.55 % Allowed : 25.26 % Favored : 72.19 % 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 aren not related in a simple way. whole: -1.12 (0.23), residues: 1369 helix: -0.24 (0.18), residues: 842 sheet: -0.62 (0.61), residues: 76 loop : -1.53 (0.30), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1144 TYR 0.017 0.001 TYR A1294 PHE 0.029 0.001 PHE A 105 TRP 0.023 0.001 TRP A 431 HIS 0.006 0.001 HIS A1050 Details of bonding type rmsd covalent geometry : bond 0.00281 (11113) covalent geometry : angle 0.71580 (15128) hydrogen bonds : bond 0.03322 ( 512) hydrogen bonds : angle 4.19639 ( 1476) Misc. bond : bond 0.00080 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2738 Ramachandran restraints generated. 1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2738 Ramachandran restraints generated. 1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 168 time to evaluate : 0.258 Fit side-chains revert: symmetry clash REVERT: A 37 LEU cc_start: 0.8510 (tt) cc_final: 0.8067 (mm) REVERT: A 74 MET cc_start: 0.6007 (ttp) cc_final: 0.4788 (mmt) REVERT: A 155 LYS cc_start: 0.8368 (pttm) cc_final: 0.7924 (tptt) REVERT: A 165 ILE cc_start: 0.7825 (OUTLIER) cc_final: 0.7528 (tt) REVERT: A 247 ASP cc_start: 0.7764 (t0) cc_final: 0.7532 (t0) REVERT: A 250 GLN cc_start: 0.8156 (OUTLIER) cc_final: 0.7918 (tm-30) REVERT: A 421 MET cc_start: 0.8170 (OUTLIER) cc_final: 0.7952 (ptm) REVERT: A 474 ARG cc_start: 0.7925 (mmp80) cc_final: 0.7692 (mtm180) REVERT: A 493 GLU cc_start: 0.8528 (tm-30) cc_final: 0.8255 (tm-30) REVERT: A 496 ASN cc_start: 0.8908 (m-40) cc_final: 0.8171 (m110) REVERT: A 504 TYR cc_start: 0.8243 (p90) cc_final: 0.7495 (p90) REVERT: A 551 LEU cc_start: 0.9492 (OUTLIER) cc_final: 0.9233 (mm) REVERT: A 678 MET cc_start: 0.8185 (tpt) cc_final: 0.7332 (tpp) REVERT: A 832 MET cc_start: 0.7950 (tmm) cc_final: 0.7500 (tmm) REVERT: A 1094 PHE cc_start: 0.8831 (t80) cc_final: 0.8378 (t80) REVERT: A 1145 SER cc_start: 0.8906 (m) cc_final: 0.8533 (p) REVERT: A 1195 LEU cc_start: 0.8453 (OUTLIER) cc_final: 0.8068 (tp) REVERT: A 1232 TYR cc_start: 0.8361 (OUTLIER) cc_final: 0.7512 (m-10) REVERT: A 1449 LEU cc_start: 0.8926 (tt) cc_final: 0.8402 (pp) outliers start: 30 outliers final: 21 residues processed: 185 average time/residue: 0.0741 time to fit residues: 21.2048 Evaluate side-chains 183 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 156 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 82 CYS Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 89 PHE Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 140 PHE Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 250 GLN Chi-restraints excluded: chain A residue 314 SER Chi-restraints excluded: chain A residue 339 ILE Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 421 MET Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 544 PHE Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 592 LEU Chi-restraints excluded: chain A residue 602 ILE Chi-restraints excluded: chain A residue 606 LEU Chi-restraints excluded: chain A residue 1098 ILE Chi-restraints excluded: chain A residue 1112 THR Chi-restraints excluded: chain A residue 1175 ASP Chi-restraints excluded: chain A residue 1195 LEU Chi-restraints excluded: chain A residue 1232 TYR Chi-restraints excluded: chain A residue 1249 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 64 optimal weight: 0.1980 chunk 26 optimal weight: 0.9980 chunk 92 optimal weight: 0.5980 chunk 117 optimal weight: 0.7980 chunk 37 optimal weight: 0.9990 chunk 42 optimal weight: 0.0570 chunk 119 optimal weight: 1.9990 chunk 4 optimal weight: 7.9990 chunk 98 optimal weight: 1.9990 chunk 58 optimal weight: 0.5980 chunk 88 optimal weight: 1.9990 overall best weight: 0.4498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 328 ASN ** A 997 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.155860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.110601 restraints weight = 18233.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.109615 restraints weight = 10382.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.110961 restraints weight = 7554.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.111877 restraints weight = 6501.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.111990 restraints weight = 5748.825| |-----------------------------------------------------------------------------| r_work (final): 0.3508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.3007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11115 Z= 0.121 Angle : 0.707 12.762 15128 Z= 0.334 Chirality : 0.043 0.168 1768 Planarity : 0.005 0.088 1883 Dihedral : 6.362 130.397 1619 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 2.64 % Allowed : 25.68 % Favored : 71.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.03 (0.23), residues: 1369 helix: -0.19 (0.18), residues: 850 sheet: -0.66 (0.60), residues: 76 loop : -1.46 (0.30), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1144 TYR 0.012 0.001 TYR A 231 PHE 0.030 0.001 PHE A1059 TRP 0.023 0.001 TRP A 431 HIS 0.005 0.001 HIS A1050 Details of bonding type rmsd covalent geometry : bond 0.00271 (11113) covalent geometry : angle 0.70658 (15128) hydrogen bonds : bond 0.03261 ( 512) hydrogen bonds : angle 4.15738 ( 1476) Misc. bond : bond 0.00078 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1770.10 seconds wall clock time: 31 minutes 20.39 seconds (1880.39 seconds total)