Starting phenix.real_space_refine on Wed Mar 4 12:46:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7v6b_31741/03_2026/7v6b_31741.cif Found real_map, /net/cci-nas-00/data/ceres_data/7v6b_31741/03_2026/7v6b_31741.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7v6b_31741/03_2026/7v6b_31741.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7v6b_31741/03_2026/7v6b_31741.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7v6b_31741/03_2026/7v6b_31741.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7v6b_31741/03_2026/7v6b_31741.map" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.007 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 80 5.16 5 C 8758 2.51 5 N 2306 2.21 5 O 2489 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 32 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13633 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 12164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1496, 12164 Classifications: {'peptide': 1496} Link IDs: {'PTRANS': 61, 'TRANS': 1434} Chain breaks: 14 Chain: "B" Number of atoms: 1469 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1469 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 5, 'TRANS': 176} Chain breaks: 3 Time building chain proxies: 2.86, per 1000 atoms: 0.21 Number of scatterers: 13633 At special positions: 0 Unit cell: (93.375, 158.115, 140.685, 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 80 16.00 O 2489 8.00 N 2306 7.00 C 8758 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.09 Conformation dependent library (CDL) restraints added in 694.4 milliseconds 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3228 Finding SS restraints... Secondary structure from input PDB file: 74 helices and 12 sheets defined 54.8% alpha, 9.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.69 Creating SS restraints... Processing helix chain 'A' and resid 10 through 22 Processing helix chain 'A' and resid 33 through 45 Processing helix chain 'A' and resid 52 through 56 removed outlier: 3.845A pdb=" N GLY A 56 " --> pdb=" O ILE A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 66 through 81 Processing helix chain 'A' and resid 89 through 93 Processing helix chain 'A' and resid 98 through 109 removed outlier: 3.524A pdb=" N ILE A 106 " --> pdb=" O TRP A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 125 Processing helix chain 'A' and resid 129 through 131 No H-bonds generated for 'chain 'A' and resid 129 through 131' Processing helix chain 'A' and resid 141 through 144 Processing helix chain 'A' and resid 148 through 158 Processing helix chain 'A' and resid 183 through 196 Processing helix chain 'A' and resid 232 through 251 removed outlier: 3.867A pdb=" N ARG A 236 " --> pdb=" O LEU A 232 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LEU A 251 " --> pdb=" O VAL A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 292 Processing helix chain 'A' and resid 292 through 313 removed outlier: 3.760A pdb=" N ILE A 298 " --> pdb=" O TYR A 294 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ILE A 301 " --> pdb=" O SER A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 343 removed outlier: 3.513A pdb=" N LEU A 327 " --> pdb=" O HIS A 323 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU A 341 " --> pdb=" O LEU A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 362 removed outlier: 3.834A pdb=" N ASN A 361 " --> pdb=" O GLU A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 378 Processing helix chain 'A' and resid 394 through 412 removed outlier: 3.594A pdb=" N CYS A 398 " --> pdb=" O ARG A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 437 through 453 removed outlier: 3.686A pdb=" N LYS A 441 " --> pdb=" O VAL A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 484 through 495 removed outlier: 3.573A pdb=" N ARG A 494 " --> pdb=" O GLN A 490 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ALA A 495 " --> pdb=" O SER A 491 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 535 removed outlier: 3.692A pdb=" N ARG A 535 " --> pdb=" O TYR A 531 " (cutoff:3.500A) Processing helix chain 'A' and resid 570 through 582A Processing helix chain 'A' and resid 598 through 606 Processing helix chain 'A' and resid 607 through 611 Processing helix chain 'A' and resid 638 through 656 Processing helix chain 'A' and resid 667 through 681 removed outlier: 3.714A pdb=" N ILE A 675 " --> pdb=" O ARG A 671 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N ASP A 677 " --> pdb=" O ALA A 673 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N VAL A 678 " --> pdb=" O SER A 674 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLU A 681 " --> pdb=" O ASP A 677 " (cutoff:3.500A) Processing helix chain 'A' and resid 682 through 687 removed outlier: 4.175A pdb=" N TYR A 686 " --> pdb=" O HIS A 682 " (cutoff:3.500A) Processing helix chain 'A' and resid 741 through 749 removed outlier: 3.654A pdb=" N LEU A 746 " --> pdb=" O GLU A 742 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N ASN A 747 " --> pdb=" O HIS A 743 " (cutoff:3.500A) Processing helix chain 'A' and resid 793 through 809 removed outlier: 3.504A pdb=" N GLU A 797 " --> pdb=" O SER A 793 " (cutoff:3.500A) Processing helix chain 'A' and resid 845 through 852 removed outlier: 3.503A pdb=" N MET A 849 " --> pdb=" O ASP A 845 " (cutoff:3.500A) Processing helix chain 'A' and resid 862 through 869 removed outlier: 3.849A pdb=" N GLN A 868 " --> pdb=" O GLN A 864 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N GLN A 869 " --> pdb=" O GLN A 865 " (cutoff:3.500A) Processing helix chain 'A' and resid 874 through 878 Processing helix chain 'A' and resid 918 through 925 Processing helix chain 'A' and resid 982 through 991 removed outlier: 3.874A pdb=" N LYS A 988 " --> pdb=" O ASP A 984 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N PHE A 991 " --> pdb=" O LEU A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 991 through 1016 Processing helix chain 'A' and resid 1087 through 1091 Processing helix chain 'A' and resid 1103 through 1116 removed outlier: 3.860A pdb=" N LEU A1107 " --> pdb=" O TYR A1103 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ASP A1108 " --> pdb=" O PRO A1104 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N TYR A1111 " --> pdb=" O LEU A1107 " (cutoff:3.500A) Processing helix chain 'A' and resid 1174 through 1182 Processing helix chain 'A' and resid 1183 through 1186 Processing helix chain 'A' and resid 1190 through 1199 Processing helix chain 'A' and resid 1200 through 1204 Processing helix chain 'A' and resid 1209 through 1232 removed outlier: 3.619A pdb=" N ILE A1214 " --> pdb=" O GLU A1210 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N LEU A1215 " --> pdb=" O ARG A1211 " (cutoff:3.500A) Processing helix chain 'A' and resid 1236 through 1248 Processing helix chain 'A' and resid 1249 through 1260 Processing helix chain 'A' and resid 1261 through 1265 removed outlier: 3.920A pdb=" N LYS A1264 " --> pdb=" O ASP A1261 " (cutoff:3.500A) Processing helix chain 'A' and resid 1285 through 1295 Processing helix chain 'A' and resid 1295 through 1302 removed outlier: 3.783A pdb=" N ILE A1301 " --> pdb=" O GLU A1297 " (cutoff:3.500A) Processing helix chain 'A' and resid 1303 through 1309 Processing helix chain 'A' and resid 1313 through 1318 Processing helix chain 'A' and resid 1324 through 1341 removed outlier: 3.908A pdb=" N GLY A1339 " --> pdb=" O CYS A1335 " (cutoff:3.500A) Processing helix chain 'A' and resid 1348 through 1357 removed outlier: 4.265A pdb=" N PHE A1354 " --> pdb=" O SER A1350 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N CYS A1355 " --> pdb=" O GLU A1351 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL A1356 " --> pdb=" O VAL A1352 " (cutoff:3.500A) Processing helix chain 'A' and resid 1363 through 1393 removed outlier: 4.161A pdb=" N ALA A1367 " --> pdb=" O ASN A1363 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N LEU A1383 " --> pdb=" O LYS A1379 " (cutoff:3.500A) removed outlier: 9.720A pdb=" N GLN A1384 " --> pdb=" O ASN A1380 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N HIS A1385 " --> pdb=" O TYR A1381 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N MET A1389 " --> pdb=" O HIS A1385 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU A1390 " --> pdb=" O ALA A1386 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLU A1391 " --> pdb=" O PHE A1387 " (cutoff:3.500A) Processing helix chain 'A' and resid 1404 through 1408 removed outlier: 4.439A pdb=" N LEU A1408 " --> pdb=" O THR A1405 " (cutoff:3.500A) Processing helix chain 'A' and resid 1423 through 1430 removed outlier: 4.045A pdb=" N PHE A1429 " --> pdb=" O GLU A1425 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU A1430 " --> pdb=" O ILE A1426 " (cutoff:3.500A) Processing helix chain 'A' and resid 1432 through 1441 removed outlier: 3.510A pdb=" N LEU A1436 " --> pdb=" O ASN A1432 " (cutoff:3.500A) Processing helix chain 'A' and resid 1447 through 1455 Processing helix chain 'A' and resid 1468 through 1491 removed outlier: 3.680A pdb=" N PHE A1473 " --> pdb=" O GLN A1469 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ILE A1474 " --> pdb=" O GLU A1470 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ALA A1477 " --> pdb=" O PHE A1473 " (cutoff:3.500A) Processing helix chain 'A' and resid 1495 through 1507 Processing helix chain 'A' and resid 1510 through 1519 removed outlier: 3.636A pdb=" N ILE A1515 " --> pdb=" O THR A1511 " (cutoff:3.500A) Processing helix chain 'A' and resid 1521 through 1525 removed outlier: 3.737A pdb=" N PHE A1524 " --> pdb=" O LEU A1521 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ILE A1525 " --> pdb=" O HIS A1522 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1521 through 1525' Processing helix chain 'A' and resid 1529 through 1547 removed outlier: 3.545A pdb=" N SER A1545 " --> pdb=" O ASN A1541 " (cutoff:3.500A) Processing helix chain 'A' and resid 1551 through 1557 Processing helix chain 'A' and resid 1610 through 1628 removed outlier: 3.549A pdb=" N LEU A1616 " --> pdb=" O LEU A1612 " (cutoff:3.500A) Processing helix chain 'A' and resid 1629 through 1651 removed outlier: 3.593A pdb=" N VAL A1636 " --> pdb=" O ARG A1632 " (cutoff:3.500A) Proline residue: A1643 - end of helix Processing helix chain 'A' and resid 1655 through 1662 Processing helix chain 'A' and resid 1701 through 1720 removed outlier: 3.574A pdb=" N LEU A1707 " --> pdb=" O ASP A1703 " (cutoff:3.500A) Processing helix chain 'B' and resid 96 through 107 Processing helix chain 'B' and resid 145 through 164 removed outlier: 3.845A pdb=" N ARG B 150 " --> pdb=" O LYS B 146 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLN B 151 " --> pdb=" O LYS B 147 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ARG B 152 " --> pdb=" O ASP B 148 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ASN B 164 " --> pdb=" O LEU B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 198 removed outlier: 4.456A pdb=" N LEU B 193 " --> pdb=" O SER B 189 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLU B 194 " --> pdb=" O MET B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 210 removed outlier: 3.530A pdb=" N ALA B 210 " --> pdb=" O GLU B 206 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 225 removed outlier: 4.086A pdb=" N HIS B 224 " --> pdb=" O CYS B 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 244 Processing helix chain 'B' and resid 251 through 261 removed outlier: 3.584A pdb=" N ASP B 256 " --> pdb=" O ASP B 252 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU B 261 " --> pdb=" O VAL B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 310 removed outlier: 4.442A pdb=" N TYR B 299 " --> pdb=" O GLU B 295 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N ASP B 300 " --> pdb=" O THR B 296 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ILE B 303 " --> pdb=" O TYR B 299 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 85 through 88 removed outlier: 5.810A pdb=" N GLY A 86 " --> pdb=" O VAL A 113 " (cutoff:3.500A) removed outlier: 8.331A pdb=" N THR A 115 " --> pdb=" O GLY A 86 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N TYR A 88 " --> pdb=" O THR A 115 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N ALA A 60 " --> pdb=" O LEU A 112 " (cutoff:3.500A) removed outlier: 7.717A pdb=" N GLY A 114 " --> pdb=" O ALA A 60 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N PHE A 62 " --> pdb=" O GLY A 114 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N ARG A 59 " --> pdb=" O VAL A 135 " (cutoff:3.500A) removed outlier: 8.565A pdb=" N ILE A 137 " --> pdb=" O ARG A 59 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N LEU A 61 " --> pdb=" O ILE A 137 " (cutoff:3.500A) removed outlier: 7.700A pdb=" N ASP A 139 " --> pdb=" O LEU A 61 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N MET A 63 " --> pdb=" O ASP A 139 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N SER A 134 " --> pdb=" O ARG A 167 " (cutoff:3.500A) removed outlier: 8.190A pdb=" N VAL A 169 " --> pdb=" O SER A 134 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N VAL A 136 " --> pdb=" O VAL A 169 " (cutoff:3.500A) removed outlier: 7.834A pdb=" N LEU A 171 " --> pdb=" O VAL A 136 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N ILE A 138 " --> pdb=" O LEU A 171 " (cutoff:3.500A) removed outlier: 5.760A pdb=" N ILE A 25A" --> pdb=" O ILE A 200 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 219 through 223 removed outlier: 6.483A pdb=" N THR A 219 " --> pdb=" O PHE A 502 " (cutoff:3.500A) removed outlier: 8.106A pdb=" N LEU A 504 " --> pdb=" O THR A 219 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N VAL A 221 " --> pdb=" O LEU A 504 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N VAL A 476 " --> pdb=" O VAL A 503 " (cutoff:3.500A) removed outlier: 7.840A pdb=" N PHE A 505 " --> pdb=" O VAL A 476 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N ILE A 478 " --> pdb=" O PHE A 505 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N LEU A 389 " --> pdb=" O PHE A 477 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N CYS A 388 " --> pdb=" O MET A 458 " (cutoff:3.500A) removed outlier: 7.754A pdb=" N CYS A 460 " --> pdb=" O CYS A 388 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N VAL A 390 " --> pdb=" O CYS A 460 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N GLN A 422 " --> pdb=" O ILE A 459 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 558 through 559 removed outlier: 3.580A pdb=" N PHE A 558 " --> pdb=" O LEU A 566 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 593 through 596 Processing sheet with id=AA5, first strand: chain 'A' and resid 702 through 706 Processing sheet with id=AA6, first strand: chain 'A' and resid 768A through 770 Processing sheet with id=AA7, first strand: chain 'A' and resid 768A through 770 removed outlier: 4.598A pdb=" N TYR A 754 " --> pdb=" O ILE A 729 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 819 through 820 Processing sheet with id=AA9, first strand: chain 'A' and resid 939 through 944 removed outlier: 3.918A pdb=" N LYS A 897 " --> pdb=" O GLU A 941 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N ARG A 943 " --> pdb=" O VAL A 895 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N VAL A 895 " --> pdb=" O ARG A 943 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ILE A 881 " --> pdb=" O PHE A 979 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 1669 through 1670 removed outlier: 3.721A pdb=" N CYS A1688 " --> pdb=" O LYS A1691 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 114 through 116 removed outlier: 3.543A pdb=" N CYS B 132 " --> pdb=" O ARG B 139 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 265 through 266 removed outlier: 3.764A pdb=" N ALA B 293 " --> pdb=" O LEU B 279 " (cutoff:3.500A) 637 hydrogen bonds defined for protein. 1797 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.08 Time building geometry restraints manager: 1.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2239 1.31 - 1.44: 3671 1.44 - 1.57: 7884 1.57 - 1.70: 0 1.70 - 1.82: 124 Bond restraints: 13918 Sorted by residual: bond pdb=" C GLU A 530 " pdb=" O GLU A 530 " ideal model delta sigma weight residual 1.236 1.304 -0.068 1.15e-02 7.56e+03 3.46e+01 bond pdb=" C ARG A 395 " pdb=" O ARG A 395 " ideal model delta sigma weight residual 1.236 1.296 -0.060 1.19e-02 7.06e+03 2.58e+01 bond pdb=" CA SER A 46 " pdb=" CB SER A 46 " ideal model delta sigma weight residual 1.528 1.462 0.065 1.35e-02 5.49e+03 2.33e+01 bond pdb=" C ILE A1487 " pdb=" O ILE A1487 " ideal model delta sigma weight residual 1.237 1.186 0.051 1.13e-02 7.83e+03 2.04e+01 bond pdb=" C ASN A 997 " pdb=" O ASN A 997 " ideal model delta sigma weight residual 1.236 1.287 -0.051 1.15e-02 7.56e+03 1.93e+01 ... (remaining 13913 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.93: 14366 1.93 - 3.86: 4027 3.86 - 5.78: 366 5.78 - 7.71: 46 7.71 - 9.64: 8 Bond angle restraints: 18813 Sorted by residual: angle pdb=" N ILE A 995 " pdb=" CA ILE A 995 " pdb=" C ILE A 995 " ideal model delta sigma weight residual 110.82 104.03 6.79 9.70e-01 1.06e+00 4.90e+01 angle pdb=" N ILE A 528 " pdb=" CA ILE A 528 " pdb=" C ILE A 528 " ideal model delta sigma weight residual 110.62 103.85 6.77 1.02e+00 9.61e-01 4.41e+01 angle pdb=" N ILE B 302 " pdb=" CA ILE B 302 " pdb=" C ILE B 302 " ideal model delta sigma weight residual 110.42 104.24 6.18 9.60e-01 1.09e+00 4.14e+01 angle pdb=" N LYS B 251 " pdb=" CA LYS B 251 " pdb=" C LYS B 251 " ideal model delta sigma weight residual 113.30 105.00 8.30 1.34e+00 5.57e-01 3.83e+01 angle pdb=" C GLU A1472 " pdb=" CA GLU A1472 " pdb=" CB GLU A1472 " ideal model delta sigma weight residual 110.88 101.24 9.64 1.57e+00 4.06e-01 3.77e+01 ... (remaining 18808 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.60: 7657 17.60 - 35.21: 602 35.21 - 52.81: 132 52.81 - 70.41: 28 70.41 - 88.02: 7 Dihedral angle restraints: 8426 sinusoidal: 3467 harmonic: 4959 Sorted by residual: dihedral pdb=" C PHE A1001 " pdb=" N PHE A1001 " pdb=" CA PHE A1001 " pdb=" CB PHE A1001 " ideal model delta harmonic sigma weight residual -122.60 -133.97 11.37 0 2.50e+00 1.60e-01 2.07e+01 dihedral pdb=" CA GLY A1382 " pdb=" C GLY A1382 " pdb=" N LEU A1383 " pdb=" CA LEU A1383 " ideal model delta harmonic sigma weight residual -180.00 -159.09 -20.91 0 5.00e+00 4.00e-02 1.75e+01 dihedral pdb=" C GLU A1472 " pdb=" N GLU A1472 " pdb=" CA GLU A1472 " pdb=" CB GLU A1472 " ideal model delta harmonic sigma weight residual -122.60 -112.66 -9.94 0 2.50e+00 1.60e-01 1.58e+01 ... (remaining 8423 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 1067 0.065 - 0.129: 747 0.129 - 0.194: 262 0.194 - 0.259: 35 0.259 - 0.323: 7 Chirality restraints: 2118 Sorted by residual: chirality pdb=" CA PHE A1001 " pdb=" N PHE A1001 " pdb=" C PHE A1001 " pdb=" CB PHE A1001 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.62e+00 chirality pdb=" CA ARG A 535 " pdb=" N ARG A 535 " pdb=" C ARG A 535 " pdb=" CB ARG A 535 " both_signs ideal model delta sigma weight residual False 2.51 2.82 -0.31 2.00e-01 2.50e+01 2.44e+00 chirality pdb=" CA TYR A1000 " pdb=" N TYR A1000 " pdb=" C TYR A1000 " pdb=" CB TYR A1000 " both_signs ideal model delta sigma weight residual False 2.51 2.82 -0.31 2.00e-01 2.50e+01 2.38e+00 ... (remaining 2115 not shown) Planarity restraints: 2388 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A1000 " 0.058 2.00e-02 2.50e+03 3.48e-02 2.42e+01 pdb=" CG TYR A1000 " -0.076 2.00e-02 2.50e+03 pdb=" CD1 TYR A1000 " -0.009 2.00e-02 2.50e+03 pdb=" CD2 TYR A1000 " -0.009 2.00e-02 2.50e+03 pdb=" CE1 TYR A1000 " 0.009 2.00e-02 2.50e+03 pdb=" CE2 TYR A1000 " 0.006 2.00e-02 2.50e+03 pdb=" CZ TYR A1000 " 0.013 2.00e-02 2.50e+03 pdb=" OH TYR A1000 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A1488 " -0.019 2.00e-02 2.50e+03 3.77e-02 1.42e+01 pdb=" C PHE A1488 " 0.065 2.00e-02 2.50e+03 pdb=" O PHE A1488 " -0.024 2.00e-02 2.50e+03 pdb=" N GLU A1489 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN A1013 " 0.017 2.00e-02 2.50e+03 3.58e-02 1.28e+01 pdb=" C ASN A1013 " -0.062 2.00e-02 2.50e+03 pdb=" O ASN A1013 " 0.023 2.00e-02 2.50e+03 pdb=" N THR A1014 " 0.021 2.00e-02 2.50e+03 ... (remaining 2385 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 3598 2.83 - 3.35: 13155 3.35 - 3.86: 21385 3.86 - 4.38: 26921 4.38 - 4.90: 43830 Nonbonded interactions: 108889 Sorted by model distance: nonbonded pdb=" OG SER A1202 " pdb=" O THR A1268 " model vdw 2.312 3.040 nonbonded pdb=" O VAL A 77 " pdb=" OG1 THR A 81 " model vdw 2.397 3.040 nonbonded pdb=" O THR A1276 " pdb=" OG1 THR A1276 " model vdw 2.449 3.040 nonbonded pdb=" O GLN A 313 " pdb=" CB GLN A 313 " model vdw 2.477 2.752 nonbonded pdb=" O PRO A 751 " pdb=" CB PRO A 751 " model vdw 2.497 2.752 ... (remaining 108884 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.370 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: 0.150 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 14.420 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6845 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 : 0.012 0.068 13918 Z= 0.900 Angle : 1.651 9.641 18813 Z= 1.254 Chirality : 0.088 0.323 2118 Planarity : 0.006 0.038 2388 Dihedral : 13.687 88.017 5198 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 5.01 % Allowed : 8.38 % Favored : 86.61 % Cbeta Deviations : 0.19 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.67 (0.19), residues: 1640 helix: -0.63 (0.16), residues: 812 sheet: -1.95 (0.37), residues: 164 loop : -1.30 (0.22), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 780 TYR 0.076 0.005 TYR A1000 PHE 0.032 0.005 PHE A 647 TRP 0.022 0.004 TRP A1086 HIS 0.011 0.002 HIS A1456 Details of bonding type rmsd covalent geometry : bond 0.01203 (13918) covalent geometry : angle 1.65072 (18813) hydrogen bonds : bond 0.22252 ( 629) hydrogen bonds : angle 8.01379 ( 1797) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 453 residues out of total 1516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 377 time to evaluate : 0.510 Fit side-chains revert: symmetry clash REVERT: A 128 VAL cc_start: 0.8367 (t) cc_final: 0.8055 (p) REVERT: A 174 VAL cc_start: 0.8255 (t) cc_final: 0.7895 (m) REVERT: A 183 ASN cc_start: 0.6130 (p0) cc_final: 0.5868 (p0) REVERT: A 217 LYS cc_start: 0.7323 (mtmm) cc_final: 0.7056 (mmtp) REVERT: A 289 LYS cc_start: 0.7776 (mttt) cc_final: 0.7224 (ttpp) REVERT: A 290 GLU cc_start: 0.7376 (mt-10) cc_final: 0.7030 (tp30) REVERT: A 298 ILE cc_start: 0.7948 (OUTLIER) cc_final: 0.7684 (mm) REVERT: A 356 GLU cc_start: 0.5788 (tt0) cc_final: 0.5563 (pt0) REVERT: A 361 ASN cc_start: 0.6290 (t0) cc_final: 0.5638 (t0) REVERT: A 410 GLN cc_start: 0.5242 (tt0) cc_final: 0.4683 (tp40) REVERT: A 425 VAL cc_start: 0.8241 (m) cc_final: 0.7907 (m) REVERT: A 439 GLU cc_start: 0.7239 (tp30) cc_final: 0.6958 (tt0) REVERT: A 444 LYS cc_start: 0.7967 (ttpp) cc_final: 0.7711 (mttt) REVERT: A 464 LEU cc_start: 0.5062 (OUTLIER) cc_final: 0.4834 (mm) REVERT: A 483 LYS cc_start: 0.7496 (mttt) cc_final: 0.6730 (tptt) REVERT: A 519 TYR cc_start: 0.6611 (m-80) cc_final: 0.6382 (m-10) REVERT: A 527 ASP cc_start: 0.6711 (m-30) cc_final: 0.6463 (m-30) REVERT: A 531 TYR cc_start: 0.6168 (t80) cc_final: 0.5755 (t80) REVERT: A 625 MET cc_start: 0.6163 (mtp) cc_final: 0.5603 (mtp) REVERT: A 656 LEU cc_start: 0.6941 (mt) cc_final: 0.6578 (mp) REVERT: A 658 GLU cc_start: 0.8148 (mm-30) cc_final: 0.7846 (mm-30) REVERT: A 670 GLU cc_start: 0.7043 (tm-30) cc_final: 0.6688 (tm-30) REVERT: A 686 TYR cc_start: 0.7269 (m-80) cc_final: 0.6978 (m-80) REVERT: A 689 SER cc_start: 0.6904 (m) cc_final: 0.6332 (p) REVERT: A 708 GLU cc_start: 0.7805 (mt-10) cc_final: 0.7553 (mt-10) REVERT: A 719 ARG cc_start: 0.6772 (mtt180) cc_final: 0.6383 (mtt90) REVERT: A 728 GLU cc_start: 0.7808 (OUTLIER) cc_final: 0.7499 (tt0) REVERT: A 792 ASN cc_start: 0.7004 (m-40) cc_final: 0.6493 (t0) REVERT: A 899 HIS cc_start: 0.5429 (m90) cc_final: 0.5225 (m170) REVERT: A 954 HIS cc_start: 0.5505 (t-90) cc_final: 0.4929 (p-80) REVERT: A 969 VAL cc_start: 0.7162 (OUTLIER) cc_final: 0.6856 (t) REVERT: A 1029 MET cc_start: 0.8373 (tpp) cc_final: 0.7845 (tpp) REVERT: A 1091 GLU cc_start: 0.6400 (tt0) cc_final: 0.5898 (tp30) REVERT: A 1143 ASN cc_start: 0.7300 (m-40) cc_final: 0.6237 (p0) REVERT: A 1183 LYS cc_start: 0.6583 (mttt) cc_final: 0.6111 (mmmt) REVERT: A 1184 GLU cc_start: 0.7507 (mt-10) cc_final: 0.7235 (tm-30) REVERT: A 1222 LEU cc_start: 0.7904 (OUTLIER) cc_final: 0.7652 (tp) REVERT: A 1223 SER cc_start: 0.8624 (t) cc_final: 0.8280 (p) REVERT: A 1269 ILE cc_start: 0.8008 (tt) cc_final: 0.7583 (pt) REVERT: A 1351 GLU cc_start: 0.7157 (mt-10) cc_final: 0.6771 (mm-30) REVERT: A 1354 PHE cc_start: 0.7080 (OUTLIER) cc_final: 0.6247 (p90) REVERT: A 1355 CYS cc_start: 0.6784 (m) cc_final: 0.6258 (m) REVERT: A 1389 MET cc_start: 0.7942 (mmp) cc_final: 0.7531 (mmp) REVERT: A 1404 LEU cc_start: 0.6484 (OUTLIER) cc_final: 0.6232 (tp) REVERT: A 1425 GLU cc_start: 0.7221 (mt-10) cc_final: 0.6862 (tt0) REVERT: A 1448 ARG cc_start: 0.7586 (ttt180) cc_final: 0.7178 (ttm170) REVERT: A 1529 ASN cc_start: 0.7952 (t0) cc_final: 0.7638 (t0) REVERT: A 1531 LYS cc_start: 0.6686 (mtpt) cc_final: 0.5900 (mtmt) REVERT: A 1553 TYR cc_start: 0.5472 (m-80) cc_final: 0.5233 (m-10) REVERT: A 1560 GLU cc_start: 0.7038 (tm-30) cc_final: 0.6317 (mm-30) REVERT: A 1651 LYS cc_start: 0.6228 (mttt) cc_final: 0.5652 (ttpp) REVERT: B 96 MET cc_start: 0.4525 (mmt) cc_final: 0.3985 (mmt) REVERT: B 107 ARG cc_start: 0.6988 (tpp-160) cc_final: 0.6578 (tpp-160) REVERT: B 190 MET cc_start: 0.5120 (mtp) cc_final: 0.4769 (mmt) REVERT: B 202 THR cc_start: 0.3771 (p) cc_final: 0.3463 (p) REVERT: B 218 MET cc_start: 0.5984 (mmt) cc_final: 0.5295 (ptt) REVERT: B 219 ARG cc_start: 0.6150 (mtt180) cc_final: 0.5814 (mtp180) REVERT: B 287 PHE cc_start: 0.6211 (OUTLIER) cc_final: 0.6007 (t80) REVERT: B 298 ILE cc_start: 0.7903 (OUTLIER) cc_final: 0.7530 (pt) REVERT: B 303 ILE cc_start: 0.7460 (OUTLIER) cc_final: 0.7180 (pt) outliers start: 76 outliers final: 14 residues processed: 427 average time/residue: 0.1251 time to fit residues: 75.8360 Evaluate side-chains 267 residues out of total 1516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 243 time to evaluate : 0.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 355 THR Chi-restraints excluded: chain A residue 400 CYS Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 484 THR Chi-restraints excluded: chain A residue 728 GLU Chi-restraints excluded: chain A residue 786 LEU Chi-restraints excluded: chain A residue 788 VAL Chi-restraints excluded: chain A residue 881 ILE Chi-restraints excluded: chain A residue 969 VAL Chi-restraints excluded: chain A residue 1094 ASP Chi-restraints excluded: chain A residue 1108 ASP Chi-restraints excluded: chain A residue 1137 PHE Chi-restraints excluded: chain A residue 1222 LEU Chi-restraints excluded: chain A residue 1354 PHE Chi-restraints excluded: chain A residue 1404 LEU Chi-restraints excluded: chain A residue 1431 ILE Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 287 PHE Chi-restraints excluded: chain B residue 298 ILE Chi-restraints excluded: chain B residue 303 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 98 optimal weight: 0.8980 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 0.6980 chunk 149 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 ASN A 142 HIS A 161 ASN A 570 ASN A 660 ASN A 743 HIS A 783 ASN A 795 GLN A 803 HIS A 841 GLN A 857 GLN A1191 GLN A1250 ASN ** A1338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1509 ASN A1546 GLN A1639 ASN B 119 GLN B 224 HIS B 225 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.186112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.149072 restraints weight = 15875.014| |-----------------------------------------------------------------------------| r_work (start): 0.3650 rms_B_bonded: 2.57 r_work: 0.3315 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 moved from start: 0.2539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13918 Z= 0.141 Angle : 0.582 9.668 18813 Z= 0.314 Chirality : 0.041 0.180 2118 Planarity : 0.005 0.069 2388 Dihedral : 6.144 54.036 1861 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 3.03 % Allowed : 12.73 % Favored : 84.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.28 (0.20), residues: 1640 helix: 0.71 (0.17), residues: 830 sheet: -1.15 (0.38), residues: 174 loop : -1.00 (0.23), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 312 TYR 0.027 0.002 TYR A1343 PHE 0.029 0.002 PHE B 306 TRP 0.011 0.001 TRP A 885 HIS 0.007 0.001 HIS A1019 Details of bonding type rmsd covalent geometry : bond 0.00303 (13918) covalent geometry : angle 0.58177 (18813) hydrogen bonds : bond 0.05723 ( 629) hydrogen bonds : angle 4.94264 ( 1797) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 1516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 248 time to evaluate : 0.448 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 190 GLU cc_start: 0.7513 (mt-10) cc_final: 0.7083 (pt0) REVERT: A 222 MET cc_start: 0.6555 (tpp) cc_final: 0.6297 (tpp) REVERT: A 246 TYR cc_start: 0.5815 (m-80) cc_final: 0.5571 (m-80) REVERT: A 298 ILE cc_start: 0.8363 (OUTLIER) cc_final: 0.8161 (mp) REVERT: A 361 ASN cc_start: 0.6049 (t0) cc_final: 0.5815 (t0) REVERT: A 393 GLU cc_start: 0.7367 (tp30) cc_final: 0.7115 (tt0) REVERT: A 483 LYS cc_start: 0.8291 (mttt) cc_final: 0.7493 (tptt) REVERT: A 504 LEU cc_start: 0.7891 (OUTLIER) cc_final: 0.7661 (tt) REVERT: A 506 THR cc_start: 0.8550 (p) cc_final: 0.8126 (p) REVERT: A 567 LEU cc_start: 0.7445 (mt) cc_final: 0.7154 (mt) REVERT: A 635 MET cc_start: 0.6614 (mmm) cc_final: 0.6117 (mtp) REVERT: A 654 TYR cc_start: 0.8260 (t80) cc_final: 0.7941 (t80) REVERT: A 708 GLU cc_start: 0.8013 (mt-10) cc_final: 0.7752 (mt-10) REVERT: A 768 MET cc_start: 0.8892 (ptp) cc_final: 0.8671 (ptp) REVERT: A 805 MET cc_start: 0.8868 (tmm) cc_final: 0.8514 (tmm) REVERT: A 1029 MET cc_start: 0.8693 (tpp) cc_final: 0.8414 (tpp) REVERT: A 1031 ARG cc_start: 0.8528 (mtp180) cc_final: 0.7993 (mtp85) REVERT: A 1143 ASN cc_start: 0.6965 (m-40) cc_final: 0.6427 (p0) REVERT: A 1222 LEU cc_start: 0.9078 (OUTLIER) cc_final: 0.8742 (tp) REVERT: A 1269 ILE cc_start: 0.8425 (tt) cc_final: 0.8201 (pt) REVERT: A 1292 TRP cc_start: 0.6080 (t60) cc_final: 0.5544 (t60) REVERT: A 1531 LYS cc_start: 0.8239 (mtpt) cc_final: 0.7600 (mtmt) REVERT: A 1560 GLU cc_start: 0.7275 (tm-30) cc_final: 0.7043 (mm-30) REVERT: A 1651 LYS cc_start: 0.7112 (mttt) cc_final: 0.6541 (ttpt) REVERT: A 1658 ARG cc_start: 0.6978 (mtp180) cc_final: 0.6314 (ttt-90) REVERT: B 96 MET cc_start: 0.5058 (mmt) cc_final: 0.4055 (mmt) REVERT: B 107 ARG cc_start: 0.7993 (tpp-160) cc_final: 0.7578 (ttm-80) REVERT: B 157 MET cc_start: 0.6568 (tpp) cc_final: 0.5851 (tpp) REVERT: B 218 MET cc_start: 0.6647 (mmt) cc_final: 0.6385 (ptt) REVERT: B 255 MET cc_start: 0.6711 (tpt) cc_final: 0.6446 (tpp) REVERT: B 263 ILE cc_start: 0.8128 (OUTLIER) cc_final: 0.7805 (mt) REVERT: B 298 ILE cc_start: 0.8295 (OUTLIER) cc_final: 0.8020 (pt) outliers start: 46 outliers final: 25 residues processed: 275 average time/residue: 0.1143 time to fit residues: 46.1340 Evaluate side-chains 232 residues out of total 1516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 202 time to evaluate : 0.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 161 ASN Chi-restraints excluded: chain A residue 243 GLU Chi-restraints excluded: chain A residue 252 MET Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 400 CYS Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 484 THR Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 637 ASN Chi-restraints excluded: chain A residue 639 LYS Chi-restraints excluded: chain A residue 770 LEU Chi-restraints excluded: chain A residue 811 LEU Chi-restraints excluded: chain A residue 881 ILE Chi-restraints excluded: chain A residue 984 ASP Chi-restraints excluded: chain A residue 990 ILE Chi-restraints excluded: chain A residue 1108 ASP Chi-restraints excluded: chain A residue 1137 PHE Chi-restraints excluded: chain A residue 1186 ILE Chi-restraints excluded: chain A residue 1222 LEU Chi-restraints excluded: chain A residue 1261 ASP Chi-restraints excluded: chain A residue 1492 THR Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 263 ILE Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 298 ILE Chi-restraints excluded: chain B residue 301 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 46 optimal weight: 10.0000 chunk 42 optimal weight: 0.1980 chunk 64 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 chunk 165 optimal weight: 7.9990 chunk 158 optimal weight: 6.9990 chunk 75 optimal weight: 1.9990 chunk 139 optimal weight: 6.9990 chunk 77 optimal weight: 2.9990 chunk 58 optimal weight: 4.9990 chunk 37 optimal weight: 1.9990 overall best weight: 1.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 183 ASN A 407 ASN A 456 ASN A 595 HIS A 827 ASN A 859 HIS A1287 ASN ** A1338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1509 ASN A1685 GLN A1715 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.183384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.146123 restraints weight = 15936.563| |-----------------------------------------------------------------------------| r_work (start): 0.3587 rms_B_bonded: 2.96 r_work: 0.3282 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.3145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 13918 Z= 0.168 Angle : 0.575 10.298 18813 Z= 0.305 Chirality : 0.042 0.197 2118 Planarity : 0.004 0.051 2388 Dihedral : 5.122 45.905 1835 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 4.16 % Allowed : 14.91 % Favored : 80.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.04 (0.20), residues: 1640 helix: 0.88 (0.17), residues: 827 sheet: -0.96 (0.36), residues: 191 loop : -0.84 (0.23), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 106 TYR 0.025 0.002 TYR A1000 PHE 0.024 0.002 PHE B 306 TRP 0.010 0.002 TRP A 885 HIS 0.007 0.001 HIS A1019 Details of bonding type rmsd covalent geometry : bond 0.00394 (13918) covalent geometry : angle 0.57489 (18813) hydrogen bonds : bond 0.05313 ( 629) hydrogen bonds : angle 4.67132 ( 1797) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 208 time to evaluate : 0.517 Fit side-chains revert: symmetry clash REVERT: A 190 GLU cc_start: 0.7642 (mt-10) cc_final: 0.7389 (mt-10) REVERT: A 239 SER cc_start: 0.7031 (m) cc_final: 0.6561 (t) REVERT: A 246 TYR cc_start: 0.5804 (m-80) cc_final: 0.5600 (m-80) REVERT: A 360 MET cc_start: 0.8064 (mmt) cc_final: 0.7784 (tpp) REVERT: A 393 GLU cc_start: 0.7407 (tp30) cc_final: 0.7084 (tt0) REVERT: A 483 LYS cc_start: 0.8154 (mttt) cc_final: 0.7332 (tptt) REVERT: A 504 LEU cc_start: 0.7893 (OUTLIER) cc_final: 0.7685 (tt) REVERT: A 506 THR cc_start: 0.8164 (p) cc_final: 0.7753 (p) REVERT: A 567 LEU cc_start: 0.7385 (OUTLIER) cc_final: 0.7055 (mt) REVERT: A 635 MET cc_start: 0.6667 (mmm) cc_final: 0.6016 (mtp) REVERT: A 654 TYR cc_start: 0.8330 (t80) cc_final: 0.7918 (t80) REVERT: A 708 GLU cc_start: 0.7994 (mt-10) cc_final: 0.7740 (mt-10) REVERT: A 768 MET cc_start: 0.8852 (ptp) cc_final: 0.8571 (ptp) REVERT: A 805 MET cc_start: 0.8831 (tmm) cc_final: 0.8412 (tmm) REVERT: A 984 ASP cc_start: 0.6615 (OUTLIER) cc_final: 0.6091 (m-30) REVERT: A 1029 MET cc_start: 0.8765 (tpp) cc_final: 0.8424 (tpp) REVERT: A 1143 ASN cc_start: 0.6906 (m-40) cc_final: 0.6377 (p0) REVERT: A 1172 LYS cc_start: 0.7481 (pttm) cc_final: 0.6973 (mmtm) REVERT: A 1183 LYS cc_start: 0.6992 (mttt) cc_final: 0.6779 (mmmt) REVERT: A 1269 ILE cc_start: 0.8485 (tt) cc_final: 0.8143 (pt) REVERT: A 1292 TRP cc_start: 0.6204 (t60) cc_final: 0.5959 (t60) REVERT: A 1531 LYS cc_start: 0.8205 (mtpt) cc_final: 0.7549 (mtmt) REVERT: A 1560 GLU cc_start: 0.7471 (tm-30) cc_final: 0.7047 (mm-30) REVERT: A 1651 LYS cc_start: 0.7226 (mttt) cc_final: 0.6607 (ttpt) REVERT: A 1689 MET cc_start: 0.2611 (mmp) cc_final: 0.1612 (tmm) REVERT: B 107 ARG cc_start: 0.7726 (tpp-160) cc_final: 0.7343 (ttm-80) REVERT: B 157 MET cc_start: 0.6636 (tpp) cc_final: 0.5620 (tpp) REVERT: B 248 GLU cc_start: 0.7796 (pp20) cc_final: 0.6831 (pm20) REVERT: B 255 MET cc_start: 0.6670 (tpt) cc_final: 0.6375 (tpp) REVERT: B 263 ILE cc_start: 0.8448 (OUTLIER) cc_final: 0.8149 (mt) REVERT: B 279 LEU cc_start: 0.6425 (OUTLIER) cc_final: 0.6131 (mt) REVERT: B 298 ILE cc_start: 0.8217 (OUTLIER) cc_final: 0.7945 (pt) outliers start: 63 outliers final: 39 residues processed: 250 average time/residue: 0.1187 time to fit residues: 43.3418 Evaluate side-chains 240 residues out of total 1516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 195 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 161 ASN Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 243 GLU Chi-restraints excluded: chain A residue 252 MET Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 355 THR Chi-restraints excluded: chain A residue 400 CYS Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 424 MET Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 480 ASP Chi-restraints excluded: chain A residue 484 THR Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 567 LEU Chi-restraints excluded: chain A residue 618 ILE Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 770 LEU Chi-restraints excluded: chain A residue 786 LEU Chi-restraints excluded: chain A residue 791 GLN Chi-restraints excluded: chain A residue 798 LEU Chi-restraints excluded: chain A residue 811 LEU Chi-restraints excluded: chain A residue 881 ILE Chi-restraints excluded: chain A residue 893 MET Chi-restraints excluded: chain A residue 946 THR Chi-restraints excluded: chain A residue 984 ASP Chi-restraints excluded: chain A residue 1108 ASP Chi-restraints excluded: chain A residue 1137 PHE Chi-restraints excluded: chain A residue 1144 ILE Chi-restraints excluded: chain A residue 1186 ILE Chi-restraints excluded: chain A residue 1317 SER Chi-restraints excluded: chain A residue 1405 THR Chi-restraints excluded: chain A residue 1492 THR Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 263 ILE Chi-restraints excluded: chain B residue 279 LEU Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 298 ILE Chi-restraints excluded: chain B residue 301 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 16 optimal weight: 7.9990 chunk 19 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 2 optimal weight: 0.4980 chunk 118 optimal weight: 3.9990 chunk 138 optimal weight: 4.9990 chunk 98 optimal weight: 5.9990 chunk 163 optimal weight: 0.6980 chunk 65 optimal weight: 1.9990 chunk 142 optimal weight: 0.8980 chunk 107 optimal weight: 0.6980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 183 ASN A 361 ASN A 410 GLN A 595 HIS ** A1338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1509 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.188386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.151201 restraints weight = 15886.585| |-----------------------------------------------------------------------------| r_work (start): 0.3603 rms_B_bonded: 2.25 r_work: 0.3304 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 moved from start: 0.3504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 13918 Z= 0.108 Angle : 0.496 9.366 18813 Z= 0.261 Chirality : 0.039 0.166 2118 Planarity : 0.004 0.042 2388 Dihedral : 4.638 46.402 1830 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 3.17 % Allowed : 16.82 % Favored : 80.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.32 (0.20), residues: 1640 helix: 1.22 (0.18), residues: 822 sheet: -0.61 (0.37), residues: 188 loop : -0.80 (0.23), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 139 TYR 0.021 0.001 TYR A1000 PHE 0.019 0.001 PHE A1342 TRP 0.010 0.001 TRP A 885 HIS 0.005 0.001 HIS A1019 Details of bonding type rmsd covalent geometry : bond 0.00234 (13918) covalent geometry : angle 0.49601 (18813) hydrogen bonds : bond 0.04318 ( 629) hydrogen bonds : angle 4.27961 ( 1797) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 216 time to evaluate : 0.466 Fit side-chains REVERT: A 183 ASN cc_start: 0.6920 (OUTLIER) cc_final: 0.6633 (p0) REVERT: A 190 GLU cc_start: 0.7601 (mt-10) cc_final: 0.7037 (pt0) REVERT: A 239 SER cc_start: 0.7000 (m) cc_final: 0.6479 (t) REVERT: A 293 ILE cc_start: 0.7856 (OUTLIER) cc_final: 0.7505 (mt) REVERT: A 393 GLU cc_start: 0.7492 (tp30) cc_final: 0.7167 (tt0) REVERT: A 424 MET cc_start: 0.7955 (ttp) cc_final: 0.7579 (ptm) REVERT: A 458 MET cc_start: 0.8338 (tpp) cc_final: 0.7526 (tpp) REVERT: A 483 LYS cc_start: 0.8111 (mttt) cc_final: 0.7203 (tptt) REVERT: A 504 LEU cc_start: 0.8004 (OUTLIER) cc_final: 0.7793 (tt) REVERT: A 506 THR cc_start: 0.8075 (p) cc_final: 0.7776 (p) REVERT: A 515 ILE cc_start: 0.7409 (mm) cc_final: 0.7204 (mt) REVERT: A 516 GLN cc_start: 0.6857 (OUTLIER) cc_final: 0.6481 (mp-120) REVERT: A 567 LEU cc_start: 0.7171 (mt) cc_final: 0.6968 (mt) REVERT: A 654 TYR cc_start: 0.8295 (t80) cc_final: 0.7876 (t80) REVERT: A 708 GLU cc_start: 0.7855 (mt-10) cc_final: 0.7574 (mt-10) REVERT: A 768 MET cc_start: 0.8740 (ptp) cc_final: 0.8438 (ptp) REVERT: A 805 MET cc_start: 0.8803 (tmm) cc_final: 0.8411 (tmm) REVERT: A 984 ASP cc_start: 0.6434 (OUTLIER) cc_final: 0.5761 (m-30) REVERT: A 1029 MET cc_start: 0.8774 (tpp) cc_final: 0.8421 (tpp) REVERT: A 1143 ASN cc_start: 0.6934 (m-40) cc_final: 0.6551 (p0) REVERT: A 1172 LYS cc_start: 0.7408 (pttm) cc_final: 0.6965 (mmtm) REVERT: A 1183 LYS cc_start: 0.6924 (mttt) cc_final: 0.6693 (mmmt) REVERT: A 1269 ILE cc_start: 0.8453 (tt) cc_final: 0.8101 (pt) REVERT: A 1292 TRP cc_start: 0.5998 (t60) cc_final: 0.5785 (t60) REVERT: A 1379 LYS cc_start: 0.8916 (ttpt) cc_final: 0.8669 (ttpp) REVERT: A 1494 MET cc_start: 0.8524 (mtp) cc_final: 0.8054 (mtp) REVERT: A 1531 LYS cc_start: 0.8016 (mtpt) cc_final: 0.7234 (mttp) REVERT: A 1560 GLU cc_start: 0.7413 (tm-30) cc_final: 0.7104 (mm-30) REVERT: A 1651 LYS cc_start: 0.7056 (mttt) cc_final: 0.6341 (ttpt) REVERT: A 1689 MET cc_start: 0.2974 (mmp) cc_final: 0.1356 (tmm) REVERT: B 107 ARG cc_start: 0.7689 (tpp-160) cc_final: 0.7398 (ttm-80) REVERT: B 157 MET cc_start: 0.6601 (tpp) cc_final: 0.5553 (tpp) REVERT: B 218 MET cc_start: 0.6436 (ptt) cc_final: 0.6174 (ptt) REVERT: B 227 PHE cc_start: 0.7759 (m-80) cc_final: 0.7545 (m-80) REVERT: B 248 GLU cc_start: 0.8120 (pp20) cc_final: 0.6974 (pm20) REVERT: B 266 LYS cc_start: 0.6804 (ttmt) cc_final: 0.6014 (tptt) REVERT: B 279 LEU cc_start: 0.6468 (OUTLIER) cc_final: 0.6213 (mt) outliers start: 48 outliers final: 29 residues processed: 245 average time/residue: 0.1050 time to fit residues: 38.7599 Evaluate side-chains 229 residues out of total 1516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 194 time to evaluate : 0.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 183 ASN Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 480 ASP Chi-restraints excluded: chain A residue 484 THR Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 516 GLN Chi-restraints excluded: chain A residue 618 ILE Chi-restraints excluded: chain A residue 674 SER Chi-restraints excluded: chain A residue 770 LEU Chi-restraints excluded: chain A residue 786 LEU Chi-restraints excluded: chain A residue 798 LEU Chi-restraints excluded: chain A residue 800 HIS Chi-restraints excluded: chain A residue 811 LEU Chi-restraints excluded: chain A residue 881 ILE Chi-restraints excluded: chain A residue 893 MET Chi-restraints excluded: chain A residue 946 THR Chi-restraints excluded: chain A residue 984 ASP Chi-restraints excluded: chain A residue 1108 ASP Chi-restraints excluded: chain A residue 1137 PHE Chi-restraints excluded: chain A residue 1144 ILE Chi-restraints excluded: chain A residue 1186 ILE Chi-restraints excluded: chain A residue 1317 SER Chi-restraints excluded: chain A residue 1352 VAL Chi-restraints excluded: chain A residue 1492 THR Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 279 LEU Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 298 ILE Chi-restraints excluded: chain B residue 301 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 144 optimal weight: 0.0770 chunk 132 optimal weight: 0.9990 chunk 84 optimal weight: 0.9990 chunk 163 optimal weight: 0.0570 chunk 96 optimal weight: 9.9990 chunk 17 optimal weight: 5.9990 chunk 63 optimal weight: 5.9990 chunk 61 optimal weight: 0.2980 chunk 78 optimal weight: 0.5980 chunk 113 optimal weight: 6.9990 chunk 1 optimal weight: 3.9990 overall best weight: 0.4058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 456 ASN A 517 GLN A 595 HIS A 801 GLN A1338 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.187601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.149933 restraints weight = 15962.343| |-----------------------------------------------------------------------------| r_work (start): 0.3662 rms_B_bonded: 2.36 r_work: 0.3366 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 moved from start: 0.3705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.059 13918 Z= 0.096 Angle : 0.472 9.282 18813 Z= 0.247 Chirality : 0.038 0.147 2118 Planarity : 0.003 0.042 2388 Dihedral : 4.364 47.558 1827 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 3.10 % Allowed : 17.35 % Favored : 79.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.56 (0.20), residues: 1640 helix: 1.45 (0.18), residues: 824 sheet: -0.56 (0.37), residues: 194 loop : -0.72 (0.23), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 106 TYR 0.020 0.001 TYR A1000 PHE 0.017 0.001 PHE A1342 TRP 0.009 0.001 TRP A 885 HIS 0.004 0.000 HIS A1019 Details of bonding type rmsd covalent geometry : bond 0.00207 (13918) covalent geometry : angle 0.47151 (18813) hydrogen bonds : bond 0.03881 ( 629) hydrogen bonds : angle 4.06773 ( 1797) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 210 time to evaluate : 0.524 Fit side-chains REVERT: A 190 GLU cc_start: 0.7628 (mt-10) cc_final: 0.7137 (pt0) REVERT: A 293 ILE cc_start: 0.7771 (OUTLIER) cc_final: 0.7473 (mt) REVERT: A 357 GLU cc_start: 0.6095 (mt-10) cc_final: 0.5577 (mp0) REVERT: A 393 GLU cc_start: 0.7485 (tp30) cc_final: 0.7187 (tt0) REVERT: A 483 LYS cc_start: 0.8124 (mttt) cc_final: 0.7176 (tptt) REVERT: A 504 LEU cc_start: 0.8059 (OUTLIER) cc_final: 0.7850 (tt) REVERT: A 506 THR cc_start: 0.8052 (p) cc_final: 0.7758 (p) REVERT: A 516 GLN cc_start: 0.6841 (OUTLIER) cc_final: 0.6454 (mp-120) REVERT: A 567 LEU cc_start: 0.7452 (mt) cc_final: 0.7228 (mt) REVERT: A 635 MET cc_start: 0.6930 (mmm) cc_final: 0.6181 (mmm) REVERT: A 654 TYR cc_start: 0.8296 (t80) cc_final: 0.7860 (t80) REVERT: A 708 GLU cc_start: 0.7935 (mt-10) cc_final: 0.7668 (mt-10) REVERT: A 768 MET cc_start: 0.8736 (ptp) cc_final: 0.8431 (ptp) REVERT: A 805 MET cc_start: 0.8858 (tmm) cc_final: 0.8603 (tmm) REVERT: A 1029 MET cc_start: 0.8730 (tpp) cc_final: 0.8391 (tpp) REVERT: A 1143 ASN cc_start: 0.7063 (m-40) cc_final: 0.6554 (p0) REVERT: A 1172 LYS cc_start: 0.7401 (pttm) cc_final: 0.7091 (mmtm) REVERT: A 1183 LYS cc_start: 0.6957 (mttt) cc_final: 0.6726 (mmmt) REVERT: A 1269 ILE cc_start: 0.8472 (tt) cc_final: 0.8133 (pt) REVERT: A 1494 MET cc_start: 0.8505 (mtp) cc_final: 0.8275 (mtp) REVERT: A 1531 LYS cc_start: 0.7938 (mtpt) cc_final: 0.7342 (mtmt) REVERT: A 1560 GLU cc_start: 0.7451 (tm-30) cc_final: 0.7131 (mm-30) REVERT: A 1651 LYS cc_start: 0.7138 (mttt) cc_final: 0.6431 (ttpt) REVERT: A 1689 MET cc_start: 0.2740 (mmp) cc_final: 0.1325 (tmm) REVERT: B 107 ARG cc_start: 0.7715 (tpp-160) cc_final: 0.7403 (ttm-80) REVERT: B 157 MET cc_start: 0.6688 (tpp) cc_final: 0.5791 (tpp) REVERT: B 266 LYS cc_start: 0.6899 (ttmt) cc_final: 0.6073 (tptt) REVERT: B 279 LEU cc_start: 0.6479 (OUTLIER) cc_final: 0.6169 (mt) outliers start: 47 outliers final: 29 residues processed: 237 average time/residue: 0.1112 time to fit residues: 38.9318 Evaluate side-chains 226 residues out of total 1516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 193 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 252 MET Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 480 ASP Chi-restraints excluded: chain A residue 484 THR Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 516 GLN Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 674 SER Chi-restraints excluded: chain A residue 770 LEU Chi-restraints excluded: chain A residue 786 LEU Chi-restraints excluded: chain A residue 798 LEU Chi-restraints excluded: chain A residue 800 HIS Chi-restraints excluded: chain A residue 811 LEU Chi-restraints excluded: chain A residue 881 ILE Chi-restraints excluded: chain A residue 946 THR Chi-restraints excluded: chain A residue 1137 PHE Chi-restraints excluded: chain A residue 1144 ILE Chi-restraints excluded: chain A residue 1186 ILE Chi-restraints excluded: chain A residue 1352 VAL Chi-restraints excluded: chain B residue 96 MET Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 279 LEU Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 298 ILE Chi-restraints excluded: chain B residue 301 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 11 optimal weight: 3.9990 chunk 114 optimal weight: 10.0000 chunk 29 optimal weight: 8.9990 chunk 137 optimal weight: 5.9990 chunk 163 optimal weight: 2.9990 chunk 139 optimal weight: 6.9990 chunk 69 optimal weight: 0.3980 chunk 74 optimal weight: 5.9990 chunk 121 optimal weight: 3.9990 chunk 82 optimal weight: 5.9990 chunk 83 optimal weight: 9.9990 overall best weight: 3.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 595 HIS A 801 GLN A 884 GLN ** A1338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1380 ASN A1509 ASN A1519 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.180418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.143715 restraints weight = 15810.815| |-----------------------------------------------------------------------------| r_work (start): 0.3512 rms_B_bonded: 2.27 r_work: 0.3213 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3082 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.3905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.076 13918 Z= 0.257 Angle : 0.659 12.652 18813 Z= 0.341 Chirality : 0.045 0.160 2118 Planarity : 0.005 0.043 2388 Dihedral : 4.970 49.983 1825 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 4.29 % Allowed : 16.75 % Favored : 78.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.12 (0.20), residues: 1640 helix: 0.82 (0.17), residues: 821 sheet: -0.64 (0.37), residues: 185 loop : -1.02 (0.23), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 78 TYR 0.036 0.002 TYR A1000 PHE 0.029 0.003 PHE A 423 TRP 0.012 0.002 TRP A1132 HIS 0.008 0.002 HIS A1456 Details of bonding type rmsd covalent geometry : bond 0.00632 (13918) covalent geometry : angle 0.65896 (18813) hydrogen bonds : bond 0.05667 ( 629) hydrogen bonds : angle 4.59017 ( 1797) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 190 time to evaluate : 0.575 Fit side-chains revert: symmetry clash REVERT: A 275 SER cc_start: 0.6451 (t) cc_final: 0.5943 (p) REVERT: A 303 LEU cc_start: 0.9123 (OUTLIER) cc_final: 0.8876 (tp) REVERT: A 357 GLU cc_start: 0.6141 (mt-10) cc_final: 0.5591 (mp0) REVERT: A 393 GLU cc_start: 0.7935 (tp30) cc_final: 0.7436 (tt0) REVERT: A 464 LEU cc_start: 0.5082 (OUTLIER) cc_final: 0.4809 (mm) REVERT: A 483 LYS cc_start: 0.8420 (mttt) cc_final: 0.7277 (tptt) REVERT: A 506 THR cc_start: 0.8072 (p) cc_final: 0.7757 (p) REVERT: A 527 ASP cc_start: 0.7576 (m-30) cc_final: 0.7083 (m-30) REVERT: A 567 LEU cc_start: 0.7319 (OUTLIER) cc_final: 0.6989 (mt) REVERT: A 654 TYR cc_start: 0.8246 (t80) cc_final: 0.7811 (t80) REVERT: A 768 MET cc_start: 0.8957 (ptp) cc_final: 0.8658 (ptp) REVERT: A 908 MET cc_start: 0.6880 (ptt) cc_final: 0.6014 (ptp) REVERT: A 1029 MET cc_start: 0.8987 (tpp) cc_final: 0.8776 (tpp) REVERT: A 1143 ASN cc_start: 0.7223 (m-40) cc_final: 0.6722 (p0) REVERT: A 1172 LYS cc_start: 0.7650 (pttm) cc_final: 0.7077 (mmtm) REVERT: A 1183 LYS cc_start: 0.7112 (mttt) cc_final: 0.6515 (mttp) REVERT: A 1269 ILE cc_start: 0.8590 (tt) cc_final: 0.8260 (pt) REVERT: A 1404 LEU cc_start: 0.7817 (OUTLIER) cc_final: 0.7567 (mt) REVERT: A 1531 LYS cc_start: 0.8215 (mtpt) cc_final: 0.7530 (mttp) REVERT: A 1560 GLU cc_start: 0.7677 (tm-30) cc_final: 0.7117 (mm-30) REVERT: A 1651 LYS cc_start: 0.7440 (mttt) cc_final: 0.6532 (ttpt) REVERT: A 1689 MET cc_start: 0.2627 (mmp) cc_final: 0.1526 (tmm) REVERT: B 227 PHE cc_start: 0.7907 (m-80) cc_final: 0.7678 (m-80) REVERT: B 266 LYS cc_start: 0.7237 (ttmt) cc_final: 0.6386 (tptt) REVERT: B 279 LEU cc_start: 0.6644 (OUTLIER) cc_final: 0.6332 (mt) outliers start: 65 outliers final: 42 residues processed: 237 average time/residue: 0.1202 time to fit residues: 41.9730 Evaluate side-chains 227 residues out of total 1516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 180 time to evaluate : 0.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 252 MET Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 355 THR Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 399 LYS Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 480 ASP Chi-restraints excluded: chain A residue 484 THR Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 567 LEU Chi-restraints excluded: chain A residue 618 ILE Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 674 SER Chi-restraints excluded: chain A residue 770 LEU Chi-restraints excluded: chain A residue 786 LEU Chi-restraints excluded: chain A residue 791 GLN Chi-restraints excluded: chain A residue 798 LEU Chi-restraints excluded: chain A residue 811 LEU Chi-restraints excluded: chain A residue 835 ILE Chi-restraints excluded: chain A residue 942 VAL Chi-restraints excluded: chain A residue 946 THR Chi-restraints excluded: chain A residue 1137 PHE Chi-restraints excluded: chain A residue 1144 ILE Chi-restraints excluded: chain A residue 1186 ILE Chi-restraints excluded: chain A residue 1305 HIS Chi-restraints excluded: chain A residue 1317 SER Chi-restraints excluded: chain A residue 1404 LEU Chi-restraints excluded: chain A residue 1405 THR Chi-restraints excluded: chain A residue 1492 THR Chi-restraints excluded: chain B residue 96 MET Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 279 LEU Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 298 ILE Chi-restraints excluded: chain B residue 301 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 37 optimal weight: 0.9990 chunk 48 optimal weight: 0.9980 chunk 154 optimal weight: 5.9990 chunk 40 optimal weight: 3.9990 chunk 152 optimal weight: 5.9990 chunk 141 optimal weight: 0.9980 chunk 3 optimal weight: 0.9980 chunk 109 optimal weight: 0.9980 chunk 140 optimal weight: 1.9990 chunk 21 optimal weight: 9.9990 chunk 32 optimal weight: 0.4980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 410 GLN A 595 HIS ** A1338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1380 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.186314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.150098 restraints weight = 15752.689| |-----------------------------------------------------------------------------| r_work (start): 0.3584 rms_B_bonded: 2.08 r_work: 0.3276 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.4108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 13918 Z= 0.112 Angle : 0.506 13.496 18813 Z= 0.264 Chirality : 0.039 0.181 2118 Planarity : 0.004 0.044 2388 Dihedral : 4.424 44.542 1823 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 2.90 % Allowed : 18.21 % Favored : 78.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.20), residues: 1640 helix: 1.22 (0.18), residues: 819 sheet: -0.44 (0.38), residues: 182 loop : -0.89 (0.23), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 535 TYR 0.022 0.001 TYR A1000 PHE 0.019 0.001 PHE A1342 TRP 0.020 0.001 TRP A1292 HIS 0.006 0.001 HIS A1019 Details of bonding type rmsd covalent geometry : bond 0.00254 (13918) covalent geometry : angle 0.50646 (18813) hydrogen bonds : bond 0.04184 ( 629) hydrogen bonds : angle 4.14657 ( 1797) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 198 time to evaluate : 0.584 Fit side-chains REVERT: A 286 TYR cc_start: 0.8406 (t80) cc_final: 0.7977 (t80) REVERT: A 293 ILE cc_start: 0.7993 (OUTLIER) cc_final: 0.7623 (mt) REVERT: A 357 GLU cc_start: 0.6039 (mt-10) cc_final: 0.5494 (mp0) REVERT: A 393 GLU cc_start: 0.7781 (tp30) cc_final: 0.7342 (tt0) REVERT: A 464 LEU cc_start: 0.5131 (OUTLIER) cc_final: 0.4874 (mm) REVERT: A 483 LYS cc_start: 0.8321 (mttt) cc_final: 0.7080 (tptt) REVERT: A 506 THR cc_start: 0.8018 (p) cc_final: 0.7715 (p) REVERT: A 567 LEU cc_start: 0.7301 (mt) cc_final: 0.7089 (mt) REVERT: A 654 TYR cc_start: 0.8129 (t80) cc_final: 0.7713 (t80) REVERT: A 768 MET cc_start: 0.8727 (ptp) cc_final: 0.8413 (ptp) REVERT: A 822 ARG cc_start: 0.7372 (mtt90) cc_final: 0.7090 (mmt-90) REVERT: A 885 TRP cc_start: 0.6428 (t60) cc_final: 0.6051 (t60) REVERT: A 908 MET cc_start: 0.7357 (ptt) cc_final: 0.6121 (ptp) REVERT: A 1029 MET cc_start: 0.8857 (tpp) cc_final: 0.8571 (tpp) REVERT: A 1143 ASN cc_start: 0.7020 (m-40) cc_final: 0.6783 (p0) REVERT: A 1172 LYS cc_start: 0.7447 (pttm) cc_final: 0.7077 (mmtm) REVERT: A 1183 LYS cc_start: 0.7029 (mttt) cc_final: 0.6820 (mmmt) REVERT: A 1269 ILE cc_start: 0.8517 (tt) cc_final: 0.8204 (pt) REVERT: A 1531 LYS cc_start: 0.8051 (mtpt) cc_final: 0.7447 (mttp) REVERT: A 1560 GLU cc_start: 0.7431 (tm-30) cc_final: 0.7054 (mm-30) REVERT: A 1651 LYS cc_start: 0.7075 (mttt) cc_final: 0.6525 (ttpt) REVERT: A 1689 MET cc_start: 0.2588 (mmp) cc_final: 0.1562 (tmm) REVERT: B 106 ARG cc_start: 0.7578 (ttp-110) cc_final: 0.7366 (ttp-110) REVERT: B 107 ARG cc_start: 0.7782 (tpp-160) cc_final: 0.7297 (ttm-80) REVERT: B 157 MET cc_start: 0.6790 (tpp) cc_final: 0.5633 (tpp) REVERT: B 266 LYS cc_start: 0.7103 (ttmt) cc_final: 0.6245 (tptt) REVERT: B 279 LEU cc_start: 0.6447 (OUTLIER) cc_final: 0.6044 (mt) outliers start: 44 outliers final: 33 residues processed: 229 average time/residue: 0.1120 time to fit residues: 37.9347 Evaluate side-chains 225 residues out of total 1516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 189 time to evaluate : 0.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 252 MET Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 355 THR Chi-restraints excluded: chain A residue 400 CYS Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 480 ASP Chi-restraints excluded: chain A residue 484 THR Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 674 SER Chi-restraints excluded: chain A residue 770 LEU Chi-restraints excluded: chain A residue 786 LEU Chi-restraints excluded: chain A residue 791 GLN Chi-restraints excluded: chain A residue 798 LEU Chi-restraints excluded: chain A residue 800 HIS Chi-restraints excluded: chain A residue 811 LEU Chi-restraints excluded: chain A residue 946 THR Chi-restraints excluded: chain A residue 1137 PHE Chi-restraints excluded: chain A residue 1144 ILE Chi-restraints excluded: chain A residue 1186 ILE Chi-restraints excluded: chain A residue 1317 SER Chi-restraints excluded: chain A residue 1410 LEU Chi-restraints excluded: chain A residue 1492 THR Chi-restraints excluded: chain B residue 96 MET Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 279 LEU Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 301 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 109 optimal weight: 2.9990 chunk 58 optimal weight: 0.9980 chunk 75 optimal weight: 9.9990 chunk 87 optimal weight: 0.0000 chunk 37 optimal weight: 2.9990 chunk 108 optimal weight: 0.7980 chunk 85 optimal weight: 8.9990 chunk 50 optimal weight: 2.9990 chunk 77 optimal weight: 4.9990 chunk 69 optimal weight: 2.9990 chunk 166 optimal weight: 0.8980 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 595 HIS ** A1338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1509 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.185635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.149797 restraints weight = 15763.945| |-----------------------------------------------------------------------------| r_work (start): 0.3576 rms_B_bonded: 2.03 r_work: 0.3266 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3135 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.4215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 13918 Z= 0.124 Angle : 0.517 13.399 18813 Z= 0.267 Chirality : 0.039 0.177 2118 Planarity : 0.004 0.043 2388 Dihedral : 4.219 38.267 1821 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.97 % Allowed : 18.54 % Favored : 78.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.41 (0.20), residues: 1640 helix: 1.30 (0.18), residues: 819 sheet: -0.42 (0.38), residues: 182 loop : -0.80 (0.23), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 106 TYR 0.023 0.001 TYR A1000 PHE 0.020 0.001 PHE A1342 TRP 0.022 0.001 TRP A1292 HIS 0.005 0.001 HIS A1019 Details of bonding type rmsd covalent geometry : bond 0.00290 (13918) covalent geometry : angle 0.51717 (18813) hydrogen bonds : bond 0.04198 ( 629) hydrogen bonds : angle 4.10105 ( 1797) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 187 time to evaluate : 0.523 Fit side-chains REVERT: A 275 SER cc_start: 0.6433 (t) cc_final: 0.6030 (p) REVERT: A 357 GLU cc_start: 0.6051 (mt-10) cc_final: 0.5467 (mp0) REVERT: A 393 GLU cc_start: 0.8026 (tp30) cc_final: 0.7493 (tt0) REVERT: A 464 LEU cc_start: 0.4606 (OUTLIER) cc_final: 0.4261 (mm) REVERT: A 483 LYS cc_start: 0.8437 (mttt) cc_final: 0.7135 (tptt) REVERT: A 506 THR cc_start: 0.8091 (p) cc_final: 0.7799 (p) REVERT: A 567 LEU cc_start: 0.7267 (mt) cc_final: 0.7053 (mt) REVERT: A 654 TYR cc_start: 0.8184 (t80) cc_final: 0.7763 (t80) REVERT: A 768 MET cc_start: 0.8890 (ptp) cc_final: 0.8602 (ptp) REVERT: A 822 ARG cc_start: 0.7256 (mtt90) cc_final: 0.7002 (mmt-90) REVERT: A 885 TRP cc_start: 0.6336 (t60) cc_final: 0.5977 (t60) REVERT: A 908 MET cc_start: 0.7318 (ptt) cc_final: 0.6079 (ptp) REVERT: A 1029 MET cc_start: 0.8955 (tpp) cc_final: 0.8687 (tpp) REVERT: A 1143 ASN cc_start: 0.7144 (m-40) cc_final: 0.6843 (p0) REVERT: A 1172 LYS cc_start: 0.7570 (pttm) cc_final: 0.7079 (mmtm) REVERT: A 1183 LYS cc_start: 0.7029 (mttt) cc_final: 0.6784 (mmmt) REVERT: A 1269 ILE cc_start: 0.8607 (tt) cc_final: 0.8253 (pt) REVERT: A 1308 ARG cc_start: 0.7742 (mmt90) cc_final: 0.7541 (mmt90) REVERT: A 1494 MET cc_start: 0.8508 (mtp) cc_final: 0.7940 (mtp) REVERT: A 1531 LYS cc_start: 0.8306 (mtpt) cc_final: 0.7701 (mttp) REVERT: A 1560 GLU cc_start: 0.7619 (tm-30) cc_final: 0.7089 (mm-30) REVERT: A 1651 LYS cc_start: 0.7196 (mttt) cc_final: 0.6477 (ttpt) REVERT: A 1689 MET cc_start: 0.2591 (mmp) cc_final: 0.1569 (tmm) REVERT: B 107 ARG cc_start: 0.7832 (tpp-160) cc_final: 0.7275 (ttm-80) REVERT: B 157 MET cc_start: 0.6953 (tpp) cc_final: 0.5845 (tpp) REVERT: B 227 PHE cc_start: 0.7877 (m-80) cc_final: 0.7557 (m-80) REVERT: B 266 LYS cc_start: 0.7251 (ttmt) cc_final: 0.6371 (tptt) outliers start: 45 outliers final: 34 residues processed: 218 average time/residue: 0.1101 time to fit residues: 35.6809 Evaluate side-chains 221 residues out of total 1516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 186 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 252 MET Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 400 CYS Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 480 ASP Chi-restraints excluded: chain A residue 484 THR Chi-restraints excluded: chain A residue 501 LYS Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 618 ILE Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 674 SER Chi-restraints excluded: chain A residue 770 LEU Chi-restraints excluded: chain A residue 786 LEU Chi-restraints excluded: chain A residue 789 ILE Chi-restraints excluded: chain A residue 791 GLN Chi-restraints excluded: chain A residue 798 LEU Chi-restraints excluded: chain A residue 811 LEU Chi-restraints excluded: chain A residue 946 THR Chi-restraints excluded: chain A residue 1137 PHE Chi-restraints excluded: chain A residue 1144 ILE Chi-restraints excluded: chain A residue 1186 ILE Chi-restraints excluded: chain A residue 1317 SER Chi-restraints excluded: chain A residue 1405 THR Chi-restraints excluded: chain A residue 1410 LEU Chi-restraints excluded: chain A residue 1492 THR Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 301 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 0 optimal weight: 5.9990 chunk 92 optimal weight: 0.0770 chunk 34 optimal weight: 0.8980 chunk 48 optimal weight: 0.7980 chunk 133 optimal weight: 0.7980 chunk 148 optimal weight: 5.9990 chunk 14 optimal weight: 3.9990 chunk 52 optimal weight: 4.9990 chunk 138 optimal weight: 5.9990 chunk 162 optimal weight: 0.9980 chunk 59 optimal weight: 0.9980 overall best weight: 0.7138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 595 HIS A1509 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.187691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.150711 restraints weight = 15939.392| |-----------------------------------------------------------------------------| r_work (start): 0.3629 rms_B_bonded: 2.33 r_work: 0.3349 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 moved from start: 0.4342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 13918 Z= 0.105 Angle : 0.506 13.996 18813 Z= 0.259 Chirality : 0.039 0.165 2118 Planarity : 0.004 0.043 2388 Dihedral : 4.092 37.253 1821 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 2.44 % Allowed : 18.67 % Favored : 78.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.54 (0.21), residues: 1640 helix: 1.42 (0.18), residues: 821 sheet: -0.50 (0.38), residues: 189 loop : -0.73 (0.24), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 928 TYR 0.021 0.001 TYR A1000 PHE 0.018 0.001 PHE A1342 TRP 0.024 0.001 TRP A1292 HIS 0.005 0.001 HIS A1019 Details of bonding type rmsd covalent geometry : bond 0.00240 (13918) covalent geometry : angle 0.50555 (18813) hydrogen bonds : bond 0.03823 ( 629) hydrogen bonds : angle 4.00576 ( 1797) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 197 time to evaluate : 0.540 Fit side-chains REVERT: A 190 GLU cc_start: 0.7344 (mt-10) cc_final: 0.6681 (pt0) REVERT: A 239 SER cc_start: 0.6881 (m) cc_final: 0.6510 (t) REVERT: A 275 SER cc_start: 0.6171 (t) cc_final: 0.5898 (p) REVERT: A 393 GLU cc_start: 0.7714 (tp30) cc_final: 0.7271 (tt0) REVERT: A 410 GLN cc_start: 0.7260 (tp40) cc_final: 0.6781 (tt0) REVERT: A 464 LEU cc_start: 0.4641 (OUTLIER) cc_final: 0.4357 (mm) REVERT: A 483 LYS cc_start: 0.8261 (mttt) cc_final: 0.7083 (tptt) REVERT: A 506 THR cc_start: 0.8032 (p) cc_final: 0.7753 (p) REVERT: A 567 LEU cc_start: 0.7447 (mt) cc_final: 0.7221 (mt) REVERT: A 654 TYR cc_start: 0.8116 (t80) cc_final: 0.7683 (t80) REVERT: A 768 MET cc_start: 0.8740 (ptp) cc_final: 0.8429 (ptp) REVERT: A 885 TRP cc_start: 0.6309 (t60) cc_final: 0.6001 (t60) REVERT: A 908 MET cc_start: 0.7386 (ptt) cc_final: 0.6135 (ptp) REVERT: A 922 MET cc_start: 0.6693 (tpt) cc_final: 0.6327 (mmm) REVERT: A 1029 MET cc_start: 0.8843 (tpp) cc_final: 0.8588 (tpp) REVERT: A 1172 LYS cc_start: 0.7408 (pttm) cc_final: 0.7158 (mmtm) REVERT: A 1183 LYS cc_start: 0.6972 (mttt) cc_final: 0.6770 (mmmt) REVERT: A 1269 ILE cc_start: 0.8482 (tt) cc_final: 0.8216 (pt) REVERT: A 1308 ARG cc_start: 0.7584 (mmt90) cc_final: 0.7380 (mmt90) REVERT: A 1531 LYS cc_start: 0.8116 (mtpt) cc_final: 0.7552 (mttp) REVERT: A 1560 GLU cc_start: 0.7471 (tm-30) cc_final: 0.7066 (mm-30) REVERT: A 1651 LYS cc_start: 0.7173 (mttt) cc_final: 0.6523 (ttpt) REVERT: A 1689 MET cc_start: 0.2361 (mmp) cc_final: 0.1772 (tmm) REVERT: B 157 MET cc_start: 0.6896 (tpp) cc_final: 0.5808 (tpp) REVERT: B 266 LYS cc_start: 0.6932 (ttmt) cc_final: 0.6178 (tptt) outliers start: 37 outliers final: 33 residues processed: 225 average time/residue: 0.1144 time to fit residues: 37.8696 Evaluate side-chains 221 residues out of total 1516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 187 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 252 MET Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 400 CYS Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 480 ASP Chi-restraints excluded: chain A residue 484 THR Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 674 SER Chi-restraints excluded: chain A residue 770 LEU Chi-restraints excluded: chain A residue 786 LEU Chi-restraints excluded: chain A residue 789 ILE Chi-restraints excluded: chain A residue 791 GLN Chi-restraints excluded: chain A residue 798 LEU Chi-restraints excluded: chain A residue 800 HIS Chi-restraints excluded: chain A residue 811 LEU Chi-restraints excluded: chain A residue 946 THR Chi-restraints excluded: chain A residue 1137 PHE Chi-restraints excluded: chain A residue 1144 ILE Chi-restraints excluded: chain A residue 1186 ILE Chi-restraints excluded: chain A residue 1317 SER Chi-restraints excluded: chain A residue 1405 THR Chi-restraints excluded: chain A residue 1410 LEU Chi-restraints excluded: chain A residue 1492 THR Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 301 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 3 optimal weight: 1.9990 chunk 154 optimal weight: 9.9990 chunk 89 optimal weight: 0.6980 chunk 136 optimal weight: 2.9990 chunk 135 optimal weight: 0.2980 chunk 43 optimal weight: 0.9990 chunk 36 optimal weight: 4.9990 chunk 119 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 99 optimal weight: 4.9990 chunk 138 optimal weight: 0.1980 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 595 HIS A1462 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.184967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.148679 restraints weight = 15845.887| |-----------------------------------------------------------------------------| r_work (start): 0.3608 rms_B_bonded: 2.42 r_work: 0.3274 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.4426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 13918 Z= 0.111 Angle : 0.510 13.870 18813 Z= 0.261 Chirality : 0.039 0.160 2118 Planarity : 0.004 0.043 2388 Dihedral : 4.036 36.991 1821 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 2.44 % Allowed : 18.87 % Favored : 78.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.21), residues: 1640 helix: 1.46 (0.18), residues: 818 sheet: -0.56 (0.38), residues: 187 loop : -0.65 (0.24), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 822 TYR 0.023 0.001 TYR A1000 PHE 0.019 0.001 PHE A1342 TRP 0.024 0.001 TRP A1292 HIS 0.005 0.001 HIS A1019 Details of bonding type rmsd covalent geometry : bond 0.00256 (13918) covalent geometry : angle 0.50996 (18813) hydrogen bonds : bond 0.03837 ( 629) hydrogen bonds : angle 3.99504 ( 1797) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 186 time to evaluate : 0.387 Fit side-chains REVERT: A 190 GLU cc_start: 0.7411 (mt-10) cc_final: 0.6785 (pt0) REVERT: A 239 SER cc_start: 0.6910 (m) cc_final: 0.6522 (t) REVERT: A 246 TYR cc_start: 0.6160 (m-80) cc_final: 0.5383 (m-80) REVERT: A 275 SER cc_start: 0.6374 (t) cc_final: 0.6001 (p) REVERT: A 282 ASN cc_start: 0.8025 (m-40) cc_final: 0.7290 (m110) REVERT: A 393 GLU cc_start: 0.7802 (tp30) cc_final: 0.7315 (tt0) REVERT: A 410 GLN cc_start: 0.7316 (tp40) cc_final: 0.6805 (tt0) REVERT: A 464 LEU cc_start: 0.4671 (OUTLIER) cc_final: 0.4347 (mm) REVERT: A 483 LYS cc_start: 0.8342 (mttt) cc_final: 0.7047 (tptt) REVERT: A 506 THR cc_start: 0.8058 (p) cc_final: 0.7759 (p) REVERT: A 567 LEU cc_start: 0.7432 (mt) cc_final: 0.7106 (mt) REVERT: A 654 TYR cc_start: 0.8262 (t80) cc_final: 0.7815 (t80) REVERT: A 768 MET cc_start: 0.8797 (ptp) cc_final: 0.8495 (ptp) REVERT: A 885 TRP cc_start: 0.6367 (t60) cc_final: 0.6083 (t60) REVERT: A 908 MET cc_start: 0.7415 (ptt) cc_final: 0.6184 (ptp) REVERT: A 1029 MET cc_start: 0.8886 (tpp) cc_final: 0.8639 (tpp) REVERT: A 1172 LYS cc_start: 0.7458 (pttm) cc_final: 0.7169 (mmtm) REVERT: A 1183 LYS cc_start: 0.7000 (mttt) cc_final: 0.6790 (mmmt) REVERT: A 1269 ILE cc_start: 0.8514 (tt) cc_final: 0.8250 (pt) REVERT: A 1531 LYS cc_start: 0.8210 (mtpt) cc_final: 0.7663 (mttp) REVERT: A 1544 GLU cc_start: 0.7682 (tp30) cc_final: 0.7210 (tp30) REVERT: A 1560 GLU cc_start: 0.7537 (tm-30) cc_final: 0.7097 (mm-30) REVERT: A 1651 LYS cc_start: 0.7176 (mttt) cc_final: 0.6511 (ttpt) REVERT: A 1689 MET cc_start: 0.2654 (mmp) cc_final: 0.1936 (tmm) REVERT: B 106 ARG cc_start: 0.7429 (ttp-110) cc_final: 0.6985 (ttp-110) REVERT: B 157 MET cc_start: 0.7028 (tpp) cc_final: 0.6036 (tpp) REVERT: B 255 MET cc_start: 0.6509 (tpp) cc_final: 0.6260 (tpp) REVERT: B 266 LYS cc_start: 0.7013 (ttmt) cc_final: 0.6134 (tptm) outliers start: 37 outliers final: 34 residues processed: 215 average time/residue: 0.1113 time to fit residues: 35.6260 Evaluate side-chains 217 residues out of total 1516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 182 time to evaluate : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 252 MET Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 400 CYS Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 480 ASP Chi-restraints excluded: chain A residue 484 THR Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 674 SER Chi-restraints excluded: chain A residue 770 LEU Chi-restraints excluded: chain A residue 786 LEU Chi-restraints excluded: chain A residue 789 ILE Chi-restraints excluded: chain A residue 791 GLN Chi-restraints excluded: chain A residue 798 LEU Chi-restraints excluded: chain A residue 800 HIS Chi-restraints excluded: chain A residue 811 LEU Chi-restraints excluded: chain A residue 946 THR Chi-restraints excluded: chain A residue 1137 PHE Chi-restraints excluded: chain A residue 1144 ILE Chi-restraints excluded: chain A residue 1186 ILE Chi-restraints excluded: chain A residue 1317 SER Chi-restraints excluded: chain A residue 1405 THR Chi-restraints excluded: chain A residue 1410 LEU Chi-restraints excluded: chain A residue 1492 THR Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 301 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 81 optimal weight: 6.9990 chunk 88 optimal weight: 0.0040 chunk 72 optimal weight: 5.9990 chunk 113 optimal weight: 4.9990 chunk 98 optimal weight: 5.9990 chunk 40 optimal weight: 3.9990 chunk 139 optimal weight: 0.9990 chunk 8 optimal weight: 4.9990 chunk 166 optimal weight: 2.9990 chunk 140 optimal weight: 3.9990 chunk 86 optimal weight: 6.9990 overall best weight: 2.4000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 517 GLN A 595 HIS A1380 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.181625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.145720 restraints weight = 15982.309| |-----------------------------------------------------------------------------| r_work (start): 0.3536 rms_B_bonded: 2.62 r_work: 0.3184 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.4439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 13918 Z= 0.196 Angle : 0.598 13.850 18813 Z= 0.305 Chirality : 0.042 0.203 2118 Planarity : 0.004 0.043 2388 Dihedral : 4.392 41.590 1821 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.57 % Allowed : 18.80 % Favored : 78.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.20), residues: 1640 helix: 1.10 (0.18), residues: 821 sheet: -0.43 (0.39), residues: 180 loop : -0.78 (0.24), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A1463 TYR 0.031 0.002 TYR A1000 PHE 0.022 0.002 PHE A 423 TRP 0.019 0.002 TRP A1292 HIS 0.007 0.001 HIS A1019 Details of bonding type rmsd covalent geometry : bond 0.00482 (13918) covalent geometry : angle 0.59752 (18813) hydrogen bonds : bond 0.04790 ( 629) hydrogen bonds : angle 4.26978 ( 1797) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3070.55 seconds wall clock time: 53 minutes 18.15 seconds (3198.15 seconds total)