Starting phenix.real_space_refine on Sat Sep 12 06:32:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6kwx_0780/09_2026/6kwx_0780.cif Found real_map, /net/cci-nas-00/data/ceres_data/6kwx_0780/09_2026/6kwx_0780.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.75 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6kwx_0780/09_2026/6kwx_0780.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6kwx_0780/09_2026/6kwx_0780.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6kwx_0780/09_2026/6kwx_0780.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6kwx_0780/09_2026/6kwx_0780.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6kwx_0780/09_2026/6kwx_0780.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6kwx_0780/09_2026/6kwx_0780.cif" } resolution = 3.75 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= -0.010 sd= 1.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 33 atoms to isotropic. 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: 5 Type Number sf(0) Gaussians P 14 5.49 5 S 79 5.16 5 C 9117 2.51 5 N 2414 2.21 5 O 2603 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 40 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14227 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 14147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1751, 14147 Classifications: {'peptide': 1751} Link IDs: {'PCIS': 1, 'PTRANS': 91, 'TRANS': 1658} Chain breaks: 3 Chain: "A" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 80 Unusual residues: {'IHP': 1, 'K0W': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 3.14, per 1000 atoms: 0.22 Number of scatterers: 14227 At special positions: 0 Unit cell: (133.12, 86.32, 121.68, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 79 16.00 P 14 15.00 O 2603 8.00 N 2414 7.00 C 9117 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.23 Conformation dependent library (CDL) restraints added in 731.6 milliseconds 3486 Ramachandran restraints generated. 1743 Oldfield, 0 Emsley, 1743 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3346 Finding SS restraints... Secondary structure from input PDB file: 95 helices and 2 sheets defined 66.4% alpha, 0.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.52 Creating SS restraints... Processing helix chain 'A' and resid 32 through 36 removed outlier: 3.761A pdb=" N ASN A 35 " --> pdb=" O ILE A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 66 removed outlier: 4.692A pdb=" N ALA A 46 " --> pdb=" O GLU A 42 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LEU A 50 " --> pdb=" O ALA A 46 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ALA A 62 " --> pdb=" O ASN A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 87 Processing helix chain 'A' and resid 91 through 105 removed outlier: 3.715A pdb=" N LEU A 97 " --> pdb=" O GLU A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 128 removed outlier: 4.521A pdb=" N GLY A 118 " --> pdb=" O SER A 114 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N PHE A 119 " --> pdb=" O MET A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 133 removed outlier: 3.513A pdb=" N LEU A 132 " --> pdb=" O LYS A 129 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU A 133 " --> pdb=" O LYS A 130 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 129 through 133' Processing helix chain 'A' and resid 142 through 151 Processing helix chain 'A' and resid 169 through 181 removed outlier: 3.780A pdb=" N THR A 175 " --> pdb=" O ASN A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 184 No H-bonds generated for 'chain 'A' and resid 182 through 184' Processing helix chain 'A' and resid 185 through 186 No H-bonds generated for 'chain 'A' and resid 185 through 186' Processing helix chain 'A' and resid 187 through 193 Processing helix chain 'A' and resid 196 through 200 Processing helix chain 'A' and resid 205 through 218 removed outlier: 3.544A pdb=" N LYS A 209 " --> pdb=" O VAL A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 233 removed outlier: 3.597A pdb=" N HIS A 227 " --> pdb=" O PRO A 224 " (cutoff:3.500A) removed outlier: 5.487A pdb=" N HIS A 228 " --> pdb=" O GLU A 225 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LYS A 229 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N PHE A 231 " --> pdb=" O HIS A 228 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N LYS A 232 " --> pdb=" O LYS A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 245 removed outlier: 3.673A pdb=" N VAL A 245 " --> pdb=" O LEU A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 266 removed outlier: 4.035A pdb=" N GLY A 253 " --> pdb=" O PRO A 249 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N GLN A 254 " --> pdb=" O GLN A 250 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ARG A 261 " --> pdb=" O ASN A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 287 removed outlier: 4.080A pdb=" N THR A 281 " --> pdb=" O PRO A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 319 removed outlier: 3.670A pdb=" N ILE A 313 " --> pdb=" O GLY A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 337 Processing helix chain 'A' and resid 342 through 346 removed outlier: 4.096A pdb=" N ASN A 346 " --> pdb=" O PRO A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 348 No H-bonds generated for 'chain 'A' and resid 347 through 348' Processing helix chain 'A' and resid 349 through 372 removed outlier: 3.760A pdb=" N LYS A 355 " --> pdb=" O ASN A 351 " (cutoff:3.500A) Proline residue: A 361 - end of helix Processing helix chain 'A' and resid 383 through 387 removed outlier: 3.765A pdb=" N LYS A 387 " --> pdb=" O ASP A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 409 removed outlier: 3.657A pdb=" N PHE A 396 " --> pdb=" O ASP A 392 " (cutoff:3.500A) removed outlier: 5.379A pdb=" N GLN A 402 " --> pdb=" O GLN A 398 " (cutoff:3.500A) Proline residue: A 403 - end of helix removed outlier: 4.347A pdb=" N PHE A 409 " --> pdb=" O LEU A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 428 removed outlier: 3.954A pdb=" N ALA A 420 " --> pdb=" O GLU A 416 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N MET A 427 " --> pdb=" O ASN A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 428 through 439 removed outlier: 3.560A pdb=" N VAL A 432 " --> pdb=" O ARG A 428 " (cutoff:3.500A) Proline residue: A 434 - end of helix Processing helix chain 'A' and resid 439 through 444 removed outlier: 3.691A pdb=" N ALA A 443 " --> pdb=" O ARG A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 462 removed outlier: 4.116A pdb=" N THR A 454 " --> pdb=" O PRO A 450 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ALA A 455 " --> pdb=" O HIS A 451 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N VAL A 460 " --> pdb=" O THR A 456 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLY A 462 " --> pdb=" O SER A 458 " (cutoff:3.500A) Processing helix chain 'A' and resid 463 through 468 Processing helix chain 'A' and resid 476 through 479 Processing helix chain 'A' and resid 480 through 488 Processing helix chain 'A' and resid 489 through 492 Processing helix chain 'A' and resid 496 through 508 removed outlier: 3.616A pdb=" N CYS A 500 " --> pdb=" O ASP A 496 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ILE A 502 " --> pdb=" O SER A 498 " (cutoff:3.500A) Processing helix chain 'A' and resid 530 through 538 removed outlier: 3.529A pdb=" N GLU A 535 " --> pdb=" O GLU A 531 " (cutoff:3.500A) Processing helix chain 'A' and resid 539 through 542 removed outlier: 3.504A pdb=" N GLU A 542 " --> pdb=" O ALA A 539 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 539 through 542' Processing helix chain 'A' and resid 543 through 548 Processing helix chain 'A' and resid 548 through 560 Processing helix chain 'A' and resid 583 through 596 removed outlier: 3.612A pdb=" N GLN A 596 " --> pdb=" O THR A 592 " (cutoff:3.500A) Processing helix chain 'A' and resid 598 through 616 removed outlier: 4.027A pdb=" N VAL A 604 " --> pdb=" O GLU A 600 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N HIS A 616 " --> pdb=" O PHE A 612 " (cutoff:3.500A) Processing helix chain 'A' and resid 622 through 638 removed outlier: 3.547A pdb=" N ASP A 629 " --> pdb=" O ARG A 625 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA A 633 " --> pdb=" O ASP A 629 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ALA A 634 " --> pdb=" O MET A 630 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N CYS A 638 " --> pdb=" O ALA A 634 " (cutoff:3.500A) Processing helix chain 'A' and resid 638 through 658 removed outlier: 4.102A pdb=" N LYS A 644 " --> pdb=" O GLU A 640 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LEU A 645 " --> pdb=" O GLU A 641 " (cutoff:3.500A) Proline residue: A 648 - end of helix Processing helix chain 'A' and resid 671 through 684 removed outlier: 3.810A pdb=" N TRP A 675 " --> pdb=" O LYS A 671 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N THR A 684 " --> pdb=" O LEU A 680 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 692 removed outlier: 3.716A pdb=" N LEU A 692 " --> pdb=" O ARG A 689 " (cutoff:3.500A) Processing helix chain 'A' and resid 695 through 700 Processing helix chain 'A' and resid 701 through 706 removed outlier: 3.651A pdb=" N THR A 705 " --> pdb=" O ILE A 701 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LEU A 706 " --> pdb=" O LEU A 702 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 701 through 706' Processing helix chain 'A' and resid 714 through 730 removed outlier: 3.876A pdb=" N LEU A 720 " --> pdb=" O LEU A 716 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N THR A 728 " --> pdb=" O LEU A 724 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEU A 730 " --> pdb=" O ARG A 726 " (cutoff:3.500A) Processing helix chain 'A' and resid 751 through 755 removed outlier: 3.629A pdb=" N LYS A 754 " --> pdb=" O PHE A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 773 through 788 Processing helix chain 'A' and resid 788 through 800 Processing helix chain 'A' and resid 806 through 824 removed outlier: 3.504A pdb=" N GLN A 812 " --> pdb=" O ASP A 808 " (cutoff:3.500A) Processing helix chain 'A' and resid 863 through 883 removed outlier: 3.890A pdb=" N VAL A 867 " --> pdb=" O ASN A 863 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ILE A 868 " --> pdb=" O HIS A 864 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LYS A 874 " --> pdb=" O THR A 870 " (cutoff:3.500A) Processing helix chain 'A' and resid 888 through 901 removed outlier: 3.758A pdb=" N LEU A 892 " --> pdb=" O LYS A 888 " (cutoff:3.500A) Processing helix chain 'A' and resid 907 through 925 Processing helix chain 'A' and resid 936 through 954 removed outlier: 3.617A pdb=" N VAL A 944 " --> pdb=" O LEU A 940 " (cutoff:3.500A) Processing helix chain 'A' and resid 962 through 976 removed outlier: 3.525A pdb=" N LEU A 974 " --> pdb=" O ASP A 970 " (cutoff:3.500A) Processing helix chain 'A' and resid 979 through 995 removed outlier: 3.648A pdb=" N GLN A 988 " --> pdb=" O ASN A 984 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N THR A 989 " --> pdb=" O LYS A 985 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLY A 995 " --> pdb=" O PHE A 991 " (cutoff:3.500A) Processing helix chain 'A' and resid 1004 through 1009 Processing helix chain 'A' and resid 1020 through 1033 Processing helix chain 'A' and resid 1048 through 1059 removed outlier: 3.575A pdb=" N THR A1052 " --> pdb=" O CYS A1048 " (cutoff:3.500A) Proline residue: A1054 - end of helix Processing helix chain 'A' and resid 1069 through 1087 removed outlier: 3.637A pdb=" N VAL A1073 " --> pdb=" O LYS A1069 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ARG A1074 " --> pdb=" O PRO A1070 " (cutoff:3.500A) Processing helix chain 'A' and resid 1099 through 1106 removed outlier: 3.923A pdb=" N LEU A1106 " --> pdb=" O GLU A1102 " (cutoff:3.500A) Processing helix chain 'A' and resid 1126 through 1136 Processing helix chain 'A' and resid 1137 through 1155 removed outlier: 3.847A pdb=" N GLU A1155 " --> pdb=" O LEU A1151 " (cutoff:3.500A) Processing helix chain 'A' and resid 1160 through 1173 Processing helix chain 'A' and resid 1182 through 1192 Processing helix chain 'A' and resid 1197 through 1215 Processing helix chain 'A' and resid 1246 through 1250 Processing helix chain 'A' and resid 1259 through 1265 Processing helix chain 'A' and resid 1305 through 1314 removed outlier: 3.740A pdb=" N ILE A1309 " --> pdb=" O ALA A1305 " (cutoff:3.500A) Processing helix chain 'A' and resid 1315 through 1326 removed outlier: 3.683A pdb=" N VAL A1319 " --> pdb=" O ASP A1315 " (cutoff:3.500A) Processing helix chain 'A' and resid 1338 through 1352 Processing helix chain 'A' and resid 1355 through 1368 removed outlier: 4.107A pdb=" N VAL A1359 " --> pdb=" O ALA A1355 " (cutoff:3.500A) Proline residue: A1362 - end of helix removed outlier: 3.593A pdb=" N VAL A1368 " --> pdb=" O LEU A1364 " (cutoff:3.500A) Processing helix chain 'A' and resid 1373 through 1390 Processing helix chain 'A' and resid 1391 through 1393 No H-bonds generated for 'chain 'A' and resid 1391 through 1393' Processing helix chain 'A' and resid 1394 through 1415 Proline residue: A1407 - end of helix Processing helix chain 'A' and resid 1420 through 1432 removed outlier: 4.124A pdb=" N ALA A1426 " --> pdb=" O ASN A1422 " (cutoff:3.500A) Processing helix chain 'A' and resid 1441 through 1448 Processing helix chain 'A' and resid 1459 through 1475 removed outlier: 3.613A pdb=" N GLN A1469 " --> pdb=" O LEU A1465 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLN A1475 " --> pdb=" O GLY A1471 " (cutoff:3.500A) Processing helix chain 'A' and resid 1479 through 1491 removed outlier: 3.757A pdb=" N LEU A1483 " --> pdb=" O VAL A1479 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N ARG A1485 " --> pdb=" O GLU A1481 " (cutoff:3.500A) Processing helix chain 'A' and resid 1492 through 1494 No H-bonds generated for 'chain 'A' and resid 1492 through 1494' Processing helix chain 'A' and resid 1498 through 1513 removed outlier: 3.770A pdb=" N GLU A1503 " --> pdb=" O LYS A1499 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ARG A1504 " --> pdb=" O ASN A1500 " (cutoff:3.500A) Processing helix chain 'A' and resid 1529 through 1541 removed outlier: 3.667A pdb=" N ARG A1536 " --> pdb=" O GLU A1532 " (cutoff:3.500A) Processing helix chain 'A' and resid 1542 through 1545 Processing helix chain 'A' and resid 1567 through 1585 removed outlier: 3.504A pdb=" N ALA A1583 " --> pdb=" O LYS A1579 " (cutoff:3.500A) Processing helix chain 'A' and resid 1599 through 1605 removed outlier: 3.640A pdb=" N LYS A1605 " --> pdb=" O PRO A1601 " (cutoff:3.500A) Processing helix chain 'A' and resid 1618 through 1631 removed outlier: 3.889A pdb=" N GLN A1631 " --> pdb=" O SER A1627 " (cutoff:3.500A) Processing helix chain 'A' and resid 1638 through 1649 removed outlier: 3.649A pdb=" N LEU A1643 " --> pdb=" O VAL A1639 " (cutoff:3.500A) Processing helix chain 'A' and resid 1654 through 1671 removed outlier: 3.687A pdb=" N LEU A1662 " --> pdb=" O ARG A1658 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N PHE A1670 " --> pdb=" O GLN A1666 " (cutoff:3.500A) Processing helix chain 'A' and resid 1672 through 1678 removed outlier: 4.172A pdb=" N PHE A1676 " --> pdb=" O ASN A1672 " (cutoff:3.500A) Processing helix chain 'A' and resid 1679 through 1694 removed outlier: 3.710A pdb=" N LYS A1684 " --> pdb=" O GLU A1680 " (cutoff:3.500A) Processing helix chain 'A' and resid 1698 through 1715 Processing helix chain 'A' and resid 1721 through 1733 removed outlier: 3.605A pdb=" N LYS A1733 " --> pdb=" O GLU A1729 " (cutoff:3.500A) Processing helix chain 'A' and resid 1755 through 1772 Processing helix chain 'A' and resid 1780 through 1790 removed outlier: 3.580A pdb=" N ASN A1787 " --> pdb=" O GLN A1783 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU A1788 " --> pdb=" O LEU A1784 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA A1790 " --> pdb=" O MET A1786 " (cutoff:3.500A) Processing helix chain 'A' and resid 1797 through 1813 removed outlier: 3.914A pdb=" N THR A1812 " --> pdb=" O ASN A1808 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 732 through 733 Processing sheet with id=AA2, first strand: chain 'A' and resid 1240 through 1241 removed outlier: 6.914A pdb=" N ALA A1240 " --> pdb=" O THR A1523 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 685 hydrogen bonds defined for protein. 2007 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: 2.80 Time building geometry restraints manager: 1.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3151 1.33 - 1.45: 3074 1.45 - 1.57: 8196 1.57 - 1.69: 17 1.69 - 1.81: 118 Bond restraints: 14556 Sorted by residual: bond pdb=" C VAL A 276 " pdb=" N PRO A 277 " ideal model delta sigma weight residual 1.337 1.376 -0.039 9.80e-03 1.04e+04 1.62e+01 bond pdb=" C GLN A 789 " pdb=" N PRO A 790 " ideal model delta sigma weight residual 1.335 1.384 -0.049 1.36e-02 5.41e+03 1.28e+01 bond pdb=" C TRP A 164 " pdb=" N PHE A 165 " ideal model delta sigma weight residual 1.331 1.281 0.050 1.48e-02 4.57e+03 1.14e+01 bond pdb=" O12 IHP A1902 " pdb=" P2 IHP A1902 " ideal model delta sigma weight residual 1.675 1.610 0.065 2.00e-02 2.50e+03 1.07e+01 bond pdb=" O15 IHP A1902 " pdb=" P5 IHP A1902 " ideal model delta sigma weight residual 1.675 1.610 0.065 2.00e-02 2.50e+03 1.06e+01 ... (remaining 14551 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.84: 19138 3.84 - 7.67: 507 7.67 - 11.51: 93 11.51 - 15.34: 22 15.34 - 19.18: 5 Bond angle restraints: 19765 Sorted by residual: angle pdb=" N THR A 303 " pdb=" CA THR A 303 " pdb=" C THR A 303 " ideal model delta sigma weight residual 111.28 124.44 -13.16 1.09e+00 8.42e-01 1.46e+02 angle pdb=" N GLU A1270 " pdb=" CA GLU A1270 " pdb=" C GLU A1270 " ideal model delta sigma weight residual 111.36 122.77 -11.41 1.09e+00 8.42e-01 1.10e+02 angle pdb=" C ASN A1112 " pdb=" N PRO A1113 " pdb=" CA PRO A1113 " ideal model delta sigma weight residual 119.84 131.70 -11.86 1.25e+00 6.40e-01 9.00e+01 angle pdb=" N ILE A1125 " pdb=" CA ILE A1125 " pdb=" C ILE A1125 " ideal model delta sigma weight residual 112.83 103.93 8.90 9.90e-01 1.02e+00 8.09e+01 angle pdb=" N LEU A1673 " pdb=" CA LEU A1673 " pdb=" C LEU A1673 " ideal model delta sigma weight residual 111.28 118.95 -7.67 1.09e+00 8.42e-01 4.95e+01 ... (remaining 19760 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.79: 8079 16.79 - 33.57: 590 33.57 - 50.36: 150 50.36 - 67.15: 21 67.15 - 83.94: 13 Dihedral angle restraints: 8853 sinusoidal: 3716 harmonic: 5137 Sorted by residual: dihedral pdb=" CA ASP A 670 " pdb=" C ASP A 670 " pdb=" N LYS A 671 " pdb=" CA LYS A 671 " ideal model delta harmonic sigma weight residual 180.00 -150.64 -29.36 0 5.00e+00 4.00e-02 3.45e+01 dihedral pdb=" CA TYR A 750 " pdb=" C TYR A 750 " pdb=" N PHE A 751 " pdb=" CA PHE A 751 " ideal model delta harmonic sigma weight residual -180.00 -150.73 -29.27 0 5.00e+00 4.00e-02 3.43e+01 dihedral pdb=" CA GLY A 713 " pdb=" C GLY A 713 " pdb=" N TYR A 714 " pdb=" CA TYR A 714 " ideal model delta harmonic sigma weight residual 180.00 150.73 29.27 0 5.00e+00 4.00e-02 3.43e+01 ... (remaining 8850 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.005: 2241 1.005 - 2.010: 0 2.010 - 3.016: 0 3.016 - 4.021: 0 4.021 - 5.026: 2 Chirality restraints: 2243 Sorted by residual: chirality pdb=" C2 IHP A1902 " pdb=" C1 IHP A1902 " pdb=" C3 IHP A1902 " pdb=" O12 IHP A1902 " both_signs ideal model delta sigma weight residual False -2.52 2.51 -5.03 2.00e-01 2.50e+01 6.32e+02 chirality pdb=" C3 IHP A1902 " pdb=" C2 IHP A1902 " pdb=" C4 IHP A1902 " pdb=" O13 IHP A1902 " both_signs ideal model delta sigma weight residual False -2.34 2.53 -4.87 2.00e-01 2.50e+01 5.92e+02 chirality pdb=" CB VAL A 463 " pdb=" CA VAL A 463 " pdb=" CG1 VAL A 463 " pdb=" CG2 VAL A 463 " both_signs ideal model delta sigma weight residual False -2.63 -2.07 -0.56 2.00e-01 2.50e+01 7.91e+00 ... (remaining 2240 not shown) Planarity restraints: 2483 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR A 373 " -0.025 2.00e-02 2.50e+03 5.20e-02 2.70e+01 pdb=" C TYR A 373 " 0.090 2.00e-02 2.50e+03 pdb=" O TYR A 373 " -0.034 2.00e-02 2.50e+03 pdb=" N LYS A 374 " -0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A1482 " -0.024 2.00e-02 2.50e+03 4.75e-02 2.25e+01 pdb=" C LEU A1482 " 0.082 2.00e-02 2.50e+03 pdb=" O LEU A1482 " -0.030 2.00e-02 2.50e+03 pdb=" N LEU A1483 " -0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 314 " 0.042 2.00e-02 2.50e+03 2.96e-02 2.19e+01 pdb=" CG TRP A 314 " -0.076 2.00e-02 2.50e+03 pdb=" CD1 TRP A 314 " 0.031 2.00e-02 2.50e+03 pdb=" CD2 TRP A 314 " -0.008 2.00e-02 2.50e+03 pdb=" NE1 TRP A 314 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 314 " -0.007 2.00e-02 2.50e+03 pdb=" CE3 TRP A 314 " -0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 314 " 0.006 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 314 " 0.008 2.00e-02 2.50e+03 pdb=" CH2 TRP A 314 " 0.008 2.00e-02 2.50e+03 ... (remaining 2480 not shown) Histogram of nonbonded interaction distances: 1.63 - 2.28: 21 2.28 - 2.94: 5756 2.94 - 3.59: 21138 3.59 - 4.25: 35172 4.25 - 4.90: 56976 Nonbonded interactions: 119063 Sorted by model distance: nonbonded pdb=" O LYS A 324 " pdb=" N VAL A 326 " model vdw 1.627 3.120 nonbonded pdb=" OG SER A 975 " pdb=" SG CYS A1030 " model vdw 1.747 3.400 nonbonded pdb=" OH TYR A1286 " pdb=" O42 IHP A1902 " model vdw 1.874 3.040 nonbonded pdb=" NH2 ARG A 300 " pdb=" O GLN A1631 " model vdw 1.911 3.120 nonbonded pdb=" O THR A 887 " pdb=" CE1 PHE A 891 " model vdw 1.964 3.340 ... (remaining 119058 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.010 Extract box with map and model: 0.190 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 14.730 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7235 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.014 0.776 14558 Z= 0.895 Angle : 1.576 19.179 19765 Z= 0.820 Chirality : 0.168 5.026 2243 Planarity : 0.009 0.070 2483 Dihedral : 13.148 83.936 5507 Min Nonbonded Distance : 1.627 Molprobity Statistics. All-atom Clashscore : 13.84 Ramachandran Plot: Outliers : 0.34 % Allowed : 9.01 % Favored : 90.65 % Rotamer: Outliers : 1.69 % Allowed : 7.72 % Favored : 90.58 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 1.09 % 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: -4.69 (0.15), residues: 1743 helix: -3.00 (0.11), residues: 1072 sheet: None (None), residues: 0 loop : -3.07 (0.20), residues: 671 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.002 ARG A1217 TYR 0.052 0.004 TYR A 997 PHE 0.048 0.004 PHE A 214 TRP 0.076 0.005 TRP A 314 HIS 0.028 0.004 HIS A 227 Details of bonding type rmsd/Z covalent geometry : bond 0.01137 / 0.47 (14556) covalent geometry : angle 1.57590 / 0.82 (19765) hydrogen bonds : bond 0.23092 / 14.94 ( 685) hydrogen bonds : angle 8.63247 / 6.04 ( 2007) Misc. bond : bond 0.64963 / 31.90 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3486 Ramachandran restraints generated. 1743 Oldfield, 0 Emsley, 1743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3486 Ramachandran restraints generated. 1743 Oldfield, 0 Emsley, 1743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 647 residues out of total 1593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 620 time to evaluate : 0.574 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 146 TYR cc_start: 0.7763 (t80) cc_final: 0.7554 (t80) REVERT: A 172 ILE cc_start: 0.8917 (OUTLIER) cc_final: 0.8197 (mm) REVERT: A 406 LEU cc_start: 0.8453 (tp) cc_final: 0.8147 (mt) REVERT: A 729 THR cc_start: 0.7906 (m) cc_final: 0.7665 (m) REVERT: A 843 MET cc_start: 0.7303 (mtp) cc_final: 0.7054 (mtp) REVERT: A 1015 ASP cc_start: 0.7483 (p0) cc_final: 0.7254 (p0) REVERT: A 1116 ASN cc_start: 0.7435 (t160) cc_final: 0.6953 (p0) REVERT: A 1132 GLN cc_start: 0.8018 (tp40) cc_final: 0.7761 (tp40) REVERT: A 1255 THR cc_start: 0.7440 (t) cc_final: 0.7105 (m) REVERT: A 1259 THR cc_start: 0.8599 (p) cc_final: 0.8316 (p) REVERT: A 1260 LYS cc_start: 0.8467 (tmtt) cc_final: 0.8170 (tptt) REVERT: A 1500 ASN cc_start: 0.5560 (p0) cc_final: 0.4750 (t0) outliers start: 27 outliers final: 6 residues processed: 637 average time/residue: 0.1301 time to fit residues: 119.8438 Evaluate side-chains 331 residues out of total 1593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 324 time to evaluate : 0.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 ILE Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 940 LEU Chi-restraints excluded: chain A residue 1443 LEU Chi-restraints excluded: chain A residue 1452 LEU Chi-restraints excluded: chain A residue 1468 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 0.0070 chunk 103 optimal weight: 8.9990 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 0.9980 chunk 149 optimal weight: 3.9990 overall best weight: 1.1602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 35 ASN A 51 GLN A 125 ASN A 208 GLN A 250 GLN ** A 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 304 ASN A 310 HIS A 527 ASN A 596 GLN A 607 GLN A 697 GLN A 703 GLN ** A 719 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 722 HIS A 819 ASN A 838 ASN A 864 HIS A 904 GLN A1021 GLN A1084 HIS A1109 GLN A1116 ASN A1132 GLN A1142 ASN A1246 ASN A1250 HIS A1307 GLN A1312 HIS A1351 ASN A1363 HIS A1569 GLN A1613 ASN A1679 ASN A1787 ASN A1791 HIS Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.145986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.121094 restraints weight = 24304.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.125478 restraints weight = 12091.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.128394 restraints weight = 7451.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.130298 restraints weight = 5268.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.131631 restraints weight = 4122.537| |-----------------------------------------------------------------------------| r_work (final): 0.3653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 moved from start: 0.3848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 14558 Z= 0.176 Angle : 0.896 12.718 19765 Z= 0.439 Chirality : 0.051 0.614 2243 Planarity : 0.007 0.061 2483 Dihedral : 8.825 58.251 1970 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 13.60 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.06 % Favored : 92.89 % Rotamer: Outliers : 5.02 % Allowed : 15.94 % Favored : 79.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.79 (0.18), residues: 1743 helix: -1.24 (0.15), residues: 1084 sheet: None (None), residues: 0 loop : -2.79 (0.21), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 261 TYR 0.035 0.002 TYR A 714 PHE 0.032 0.002 PHE A 602 TRP 0.027 0.002 TRP A 314 HIS 0.008 0.001 HIS A 227 Details of bonding type rmsd/Z covalent geometry : bond 0.00397 / 0.18 (14556) covalent geometry : angle 0.89569 / 0.44 (19765) hydrogen bonds : bond 0.04762 / 3.04 ( 685) hydrogen bonds : angle 4.98017 / 3.51 ( 2007) Misc. bond : bond 0.00143 / 0.07 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3486 Ramachandran restraints generated. 1743 Oldfield, 0 Emsley, 1743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3486 Ramachandran restraints generated. 1743 Oldfield, 0 Emsley, 1743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 493 residues out of total 1593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 413 time to evaluate : 0.634 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 TRP cc_start: 0.7983 (t60) cc_final: 0.7698 (t60) REVERT: A 86 TYR cc_start: 0.8359 (m-80) cc_final: 0.8058 (m-10) REVERT: A 172 ILE cc_start: 0.8310 (OUTLIER) cc_final: 0.7602 (mm) REVERT: A 302 LEU cc_start: 0.6525 (OUTLIER) cc_final: 0.5849 (mp) REVERT: A 399 CYS cc_start: 0.8388 (p) cc_final: 0.8027 (p) REVERT: A 501 MET cc_start: 0.8460 (mmm) cc_final: 0.8172 (mmt) REVERT: A 516 LEU cc_start: 0.8839 (OUTLIER) cc_final: 0.8575 (pp) REVERT: A 593 ILE cc_start: 0.8785 (mm) cc_final: 0.8335 (mt) REVERT: A 649 HIS cc_start: 0.6329 (t70) cc_final: 0.5737 (t-90) REVERT: A 828 LEU cc_start: 0.9268 (OUTLIER) cc_final: 0.8877 (pp) REVERT: A 899 ASP cc_start: 0.8514 (m-30) cc_final: 0.8154 (m-30) REVERT: A 903 PHE cc_start: 0.8768 (t80) cc_final: 0.8551 (t80) REVERT: A 924 SER cc_start: 0.8964 (m) cc_final: 0.8547 (t) REVERT: A 926 GLU cc_start: 0.8682 (tp30) cc_final: 0.8030 (tt0) REVERT: A 961 LYS cc_start: 0.8786 (mttt) cc_final: 0.8363 (mmtp) REVERT: A 966 ASP cc_start: 0.8192 (m-30) cc_final: 0.7592 (t0) REVERT: A 1029 TYR cc_start: 0.8241 (OUTLIER) cc_final: 0.6897 (t80) REVERT: A 1043 LEU cc_start: 0.9000 (OUTLIER) cc_final: 0.8743 (mp) REVERT: A 1045 ASP cc_start: 0.7877 (m-30) cc_final: 0.7521 (m-30) REVERT: A 1116 ASN cc_start: 0.7613 (t0) cc_final: 0.6956 (p0) REVERT: A 1132 GLN cc_start: 0.8801 (tp-100) cc_final: 0.8240 (tp-100) REVERT: A 1242 ASP cc_start: 0.7558 (m-30) cc_final: 0.7248 (m-30) REVERT: A 1260 LYS cc_start: 0.8054 (tmtt) cc_final: 0.7754 (tptt) REVERT: A 1302 MET cc_start: 0.7991 (mmm) cc_final: 0.7628 (mmt) REVERT: A 1326 LEU cc_start: 0.8448 (OUTLIER) cc_final: 0.8209 (tt) REVERT: A 1338 ASN cc_start: 0.7753 (t0) cc_final: 0.7056 (t0) REVERT: A 1395 PHE cc_start: 0.7392 (t80) cc_final: 0.7166 (t80) REVERT: A 1459 PHE cc_start: 0.6905 (t80) cc_final: 0.6555 (t80) REVERT: A 1477 TRP cc_start: 0.9010 (OUTLIER) cc_final: 0.8374 (t60) REVERT: A 1500 ASN cc_start: 0.7524 (p0) cc_final: 0.6095 (t0) REVERT: A 1519 LEU cc_start: 0.8868 (OUTLIER) cc_final: 0.8661 (tt) REVERT: A 1621 ASP cc_start: 0.8358 (t0) cc_final: 0.8156 (t0) REVERT: A 1704 MET cc_start: 0.8559 (mmm) cc_final: 0.8237 (mmt) REVERT: A 1786 MET cc_start: 0.5446 (tpp) cc_final: 0.5232 (tpp) outliers start: 80 outliers final: 33 residues processed: 463 average time/residue: 0.1089 time to fit residues: 77.5542 Evaluate side-chains 346 residues out of total 1593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 304 time to evaluate : 0.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 ASP Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 155 SER Chi-restraints excluded: chain A residue 172 ILE Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 378 TRP Chi-restraints excluded: chain A residue 392 ASP Chi-restraints excluded: chain A residue 395 ASP Chi-restraints excluded: chain A residue 512 THR Chi-restraints excluded: chain A residue 516 LEU Chi-restraints excluded: chain A residue 523 LEU Chi-restraints excluded: chain A residue 647 VAL Chi-restraints excluded: chain A residue 715 THR Chi-restraints excluded: chain A residue 719 ASN Chi-restraints excluded: chain A residue 724 LEU Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 827 LEU Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 890 LEU Chi-restraints excluded: chain A residue 939 LEU Chi-restraints excluded: chain A residue 940 LEU Chi-restraints excluded: chain A residue 1029 TYR Chi-restraints excluded: chain A residue 1043 LEU Chi-restraints excluded: chain A residue 1049 ILE Chi-restraints excluded: chain A residue 1147 VAL Chi-restraints excluded: chain A residue 1150 LEU Chi-restraints excluded: chain A residue 1177 ASP Chi-restraints excluded: chain A residue 1295 LEU Chi-restraints excluded: chain A residue 1326 LEU Chi-restraints excluded: chain A residue 1344 LEU Chi-restraints excluded: chain A residue 1401 LEU Chi-restraints excluded: chain A residue 1433 GLU Chi-restraints excluded: chain A residue 1443 LEU Chi-restraints excluded: chain A residue 1477 TRP Chi-restraints excluded: chain A residue 1519 LEU Chi-restraints excluded: chain A residue 1576 THR Chi-restraints excluded: chain A residue 1593 VAL Chi-restraints excluded: chain A residue 1602 LEU Chi-restraints excluded: chain A residue 1627 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 125 optimal weight: 6.9990 chunk 96 optimal weight: 4.9990 chunk 107 optimal weight: 7.9990 chunk 172 optimal weight: 0.9990 chunk 100 optimal weight: 7.9990 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 3.9990 chunk 111 optimal weight: 7.9990 chunk 32 optimal weight: 5.9990 chunk 115 optimal weight: 0.5980 chunk 83 optimal weight: 6.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 51 GLN A 250 GLN ** A 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 676 ASN ** A 719 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 947 GLN A1165 HIS A1194 ASN A1246 ASN A1569 GLN ** A1631 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1666 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.138181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.113477 restraints weight = 25059.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.117567 restraints weight = 12584.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.120285 restraints weight = 7851.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.121978 restraints weight = 5649.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.123291 restraints weight = 4512.893| |-----------------------------------------------------------------------------| r_work (final): 0.3542 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.4976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 14558 Z= 0.190 Angle : 0.841 12.927 19765 Z= 0.410 Chirality : 0.048 0.318 2243 Planarity : 0.005 0.045 2483 Dihedral : 7.920 54.982 1966 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 13.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.11 % Favored : 92.89 % Rotamer: Outliers : 5.65 % Allowed : 18.46 % Favored : 75.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -1.77 (0.20), residues: 1743 helix: -0.42 (0.16), residues: 1099 sheet: None (None), residues: 0 loop : -2.46 (0.23), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A1299 TYR 0.029 0.002 TYR A 714 PHE 0.025 0.002 PHE A1728 TRP 0.018 0.002 TRP A1477 HIS 0.006 0.001 HIS A1044 Details of bonding type rmsd/Z covalent geometry : bond 0.00453 / 0.19 (14556) covalent geometry : angle 0.84111 / 0.41 (19765) hydrogen bonds : bond 0.04366 / 2.84 ( 685) hydrogen bonds : angle 4.54147 / 3.21 ( 2007) Misc. bond : bond 0.00093 / 0.05 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3486 Ramachandran restraints generated. 1743 Oldfield, 0 Emsley, 1743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3486 Ramachandran restraints generated. 1743 Oldfield, 0 Emsley, 1743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 454 residues out of total 1593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 364 time to evaluate : 0.559 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 195 GLU cc_start: 0.6949 (tm-30) cc_final: 0.6720 (tm-30) REVERT: A 246 GLN cc_start: 0.7901 (OUTLIER) cc_final: 0.7667 (pm20) REVERT: A 353 LEU cc_start: 0.9050 (OUTLIER) cc_final: 0.8553 (mm) REVERT: A 399 CYS cc_start: 0.8579 (p) cc_final: 0.8241 (p) REVERT: A 481 MET cc_start: 0.8664 (tmm) cc_final: 0.8099 (tmm) REVERT: A 501 MET cc_start: 0.8369 (mmm) cc_final: 0.7889 (mmt) REVERT: A 621 ARG cc_start: 0.7552 (mtm180) cc_final: 0.7173 (ttm-80) REVERT: A 649 HIS cc_start: 0.6236 (t70) cc_final: 0.5667 (t-90) REVERT: A 751 PHE cc_start: 0.6590 (OUTLIER) cc_final: 0.4651 (m-10) REVERT: A 828 LEU cc_start: 0.9285 (OUTLIER) cc_final: 0.8988 (pp) REVERT: A 903 PHE cc_start: 0.8707 (t80) cc_final: 0.8502 (t80) REVERT: A 924 SER cc_start: 0.9087 (m) cc_final: 0.8739 (t) REVERT: A 926 GLU cc_start: 0.8658 (tp30) cc_final: 0.8173 (tt0) REVERT: A 961 LYS cc_start: 0.8667 (mttt) cc_final: 0.8173 (mmmt) REVERT: A 1021 GLN cc_start: 0.8518 (tt0) cc_final: 0.8293 (tt0) REVERT: A 1029 TYR cc_start: 0.8339 (OUTLIER) cc_final: 0.7086 (t80) REVERT: A 1043 LEU cc_start: 0.9149 (OUTLIER) cc_final: 0.8947 (mm) REVERT: A 1045 ASP cc_start: 0.7708 (m-30) cc_final: 0.7020 (m-30) REVERT: A 1067 LEU cc_start: 0.7666 (pt) cc_final: 0.7019 (tt) REVERT: A 1116 ASN cc_start: 0.7560 (t0) cc_final: 0.7018 (p0) REVERT: A 1132 GLN cc_start: 0.8859 (tp-100) cc_final: 0.8330 (tp-100) REVERT: A 1260 LYS cc_start: 0.8271 (tmtt) cc_final: 0.7909 (tptt) REVERT: A 1302 MET cc_start: 0.7851 (mmm) cc_final: 0.7336 (mmt) REVERT: A 1338 ASN cc_start: 0.8259 (t0) cc_final: 0.7692 (t0) REVERT: A 1503 GLU cc_start: 0.7879 (tt0) cc_final: 0.7519 (mt-10) REVERT: A 1519 LEU cc_start: 0.8963 (OUTLIER) cc_final: 0.8760 (tt) outliers start: 90 outliers final: 49 residues processed: 420 average time/residue: 0.1020 time to fit residues: 66.9285 Evaluate side-chains 364 residues out of total 1593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 308 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 GLN Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 155 SER Chi-restraints excluded: chain A residue 168 SER Chi-restraints excluded: chain A residue 172 ILE Chi-restraints excluded: chain A residue 203 PHE Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 246 GLN Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 378 TRP Chi-restraints excluded: chain A residue 392 ASP Chi-restraints excluded: chain A residue 395 ASP Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 523 LEU Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 583 GLU Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 647 VAL Chi-restraints excluded: chain A residue 684 THR Chi-restraints excluded: chain A residue 715 THR Chi-restraints excluded: chain A residue 719 ASN Chi-restraints excluded: chain A residue 724 LEU Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain A residue 731 ILE Chi-restraints excluded: chain A residue 743 PHE Chi-restraints excluded: chain A residue 751 PHE Chi-restraints excluded: chain A residue 784 LEU Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 827 LEU Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 890 LEU Chi-restraints excluded: chain A residue 940 LEU Chi-restraints excluded: chain A residue 1020 THR Chi-restraints excluded: chain A residue 1029 TYR Chi-restraints excluded: chain A residue 1043 LEU Chi-restraints excluded: chain A residue 1147 VAL Chi-restraints excluded: chain A residue 1150 LEU Chi-restraints excluded: chain A residue 1177 ASP Chi-restraints excluded: chain A residue 1259 THR Chi-restraints excluded: chain A residue 1295 LEU Chi-restraints excluded: chain A residue 1341 ARG Chi-restraints excluded: chain A residue 1401 LEU Chi-restraints excluded: chain A residue 1433 GLU Chi-restraints excluded: chain A residue 1443 LEU Chi-restraints excluded: chain A residue 1477 TRP Chi-restraints excluded: chain A residue 1519 LEU Chi-restraints excluded: chain A residue 1576 THR Chi-restraints excluded: chain A residue 1593 VAL Chi-restraints excluded: chain A residue 1602 LEU Chi-restraints excluded: chain A residue 1626 LEU Chi-restraints excluded: chain A residue 1627 SER Chi-restraints excluded: chain A residue 1666 GLN Chi-restraints excluded: chain A residue 1694 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 166 optimal weight: 3.9990 chunk 128 optimal weight: 4.9990 chunk 153 optimal weight: 3.9990 chunk 68 optimal weight: 2.9990 chunk 45 optimal weight: 0.9990 chunk 148 optimal weight: 5.9990 chunk 13 optimal weight: 2.9990 chunk 117 optimal weight: 0.0770 chunk 70 optimal weight: 0.0970 chunk 155 optimal weight: 0.5980 chunk 3 optimal weight: 8.9990 overall best weight: 0.9540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 58 ASN A 257 ASN ** A 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 719 ASN A 812 GLN A 819 ASN A1156 GLN A1569 GLN ** A1631 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1808 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.140099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.115352 restraints weight = 24783.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.119470 restraints weight = 12526.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.122226 restraints weight = 7827.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.124001 restraints weight = 5614.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.125229 restraints weight = 4446.041| |-----------------------------------------------------------------------------| r_work (final): 0.3562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.5534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14558 Z= 0.147 Angle : 0.812 10.841 19765 Z= 0.389 Chirality : 0.046 0.259 2243 Planarity : 0.005 0.086 2483 Dihedral : 7.513 53.104 1966 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 13.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.06 % Favored : 92.94 % Rotamer: Outliers : 5.02 % Allowed : 21.66 % Favored : 73.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.33 (0.20), residues: 1743 helix: -0.11 (0.16), residues: 1093 sheet: None (None), residues: 0 loop : -2.17 (0.24), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 726 TYR 0.030 0.002 TYR A 714 PHE 0.021 0.002 PHE A 990 TRP 0.020 0.002 TRP A1477 HIS 0.005 0.001 HIS A 227 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.15 (14556) covalent geometry : angle 0.81190 / 0.39 (19765) hydrogen bonds : bond 0.03961 / 2.56 ( 685) hydrogen bonds : angle 4.42683 / 3.15 ( 2007) Misc. bond : bond 0.00067 / 0.04 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3486 Ramachandran restraints generated. 1743 Oldfield, 0 Emsley, 1743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3486 Ramachandran restraints generated. 1743 Oldfield, 0 Emsley, 1743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 1593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 339 time to evaluate : 0.463 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 MET cc_start: 0.8497 (ttp) cc_final: 0.8039 (tmm) REVERT: A 195 GLU cc_start: 0.7008 (tm-30) cc_final: 0.6724 (tm-30) REVERT: A 353 LEU cc_start: 0.8941 (OUTLIER) cc_final: 0.8449 (mm) REVERT: A 481 MET cc_start: 0.8720 (tmm) cc_final: 0.8255 (tmm) REVERT: A 531 GLU cc_start: 0.7389 (tm-30) cc_final: 0.6983 (tm-30) REVERT: A 535 GLU cc_start: 0.8280 (pt0) cc_final: 0.8009 (pt0) REVERT: A 621 ARG cc_start: 0.7534 (mtm180) cc_final: 0.7152 (ttm-80) REVERT: A 649 HIS cc_start: 0.6186 (t70) cc_final: 0.5817 (t70) REVERT: A 730 LEU cc_start: 0.7415 (OUTLIER) cc_final: 0.7122 (mp) REVERT: A 751 PHE cc_start: 0.6651 (OUTLIER) cc_final: 0.4692 (m-10) REVERT: A 828 LEU cc_start: 0.9170 (OUTLIER) cc_final: 0.8908 (pp) REVERT: A 924 SER cc_start: 0.9054 (m) cc_final: 0.8794 (t) REVERT: A 926 GLU cc_start: 0.8675 (tp30) cc_final: 0.8213 (tt0) REVERT: A 959 GLU cc_start: 0.7047 (tp30) cc_final: 0.6444 (tp30) REVERT: A 961 LYS cc_start: 0.8670 (mttt) cc_final: 0.7951 (mmtp) REVERT: A 966 ASP cc_start: 0.8390 (m-30) cc_final: 0.7624 (t70) REVERT: A 1021 GLN cc_start: 0.8482 (tt0) cc_final: 0.8232 (tt0) REVERT: A 1029 TYR cc_start: 0.8214 (OUTLIER) cc_final: 0.7114 (t80) REVERT: A 1043 LEU cc_start: 0.9295 (OUTLIER) cc_final: 0.8988 (mp) REVERT: A 1067 LEU cc_start: 0.7853 (pt) cc_final: 0.7253 (tt) REVERT: A 1116 ASN cc_start: 0.7509 (t0) cc_final: 0.6933 (p0) REVERT: A 1191 GLU cc_start: 0.8214 (tp30) cc_final: 0.7859 (tp30) REVERT: A 1283 MET cc_start: 0.7430 (tpt) cc_final: 0.7180 (tpt) REVERT: A 1302 MET cc_start: 0.7716 (mmm) cc_final: 0.7327 (mmt) REVERT: A 1338 ASN cc_start: 0.8063 (t0) cc_final: 0.7473 (t0) REVERT: A 1393 TRP cc_start: 0.8904 (m-10) cc_final: 0.8551 (m100) REVERT: A 1488 LYS cc_start: 0.9071 (mmmm) cc_final: 0.8561 (mtpt) REVERT: A 1514 MET cc_start: 0.8390 (ttp) cc_final: 0.7821 (ptm) REVERT: A 1519 LEU cc_start: 0.8928 (OUTLIER) cc_final: 0.8711 (tt) REVERT: A 1716 ASN cc_start: 0.8534 (m-40) cc_final: 0.7604 (t0) REVERT: A 1717 PHE cc_start: 0.8557 (t80) cc_final: 0.8210 (t80) outliers start: 80 outliers final: 43 residues processed: 391 average time/residue: 0.0983 time to fit residues: 60.2544 Evaluate side-chains 349 residues out of total 1593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 299 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 GLU Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 155 SER Chi-restraints excluded: chain A residue 167 ASN Chi-restraints excluded: chain A residue 172 ILE Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 203 PHE Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 378 TRP Chi-restraints excluded: chain A residue 395 ASP Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 583 GLU Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 684 THR Chi-restraints excluded: chain A residue 715 THR Chi-restraints excluded: chain A residue 719 ASN Chi-restraints excluded: chain A residue 724 LEU Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain A residue 730 LEU Chi-restraints excluded: chain A residue 743 PHE Chi-restraints excluded: chain A residue 751 PHE Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 827 LEU Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 890 LEU Chi-restraints excluded: chain A residue 939 LEU Chi-restraints excluded: chain A residue 940 LEU Chi-restraints excluded: chain A residue 994 LEU Chi-restraints excluded: chain A residue 1020 THR Chi-restraints excluded: chain A residue 1028 LEU Chi-restraints excluded: chain A residue 1029 TYR Chi-restraints excluded: chain A residue 1043 LEU Chi-restraints excluded: chain A residue 1147 VAL Chi-restraints excluded: chain A residue 1177 ASP Chi-restraints excluded: chain A residue 1193 LEU Chi-restraints excluded: chain A residue 1401 LEU Chi-restraints excluded: chain A residue 1433 GLU Chi-restraints excluded: chain A residue 1477 TRP Chi-restraints excluded: chain A residue 1519 LEU Chi-restraints excluded: chain A residue 1523 THR Chi-restraints excluded: chain A residue 1569 GLN Chi-restraints excluded: chain A residue 1576 THR Chi-restraints excluded: chain A residue 1588 SER Chi-restraints excluded: chain A residue 1593 VAL Chi-restraints excluded: chain A residue 1626 LEU Chi-restraints excluded: chain A residue 1694 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 88 optimal weight: 6.9990 chunk 104 optimal weight: 0.9980 chunk 153 optimal weight: 0.8980 chunk 152 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 chunk 55 optimal weight: 0.7980 chunk 115 optimal weight: 8.9990 chunk 144 optimal weight: 0.8980 chunk 32 optimal weight: 6.9990 chunk 145 optimal weight: 6.9990 chunk 63 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 51 GLN A 902 GLN A 919 ASN A1044 HIS ** A1338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1569 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1631 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1666 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.146705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.121844 restraints weight = 25262.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.126114 restraints weight = 12784.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.128953 restraints weight = 7976.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.130815 restraints weight = 5699.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.132105 restraints weight = 4501.988| |-----------------------------------------------------------------------------| r_work (final): 0.3646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.5960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 14558 Z= 0.146 Angle : 0.789 10.635 19765 Z= 0.379 Chirality : 0.047 0.310 2243 Planarity : 0.005 0.047 2483 Dihedral : 7.208 53.889 1964 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 13.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.66 % Favored : 93.34 % Rotamer: Outliers : 5.02 % Allowed : 23.29 % Favored : 71.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 0.00 % Twisted Proline : 1.09 % Twisted General : 0.06 % 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: -1.06 (0.20), residues: 1743 helix: 0.07 (0.16), residues: 1100 sheet: None (None), residues: 0 loop : -2.01 (0.24), residues: 643 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 472 TYR 0.030 0.002 TYR A 714 PHE 0.021 0.002 PHE A 590 TRP 0.020 0.001 TRP A1477 HIS 0.005 0.001 HIS A 227 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.15 (14556) covalent geometry : angle 0.78916 / 0.38 (19765) hydrogen bonds : bond 0.03823 / 2.50 ( 685) hydrogen bonds : angle 4.38012 / 3.13 ( 2007) Misc. bond : bond 0.00068 / 0.04 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3486 Ramachandran restraints generated. 1743 Oldfield, 0 Emsley, 1743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3486 Ramachandran restraints generated. 1743 Oldfield, 0 Emsley, 1743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 1593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 323 time to evaluate : 0.519 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 172 ILE cc_start: 0.7925 (OUTLIER) cc_final: 0.6881 (mm) REVERT: A 195 GLU cc_start: 0.7007 (tm-30) cc_final: 0.6695 (tm-30) REVERT: A 353 LEU cc_start: 0.8912 (OUTLIER) cc_final: 0.8430 (mm) REVERT: A 481 MET cc_start: 0.8690 (tmm) cc_final: 0.8206 (tmm) REVERT: A 501 MET cc_start: 0.8027 (mmm) cc_final: 0.7782 (mmm) REVERT: A 531 GLU cc_start: 0.7441 (tm-30) cc_final: 0.6983 (tm-30) REVERT: A 535 GLU cc_start: 0.8231 (pt0) cc_final: 0.7889 (pt0) REVERT: A 621 ARG cc_start: 0.7437 (mtm180) cc_final: 0.7073 (ttt-90) REVERT: A 649 HIS cc_start: 0.6117 (t70) cc_final: 0.5832 (t70) REVERT: A 751 PHE cc_start: 0.6337 (OUTLIER) cc_final: 0.4646 (m-80) REVERT: A 828 LEU cc_start: 0.9232 (OUTLIER) cc_final: 0.8931 (pp) REVERT: A 924 SER cc_start: 0.9096 (m) cc_final: 0.8854 (t) REVERT: A 926 GLU cc_start: 0.8581 (tp30) cc_final: 0.8189 (tt0) REVERT: A 1021 GLN cc_start: 0.8433 (tt0) cc_final: 0.8197 (tt0) REVERT: A 1029 TYR cc_start: 0.8462 (OUTLIER) cc_final: 0.6963 (t80) REVERT: A 1043 LEU cc_start: 0.9257 (OUTLIER) cc_final: 0.8958 (mp) REVERT: A 1053 TRP cc_start: 0.8650 (m-10) cc_final: 0.8293 (m-10) REVERT: A 1067 LEU cc_start: 0.8016 (pt) cc_final: 0.7478 (tt) REVERT: A 1074 ARG cc_start: 0.8522 (ttm-80) cc_final: 0.8199 (tmm-80) REVERT: A 1116 ASN cc_start: 0.7307 (t0) cc_final: 0.6810 (p0) REVERT: A 1283 MET cc_start: 0.7809 (tpt) cc_final: 0.7428 (tpt) REVERT: A 1302 MET cc_start: 0.7560 (mmm) cc_final: 0.7258 (mmt) REVERT: A 1335 ASP cc_start: 0.7363 (t0) cc_final: 0.7161 (t70) REVERT: A 1338 ASN cc_start: 0.8064 (t0) cc_final: 0.7572 (t0) REVERT: A 1393 TRP cc_start: 0.8901 (m-10) cc_final: 0.8551 (m100) REVERT: A 1488 LYS cc_start: 0.9037 (mmmm) cc_final: 0.8560 (mtpt) REVERT: A 1514 MET cc_start: 0.8349 (ttp) cc_final: 0.7840 (ptm) REVERT: A 1519 LEU cc_start: 0.8945 (OUTLIER) cc_final: 0.8720 (mp) REVERT: A 1578 LEU cc_start: 0.8783 (OUTLIER) cc_final: 0.8501 (mp) REVERT: A 1659 TYR cc_start: 0.8199 (t80) cc_final: 0.7965 (t80) REVERT: A 1716 ASN cc_start: 0.8652 (m-40) cc_final: 0.7716 (t0) REVERT: A 1717 PHE cc_start: 0.8626 (t80) cc_final: 0.8301 (t80) outliers start: 80 outliers final: 49 residues processed: 369 average time/residue: 0.1002 time to fit residues: 58.2237 Evaluate side-chains 352 residues out of total 1593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 295 time to evaluate : 0.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 GLU Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 155 SER Chi-restraints excluded: chain A residue 167 ASN Chi-restraints excluded: chain A residue 168 SER Chi-restraints excluded: chain A residue 172 ILE Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 203 PHE Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 378 TRP Chi-restraints excluded: chain A residue 395 ASP Chi-restraints excluded: chain A residue 424 LEU Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 583 GLU Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 684 THR Chi-restraints excluded: chain A residue 715 THR Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain A residue 743 PHE Chi-restraints excluded: chain A residue 751 PHE Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 827 LEU Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 939 LEU Chi-restraints excluded: chain A residue 940 LEU Chi-restraints excluded: chain A residue 994 LEU Chi-restraints excluded: chain A residue 1020 THR Chi-restraints excluded: chain A residue 1028 LEU Chi-restraints excluded: chain A residue 1029 TYR Chi-restraints excluded: chain A residue 1043 LEU Chi-restraints excluded: chain A residue 1061 LEU Chi-restraints excluded: chain A residue 1090 ILE Chi-restraints excluded: chain A residue 1147 VAL Chi-restraints excluded: chain A residue 1150 LEU Chi-restraints excluded: chain A residue 1177 ASP Chi-restraints excluded: chain A residue 1193 LEU Chi-restraints excluded: chain A residue 1401 LEU Chi-restraints excluded: chain A residue 1433 GLU Chi-restraints excluded: chain A residue 1477 TRP Chi-restraints excluded: chain A residue 1519 LEU Chi-restraints excluded: chain A residue 1523 THR Chi-restraints excluded: chain A residue 1537 ILE Chi-restraints excluded: chain A residue 1576 THR Chi-restraints excluded: chain A residue 1578 LEU Chi-restraints excluded: chain A residue 1593 VAL Chi-restraints excluded: chain A residue 1602 LEU Chi-restraints excluded: chain A residue 1626 LEU Chi-restraints excluded: chain A residue 1666 GLN Chi-restraints excluded: chain A residue 1694 LEU Chi-restraints excluded: chain A residue 1735 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 98 optimal weight: 5.9990 chunk 106 optimal weight: 0.6980 chunk 9 optimal weight: 0.8980 chunk 5 optimal weight: 0.7980 chunk 123 optimal weight: 2.9990 chunk 173 optimal weight: 9.9990 chunk 140 optimal weight: 0.9990 chunk 110 optimal weight: 10.0000 chunk 130 optimal weight: 6.9990 chunk 169 optimal weight: 2.9990 chunk 143 optimal weight: 5.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 66 GLN A 95 HIS A 770 HIS A1142 ASN A1338 ASN A1351 ASN ** A1666 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.143227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.118806 restraints weight = 25348.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.122940 restraints weight = 12635.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.125714 restraints weight = 7830.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.127533 restraints weight = 5599.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.128708 restraints weight = 4428.509| |-----------------------------------------------------------------------------| r_work (final): 0.3609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.6304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 14558 Z= 0.148 Angle : 0.768 10.443 19765 Z= 0.370 Chirality : 0.047 0.284 2243 Planarity : 0.005 0.073 2483 Dihedral : 6.927 54.835 1964 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 14.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.94 % Favored : 93.06 % Rotamer: Outliers : 5.27 % Allowed : 23.10 % Favored : 71.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 0.00 % Twisted Proline : 1.09 % Twisted General : 0.06 % 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: -0.86 (0.21), residues: 1743 helix: 0.27 (0.16), residues: 1089 sheet: None (None), residues: 0 loop : -2.01 (0.24), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 726 TYR 0.027 0.002 TYR A 714 PHE 0.017 0.002 PHE A 990 TRP 0.020 0.002 TRP A1477 HIS 0.004 0.001 HIS A 227 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.15 (14556) covalent geometry : angle 0.76774 / 0.37 (19765) hydrogen bonds : bond 0.03752 / 2.48 ( 685) hydrogen bonds : angle 4.36260 / 3.11 ( 2007) Misc. bond : bond 0.00060 / 0.03 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3486 Ramachandran restraints generated. 1743 Oldfield, 0 Emsley, 1743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3486 Ramachandran restraints generated. 1743 Oldfield, 0 Emsley, 1743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 1593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 311 time to evaluate : 0.533 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 ARG cc_start: 0.8242 (OUTLIER) cc_final: 0.7990 (ttp80) REVERT: A 116 MET cc_start: 0.8399 (ttp) cc_final: 0.8020 (tmm) REVERT: A 195 GLU cc_start: 0.7117 (tm-30) cc_final: 0.6785 (tm-30) REVERT: A 213 TYR cc_start: 0.8717 (m-80) cc_final: 0.8065 (m-80) REVERT: A 267 ILE cc_start: 0.8678 (OUTLIER) cc_final: 0.8454 (mm) REVERT: A 353 LEU cc_start: 0.8816 (OUTLIER) cc_final: 0.8297 (mm) REVERT: A 371 GLU cc_start: 0.7042 (mt-10) cc_final: 0.6700 (mt-10) REVERT: A 481 MET cc_start: 0.8676 (tmm) cc_final: 0.8156 (tmm) REVERT: A 501 MET cc_start: 0.8021 (mmm) cc_final: 0.7761 (mmm) REVERT: A 531 GLU cc_start: 0.7469 (tm-30) cc_final: 0.7200 (tm-30) REVERT: A 612 PHE cc_start: 0.7943 (t80) cc_final: 0.7563 (t80) REVERT: A 621 ARG cc_start: 0.7499 (mtm180) cc_final: 0.7203 (ttt90) REVERT: A 649 HIS cc_start: 0.6196 (t70) cc_final: 0.5961 (t70) REVERT: A 751 PHE cc_start: 0.6452 (OUTLIER) cc_final: 0.4772 (m-80) REVERT: A 828 LEU cc_start: 0.9213 (OUTLIER) cc_final: 0.8806 (pp) REVERT: A 926 GLU cc_start: 0.8581 (tp30) cc_final: 0.8191 (tt0) REVERT: A 1021 GLN cc_start: 0.8402 (tt0) cc_final: 0.8168 (tt0) REVERT: A 1029 TYR cc_start: 0.8641 (OUTLIER) cc_final: 0.7183 (t80) REVERT: A 1043 LEU cc_start: 0.9323 (OUTLIER) cc_final: 0.8702 (mp) REVERT: A 1067 LEU cc_start: 0.8132 (pt) cc_final: 0.7716 (tt) REVERT: A 1074 ARG cc_start: 0.8505 (ttm-80) cc_final: 0.8217 (tmm-80) REVERT: A 1087 TYR cc_start: 0.8951 (t80) cc_final: 0.8604 (t80) REVERT: A 1116 ASN cc_start: 0.7333 (t0) cc_final: 0.6874 (p0) REVERT: A 1191 GLU cc_start: 0.8638 (tp30) cc_final: 0.8356 (tp30) REVERT: A 1283 MET cc_start: 0.8011 (tpt) cc_final: 0.7508 (tpt) REVERT: A 1338 ASN cc_start: 0.8062 (t0) cc_final: 0.7651 (t0) REVERT: A 1393 TRP cc_start: 0.8949 (m-10) cc_final: 0.8546 (m100) REVERT: A 1488 LYS cc_start: 0.8952 (mmmm) cc_final: 0.8673 (mtpt) REVERT: A 1514 MET cc_start: 0.8359 (ttp) cc_final: 0.7811 (ptm) REVERT: A 1519 LEU cc_start: 0.8948 (OUTLIER) cc_final: 0.8733 (mp) REVERT: A 1660 THR cc_start: 0.8876 (t) cc_final: 0.8660 (t) REVERT: A 1703 GLU cc_start: 0.8538 (pp20) cc_final: 0.8007 (pt0) REVERT: A 1716 ASN cc_start: 0.8588 (m-40) cc_final: 0.7748 (t0) REVERT: A 1717 PHE cc_start: 0.8740 (t80) cc_final: 0.8398 (t80) outliers start: 84 outliers final: 52 residues processed: 365 average time/residue: 0.1027 time to fit residues: 58.5674 Evaluate side-chains 348 residues out of total 1593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 288 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 GLU Chi-restraints excluded: chain A residue 84 ARG Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 155 SER Chi-restraints excluded: chain A residue 167 ASN Chi-restraints excluded: chain A residue 168 SER Chi-restraints excluded: chain A residue 203 PHE Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 378 TRP Chi-restraints excluded: chain A residue 395 ASP Chi-restraints excluded: chain A residue 424 LEU Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 583 GLU Chi-restraints excluded: chain A residue 684 THR Chi-restraints excluded: chain A residue 715 THR Chi-restraints excluded: chain A residue 724 LEU Chi-restraints excluded: chain A residue 743 PHE Chi-restraints excluded: chain A residue 751 PHE Chi-restraints excluded: chain A residue 770 HIS Chi-restraints excluded: chain A residue 784 LEU Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 939 LEU Chi-restraints excluded: chain A residue 940 LEU Chi-restraints excluded: chain A residue 975 SER Chi-restraints excluded: chain A residue 994 LEU Chi-restraints excluded: chain A residue 1020 THR Chi-restraints excluded: chain A residue 1028 LEU Chi-restraints excluded: chain A residue 1029 TYR Chi-restraints excluded: chain A residue 1043 LEU Chi-restraints excluded: chain A residue 1061 LEU Chi-restraints excluded: chain A residue 1147 VAL Chi-restraints excluded: chain A residue 1150 LEU Chi-restraints excluded: chain A residue 1177 ASP Chi-restraints excluded: chain A residue 1193 LEU Chi-restraints excluded: chain A residue 1343 CYS Chi-restraints excluded: chain A residue 1401 LEU Chi-restraints excluded: chain A residue 1434 SER Chi-restraints excluded: chain A residue 1459 PHE Chi-restraints excluded: chain A residue 1477 TRP Chi-restraints excluded: chain A residue 1519 LEU Chi-restraints excluded: chain A residue 1523 THR Chi-restraints excluded: chain A residue 1537 ILE Chi-restraints excluded: chain A residue 1578 LEU Chi-restraints excluded: chain A residue 1588 SER Chi-restraints excluded: chain A residue 1593 VAL Chi-restraints excluded: chain A residue 1602 LEU Chi-restraints excluded: chain A residue 1626 LEU Chi-restraints excluded: chain A residue 1639 VAL Chi-restraints excluded: chain A residue 1694 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 55 optimal weight: 5.9990 chunk 46 optimal weight: 1.9990 chunk 49 optimal weight: 6.9990 chunk 72 optimal weight: 0.9990 chunk 6 optimal weight: 0.9980 chunk 15 optimal weight: 0.8980 chunk 155 optimal weight: 3.9990 chunk 29 optimal weight: 0.6980 chunk 142 optimal weight: 8.9990 chunk 152 optimal weight: 10.0000 chunk 146 optimal weight: 6.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 770 HIS ** A1214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1569 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1596 GLN ** A1666 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.143249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.119266 restraints weight = 25229.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.123327 restraints weight = 12581.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.126052 restraints weight = 7784.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.127873 restraints weight = 5554.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.128993 restraints weight = 4362.958| |-----------------------------------------------------------------------------| r_work (final): 0.3603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.6566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 14558 Z= 0.142 Angle : 0.772 10.860 19765 Z= 0.372 Chirality : 0.046 0.327 2243 Planarity : 0.005 0.059 2483 Dihedral : 6.667 55.581 1960 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 13.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.94 % Favored : 93.06 % Rotamer: Outliers : 4.90 % Allowed : 24.61 % Favored : 70.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 0.00 % Twisted Proline : 1.09 % Twisted General : 0.06 % 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: -0.78 (0.21), residues: 1743 helix: 0.37 (0.16), residues: 1087 sheet: None (None), residues: 0 loop : -2.02 (0.24), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1377 TYR 0.026 0.002 TYR A 714 PHE 0.017 0.002 PHE A 990 TRP 0.020 0.001 TRP A1477 HIS 0.015 0.001 HIS A 770 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.14 (14556) covalent geometry : angle 0.77213 / 0.37 (19765) hydrogen bonds : bond 0.03665 / 2.42 ( 685) hydrogen bonds : angle 4.38353 / 3.14 ( 2007) Misc. bond : bond 0.00063 / 0.03 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3486 Ramachandran restraints generated. 1743 Oldfield, 0 Emsley, 1743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3486 Ramachandran restraints generated. 1743 Oldfield, 0 Emsley, 1743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 1593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 312 time to evaluate : 0.566 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 ARG cc_start: 0.8236 (OUTLIER) cc_final: 0.8004 (ttp80) REVERT: A 116 MET cc_start: 0.8319 (ttp) cc_final: 0.7969 (tmm) REVERT: A 195 GLU cc_start: 0.7161 (tm-30) cc_final: 0.6812 (tm-30) REVERT: A 208 GLN cc_start: 0.7618 (tp40) cc_final: 0.7354 (tp-100) REVERT: A 353 LEU cc_start: 0.8814 (OUTLIER) cc_final: 0.8310 (mm) REVERT: A 405 LEU cc_start: 0.8553 (mm) cc_final: 0.8339 (mp) REVERT: A 481 MET cc_start: 0.8809 (tmm) cc_final: 0.8210 (tmm) REVERT: A 501 MET cc_start: 0.7894 (mmm) cc_final: 0.7527 (mmt) REVERT: A 535 GLU cc_start: 0.8173 (pt0) cc_final: 0.7747 (tp30) REVERT: A 612 PHE cc_start: 0.7994 (t80) cc_final: 0.7634 (t80) REVERT: A 621 ARG cc_start: 0.7503 (mtm180) cc_final: 0.7271 (ttt90) REVERT: A 681 SER cc_start: 0.9273 (t) cc_final: 0.8890 (p) REVERT: A 751 PHE cc_start: 0.6428 (OUTLIER) cc_final: 0.4857 (m-10) REVERT: A 805 MET cc_start: 0.8150 (ttm) cc_final: 0.7823 (mtp) REVERT: A 827 LEU cc_start: 0.8549 (OUTLIER) cc_final: 0.8317 (mm) REVERT: A 828 LEU cc_start: 0.9121 (OUTLIER) cc_final: 0.8743 (pp) REVERT: A 863 ASN cc_start: 0.8274 (t0) cc_final: 0.7990 (t0) REVERT: A 902 GLN cc_start: 0.7730 (tm-30) cc_final: 0.7306 (tm-30) REVERT: A 908 LYS cc_start: 0.8419 (ttmt) cc_final: 0.8172 (ttmt) REVERT: A 926 GLU cc_start: 0.8565 (tp30) cc_final: 0.8270 (tt0) REVERT: A 959 GLU cc_start: 0.7445 (tp30) cc_final: 0.7119 (tp30) REVERT: A 1021 GLN cc_start: 0.8364 (tt0) cc_final: 0.8155 (tt0) REVERT: A 1029 TYR cc_start: 0.8478 (OUTLIER) cc_final: 0.7060 (t80) REVERT: A 1043 LEU cc_start: 0.9341 (OUTLIER) cc_final: 0.8684 (mp) REVERT: A 1067 LEU cc_start: 0.8129 (pt) cc_final: 0.7744 (tt) REVERT: A 1074 ARG cc_start: 0.8479 (ttm-80) cc_final: 0.8235 (tmm-80) REVERT: A 1087 TYR cc_start: 0.8954 (t80) cc_final: 0.8593 (t80) REVERT: A 1116 ASN cc_start: 0.7389 (t0) cc_final: 0.6973 (p0) REVERT: A 1159 LEU cc_start: 0.8231 (tt) cc_final: 0.7998 (tt) REVERT: A 1191 GLU cc_start: 0.8652 (tp30) cc_final: 0.8365 (tp30) REVERT: A 1276 TYR cc_start: 0.8546 (t80) cc_final: 0.8282 (t80) REVERT: A 1283 MET cc_start: 0.8087 (tpt) cc_final: 0.7440 (tpt) REVERT: A 1302 MET cc_start: 0.7834 (mmt) cc_final: 0.7533 (mmt) REVERT: A 1338 ASN cc_start: 0.7962 (t0) cc_final: 0.7529 (t0) REVERT: A 1377 ARG cc_start: 0.7613 (tpp80) cc_final: 0.7360 (tpp80) REVERT: A 1393 TRP cc_start: 0.8892 (m-10) cc_final: 0.8458 (m100) REVERT: A 1488 LYS cc_start: 0.8949 (mmmm) cc_final: 0.8659 (mtpt) REVERT: A 1514 MET cc_start: 0.8377 (ttp) cc_final: 0.7800 (ptm) REVERT: A 1578 LEU cc_start: 0.8749 (OUTLIER) cc_final: 0.8359 (mp) REVERT: A 1621 ASP cc_start: 0.8613 (OUTLIER) cc_final: 0.8262 (t0) REVERT: A 1703 GLU cc_start: 0.8521 (pp20) cc_final: 0.7975 (pt0) REVERT: A 1716 ASN cc_start: 0.8538 (m-40) cc_final: 0.7800 (t0) REVERT: A 1800 MET cc_start: 0.8205 (mmp) cc_final: 0.7285 (ttt) outliers start: 78 outliers final: 45 residues processed: 359 average time/residue: 0.1061 time to fit residues: 59.5367 Evaluate side-chains 343 residues out of total 1593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 289 time to evaluate : 0.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 GLU Chi-restraints excluded: chain A residue 84 ARG Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 115 MET Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 155 SER Chi-restraints excluded: chain A residue 167 ASN Chi-restraints excluded: chain A residue 203 PHE Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 378 TRP Chi-restraints excluded: chain A residue 424 LEU Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 516 LEU Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 583 GLU Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 677 LEU Chi-restraints excluded: chain A residue 684 THR Chi-restraints excluded: chain A residue 715 THR Chi-restraints excluded: chain A residue 751 PHE Chi-restraints excluded: chain A residue 784 LEU Chi-restraints excluded: chain A residue 827 LEU Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 939 LEU Chi-restraints excluded: chain A residue 940 LEU Chi-restraints excluded: chain A residue 975 SER Chi-restraints excluded: chain A residue 1020 THR Chi-restraints excluded: chain A residue 1028 LEU Chi-restraints excluded: chain A residue 1029 TYR Chi-restraints excluded: chain A residue 1043 LEU Chi-restraints excluded: chain A residue 1061 LEU Chi-restraints excluded: chain A residue 1147 VAL Chi-restraints excluded: chain A residue 1150 LEU Chi-restraints excluded: chain A residue 1177 ASP Chi-restraints excluded: chain A residue 1193 LEU Chi-restraints excluded: chain A residue 1401 LEU Chi-restraints excluded: chain A residue 1434 SER Chi-restraints excluded: chain A residue 1459 PHE Chi-restraints excluded: chain A residue 1477 TRP Chi-restraints excluded: chain A residue 1523 THR Chi-restraints excluded: chain A residue 1578 LEU Chi-restraints excluded: chain A residue 1593 VAL Chi-restraints excluded: chain A residue 1596 GLN Chi-restraints excluded: chain A residue 1602 LEU Chi-restraints excluded: chain A residue 1621 ASP Chi-restraints excluded: chain A residue 1626 LEU Chi-restraints excluded: chain A residue 1627 SER Chi-restraints excluded: chain A residue 1694 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 45 optimal weight: 1.9990 chunk 68 optimal weight: 0.7980 chunk 104 optimal weight: 2.9990 chunk 143 optimal weight: 8.9990 chunk 142 optimal weight: 0.9980 chunk 26 optimal weight: 0.0040 chunk 32 optimal weight: 5.9990 chunk 93 optimal weight: 1.9990 chunk 164 optimal weight: 9.9990 chunk 73 optimal weight: 0.0870 chunk 153 optimal weight: 0.0970 overall best weight: 0.3968 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 722 HIS A 907 HIS A1214 GLN ** A1666 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.145717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.121518 restraints weight = 25274.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.125717 restraints weight = 12721.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.128371 restraints weight = 7878.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.130316 restraints weight = 5666.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.131586 restraints weight = 4443.469| |-----------------------------------------------------------------------------| r_work (final): 0.3639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.6815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 14558 Z= 0.136 Angle : 0.771 10.573 19765 Z= 0.372 Chirality : 0.046 0.291 2243 Planarity : 0.005 0.059 2483 Dihedral : 6.473 55.863 1958 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 12.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.88 % Favored : 93.12 % Rotamer: Outliers : 4.33 % Allowed : 25.61 % Favored : 70.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 0.00 % Twisted Proline : 1.09 % Twisted General : 0.06 % 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: -0.68 (0.21), residues: 1743 helix: 0.40 (0.16), residues: 1088 sheet: None (None), residues: 0 loop : -1.89 (0.24), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 951 TYR 0.022 0.002 TYR A 714 PHE 0.020 0.002 PHE A1395 TRP 0.021 0.001 TRP A1477 HIS 0.006 0.001 HIS A 818 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.14 (14556) covalent geometry : angle 0.77118 / 0.37 (19765) hydrogen bonds : bond 0.03552 / 2.35 ( 685) hydrogen bonds : angle 4.39465 / 3.15 ( 2007) Misc. bond : bond 0.00065 / 0.03 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3486 Ramachandran restraints generated. 1743 Oldfield, 0 Emsley, 1743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3486 Ramachandran restraints generated. 1743 Oldfield, 0 Emsley, 1743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 1593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 317 time to evaluate : 0.596 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 208 GLN cc_start: 0.7546 (tp40) cc_final: 0.7281 (tp-100) REVERT: A 353 LEU cc_start: 0.8802 (OUTLIER) cc_final: 0.8340 (mm) REVERT: A 405 LEU cc_start: 0.8416 (mm) cc_final: 0.8211 (mp) REVERT: A 481 MET cc_start: 0.8829 (tmm) cc_final: 0.8179 (tmm) REVERT: A 501 MET cc_start: 0.7989 (mmm) cc_final: 0.7715 (mmt) REVERT: A 535 GLU cc_start: 0.8082 (pt0) cc_final: 0.7696 (tp30) REVERT: A 612 PHE cc_start: 0.8009 (t80) cc_final: 0.7756 (t80) REVERT: A 677 LEU cc_start: 0.8345 (OUTLIER) cc_final: 0.8106 (mt) REVERT: A 681 SER cc_start: 0.9228 (t) cc_final: 0.8855 (p) REVERT: A 751 PHE cc_start: 0.6276 (OUTLIER) cc_final: 0.4681 (m-10) REVERT: A 805 MET cc_start: 0.8088 (ttm) cc_final: 0.7764 (mtp) REVERT: A 814 LEU cc_start: 0.8772 (OUTLIER) cc_final: 0.8438 (mm) REVERT: A 819 ASN cc_start: 0.8576 (m-40) cc_final: 0.7871 (m110) REVERT: A 827 LEU cc_start: 0.8431 (OUTLIER) cc_final: 0.8181 (mm) REVERT: A 828 LEU cc_start: 0.9069 (OUTLIER) cc_final: 0.8639 (pp) REVERT: A 863 ASN cc_start: 0.8069 (t0) cc_final: 0.7769 (t0) REVERT: A 886 ASP cc_start: 0.8163 (t0) cc_final: 0.7943 (t0) REVERT: A 908 LYS cc_start: 0.8391 (ttmt) cc_final: 0.8157 (ttmt) REVERT: A 926 GLU cc_start: 0.8465 (tp30) cc_final: 0.8189 (tt0) REVERT: A 1021 GLN cc_start: 0.8373 (tt0) cc_final: 0.8171 (tt0) REVERT: A 1029 TYR cc_start: 0.8426 (OUTLIER) cc_final: 0.7029 (t80) REVERT: A 1043 LEU cc_start: 0.9347 (OUTLIER) cc_final: 0.8962 (mp) REVERT: A 1053 TRP cc_start: 0.8643 (m-10) cc_final: 0.8408 (m-10) REVERT: A 1067 LEU cc_start: 0.8131 (pt) cc_final: 0.7762 (tt) REVERT: A 1074 ARG cc_start: 0.8452 (ttm-80) cc_final: 0.8230 (tmm-80) REVERT: A 1087 TYR cc_start: 0.8934 (t80) cc_final: 0.8545 (t80) REVERT: A 1116 ASN cc_start: 0.7342 (t0) cc_final: 0.6880 (p0) REVERT: A 1132 GLN cc_start: 0.8714 (tp40) cc_final: 0.8451 (tp40) REVERT: A 1159 LEU cc_start: 0.8008 (tt) cc_final: 0.7678 (tt) REVERT: A 1191 GLU cc_start: 0.8637 (tp30) cc_final: 0.8364 (tp30) REVERT: A 1192 ASN cc_start: 0.8528 (t0) cc_final: 0.8254 (t0) REVERT: A 1276 TYR cc_start: 0.8450 (t80) cc_final: 0.8221 (t80) REVERT: A 1283 MET cc_start: 0.8037 (tpt) cc_final: 0.7463 (tpt) REVERT: A 1338 ASN cc_start: 0.7919 (t0) cc_final: 0.7508 (t0) REVERT: A 1393 TRP cc_start: 0.8827 (m-10) cc_final: 0.8489 (m100) REVERT: A 1488 LYS cc_start: 0.8926 (mmmm) cc_final: 0.8609 (mtpt) REVERT: A 1514 MET cc_start: 0.8358 (ttp) cc_final: 0.7786 (ptm) REVERT: A 1519 LEU cc_start: 0.8920 (OUTLIER) cc_final: 0.8713 (mp) REVERT: A 1566 GLU cc_start: 0.8649 (pm20) cc_final: 0.8424 (pt0) REVERT: A 1578 LEU cc_start: 0.8617 (OUTLIER) cc_final: 0.8315 (mp) REVERT: A 1621 ASP cc_start: 0.8597 (OUTLIER) cc_final: 0.8334 (t0) REVERT: A 1646 LEU cc_start: 0.8699 (mt) cc_final: 0.8457 (mt) REVERT: A 1703 GLU cc_start: 0.8537 (pp20) cc_final: 0.7978 (pt0) REVERT: A 1704 MET cc_start: 0.8697 (mmt) cc_final: 0.8249 (mmt) REVERT: A 1716 ASN cc_start: 0.8601 (m-40) cc_final: 0.7914 (t0) REVERT: A 1717 PHE cc_start: 0.8683 (t80) cc_final: 0.8468 (t80) REVERT: A 1800 MET cc_start: 0.8229 (mmp) cc_final: 0.7453 (ttt) outliers start: 69 outliers final: 42 residues processed: 358 average time/residue: 0.0992 time to fit residues: 56.1931 Evaluate side-chains 347 residues out of total 1593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 294 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 GLU Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 155 SER Chi-restraints excluded: chain A residue 167 ASN Chi-restraints excluded: chain A residue 168 SER Chi-restraints excluded: chain A residue 203 PHE Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 319 MET Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 424 LEU Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 516 LEU Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 583 GLU Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 677 LEU Chi-restraints excluded: chain A residue 684 THR Chi-restraints excluded: chain A residue 715 THR Chi-restraints excluded: chain A residue 727 SER Chi-restraints excluded: chain A residue 751 PHE Chi-restraints excluded: chain A residue 814 LEU Chi-restraints excluded: chain A residue 827 LEU Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 939 LEU Chi-restraints excluded: chain A residue 940 LEU Chi-restraints excluded: chain A residue 975 SER Chi-restraints excluded: chain A residue 994 LEU Chi-restraints excluded: chain A residue 1019 VAL Chi-restraints excluded: chain A residue 1020 THR Chi-restraints excluded: chain A residue 1028 LEU Chi-restraints excluded: chain A residue 1029 TYR Chi-restraints excluded: chain A residue 1043 LEU Chi-restraints excluded: chain A residue 1147 VAL Chi-restraints excluded: chain A residue 1150 LEU Chi-restraints excluded: chain A residue 1177 ASP Chi-restraints excluded: chain A residue 1343 CYS Chi-restraints excluded: chain A residue 1401 LEU Chi-restraints excluded: chain A residue 1434 SER Chi-restraints excluded: chain A residue 1459 PHE Chi-restraints excluded: chain A residue 1477 TRP Chi-restraints excluded: chain A residue 1519 LEU Chi-restraints excluded: chain A residue 1523 THR Chi-restraints excluded: chain A residue 1576 THR Chi-restraints excluded: chain A residue 1578 LEU Chi-restraints excluded: chain A residue 1593 VAL Chi-restraints excluded: chain A residue 1602 LEU Chi-restraints excluded: chain A residue 1621 ASP Chi-restraints excluded: chain A residue 1626 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 104 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 chunk 82 optimal weight: 3.9990 chunk 170 optimal weight: 10.0000 chunk 92 optimal weight: 6.9990 chunk 151 optimal weight: 3.9990 chunk 50 optimal weight: 20.0000 chunk 123 optimal weight: 9.9990 chunk 55 optimal weight: 7.9990 chunk 89 optimal weight: 7.9990 chunk 85 optimal weight: 0.7980 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 288 ASN A1596 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.133726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.110502 restraints weight = 25242.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.114301 restraints weight = 12953.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.116877 restraints weight = 8187.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.118582 restraints weight = 5903.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.119764 restraints weight = 4684.692| |-----------------------------------------------------------------------------| r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.7188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 14558 Z= 0.176 Angle : 0.804 11.601 19765 Z= 0.393 Chirality : 0.048 0.251 2243 Planarity : 0.005 0.063 2483 Dihedral : 6.488 57.980 1958 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 14.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.94 % Favored : 93.06 % Rotamer: Outliers : 4.14 % Allowed : 25.93 % Favored : 69.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.62 (0.21), residues: 1743 helix: 0.42 (0.16), residues: 1093 sheet: None (None), residues: 0 loop : -1.83 (0.25), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A1131 TYR 0.021 0.002 TYR A 269 PHE 0.018 0.002 PHE A1728 TRP 0.019 0.002 TRP A 69 HIS 0.005 0.001 HIS A 227 Details of bonding type rmsd/Z covalent geometry : bond 0.00425 / 0.18 (14556) covalent geometry : angle 0.80410 / 0.39 (19765) hydrogen bonds : bond 0.03946 / 2.64 ( 685) hydrogen bonds : angle 4.47992 / 3.17 ( 2007) Misc. bond : bond 0.00070 / 0.04 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3486 Ramachandran restraints generated. 1743 Oldfield, 0 Emsley, 1743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3486 Ramachandran restraints generated. 1743 Oldfield, 0 Emsley, 1743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 1593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 300 time to evaluate : 0.602 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 GLU cc_start: 0.8213 (tp30) cc_final: 0.8013 (tp30) REVERT: A 115 MET cc_start: 0.8825 (ptt) cc_final: 0.8384 (ptp) REVERT: A 116 MET cc_start: 0.8350 (ttp) cc_final: 0.8100 (tmm) REVERT: A 196 TRP cc_start: 0.8934 (m-10) cc_final: 0.7966 (m-10) REVERT: A 213 TYR cc_start: 0.8760 (m-80) cc_final: 0.8007 (m-80) REVERT: A 257 ASN cc_start: 0.8794 (t0) cc_final: 0.8416 (m-40) REVERT: A 353 LEU cc_start: 0.8894 (OUTLIER) cc_final: 0.8403 (mm) REVERT: A 481 MET cc_start: 0.8895 (tmm) cc_final: 0.8233 (tmm) REVERT: A 501 MET cc_start: 0.8008 (mmm) cc_final: 0.7729 (mmm) REVERT: A 535 GLU cc_start: 0.8106 (pt0) cc_final: 0.7742 (tp30) REVERT: A 677 LEU cc_start: 0.8440 (OUTLIER) cc_final: 0.8222 (mt) REVERT: A 681 SER cc_start: 0.9433 (t) cc_final: 0.8970 (p) REVERT: A 749 GLU cc_start: 0.6694 (mp0) cc_final: 0.5931 (pm20) REVERT: A 751 PHE cc_start: 0.6317 (OUTLIER) cc_final: 0.4712 (m-10) REVERT: A 814 LEU cc_start: 0.8799 (OUTLIER) cc_final: 0.8448 (mm) REVERT: A 819 ASN cc_start: 0.8751 (m-40) cc_final: 0.8060 (m110) REVERT: A 827 LEU cc_start: 0.8524 (OUTLIER) cc_final: 0.8236 (mm) REVERT: A 863 ASN cc_start: 0.8388 (t0) cc_final: 0.8125 (t0) REVERT: A 908 LYS cc_start: 0.8433 (ttmt) cc_final: 0.8131 (ttmt) REVERT: A 926 GLU cc_start: 0.8494 (tp30) cc_final: 0.8205 (tt0) REVERT: A 959 GLU cc_start: 0.7422 (tp30) cc_final: 0.7201 (tp30) REVERT: A 1021 GLN cc_start: 0.8435 (tt0) cc_final: 0.8145 (tt0) REVERT: A 1029 TYR cc_start: 0.8486 (OUTLIER) cc_final: 0.7130 (t80) REVERT: A 1043 LEU cc_start: 0.9441 (OUTLIER) cc_final: 0.8702 (mp) REVERT: A 1053 TRP cc_start: 0.8879 (m-10) cc_final: 0.8672 (m-10) REVERT: A 1067 LEU cc_start: 0.8195 (pt) cc_final: 0.7875 (tt) REVERT: A 1074 ARG cc_start: 0.8511 (ttm-80) cc_final: 0.8298 (tmm-80) REVERT: A 1087 TYR cc_start: 0.9078 (t80) cc_final: 0.8759 (t80) REVERT: A 1116 ASN cc_start: 0.7393 (t0) cc_final: 0.7001 (p0) REVERT: A 1159 LEU cc_start: 0.8293 (tt) cc_final: 0.8014 (tt) REVERT: A 1191 GLU cc_start: 0.8643 (tp30) cc_final: 0.8321 (tp30) REVERT: A 1283 MET cc_start: 0.8283 (tpt) cc_final: 0.7795 (tpt) REVERT: A 1338 ASN cc_start: 0.8186 (t0) cc_final: 0.7719 (t0) REVERT: A 1488 LYS cc_start: 0.8965 (mmmm) cc_final: 0.8682 (mtpt) REVERT: A 1533 PHE cc_start: 0.8353 (t80) cc_final: 0.8097 (t80) REVERT: A 1578 LEU cc_start: 0.8931 (OUTLIER) cc_final: 0.8709 (mp) REVERT: A 1594 THR cc_start: 0.8566 (p) cc_final: 0.8322 (t) REVERT: A 1621 ASP cc_start: 0.8639 (OUTLIER) cc_final: 0.8413 (t0) REVERT: A 1646 LEU cc_start: 0.8751 (mt) cc_final: 0.8488 (mt) REVERT: A 1703 GLU cc_start: 0.8497 (pp20) cc_final: 0.8040 (pt0) REVERT: A 1704 MET cc_start: 0.8750 (mmt) cc_final: 0.8378 (mmt) REVERT: A 1716 ASN cc_start: 0.8576 (m-40) cc_final: 0.8086 (t0) REVERT: A 1800 MET cc_start: 0.8326 (mmp) cc_final: 0.7835 (ttt) outliers start: 66 outliers final: 45 residues processed: 341 average time/residue: 0.1004 time to fit residues: 54.2595 Evaluate side-chains 340 residues out of total 1593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 286 time to evaluate : 0.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 GLU Chi-restraints excluded: chain A residue 66 GLN Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 155 SER Chi-restraints excluded: chain A residue 167 ASN Chi-restraints excluded: chain A residue 203 PHE Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain A residue 288 ASN Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 424 LEU Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 516 LEU Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 583 GLU Chi-restraints excluded: chain A residue 597 CYS Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 677 LEU Chi-restraints excluded: chain A residue 684 THR Chi-restraints excluded: chain A residue 715 THR Chi-restraints excluded: chain A residue 751 PHE Chi-restraints excluded: chain A residue 814 LEU Chi-restraints excluded: chain A residue 827 LEU Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 939 LEU Chi-restraints excluded: chain A residue 940 LEU Chi-restraints excluded: chain A residue 975 SER Chi-restraints excluded: chain A residue 994 LEU Chi-restraints excluded: chain A residue 1019 VAL Chi-restraints excluded: chain A residue 1020 THR Chi-restraints excluded: chain A residue 1028 LEU Chi-restraints excluded: chain A residue 1029 TYR Chi-restraints excluded: chain A residue 1043 LEU Chi-restraints excluded: chain A residue 1045 ASP Chi-restraints excluded: chain A residue 1061 LEU Chi-restraints excluded: chain A residue 1147 VAL Chi-restraints excluded: chain A residue 1150 LEU Chi-restraints excluded: chain A residue 1177 ASP Chi-restraints excluded: chain A residue 1343 CYS Chi-restraints excluded: chain A residue 1434 SER Chi-restraints excluded: chain A residue 1477 TRP Chi-restraints excluded: chain A residue 1523 THR Chi-restraints excluded: chain A residue 1578 LEU Chi-restraints excluded: chain A residue 1593 VAL Chi-restraints excluded: chain A residue 1602 LEU Chi-restraints excluded: chain A residue 1621 ASP Chi-restraints excluded: chain A residue 1626 LEU Chi-restraints excluded: chain A residue 1627 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 89 optimal weight: 0.0980 chunk 21 optimal weight: 3.9990 chunk 33 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 69 optimal weight: 3.9990 chunk 61 optimal weight: 0.9990 chunk 56 optimal weight: 7.9990 chunk 123 optimal weight: 7.9990 chunk 92 optimal weight: 2.9990 chunk 174 optimal weight: 2.9990 chunk 106 optimal weight: 10.0000 overall best weight: 1.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 288 ASN ** A1596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.135945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.112062 restraints weight = 25086.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.115995 restraints weight = 12782.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.118669 restraints weight = 8048.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.120329 restraints weight = 5795.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.121610 restraints weight = 4640.088| |-----------------------------------------------------------------------------| r_work (final): 0.3516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.7424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 14558 Z= 0.153 Angle : 0.815 15.772 19765 Z= 0.391 Chirality : 0.047 0.270 2243 Planarity : 0.005 0.066 2483 Dihedral : 6.444 58.128 1958 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 13.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.94 % Favored : 93.06 % Rotamer: Outliers : 3.58 % Allowed : 26.74 % Favored : 69.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 1743 helix: 0.49 (0.16), residues: 1091 sheet: None (None), residues: 0 loop : -1.80 (0.25), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A1131 TYR 0.020 0.002 TYR A 86 PHE 0.063 0.002 PHE A1395 TRP 0.019 0.002 TRP A1477 HIS 0.007 0.001 HIS A 329 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.15 (14556) covalent geometry : angle 0.81459 / 0.39 (19765) hydrogen bonds : bond 0.03724 / 2.47 ( 685) hydrogen bonds : angle 4.48386 / 3.18 ( 2007) Misc. bond : bond 0.00067 / 0.04 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3486 Ramachandran restraints generated. 1743 Oldfield, 0 Emsley, 1743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3486 Ramachandran restraints generated. 1743 Oldfield, 0 Emsley, 1743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 1593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 311 time to evaluate : 0.503 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 115 MET cc_start: 0.8788 (ptt) cc_final: 0.8296 (ptp) REVERT: A 116 MET cc_start: 0.8332 (ttp) cc_final: 0.8071 (tmm) REVERT: A 196 TRP cc_start: 0.8904 (m-10) cc_final: 0.7829 (m-10) REVERT: A 213 TYR cc_start: 0.8741 (m-80) cc_final: 0.7927 (m-80) REVERT: A 353 LEU cc_start: 0.8966 (OUTLIER) cc_final: 0.8510 (mm) REVERT: A 395 ASP cc_start: 0.8599 (t0) cc_final: 0.8200 (t0) REVERT: A 481 MET cc_start: 0.8924 (tmm) cc_final: 0.8241 (tmm) REVERT: A 501 MET cc_start: 0.8042 (mmm) cc_final: 0.7765 (mmm) REVERT: A 535 GLU cc_start: 0.8025 (pt0) cc_final: 0.7634 (tp30) REVERT: A 555 PHE cc_start: 0.7853 (m-80) cc_final: 0.7619 (m-80) REVERT: A 662 ASP cc_start: 0.7740 (m-30) cc_final: 0.7522 (t0) REVERT: A 681 SER cc_start: 0.9408 (t) cc_final: 0.8957 (p) REVERT: A 751 PHE cc_start: 0.6308 (OUTLIER) cc_final: 0.4743 (m-10) REVERT: A 814 LEU cc_start: 0.8801 (OUTLIER) cc_final: 0.8475 (mm) REVERT: A 819 ASN cc_start: 0.8647 (m-40) cc_final: 0.7990 (m110) REVERT: A 827 LEU cc_start: 0.8519 (OUTLIER) cc_final: 0.8299 (mm) REVERT: A 863 ASN cc_start: 0.8312 (t0) cc_final: 0.8040 (t0) REVERT: A 908 LYS cc_start: 0.8372 (ttmt) cc_final: 0.8049 (ttmt) REVERT: A 926 GLU cc_start: 0.8448 (tp30) cc_final: 0.8247 (tt0) REVERT: A 959 GLU cc_start: 0.7420 (tp30) cc_final: 0.7151 (tp30) REVERT: A 1020 THR cc_start: 0.8165 (OUTLIER) cc_final: 0.7915 (p) REVERT: A 1021 GLN cc_start: 0.8410 (tt0) cc_final: 0.8000 (tt0) REVERT: A 1029 TYR cc_start: 0.8415 (OUTLIER) cc_final: 0.7174 (t80) REVERT: A 1043 LEU cc_start: 0.9476 (mm) cc_final: 0.9078 (mp) REVERT: A 1067 LEU cc_start: 0.8178 (pt) cc_final: 0.7932 (tt) REVERT: A 1087 TYR cc_start: 0.9013 (t80) cc_final: 0.8656 (t80) REVERT: A 1116 ASN cc_start: 0.7342 (t0) cc_final: 0.6953 (p0) REVERT: A 1159 LEU cc_start: 0.8175 (tt) cc_final: 0.7862 (tt) REVERT: A 1191 GLU cc_start: 0.8601 (tp30) cc_final: 0.8310 (tp30) REVERT: A 1192 ASN cc_start: 0.8524 (t0) cc_final: 0.8233 (t0) REVERT: A 1245 ASP cc_start: 0.8113 (p0) cc_final: 0.7849 (p0) REVERT: A 1283 MET cc_start: 0.8119 (tpt) cc_final: 0.7503 (tpt) REVERT: A 1338 ASN cc_start: 0.8045 (t0) cc_final: 0.7562 (t0) REVERT: A 1488 LYS cc_start: 0.8909 (mmmm) cc_final: 0.8656 (mtpt) REVERT: A 1532 GLU cc_start: 0.7681 (mm-30) cc_final: 0.7422 (tp30) REVERT: A 1594 THR cc_start: 0.8439 (p) cc_final: 0.8221 (t) REVERT: A 1716 ASN cc_start: 0.8519 (m-40) cc_final: 0.8151 (t0) REVERT: A 1800 MET cc_start: 0.8383 (mmp) cc_final: 0.7986 (ttt) outliers start: 57 outliers final: 38 residues processed: 347 average time/residue: 0.0961 time to fit residues: 52.8636 Evaluate side-chains 334 residues out of total 1593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 290 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 GLU Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 155 SER Chi-restraints excluded: chain A residue 167 ASN Chi-restraints excluded: chain A residue 203 PHE Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 424 LEU Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 583 GLU Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 684 THR Chi-restraints excluded: chain A residue 715 THR Chi-restraints excluded: chain A residue 751 PHE Chi-restraints excluded: chain A residue 814 LEU Chi-restraints excluded: chain A residue 827 LEU Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 939 LEU Chi-restraints excluded: chain A residue 940 LEU Chi-restraints excluded: chain A residue 975 SER Chi-restraints excluded: chain A residue 1019 VAL Chi-restraints excluded: chain A residue 1020 THR Chi-restraints excluded: chain A residue 1028 LEU Chi-restraints excluded: chain A residue 1029 TYR Chi-restraints excluded: chain A residue 1147 VAL Chi-restraints excluded: chain A residue 1150 LEU Chi-restraints excluded: chain A residue 1177 ASP Chi-restraints excluded: chain A residue 1343 CYS Chi-restraints excluded: chain A residue 1356 PHE Chi-restraints excluded: chain A residue 1434 SER Chi-restraints excluded: chain A residue 1477 TRP Chi-restraints excluded: chain A residue 1523 THR Chi-restraints excluded: chain A residue 1593 VAL Chi-restraints excluded: chain A residue 1602 LEU Chi-restraints excluded: chain A residue 1627 SER Chi-restraints excluded: chain A residue 1694 LEU Chi-restraints excluded: chain A residue 1724 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 22 optimal weight: 4.9990 chunk 12 optimal weight: 6.9990 chunk 147 optimal weight: 0.8980 chunk 82 optimal weight: 4.9990 chunk 62 optimal weight: 0.5980 chunk 59 optimal weight: 0.9980 chunk 171 optimal weight: 8.9990 chunk 169 optimal weight: 10.0000 chunk 156 optimal weight: 20.0000 chunk 58 optimal weight: 3.9990 chunk 90 optimal weight: 0.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.134030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.110044 restraints weight = 25464.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.113976 restraints weight = 13199.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.116576 restraints weight = 8369.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.118358 restraints weight = 6080.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.119463 restraints weight = 4841.209| |-----------------------------------------------------------------------------| r_work (final): 0.3500 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.7603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 14558 Z= 0.159 Angle : 0.812 11.791 19765 Z= 0.394 Chirality : 0.048 0.288 2243 Planarity : 0.005 0.067 2483 Dihedral : 6.612 49.253 1958 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 14.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.34 % Favored : 92.66 % Rotamer: Outliers : 3.26 % Allowed : 27.24 % Favored : 69.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.49 (0.21), residues: 1743 helix: 0.52 (0.16), residues: 1095 sheet: None (None), residues: 0 loop : -1.76 (0.25), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A1131 TYR 0.020 0.002 TYR A 86 PHE 0.021 0.002 PHE A1395 TRP 0.056 0.002 TRP A1053 HIS 0.010 0.001 HIS A 329 Details of bonding type rmsd/Z covalent geometry : bond 0.00381 / 0.16 (14556) covalent geometry : angle 0.81178 / 0.39 (19765) hydrogen bonds : bond 0.03820 / 2.54 ( 685) hydrogen bonds : angle 4.48860 / 3.18 ( 2007) Misc. bond : bond 0.00429 / 0.23 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2427.61 seconds wall clock time: 42 minutes 52.11 seconds (2572.11 seconds total)