Starting phenix.real_space_refine on Wed Feb 4 13:40:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9lgb_63060/02_2026/9lgb_63060_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9lgb_63060/02_2026/9lgb_63060.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.34 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9lgb_63060/02_2026/9lgb_63060.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9lgb_63060/02_2026/9lgb_63060.map" model { file = "/net/cci-nas-00/data/ceres_data/9lgb_63060/02_2026/9lgb_63060_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9lgb_63060/02_2026/9lgb_63060_neut.cif" } resolution = 3.34 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= -0.001 sd= 0.068 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 57 5.16 5 C 6926 2.51 5 N 1758 2.21 5 O 1891 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 23 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10632 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 10589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1332, 10589 Classifications: {'peptide': 1332} Link IDs: {'PTRANS': 49, 'TRANS': 1282} Chain breaks: 10 Chain: "A" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'LTX': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.60, per 1000 atoms: 0.24 Number of scatterers: 10632 At special positions: 0 Unit cell: (79.04, 113.36, 151.84, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 57 16.00 O 1891 8.00 N 1758 7.00 C 6926 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.92 Conformation dependent library (CDL) restraints added in 528.4 milliseconds 2620 Ramachandran restraints generated. 1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2524 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 5 sheets defined 71.6% alpha, 7.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.44 Creating SS restraints... Processing helix chain 'A' and resid 30 through 60 removed outlier: 3.960A pdb=" N LEU A 38 " --> pdb=" O GLN A 34 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N VAL A 39 " --> pdb=" O ASN A 35 " (cutoff:3.500A) Proline residue: A 42 - end of helix removed outlier: 3.857A pdb=" N CYS A 49 " --> pdb=" O TYR A 45 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N PHE A 50 " --> pdb=" O LEU A 46 " (cutoff:3.500A) Proline residue: A 51 - end of helix removed outlier: 3.994A pdb=" N LEU A 55 " --> pdb=" O PRO A 51 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N TYR A 56 " --> pdb=" O PHE A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 68 through 94 removed outlier: 3.696A pdb=" N LEU A 89 " --> pdb=" O CYS A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 130 removed outlier: 3.577A pdb=" N VAL A 108 " --> pdb=" O PRO A 104 " (cutoff:3.500A) Proline residue: A 110 - end of helix Processing helix chain 'A' and resid 136 through 160 removed outlier: 4.530A pdb=" N TRP A 142 " --> pdb=" O MET A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 191 removed outlier: 3.545A pdb=" N PHE A 175 " --> pdb=" O ARG A 171 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N PHE A 191 " --> pdb=" O VAL A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 221 Processing helix chain 'A' and resid 224 through 234 removed outlier: 3.858A pdb=" N ARG A 233 " --> pdb=" O VAL A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 268 Proline residue: A 255 - end of helix Processing helix chain 'A' and resid 314 through 319 Processing helix chain 'A' and resid 321 through 355 removed outlier: 4.251A pdb=" N MET A 327 " --> pdb=" O PRO A 323 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N SER A 328 " --> pdb=" O TYR A 324 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N PHE A 329 " --> pdb=" O PHE A 325 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU A 330 " --> pdb=" O LEU A 326 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU A 337 " --> pdb=" O ALA A 333 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N GLY A 342 " --> pdb=" O MET A 338 " (cutoff:3.500A) Proline residue: A 343 - end of helix Processing helix chain 'A' and resid 359 through 408 removed outlier: 3.892A pdb=" N GLY A 363 " --> pdb=" O PRO A 359 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LEU A 408 " --> pdb=" O TYR A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 418 Processing helix chain 'A' and resid 419 through 442 removed outlier: 3.927A pdb=" N VAL A 424 " --> pdb=" O VAL A 420 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ALA A 431 " --> pdb=" O MET A 427 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N GLN A 432 " --> pdb=" O SER A 428 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N THR A 439 " --> pdb=" O MET A 435 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N TYR A 440 " --> pdb=" O ASP A 436 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N ASN A 442 " --> pdb=" O ALA A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 442 through 463 Proline residue: A 448 - end of helix removed outlier: 4.362A pdb=" N ALA A 454 " --> pdb=" O GLN A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 464 through 511 removed outlier: 4.142A pdb=" N ALA A 468 " --> pdb=" O PRO A 464 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N VAL A 472 " --> pdb=" O ALA A 468 " (cutoff:3.500A) Proline residue: A 478 - end of helix removed outlier: 3.609A pdb=" N GLN A 491 " --> pdb=" O THR A 487 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N VAL A 492 " --> pdb=" O LYS A 488 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N SER A 497 " --> pdb=" O ALA A 493 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ASN A 506 " --> pdb=" O ILE A 502 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLU A 507 " --> pdb=" O LYS A 503 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLY A 511 " --> pdb=" O GLU A 507 " (cutoff:3.500A) Processing helix chain 'A' and resid 511 through 516 Processing helix chain 'A' and resid 520 through 572 removed outlier: 3.584A pdb=" N ILE A 531 " --> pdb=" O LYS A 527 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N VAL A 538 " --> pdb=" O GLU A 534 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N VAL A 548 " --> pdb=" O TYR A 544 " (cutoff:3.500A) Proline residue: A 557 - end of helix removed outlier: 3.632A pdb=" N SER A 563 " --> pdb=" O LEU A 559 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ASP A 572 " --> pdb=" O TYR A 568 " (cutoff:3.500A) Processing helix chain 'A' and resid 578 through 621 removed outlier: 4.257A pdb=" N PHE A 594 " --> pdb=" O ASN A 590 " (cutoff:3.500A) Proline residue: A 595 - end of helix Proline residue: A 600 - end of helix removed outlier: 3.586A pdb=" N ARG A 615 " --> pdb=" O VAL A 611 " (cutoff:3.500A) Processing helix chain 'A' and resid 683 through 692 removed outlier: 3.552A pdb=" N LEU A 688 " --> pdb=" O LYS A 684 " (cutoff:3.500A) Processing helix chain 'A' and resid 721 through 728 Processing helix chain 'A' and resid 733 through 744 removed outlier: 4.369A pdb=" N GLU A 742 " --> pdb=" O LYS A 738 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ALA A 743 " --> pdb=" O ALA A 739 " (cutoff:3.500A) Processing helix chain 'A' and resid 746 through 753 Processing helix chain 'A' and resid 755 through 759 removed outlier: 3.659A pdb=" N ARG A 758 " --> pdb=" O SER A 755 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N THR A 759 " --> pdb=" O GLY A 756 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 755 through 759' Processing helix chain 'A' and resid 769 through 785 removed outlier: 3.500A pdb=" N ASP A 785 " --> pdb=" O ALA A 781 " (cutoff:3.500A) Processing helix chain 'A' and resid 799 through 810 Processing helix chain 'A' and resid 831 through 835 Processing helix chain 'A' and resid 851 through 859 Processing helix chain 'A' and resid 860 through 869 removed outlier: 4.016A pdb=" N TYR A 869 " --> pdb=" O PHE A 865 " (cutoff:3.500A) Processing helix chain 'A' and resid 958 through 970 removed outlier: 3.922A pdb=" N TYR A 962 " --> pdb=" O LYS A 958 " (cutoff:3.500A) Processing helix chain 'A' and resid 970 through 1000 removed outlier: 3.552A pdb=" N ASP A1000 " --> pdb=" O SER A 996 " (cutoff:3.500A) Processing helix chain 'A' and resid 1010 through 1058 Processing helix chain 'A' and resid 1059 through 1066 removed outlier: 3.856A pdb=" N PHE A1063 " --> pdb=" O PRO A1059 " (cutoff:3.500A) Processing helix chain 'A' and resid 1067 through 1075 removed outlier: 3.579A pdb=" N ARG A1074 " --> pdb=" O ASN A1070 " (cutoff:3.500A) Processing helix chain 'A' and resid 1076 through 1111 removed outlier: 4.509A pdb=" N ILE A1086 " --> pdb=" O VAL A1082 " (cutoff:3.500A) Proline residue: A1087 - end of helix Processing helix chain 'A' and resid 1112 through 1116 Processing helix chain 'A' and resid 1117 through 1160 removed outlier: 3.631A pdb=" N VAL A1133 " --> pdb=" O GLN A1129 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ALA A1134 " --> pdb=" O ARG A1130 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N SER A1135 " --> pdb=" O PHE A1131 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N GLN A1138 " --> pdb=" O ALA A1134 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N SER A1144 " --> pdb=" O LYS A1140 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N SER A1146 " --> pdb=" O LEU A1142 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N SER A1148 " --> pdb=" O SER A1144 " (cutoff:3.500A) Proline residue: A1149 - end of helix removed outlier: 3.600A pdb=" N GLU A1156 " --> pdb=" O SER A1152 " (cutoff:3.500A) Processing helix chain 'A' and resid 1160 through 1168 Processing helix chain 'A' and resid 1169 through 1220 Proline residue: A1190 - end of helix removed outlier: 3.740A pdb=" N ARG A1196 " --> pdb=" O ILE A1192 " (cutoff:3.500A) Processing helix chain 'A' and resid 1225 through 1257 removed outlier: 3.814A pdb=" N THR A1240 " --> pdb=" O SER A1236 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N THR A1241 " --> pdb=" O LEU A1237 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N TYR A1242 " --> pdb=" O GLN A1238 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N ASN A1244 " --> pdb=" O THR A1240 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N TRP A1245 " --> pdb=" O THR A1241 " (cutoff:3.500A) Processing helix chain 'A' and resid 1257 through 1264 removed outlier: 3.736A pdb=" N GLU A1261 " --> pdb=" O ILE A1257 " (cutoff:3.500A) Processing helix chain 'A' and resid 1265 through 1268 removed outlier: 4.165A pdb=" N GLU A1268 " --> pdb=" O GLU A1265 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1265 through 1268' Processing helix chain 'A' and resid 1331 through 1340 removed outlier: 3.668A pdb=" N THR A1336 " --> pdb=" O LYS A1332 " (cutoff:3.500A) Processing helix chain 'A' and resid 1361 through 1368 Processing helix chain 'A' and resid 1382 through 1388 Processing helix chain 'A' and resid 1394 through 1405 Processing helix chain 'A' and resid 1407 through 1412 Processing helix chain 'A' and resid 1416 through 1420 removed outlier: 3.863A pdb=" N HIS A1420 " --> pdb=" O LYS A1417 " (cutoff:3.500A) Processing helix chain 'A' and resid 1430 through 1446 removed outlier: 3.638A pdb=" N LYS A1446 " --> pdb=" O ALA A1442 " (cutoff:3.500A) Processing helix chain 'A' and resid 1463 through 1474 removed outlier: 3.975A pdb=" N GLN A1474 " --> pdb=" O THR A1470 " (cutoff:3.500A) Processing helix chain 'A' and resid 1486 through 1493 removed outlier: 3.878A pdb=" N ILE A1490 " --> pdb=" O ARG A1486 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N ASP A1492 " --> pdb=" O ASN A1488 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N TYR A1493 " --> pdb=" O THR A1489 " (cutoff:3.500A) Processing helix chain 'A' and resid 1509 through 1514 Processing sheet with id=AA1, first strand: chain 'A' and resid 661 through 668 removed outlier: 7.039A pdb=" N HIS A 662 " --> pdb=" O THR A 650 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N THR A 650 " --> pdb=" O HIS A 662 " (cutoff:3.500A) removed outlier: 5.594A pdb=" N ILE A 664 " --> pdb=" O ASN A 648 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N VAL A 646 " --> pdb=" O VAL A 702 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N VAL A 702 " --> pdb=" O VAL A 646 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N ASN A 648 " --> pdb=" O GLY A 700 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLY A 700 " --> pdb=" O ASN A 648 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N THR A 650 " --> pdb=" O VAL A 698 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 708 through 711 removed outlier: 6.300A pdb=" N TYR A 789 " --> pdb=" O LEU A 823 " (cutoff:3.500A) removed outlier: 7.707A pdb=" N VAL A 825 " --> pdb=" O TYR A 789 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N LEU A 791 " --> pdb=" O VAL A 825 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N LEU A 673 " --> pdb=" O VAL A 837 " (cutoff:3.500A) removed outlier: 7.344A pdb=" N ILE A 839 " --> pdb=" O LEU A 673 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N ALA A 675 " --> pdb=" O ILE A 839 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1309 through 1316 removed outlier: 5.875A pdb=" N LYS A1310 " --> pdb=" O LEU A1299 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N LEU A1299 " --> pdb=" O LYS A1310 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N VAL A1314 " --> pdb=" O ARG A1295 " (cutoff:3.500A) removed outlier: 4.966A pdb=" N ARG A1295 " --> pdb=" O VAL A1314 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N ILE A1316 " --> pdb=" O GLU A1293 " (cutoff:3.500A) removed outlier: 5.197A pdb=" N GLU A1293 " --> pdb=" O ILE A1316 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1309 through 1316 removed outlier: 5.875A pdb=" N LYS A1310 " --> pdb=" O LEU A1299 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N LEU A1299 " --> pdb=" O LYS A1310 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N VAL A1314 " --> pdb=" O ARG A1295 " (cutoff:3.500A) removed outlier: 4.966A pdb=" N ARG A1295 " --> pdb=" O VAL A1314 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N ILE A1316 " --> pdb=" O GLU A1293 " (cutoff:3.500A) removed outlier: 5.197A pdb=" N GLU A1293 " --> pdb=" O ILE A1316 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1369 through 1372 removed outlier: 6.390A pdb=" N LEU A1450 " --> pdb=" O LEU A1481 " (cutoff:3.500A) removed outlier: 8.029A pdb=" N ILE A1483 " --> pdb=" O LEU A1450 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N LEU A1452 " --> pdb=" O ILE A1483 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N GLY A1323 " --> pdb=" O ILE A1497 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N LEU A1499 " --> pdb=" O GLY A1323 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N VAL A1325 " --> pdb=" O LEU A1499 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N VAL A1496 " --> pdb=" O TRP A1507 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N TRP A1507 " --> pdb=" O VAL A1496 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N VAL A1498 " --> pdb=" O GLN A1505 " (cutoff:3.500A) 672 hydrogen bonds defined for protein. 1986 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: 2.09 Time building geometry restraints manager: 1.23 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: 2171 1.33 - 1.45: 2473 1.45 - 1.57: 6129 1.57 - 1.69: 0 1.69 - 1.82: 93 Bond restraints: 10866 Sorted by residual: bond pdb=" N VAL A1289 " pdb=" CA VAL A1289 " ideal model delta sigma weight residual 1.460 1.493 -0.033 8.60e-03 1.35e+04 1.45e+01 bond pdb=" N PHE A 594 " pdb=" CA PHE A 594 " ideal model delta sigma weight residual 1.462 1.490 -0.028 7.70e-03 1.69e+04 1.29e+01 bond pdb=" N VAL A 451 " pdb=" CA VAL A 451 " ideal model delta sigma weight residual 1.454 1.496 -0.042 1.19e-02 7.06e+03 1.26e+01 bond pdb=" N TRP A1286 " pdb=" CA TRP A1286 " ideal model delta sigma weight residual 1.462 1.487 -0.025 7.70e-03 1.69e+04 1.05e+01 bond pdb=" N VAL A1210 " pdb=" CA VAL A1210 " ideal model delta sigma weight residual 1.460 1.498 -0.038 1.21e-02 6.83e+03 1.00e+01 ... (remaining 10861 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.12: 13929 2.12 - 4.25: 738 4.25 - 6.37: 58 6.37 - 8.50: 13 8.50 - 10.62: 3 Bond angle restraints: 14741 Sorted by residual: angle pdb=" N VAL A1289 " pdb=" CA VAL A1289 " pdb=" C VAL A1289 " ideal model delta sigma weight residual 113.71 107.64 6.07 9.50e-01 1.11e+00 4.08e+01 angle pdb=" C PHE A 15 " pdb=" N TRP A 16 " pdb=" CA TRP A 16 " ideal model delta sigma weight residual 122.44 114.14 8.30 1.45e+00 4.76e-01 3.28e+01 angle pdb=" N LYS A1264 " pdb=" CA LYS A1264 " pdb=" C LYS A1264 " ideal model delta sigma weight residual 112.57 106.11 6.46 1.13e+00 7.83e-01 3.27e+01 angle pdb=" CA PHE A 981 " pdb=" CB PHE A 981 " pdb=" CG PHE A 981 " ideal model delta sigma weight residual 113.80 119.49 -5.69 1.00e+00 1.00e+00 3.24e+01 angle pdb=" N PHE A 981 " pdb=" CA PHE A 981 " pdb=" C PHE A 981 " ideal model delta sigma weight residual 111.07 105.74 5.33 1.07e+00 8.73e-01 2.48e+01 ... (remaining 14736 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.93: 5892 22.93 - 45.86: 473 45.86 - 68.79: 82 68.79 - 91.71: 20 91.71 - 114.64: 2 Dihedral angle restraints: 6469 sinusoidal: 2579 harmonic: 3890 Sorted by residual: dihedral pdb=" CB2 LTX A1601 " pdb=" CA2 LTX A1601 " pdb=" N2 LTX A1601 " pdb=" CD1 LTX A1601 " ideal model delta sinusoidal sigma weight residual 176.49 -68.87 -114.64 1 3.00e+01 1.11e-03 1.51e+01 dihedral pdb=" C17 LTX A1601 " pdb=" C18 LTX A1601 " pdb=" C19 LTX A1601 " pdb=" C20 LTX A1601 " ideal model delta sinusoidal sigma weight residual -179.63 -70.91 -108.72 1 3.00e+01 1.11e-03 1.41e+01 dihedral pdb=" CG ARG A1472 " pdb=" CD ARG A1472 " pdb=" NE ARG A1472 " pdb=" CZ ARG A1472 " ideal model delta sinusoidal sigma weight residual -90.00 -40.19 -49.81 2 1.50e+01 4.44e-03 1.25e+01 ... (remaining 6466 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 1307 0.057 - 0.115: 283 0.115 - 0.172: 102 0.172 - 0.230: 22 0.230 - 0.287: 3 Chirality restraints: 1717 Sorted by residual: chirality pdb=" C6 LTX A1601 " pdb=" SG2 LTX A1601 " pdb=" C5 LTX A1601 " pdb=" C7 LTX A1601 " both_signs ideal model delta sigma weight residual False -3.19 -2.90 -0.29 2.00e-01 2.50e+01 2.06e+00 chirality pdb=" CA ASP A 204 " pdb=" N ASP A 204 " pdb=" C ASP A 204 " pdb=" CB ASP A 204 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.34e+00 chirality pdb=" CA2 LTX A1601 " pdb=" CB2 LTX A1601 " pdb=" C22 LTX A1601 " pdb=" N2 LTX A1601 " both_signs ideal model delta sigma weight residual False -2.54 -2.32 -0.23 2.00e-01 2.50e+01 1.32e+00 ... (remaining 1714 not shown) Planarity restraints: 1825 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG1 LTX A1601 " 0.158 2.00e-02 2.50e+03 1.90e-01 4.52e+02 pdb=" CD1 LTX A1601 " -0.058 2.00e-02 2.50e+03 pdb=" OE1 LTX A1601 " -0.012 2.00e-02 2.50e+03 pdb=" CA2 LTX A1601 " 0.229 2.00e-02 2.50e+03 pdb=" N2 LTX A1601 " -0.316 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 LTX A1601 " -0.096 2.00e-02 2.50e+03 7.42e-02 5.50e+01 pdb=" C11 LTX A1601 " 0.042 2.00e-02 2.50e+03 pdb=" C8 LTX A1601 " -0.042 2.00e-02 2.50e+03 pdb=" C9 LTX A1601 " 0.096 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C6 LTX A1601 " -0.027 2.00e-02 2.50e+03 4.96e-02 2.46e+01 pdb=" C7 LTX A1601 " 0.064 2.00e-02 2.50e+03 pdb=" C8 LTX A1601 " -0.065 2.00e-02 2.50e+03 pdb=" C9 LTX A1601 " 0.027 2.00e-02 2.50e+03 ... (remaining 1822 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 1778 2.77 - 3.30: 11018 3.30 - 3.83: 17946 3.83 - 4.37: 20663 4.37 - 4.90: 35833 Nonbonded interactions: 87238 Sorted by model distance: nonbonded pdb=" OD1 ASN A 992 " pdb=" OH TYR A1235 " model vdw 2.232 3.040 nonbonded pdb=" O PHE A 15 " pdb=" OG1 THR A 30 " model vdw 2.324 3.040 nonbonded pdb=" OH TYR A 404 " pdb=" OG1 THR A1157 " model vdw 2.364 3.040 nonbonded pdb=" NZ LYS A 498 " pdb=" OD2 ASP A1080 " model vdw 2.379 3.120 nonbonded pdb=" O THR A 552 " pdb=" OG1 THR A 556 " model vdw 2.401 3.040 ... (remaining 87233 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.240 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.790 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7292 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 : 0.007 0.046 10866 Z= 0.482 Angle : 0.948 10.623 14741 Z= 0.652 Chirality : 0.059 0.287 1717 Planarity : 0.010 0.190 1825 Dihedral : 16.802 114.641 3945 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 0.00 % Allowed : 18.09 % Favored : 81.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.25 (0.23), residues: 1310 helix: 0.63 (0.18), residues: 860 sheet: -0.68 (0.55), residues: 76 loop : -1.80 (0.30), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 735 TYR 0.015 0.002 TYR A 783 PHE 0.033 0.002 PHE A 981 TRP 0.016 0.001 TRP A 242 HIS 0.004 0.001 HIS A 805 Details of bonding type rmsd covalent geometry : bond 0.00689 (10866) covalent geometry : angle 0.94836 (14741) hydrogen bonds : bond 0.17600 ( 670) hydrogen bonds : angle 6.58779 ( 1986) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2620 Ramachandran restraints generated. 1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2620 Ramachandran restraints generated. 1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 266 time to evaluate : 0.422 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 VAL cc_start: 0.7592 (t) cc_final: 0.7154 (p) outliers start: 0 outliers final: 0 residues processed: 266 average time/residue: 0.1214 time to fit residues: 43.7477 Evaluate side-chains 166 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 166 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 98 optimal weight: 0.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 0.0030 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 0.6980 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 overall best weight: 0.7394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 71 ASN A 245 ASN A 575 ASN A 597 ASN A 834 GLN A 985 HIS A1008 GLN A1363 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.181625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.134962 restraints weight = 12946.950| |-----------------------------------------------------------------------------| r_work (start): 0.3693 rms_B_bonded: 2.18 r_work: 0.3484 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3340 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.2487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 10866 Z= 0.165 Angle : 0.637 7.724 14741 Z= 0.321 Chirality : 0.042 0.254 1717 Planarity : 0.005 0.042 1825 Dihedral : 9.660 121.932 1467 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 3.92 % Allowed : 19.20 % Favored : 76.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.75 (0.23), residues: 1310 helix: 1.36 (0.17), residues: 878 sheet: -0.55 (0.55), residues: 81 loop : -1.42 (0.31), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 775 TYR 0.022 0.002 TYR A 710 PHE 0.020 0.002 PHE A 583 TRP 0.012 0.001 TRP A1197 HIS 0.007 0.001 HIS A 985 Details of bonding type rmsd covalent geometry : bond 0.00380 (10866) covalent geometry : angle 0.63680 (14741) hydrogen bonds : bond 0.04968 ( 670) hydrogen bonds : angle 4.44982 ( 1986) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2620 Ramachandran restraints generated. 1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2620 Ramachandran restraints generated. 1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 186 time to evaluate : 0.323 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 PHE cc_start: 0.7094 (OUTLIER) cc_final: 0.6679 (t80) REVERT: A 67 MET cc_start: 0.7456 (tpp) cc_final: 0.7155 (tpt) REVERT: A 313 LEU cc_start: 0.7897 (mp) cc_final: 0.7279 (mp) REVERT: A 317 LEU cc_start: 0.8437 (tt) cc_final: 0.8026 (tt) REVERT: A 470 VAL cc_start: 0.8296 (OUTLIER) cc_final: 0.8077 (p) REVERT: A 701 HIS cc_start: 0.7602 (t-170) cc_final: 0.7221 (t-170) REVERT: A 775 ARG cc_start: 0.8714 (mtm-85) cc_final: 0.8388 (mtm-85) REVERT: A 804 LYS cc_start: 0.8051 (OUTLIER) cc_final: 0.7801 (tppt) REVERT: A 835 MET cc_start: 0.8594 (mmt) cc_final: 0.8237 (mmt) REVERT: A 849 MET cc_start: 0.6581 (ttt) cc_final: 0.6310 (ttt) REVERT: A 1034 MET cc_start: 0.8186 (mmm) cc_final: 0.7982 (mmm) REVERT: A 1300 ARG cc_start: 0.6610 (mmm160) cc_final: 0.5998 (mmm160) REVERT: A 1495 ARG cc_start: 0.7072 (mtt180) cc_final: 0.6642 (mtt-85) outliers start: 46 outliers final: 21 residues processed: 216 average time/residue: 0.1064 time to fit residues: 31.7675 Evaluate side-chains 181 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 157 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 PHE Chi-restraints excluded: chain A residue 71 ASN Chi-restraints excluded: chain A residue 211 SER Chi-restraints excluded: chain A residue 212 SER Chi-restraints excluded: chain A residue 388 CYS Chi-restraints excluded: chain A residue 393 MET Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 485 MET Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 597 ASN Chi-restraints excluded: chain A residue 665 THR Chi-restraints excluded: chain A residue 749 ASP Chi-restraints excluded: chain A residue 804 LYS Chi-restraints excluded: chain A residue 805 HIS Chi-restraints excluded: chain A residue 819 ASN Chi-restraints excluded: chain A residue 824 LEU Chi-restraints excluded: chain A residue 1027 ILE Chi-restraints excluded: chain A residue 1065 ARG Chi-restraints excluded: chain A residue 1072 VAL Chi-restraints excluded: chain A residue 1105 ILE Chi-restraints excluded: chain A residue 1244 ASN Chi-restraints excluded: chain A residue 1403 GLU Chi-restraints excluded: chain A residue 1498 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 109 optimal weight: 2.9990 chunk 66 optimal weight: 7.9990 chunk 71 optimal weight: 4.9990 chunk 74 optimal weight: 3.9990 chunk 86 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 93 optimal weight: 1.9990 chunk 31 optimal weight: 0.6980 chunk 96 optimal weight: 0.6980 chunk 90 optimal weight: 0.7980 chunk 127 optimal weight: 0.8980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 575 ASN A 597 ASN A 834 GLN ** A1420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1485 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.177833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.131393 restraints weight = 13133.440| |-----------------------------------------------------------------------------| r_work (start): 0.3650 rms_B_bonded: 2.17 r_work: 0.3444 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3298 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.3058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 10866 Z= 0.185 Angle : 0.612 6.384 14741 Z= 0.311 Chirality : 0.042 0.187 1717 Planarity : 0.004 0.048 1825 Dihedral : 8.980 119.035 1467 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 4.44 % Allowed : 20.39 % Favored : 75.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.95 (0.23), residues: 1310 helix: 1.45 (0.17), residues: 888 sheet: -0.36 (0.55), residues: 81 loop : -1.23 (0.32), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 775 TYR 0.020 0.002 TYR A1032 PHE 0.021 0.002 PHE A 558 TRP 0.014 0.001 TRP A 47 HIS 0.008 0.002 HIS A 985 Details of bonding type rmsd covalent geometry : bond 0.00441 (10866) covalent geometry : angle 0.61187 (14741) hydrogen bonds : bond 0.04746 ( 670) hydrogen bonds : angle 4.23432 ( 1986) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2620 Ramachandran restraints generated. 1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2620 Ramachandran restraints generated. 1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 183 time to evaluate : 0.406 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 54 PHE cc_start: 0.7042 (OUTLIER) cc_final: 0.6777 (t80) REVERT: A 67 MET cc_start: 0.7588 (tpp) cc_final: 0.7279 (tpt) REVERT: A 81 LEU cc_start: 0.6771 (mt) cc_final: 0.6570 (tp) REVERT: A 313 LEU cc_start: 0.7765 (mp) cc_final: 0.7465 (mp) REVERT: A 516 LYS cc_start: 0.8219 (ttmm) cc_final: 0.7841 (mttm) REVERT: A 701 HIS cc_start: 0.7810 (t-170) cc_final: 0.7258 (t70) REVERT: A 758 ARG cc_start: 0.7924 (mtp85) cc_final: 0.7559 (mmt90) REVERT: A 775 ARG cc_start: 0.8752 (mtm-85) cc_final: 0.8451 (mtm-85) REVERT: A 831 TYR cc_start: 0.7717 (m-80) cc_final: 0.7501 (m-10) REVERT: A 984 ASN cc_start: 0.8730 (OUTLIER) cc_final: 0.8489 (t0) REVERT: A 1209 ILE cc_start: 0.8480 (OUTLIER) cc_final: 0.8237 (tt) REVERT: A 1300 ARG cc_start: 0.6630 (mmm160) cc_final: 0.5841 (mmm160) REVERT: A 1312 ILE cc_start: 0.8781 (OUTLIER) cc_final: 0.8507 (mp) REVERT: A 1495 ARG cc_start: 0.7243 (mtt180) cc_final: 0.6720 (mtt-85) outliers start: 52 outliers final: 27 residues processed: 214 average time/residue: 0.1098 time to fit residues: 33.0725 Evaluate side-chains 189 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 158 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 54 PHE Chi-restraints excluded: chain A residue 211 SER Chi-restraints excluded: chain A residue 212 SER Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain A residue 388 CYS Chi-restraints excluded: chain A residue 393 MET Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 483 MET Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 556 THR Chi-restraints excluded: chain A residue 575 ASN Chi-restraints excluded: chain A residue 665 THR Chi-restraints excluded: chain A residue 749 ASP Chi-restraints excluded: chain A residue 805 HIS Chi-restraints excluded: chain A residue 819 ASN Chi-restraints excluded: chain A residue 984 ASN Chi-restraints excluded: chain A residue 1027 ILE Chi-restraints excluded: chain A residue 1065 ARG Chi-restraints excluded: chain A residue 1072 VAL Chi-restraints excluded: chain A residue 1105 ILE Chi-restraints excluded: chain A residue 1136 SER Chi-restraints excluded: chain A residue 1209 ILE Chi-restraints excluded: chain A residue 1244 ASN Chi-restraints excluded: chain A residue 1312 ILE Chi-restraints excluded: chain A residue 1333 SER Chi-restraints excluded: chain A residue 1342 ILE Chi-restraints excluded: chain A residue 1477 ASP Chi-restraints excluded: chain A residue 1480 VAL Chi-restraints excluded: chain A residue 1498 VAL Chi-restraints excluded: chain A residue 1504 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 68 optimal weight: 0.8980 chunk 2 optimal weight: 0.9980 chunk 122 optimal weight: 1.9990 chunk 82 optimal weight: 0.9980 chunk 61 optimal weight: 2.9990 chunk 90 optimal weight: 0.7980 chunk 7 optimal weight: 4.9990 chunk 128 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 chunk 91 optimal weight: 0.8980 chunk 72 optimal weight: 4.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 GLN A 834 GLN A1048 HIS ** A1420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1468 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.176563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.130561 restraints weight = 13153.198| |-----------------------------------------------------------------------------| r_work (start): 0.3639 rms_B_bonded: 2.12 r_work: 0.3437 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3289 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.3389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 10866 Z= 0.171 Angle : 0.592 7.469 14741 Z= 0.298 Chirality : 0.041 0.181 1717 Planarity : 0.004 0.050 1825 Dihedral : 8.538 115.094 1467 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 4.86 % Allowed : 20.14 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.13 (0.23), residues: 1310 helix: 1.62 (0.17), residues: 874 sheet: -0.37 (0.55), residues: 87 loop : -1.16 (0.32), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1291 TYR 0.019 0.001 TYR A1032 PHE 0.021 0.002 PHE A1294 TRP 0.021 0.001 TRP A 47 HIS 0.011 0.001 HIS A 985 Details of bonding type rmsd covalent geometry : bond 0.00406 (10866) covalent geometry : angle 0.59156 (14741) hydrogen bonds : bond 0.04513 ( 670) hydrogen bonds : angle 4.13774 ( 1986) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2620 Ramachandran restraints generated. 1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2620 Ramachandran restraints generated. 1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 173 time to evaluate : 0.358 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 54 PHE cc_start: 0.6992 (OUTLIER) cc_final: 0.6720 (t80) REVERT: A 194 ARG cc_start: 0.6622 (mtm110) cc_final: 0.6298 (ptt180) REVERT: A 313 LEU cc_start: 0.7808 (mp) cc_final: 0.7544 (mp) REVERT: A 485 MET cc_start: 0.8342 (OUTLIER) cc_final: 0.8098 (ptt) REVERT: A 516 LYS cc_start: 0.8161 (ttmm) cc_final: 0.7830 (mttm) REVERT: A 617 ARG cc_start: 0.8028 (OUTLIER) cc_final: 0.7209 (ttp80) REVERT: A 701 HIS cc_start: 0.7893 (t-170) cc_final: 0.7304 (t70) REVERT: A 758 ARG cc_start: 0.7972 (mtp85) cc_final: 0.7584 (mmt90) REVERT: A 775 ARG cc_start: 0.8771 (mtm-85) cc_final: 0.8546 (mtm-85) REVERT: A 831 TYR cc_start: 0.7696 (m-80) cc_final: 0.7392 (m-10) REVERT: A 849 MET cc_start: 0.6084 (ttp) cc_final: 0.5629 (ttt) REVERT: A 984 ASN cc_start: 0.8756 (OUTLIER) cc_final: 0.8518 (t0) REVERT: A 999 THR cc_start: 0.8609 (p) cc_final: 0.8232 (p) REVERT: A 1138 GLN cc_start: 0.8619 (OUTLIER) cc_final: 0.8067 (mt0) REVERT: A 1209 ILE cc_start: 0.8473 (OUTLIER) cc_final: 0.8234 (tt) REVERT: A 1300 ARG cc_start: 0.6624 (mmm160) cc_final: 0.5622 (mmm160) REVERT: A 1312 ILE cc_start: 0.8751 (OUTLIER) cc_final: 0.8516 (mp) REVERT: A 1317 ASP cc_start: 0.7475 (t0) cc_final: 0.7147 (p0) REVERT: A 1357 ILE cc_start: 0.7206 (mm) cc_final: 0.6992 (tt) REVERT: A 1407 LEU cc_start: 0.7625 (OUTLIER) cc_final: 0.7379 (tt) REVERT: A 1495 ARG cc_start: 0.7236 (mtt180) cc_final: 0.6794 (mtt-85) outliers start: 57 outliers final: 33 residues processed: 217 average time/residue: 0.0964 time to fit residues: 29.6800 Evaluate side-chains 199 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 158 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 54 PHE Chi-restraints excluded: chain A residue 211 SER Chi-restraints excluded: chain A residue 212 SER Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain A residue 388 CYS Chi-restraints excluded: chain A residue 393 MET Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 483 MET Chi-restraints excluded: chain A residue 485 MET Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 518 TYR Chi-restraints excluded: chain A residue 556 THR Chi-restraints excluded: chain A residue 597 ASN Chi-restraints excluded: chain A residue 617 ARG Chi-restraints excluded: chain A residue 665 THR Chi-restraints excluded: chain A residue 677 VAL Chi-restraints excluded: chain A residue 749 ASP Chi-restraints excluded: chain A residue 819 ASN Chi-restraints excluded: chain A residue 824 LEU Chi-restraints excluded: chain A residue 840 VAL Chi-restraints excluded: chain A residue 984 ASN Chi-restraints excluded: chain A residue 1027 ILE Chi-restraints excluded: chain A residue 1065 ARG Chi-restraints excluded: chain A residue 1072 VAL Chi-restraints excluded: chain A residue 1105 ILE Chi-restraints excluded: chain A residue 1106 ILE Chi-restraints excluded: chain A residue 1136 SER Chi-restraints excluded: chain A residue 1138 GLN Chi-restraints excluded: chain A residue 1209 ILE Chi-restraints excluded: chain A residue 1244 ASN Chi-restraints excluded: chain A residue 1312 ILE Chi-restraints excluded: chain A residue 1333 SER Chi-restraints excluded: chain A residue 1342 ILE Chi-restraints excluded: chain A residue 1363 HIS Chi-restraints excluded: chain A residue 1407 LEU Chi-restraints excluded: chain A residue 1477 ASP Chi-restraints excluded: chain A residue 1480 VAL Chi-restraints excluded: chain A residue 1498 VAL Chi-restraints excluded: chain A residue 1504 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 37 optimal weight: 0.6980 chunk 101 optimal weight: 0.6980 chunk 93 optimal weight: 1.9990 chunk 48 optimal weight: 0.7980 chunk 47 optimal weight: 0.6980 chunk 65 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 chunk 63 optimal weight: 0.5980 chunk 85 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 260 ASN A 834 GLN ** A1420 HIS ** 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 = 0.4136 r_free = 0.4136 target = 0.177494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.132121 restraints weight = 12970.703| |-----------------------------------------------------------------------------| r_work (start): 0.3674 rms_B_bonded: 2.08 r_work: 0.3472 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3327 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.3605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10866 Z= 0.143 Angle : 0.556 7.709 14741 Z= 0.279 Chirality : 0.040 0.159 1717 Planarity : 0.004 0.051 1825 Dihedral : 8.413 114.681 1467 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 4.35 % Allowed : 21.50 % Favored : 74.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.30 (0.23), residues: 1310 helix: 1.75 (0.17), residues: 874 sheet: -0.21 (0.56), residues: 87 loop : -1.13 (0.32), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1434 TYR 0.019 0.001 TYR A1032 PHE 0.021 0.001 PHE A1294 TRP 0.027 0.001 TRP A 47 HIS 0.009 0.001 HIS A 985 Details of bonding type rmsd covalent geometry : bond 0.00333 (10866) covalent geometry : angle 0.55643 (14741) hydrogen bonds : bond 0.04259 ( 670) hydrogen bonds : angle 4.03263 ( 1986) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2620 Ramachandran restraints generated. 1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2620 Ramachandran restraints generated. 1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 168 time to evaluate : 0.330 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 54 PHE cc_start: 0.6994 (OUTLIER) cc_final: 0.6766 (t80) REVERT: A 194 ARG cc_start: 0.6651 (mtm110) cc_final: 0.6314 (ptt180) REVERT: A 313 LEU cc_start: 0.7633 (mp) cc_final: 0.7349 (mp) REVERT: A 443 MET cc_start: 0.8662 (mmp) cc_final: 0.8418 (mmm) REVERT: A 485 MET cc_start: 0.8345 (ttp) cc_final: 0.8127 (ptt) REVERT: A 488 LYS cc_start: 0.8071 (ttpp) cc_final: 0.7446 (mmtt) REVERT: A 518 TYR cc_start: 0.7957 (OUTLIER) cc_final: 0.6842 (p90) REVERT: A 617 ARG cc_start: 0.7989 (OUTLIER) cc_final: 0.7135 (ttp80) REVERT: A 699 GLU cc_start: 0.7423 (tt0) cc_final: 0.7116 (tt0) REVERT: A 701 HIS cc_start: 0.7909 (t-170) cc_final: 0.7364 (t70) REVERT: A 758 ARG cc_start: 0.7992 (mtp85) cc_final: 0.7590 (mmt90) REVERT: A 831 TYR cc_start: 0.7685 (m-80) cc_final: 0.7412 (m-10) REVERT: A 849 MET cc_start: 0.5790 (ttp) cc_final: 0.5395 (ttt) REVERT: A 984 ASN cc_start: 0.8745 (OUTLIER) cc_final: 0.8516 (t0) REVERT: A 1300 ARG cc_start: 0.6657 (mmm160) cc_final: 0.5540 (mmm160) REVERT: A 1312 ILE cc_start: 0.8789 (OUTLIER) cc_final: 0.8556 (mp) REVERT: A 1317 ASP cc_start: 0.7419 (t0) cc_final: 0.7163 (p0) REVERT: A 1367 PHE cc_start: 0.7545 (m-10) cc_final: 0.7205 (m-10) REVERT: A 1407 LEU cc_start: 0.7560 (OUTLIER) cc_final: 0.7287 (tt) REVERT: A 1495 ARG cc_start: 0.7299 (mtt180) cc_final: 0.6886 (mtt-85) outliers start: 51 outliers final: 37 residues processed: 203 average time/residue: 0.0833 time to fit residues: 24.2289 Evaluate side-chains 198 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 155 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 54 PHE Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 211 SER Chi-restraints excluded: chain A residue 212 SER Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain A residue 388 CYS Chi-restraints excluded: chain A residue 393 MET Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 483 MET Chi-restraints excluded: chain A residue 508 ILE Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 518 TYR Chi-restraints excluded: chain A residue 556 THR Chi-restraints excluded: chain A residue 597 ASN Chi-restraints excluded: chain A residue 617 ARG Chi-restraints excluded: chain A residue 665 THR Chi-restraints excluded: chain A residue 691 LEU Chi-restraints excluded: chain A residue 749 ASP Chi-restraints excluded: chain A residue 819 ASN Chi-restraints excluded: chain A residue 840 VAL Chi-restraints excluded: chain A residue 984 ASN Chi-restraints excluded: chain A residue 1049 LEU Chi-restraints excluded: chain A residue 1065 ARG Chi-restraints excluded: chain A residue 1071 LEU Chi-restraints excluded: chain A residue 1072 VAL Chi-restraints excluded: chain A residue 1105 ILE Chi-restraints excluded: chain A residue 1106 ILE Chi-restraints excluded: chain A residue 1136 SER Chi-restraints excluded: chain A residue 1244 ASN Chi-restraints excluded: chain A residue 1309 LEU Chi-restraints excluded: chain A residue 1312 ILE Chi-restraints excluded: chain A residue 1333 SER Chi-restraints excluded: chain A residue 1342 ILE Chi-restraints excluded: chain A residue 1360 ILE Chi-restraints excluded: chain A residue 1363 HIS Chi-restraints excluded: chain A residue 1407 LEU Chi-restraints excluded: chain A residue 1414 LEU Chi-restraints excluded: chain A residue 1480 VAL Chi-restraints excluded: chain A residue 1498 VAL Chi-restraints excluded: chain A residue 1504 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 92 optimal weight: 0.5980 chunk 122 optimal weight: 6.9990 chunk 17 optimal weight: 0.0970 chunk 23 optimal weight: 1.9990 chunk 60 optimal weight: 0.9980 chunk 104 optimal weight: 0.9990 chunk 93 optimal weight: 0.7980 chunk 76 optimal weight: 6.9990 chunk 12 optimal weight: 0.8980 chunk 87 optimal weight: 1.9990 chunk 100 optimal weight: 0.8980 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 GLN A 834 GLN ** A1420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1468 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.177665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.131725 restraints weight = 13168.602| |-----------------------------------------------------------------------------| r_work (start): 0.3622 rms_B_bonded: 2.12 r_work: 0.3418 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3273 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.3820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10866 Z= 0.139 Angle : 0.553 7.789 14741 Z= 0.277 Chirality : 0.040 0.158 1717 Planarity : 0.004 0.052 1825 Dihedral : 8.374 115.246 1467 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 4.78 % Allowed : 21.08 % Favored : 74.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.42 (0.23), residues: 1310 helix: 1.84 (0.17), residues: 875 sheet: -0.08 (0.56), residues: 87 loop : -1.12 (0.32), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 775 TYR 0.019 0.001 TYR A1032 PHE 0.019 0.001 PHE A 558 TRP 0.017 0.001 TRP A 47 HIS 0.010 0.001 HIS A 985 Details of bonding type rmsd covalent geometry : bond 0.00322 (10866) covalent geometry : angle 0.55323 (14741) hydrogen bonds : bond 0.04132 ( 670) hydrogen bonds : angle 3.97094 ( 1986) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2620 Ramachandran restraints generated. 1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2620 Ramachandran restraints generated. 1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 161 time to evaluate : 0.435 Fit side-chains revert: symmetry clash REVERT: A 54 PHE cc_start: 0.6961 (OUTLIER) cc_final: 0.6750 (t80) REVERT: A 130 ARG cc_start: 0.7360 (mmt90) cc_final: 0.7010 (mmm-85) REVERT: A 194 ARG cc_start: 0.6655 (mtm110) cc_final: 0.6444 (ptt180) REVERT: A 236 LEU cc_start: 0.7765 (OUTLIER) cc_final: 0.6879 (mp) REVERT: A 443 MET cc_start: 0.8694 (mmp) cc_final: 0.8475 (mmm) REVERT: A 485 MET cc_start: 0.8340 (ttp) cc_final: 0.8126 (ptt) REVERT: A 488 LYS cc_start: 0.8124 (ttpp) cc_final: 0.7520 (mmtt) REVERT: A 518 TYR cc_start: 0.8093 (OUTLIER) cc_final: 0.7053 (p90) REVERT: A 617 ARG cc_start: 0.8056 (OUTLIER) cc_final: 0.7240 (ttp80) REVERT: A 696 ASP cc_start: 0.8628 (t0) cc_final: 0.7828 (m-30) REVERT: A 701 HIS cc_start: 0.7978 (t-170) cc_final: 0.7412 (t70) REVERT: A 758 ARG cc_start: 0.8134 (mtp85) cc_final: 0.7746 (mmt90) REVERT: A 775 ARG cc_start: 0.8815 (mtm-85) cc_final: 0.8560 (mtm-85) REVERT: A 835 MET cc_start: 0.8290 (mmt) cc_final: 0.8077 (mmt) REVERT: A 849 MET cc_start: 0.6008 (ttp) cc_final: 0.5531 (ttt) REVERT: A 984 ASN cc_start: 0.8742 (OUTLIER) cc_final: 0.8513 (t0) REVERT: A 999 THR cc_start: 0.8653 (p) cc_final: 0.8281 (p) REVERT: A 1209 ILE cc_start: 0.8476 (OUTLIER) cc_final: 0.8222 (tt) REVERT: A 1300 ARG cc_start: 0.6738 (mmm160) cc_final: 0.5632 (mmm160) REVERT: A 1307 LEU cc_start: 0.8084 (OUTLIER) cc_final: 0.7864 (tp) REVERT: A 1312 ILE cc_start: 0.8769 (OUTLIER) cc_final: 0.8556 (mp) REVERT: A 1317 ASP cc_start: 0.7469 (t0) cc_final: 0.7163 (p0) REVERT: A 1353 ASP cc_start: 0.6294 (m-30) cc_final: 0.6047 (t0) REVERT: A 1367 PHE cc_start: 0.7452 (m-10) cc_final: 0.7083 (m-10) REVERT: A 1407 LEU cc_start: 0.7473 (OUTLIER) cc_final: 0.7216 (tt) REVERT: A 1435 GLN cc_start: 0.8529 (OUTLIER) cc_final: 0.8024 (mp10) REVERT: A 1495 ARG cc_start: 0.7391 (mtt180) cc_final: 0.6964 (mtt-85) outliers start: 56 outliers final: 37 residues processed: 203 average time/residue: 0.1040 time to fit residues: 30.1027 Evaluate side-chains 199 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 152 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 54 PHE Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 211 SER Chi-restraints excluded: chain A residue 212 SER Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain A residue 388 CYS Chi-restraints excluded: chain A residue 393 MET Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 483 MET Chi-restraints excluded: chain A residue 508 ILE Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 518 TYR Chi-restraints excluded: chain A residue 556 THR Chi-restraints excluded: chain A residue 571 VAL Chi-restraints excluded: chain A residue 597 ASN Chi-restraints excluded: chain A residue 617 ARG Chi-restraints excluded: chain A residue 625 LEU Chi-restraints excluded: chain A residue 665 THR Chi-restraints excluded: chain A residue 749 ASP Chi-restraints excluded: chain A residue 819 ASN Chi-restraints excluded: chain A residue 840 VAL Chi-restraints excluded: chain A residue 984 ASN Chi-restraints excluded: chain A residue 1049 LEU Chi-restraints excluded: chain A residue 1071 LEU Chi-restraints excluded: chain A residue 1072 VAL Chi-restraints excluded: chain A residue 1105 ILE Chi-restraints excluded: chain A residue 1106 ILE Chi-restraints excluded: chain A residue 1136 SER Chi-restraints excluded: chain A residue 1209 ILE Chi-restraints excluded: chain A residue 1244 ASN Chi-restraints excluded: chain A residue 1307 LEU Chi-restraints excluded: chain A residue 1309 LEU Chi-restraints excluded: chain A residue 1312 ILE Chi-restraints excluded: chain A residue 1333 SER Chi-restraints excluded: chain A residue 1342 ILE Chi-restraints excluded: chain A residue 1357 ILE Chi-restraints excluded: chain A residue 1363 HIS Chi-restraints excluded: chain A residue 1407 LEU Chi-restraints excluded: chain A residue 1414 LEU Chi-restraints excluded: chain A residue 1435 GLN Chi-restraints excluded: chain A residue 1480 VAL Chi-restraints excluded: chain A residue 1498 VAL Chi-restraints excluded: chain A residue 1504 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 112 optimal weight: 6.9990 chunk 94 optimal weight: 0.5980 chunk 86 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 chunk 43 optimal weight: 2.9990 chunk 108 optimal weight: 0.9990 chunk 16 optimal weight: 5.9990 chunk 129 optimal weight: 0.9980 chunk 12 optimal weight: 0.9990 chunk 123 optimal weight: 8.9990 chunk 114 optimal weight: 1.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 834 GLN ** A1420 HIS ** 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 = 0.4112 r_free = 0.4112 target = 0.175017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.129043 restraints weight = 13119.655| |-----------------------------------------------------------------------------| r_work (start): 0.3590 rms_B_bonded: 2.14 r_work: 0.3377 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3230 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.4010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 10866 Z= 0.191 Angle : 0.602 7.444 14741 Z= 0.301 Chirality : 0.042 0.160 1717 Planarity : 0.004 0.054 1825 Dihedral : 8.426 117.142 1467 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 4.78 % Allowed : 21.67 % Favored : 73.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.21 (0.23), residues: 1310 helix: 1.67 (0.17), residues: 874 sheet: -0.18 (0.56), residues: 87 loop : -1.14 (0.32), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 775 TYR 0.021 0.002 TYR A1032 PHE 0.021 0.002 PHE A 558 TRP 0.026 0.001 TRP A 47 HIS 0.011 0.001 HIS A 985 Details of bonding type rmsd covalent geometry : bond 0.00459 (10866) covalent geometry : angle 0.60197 (14741) hydrogen bonds : bond 0.04479 ( 670) hydrogen bonds : angle 4.10435 ( 1986) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2620 Ramachandran restraints generated. 1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2620 Ramachandran restraints generated. 1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 151 time to evaluate : 0.425 Fit side-chains revert: symmetry clash REVERT: A 54 PHE cc_start: 0.6999 (OUTLIER) cc_final: 0.6783 (t80) REVERT: A 117 MET cc_start: 0.6957 (ttm) cc_final: 0.6236 (ttm) REVERT: A 194 ARG cc_start: 0.6665 (mtm110) cc_final: 0.6449 (ptt180) REVERT: A 488 LYS cc_start: 0.8088 (ttpp) cc_final: 0.7493 (mmtt) REVERT: A 503 LYS cc_start: 0.7428 (mttt) cc_final: 0.7160 (pptt) REVERT: A 518 TYR cc_start: 0.8258 (OUTLIER) cc_final: 0.6612 (p90) REVERT: A 617 ARG cc_start: 0.8129 (OUTLIER) cc_final: 0.7299 (ttp80) REVERT: A 696 ASP cc_start: 0.8681 (t0) cc_final: 0.7874 (m-30) REVERT: A 701 HIS cc_start: 0.8096 (t-170) cc_final: 0.7520 (t70) REVERT: A 758 ARG cc_start: 0.8152 (mtp85) cc_final: 0.7761 (mmt90) REVERT: A 835 MET cc_start: 0.8340 (mmt) cc_final: 0.8077 (mmt) REVERT: A 849 MET cc_start: 0.6077 (ttp) cc_final: 0.5622 (ttt) REVERT: A 984 ASN cc_start: 0.8767 (OUTLIER) cc_final: 0.8520 (t0) REVERT: A 1209 ILE cc_start: 0.8529 (OUTLIER) cc_final: 0.8238 (tt) REVERT: A 1300 ARG cc_start: 0.6583 (mmm160) cc_final: 0.5699 (mmm160) REVERT: A 1307 LEU cc_start: 0.8148 (OUTLIER) cc_final: 0.7893 (tp) REVERT: A 1312 ILE cc_start: 0.8830 (OUTLIER) cc_final: 0.8600 (mp) REVERT: A 1317 ASP cc_start: 0.7503 (t0) cc_final: 0.7194 (p0) REVERT: A 1353 ASP cc_start: 0.6440 (m-30) cc_final: 0.6190 (t0) REVERT: A 1367 PHE cc_start: 0.7464 (m-10) cc_final: 0.7108 (m-10) REVERT: A 1407 LEU cc_start: 0.7470 (OUTLIER) cc_final: 0.7199 (tt) REVERT: A 1495 ARG cc_start: 0.7362 (mtt180) cc_final: 0.7002 (mtt-85) outliers start: 56 outliers final: 41 residues processed: 193 average time/residue: 0.1084 time to fit residues: 29.6775 Evaluate side-chains 194 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 145 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 54 PHE Chi-restraints excluded: chain A residue 211 SER Chi-restraints excluded: chain A residue 212 SER Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain A residue 388 CYS Chi-restraints excluded: chain A residue 393 MET Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 483 MET Chi-restraints excluded: chain A residue 502 ILE Chi-restraints excluded: chain A residue 508 ILE Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 518 TYR Chi-restraints excluded: chain A residue 556 THR Chi-restraints excluded: chain A residue 571 VAL Chi-restraints excluded: chain A residue 580 GLN Chi-restraints excluded: chain A residue 597 ASN Chi-restraints excluded: chain A residue 617 ARG Chi-restraints excluded: chain A residue 625 LEU Chi-restraints excluded: chain A residue 665 THR Chi-restraints excluded: chain A residue 691 LEU Chi-restraints excluded: chain A residue 749 ASP Chi-restraints excluded: chain A residue 811 ILE Chi-restraints excluded: chain A residue 819 ASN Chi-restraints excluded: chain A residue 840 VAL Chi-restraints excluded: chain A residue 984 ASN Chi-restraints excluded: chain A residue 1027 ILE Chi-restraints excluded: chain A residue 1032 TYR Chi-restraints excluded: chain A residue 1065 ARG Chi-restraints excluded: chain A residue 1071 LEU Chi-restraints excluded: chain A residue 1072 VAL Chi-restraints excluded: chain A residue 1105 ILE Chi-restraints excluded: chain A residue 1106 ILE Chi-restraints excluded: chain A residue 1136 SER Chi-restraints excluded: chain A residue 1209 ILE Chi-restraints excluded: chain A residue 1244 ASN Chi-restraints excluded: chain A residue 1307 LEU Chi-restraints excluded: chain A residue 1309 LEU Chi-restraints excluded: chain A residue 1312 ILE Chi-restraints excluded: chain A residue 1342 ILE Chi-restraints excluded: chain A residue 1357 ILE Chi-restraints excluded: chain A residue 1363 HIS Chi-restraints excluded: chain A residue 1407 LEU Chi-restraints excluded: chain A residue 1414 LEU Chi-restraints excluded: chain A residue 1480 VAL Chi-restraints excluded: chain A residue 1498 VAL Chi-restraints excluded: chain A residue 1504 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 5 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 108 optimal weight: 0.4980 chunk 64 optimal weight: 2.9990 chunk 123 optimal weight: 0.7980 chunk 25 optimal weight: 0.9990 chunk 8 optimal weight: 0.9990 chunk 31 optimal weight: 0.5980 chunk 12 optimal weight: 1.9990 chunk 79 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1406 HIS ** A1420 HIS ** 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 = 0.4126 r_free = 0.4126 target = 0.175918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.130653 restraints weight = 13046.684| |-----------------------------------------------------------------------------| r_work (start): 0.3617 rms_B_bonded: 2.12 r_work: 0.3399 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3251 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.4149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10866 Z= 0.148 Angle : 0.583 11.080 14741 Z= 0.289 Chirality : 0.041 0.156 1717 Planarity : 0.004 0.055 1825 Dihedral : 8.355 114.802 1467 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 4.86 % Allowed : 21.59 % Favored : 73.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.33 (0.23), residues: 1310 helix: 1.77 (0.17), residues: 874 sheet: -0.12 (0.56), residues: 87 loop : -1.13 (0.32), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 171 TYR 0.019 0.001 TYR A1032 PHE 0.019 0.001 PHE A 558 TRP 0.027 0.001 TRP A 47 HIS 0.010 0.001 HIS A 985 Details of bonding type rmsd covalent geometry : bond 0.00348 (10866) covalent geometry : angle 0.58291 (14741) hydrogen bonds : bond 0.04186 ( 670) hydrogen bonds : angle 4.01244 ( 1986) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2620 Ramachandran restraints generated. 1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2620 Ramachandran restraints generated. 1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 152 time to evaluate : 0.417 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 488 LYS cc_start: 0.8110 (ttpp) cc_final: 0.7488 (mmtt) REVERT: A 503 LYS cc_start: 0.7572 (mttt) cc_final: 0.7238 (pptt) REVERT: A 518 TYR cc_start: 0.8218 (OUTLIER) cc_final: 0.7303 (p90) REVERT: A 617 ARG cc_start: 0.8081 (OUTLIER) cc_final: 0.7247 (ttp80) REVERT: A 696 ASP cc_start: 0.8708 (t0) cc_final: 0.7885 (m-30) REVERT: A 701 HIS cc_start: 0.8069 (t-170) cc_final: 0.7536 (t70) REVERT: A 758 ARG cc_start: 0.8177 (mtp85) cc_final: 0.7765 (mmt90) REVERT: A 835 MET cc_start: 0.8345 (mmt) cc_final: 0.8061 (mmt) REVERT: A 849 MET cc_start: 0.6007 (ttp) cc_final: 0.5557 (ttt) REVERT: A 984 ASN cc_start: 0.8745 (OUTLIER) cc_final: 0.8504 (t0) REVERT: A 1209 ILE cc_start: 0.8491 (OUTLIER) cc_final: 0.8222 (tt) REVERT: A 1300 ARG cc_start: 0.6750 (mmm160) cc_final: 0.5834 (mmm160) REVERT: A 1312 ILE cc_start: 0.8824 (mm) cc_final: 0.8601 (mp) REVERT: A 1317 ASP cc_start: 0.7472 (t0) cc_final: 0.7110 (p0) REVERT: A 1407 LEU cc_start: 0.7567 (OUTLIER) cc_final: 0.7285 (tt) REVERT: A 1435 GLN cc_start: 0.8585 (OUTLIER) cc_final: 0.8152 (mp10) REVERT: A 1495 ARG cc_start: 0.7330 (mtt180) cc_final: 0.6997 (mtt-85) outliers start: 57 outliers final: 43 residues processed: 197 average time/residue: 0.1119 time to fit residues: 31.1395 Evaluate side-chains 193 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 144 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 44 SER Chi-restraints excluded: chain A residue 130 ARG Chi-restraints excluded: chain A residue 211 SER Chi-restraints excluded: chain A residue 212 SER Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain A residue 388 CYS Chi-restraints excluded: chain A residue 393 MET Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 483 MET Chi-restraints excluded: chain A residue 502 ILE Chi-restraints excluded: chain A residue 508 ILE Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 518 TYR Chi-restraints excluded: chain A residue 556 THR Chi-restraints excluded: chain A residue 571 VAL Chi-restraints excluded: chain A residue 580 GLN Chi-restraints excluded: chain A residue 597 ASN Chi-restraints excluded: chain A residue 617 ARG Chi-restraints excluded: chain A residue 665 THR Chi-restraints excluded: chain A residue 677 VAL Chi-restraints excluded: chain A residue 691 LEU Chi-restraints excluded: chain A residue 819 ASN Chi-restraints excluded: chain A residue 839 ILE Chi-restraints excluded: chain A residue 840 VAL Chi-restraints excluded: chain A residue 984 ASN Chi-restraints excluded: chain A residue 1065 ARG Chi-restraints excluded: chain A residue 1071 LEU Chi-restraints excluded: chain A residue 1072 VAL Chi-restraints excluded: chain A residue 1105 ILE Chi-restraints excluded: chain A residue 1106 ILE Chi-restraints excluded: chain A residue 1136 SER Chi-restraints excluded: chain A residue 1209 ILE Chi-restraints excluded: chain A residue 1223 SER Chi-restraints excluded: chain A residue 1244 ASN Chi-restraints excluded: chain A residue 1309 LEU Chi-restraints excluded: chain A residue 1333 SER Chi-restraints excluded: chain A residue 1342 ILE Chi-restraints excluded: chain A residue 1357 ILE Chi-restraints excluded: chain A residue 1363 HIS Chi-restraints excluded: chain A residue 1365 LEU Chi-restraints excluded: chain A residue 1407 LEU Chi-restraints excluded: chain A residue 1414 LEU Chi-restraints excluded: chain A residue 1435 GLN Chi-restraints excluded: chain A residue 1480 VAL Chi-restraints excluded: chain A residue 1498 VAL Chi-restraints excluded: chain A residue 1504 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 96 optimal weight: 0.7980 chunk 21 optimal weight: 0.6980 chunk 130 optimal weight: 2.9990 chunk 42 optimal weight: 0.3980 chunk 29 optimal weight: 2.9990 chunk 62 optimal weight: 0.1980 chunk 98 optimal weight: 0.0870 chunk 14 optimal weight: 6.9990 chunk 125 optimal weight: 4.9990 chunk 32 optimal weight: 0.2980 chunk 77 optimal weight: 4.9990 overall best weight: 0.3358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 834 GLN ** A1420 HIS ** 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 = 0.4167 r_free = 0.4167 target = 0.180338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.135254 restraints weight = 12983.314| |-----------------------------------------------------------------------------| r_work (start): 0.3665 rms_B_bonded: 2.12 r_work: 0.3450 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3305 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.4274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10866 Z= 0.116 Angle : 0.560 11.550 14741 Z= 0.275 Chirality : 0.039 0.153 1717 Planarity : 0.004 0.054 1825 Dihedral : 8.169 113.444 1467 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 3.33 % Allowed : 23.12 % Favored : 73.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.62 (0.24), residues: 1310 helix: 2.02 (0.18), residues: 869 sheet: 0.04 (0.56), residues: 87 loop : -1.09 (0.32), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 775 TYR 0.019 0.001 TYR A1032 PHE 0.015 0.001 PHE A1294 TRP 0.028 0.001 TRP A 47 HIS 0.010 0.001 HIS A 985 Details of bonding type rmsd covalent geometry : bond 0.00255 (10866) covalent geometry : angle 0.56037 (14741) hydrogen bonds : bond 0.03782 ( 670) hydrogen bonds : angle 3.88502 ( 1986) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2620 Ramachandran restraints generated. 1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2620 Ramachandran restraints generated. 1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 151 time to evaluate : 0.420 Fit side-chains revert: symmetry clash REVERT: A 210 GLU cc_start: 0.8827 (OUTLIER) cc_final: 0.8468 (tp30) REVERT: A 488 LYS cc_start: 0.8164 (ttpp) cc_final: 0.7577 (mmtt) REVERT: A 503 LYS cc_start: 0.7617 (mttt) cc_final: 0.7311 (pptt) REVERT: A 518 TYR cc_start: 0.8075 (OUTLIER) cc_final: 0.6768 (p90) REVERT: A 534 GLU cc_start: 0.8362 (tm-30) cc_final: 0.8096 (tm-30) REVERT: A 617 ARG cc_start: 0.8061 (OUTLIER) cc_final: 0.7264 (ttp80) REVERT: A 696 ASP cc_start: 0.8820 (t0) cc_final: 0.7975 (m-30) REVERT: A 701 HIS cc_start: 0.7989 (t-170) cc_final: 0.7535 (t70) REVERT: A 758 ARG cc_start: 0.8161 (mtp85) cc_final: 0.7733 (mmt90) REVERT: A 835 MET cc_start: 0.8348 (mmt) cc_final: 0.8056 (mmt) REVERT: A 849 MET cc_start: 0.6053 (ttp) cc_final: 0.5609 (ttt) REVERT: A 984 ASN cc_start: 0.8693 (OUTLIER) cc_final: 0.8475 (t0) REVERT: A 1209 ILE cc_start: 0.8423 (OUTLIER) cc_final: 0.8145 (tt) REVERT: A 1300 ARG cc_start: 0.6741 (mmm160) cc_final: 0.5853 (mmm160) REVERT: A 1317 ASP cc_start: 0.7517 (t0) cc_final: 0.7181 (p0) REVERT: A 1407 LEU cc_start: 0.7492 (OUTLIER) cc_final: 0.7218 (tt) REVERT: A 1435 GLN cc_start: 0.8574 (OUTLIER) cc_final: 0.8177 (mp10) REVERT: A 1495 ARG cc_start: 0.7226 (mtt180) cc_final: 0.6876 (mtt-85) outliers start: 39 outliers final: 28 residues processed: 178 average time/residue: 0.1061 time to fit residues: 26.7679 Evaluate side-chains 174 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 139 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 210 GLU Chi-restraints excluded: chain A residue 212 SER Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 388 CYS Chi-restraints excluded: chain A residue 393 MET Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 483 MET Chi-restraints excluded: chain A residue 502 ILE Chi-restraints excluded: chain A residue 508 ILE Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 518 TYR Chi-restraints excluded: chain A residue 556 THR Chi-restraints excluded: chain A residue 597 ASN Chi-restraints excluded: chain A residue 617 ARG Chi-restraints excluded: chain A residue 691 LEU Chi-restraints excluded: chain A residue 819 ASN Chi-restraints excluded: chain A residue 839 ILE Chi-restraints excluded: chain A residue 840 VAL Chi-restraints excluded: chain A residue 984 ASN Chi-restraints excluded: chain A residue 1049 LEU Chi-restraints excluded: chain A residue 1065 ARG Chi-restraints excluded: chain A residue 1071 LEU Chi-restraints excluded: chain A residue 1136 SER Chi-restraints excluded: chain A residue 1209 ILE Chi-restraints excluded: chain A residue 1309 LEU Chi-restraints excluded: chain A residue 1333 SER Chi-restraints excluded: chain A residue 1357 ILE Chi-restraints excluded: chain A residue 1363 HIS Chi-restraints excluded: chain A residue 1407 LEU Chi-restraints excluded: chain A residue 1414 LEU Chi-restraints excluded: chain A residue 1435 GLN Chi-restraints excluded: chain A residue 1480 VAL Chi-restraints excluded: chain A residue 1498 VAL Chi-restraints excluded: chain A residue 1504 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 105 optimal weight: 2.9990 chunk 19 optimal weight: 0.8980 chunk 64 optimal weight: 2.9990 chunk 111 optimal weight: 3.9990 chunk 6 optimal weight: 5.9990 chunk 116 optimal weight: 2.9990 chunk 73 optimal weight: 0.6980 chunk 36 optimal weight: 1.9990 chunk 12 optimal weight: 0.5980 chunk 130 optimal weight: 0.0970 chunk 110 optimal weight: 0.7980 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 412 ASN A 834 GLN ** A1420 HIS ** 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 = 0.4144 r_free = 0.4144 target = 0.177992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.132552 restraints weight = 13019.924| |-----------------------------------------------------------------------------| r_work (start): 0.3631 rms_B_bonded: 2.09 r_work: 0.3424 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3277 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.4364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10866 Z= 0.136 Angle : 0.580 11.584 14741 Z= 0.285 Chirality : 0.040 0.153 1717 Planarity : 0.004 0.054 1825 Dihedral : 8.109 115.954 1467 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 3.58 % Allowed : 22.87 % Favored : 73.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.53 (0.23), residues: 1310 helix: 1.92 (0.17), residues: 875 sheet: 0.04 (0.56), residues: 87 loop : -1.10 (0.32), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 775 TYR 0.021 0.001 TYR A1032 PHE 0.028 0.001 PHE A 558 TRP 0.022 0.001 TRP A 47 HIS 0.011 0.001 HIS A 985 Details of bonding type rmsd covalent geometry : bond 0.00314 (10866) covalent geometry : angle 0.57998 (14741) hydrogen bonds : bond 0.03959 ( 670) hydrogen bonds : angle 3.92763 ( 1986) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2620 Ramachandran restraints generated. 1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2620 Ramachandran restraints generated. 1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 143 time to evaluate : 0.337 Fit side-chains revert: symmetry clash REVERT: A 171 ARG cc_start: 0.6856 (ttm110) cc_final: 0.6191 (mtp85) REVERT: A 210 GLU cc_start: 0.8830 (OUTLIER) cc_final: 0.8464 (tp30) REVERT: A 488 LYS cc_start: 0.8173 (ttpp) cc_final: 0.7600 (mmtm) REVERT: A 503 LYS cc_start: 0.7620 (mttt) cc_final: 0.7320 (pptt) REVERT: A 518 TYR cc_start: 0.8146 (OUTLIER) cc_final: 0.7015 (p90) REVERT: A 617 ARG cc_start: 0.8077 (OUTLIER) cc_final: 0.7292 (ttp80) REVERT: A 695 MET cc_start: 0.8847 (mmm) cc_final: 0.7950 (mmt) REVERT: A 696 ASP cc_start: 0.8802 (t0) cc_final: 0.7979 (m-30) REVERT: A 701 HIS cc_start: 0.8018 (t-170) cc_final: 0.7546 (t70) REVERT: A 758 ARG cc_start: 0.8274 (mtp85) cc_final: 0.7836 (mmt90) REVERT: A 835 MET cc_start: 0.8395 (mmt) cc_final: 0.8112 (mmt) REVERT: A 849 MET cc_start: 0.6059 (ttp) cc_final: 0.5611 (ttt) REVERT: A 1209 ILE cc_start: 0.8453 (OUTLIER) cc_final: 0.8201 (tt) REVERT: A 1300 ARG cc_start: 0.6757 (mmm160) cc_final: 0.5609 (mmm160) REVERT: A 1317 ASP cc_start: 0.7504 (t0) cc_final: 0.7198 (p0) REVERT: A 1407 LEU cc_start: 0.7510 (OUTLIER) cc_final: 0.7230 (tt) REVERT: A 1435 GLN cc_start: 0.8579 (OUTLIER) cc_final: 0.8177 (mp10) REVERT: A 1452 LEU cc_start: 0.7704 (OUTLIER) cc_final: 0.6969 (tt) REVERT: A 1495 ARG cc_start: 0.7320 (mtt180) cc_final: 0.6946 (mtt-85) outliers start: 42 outliers final: 29 residues processed: 176 average time/residue: 0.1097 time to fit residues: 27.6620 Evaluate side-chains 178 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 142 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 210 GLU Chi-restraints excluded: chain A residue 212 SER Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 388 CYS Chi-restraints excluded: chain A residue 393 MET Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 483 MET Chi-restraints excluded: chain A residue 502 ILE Chi-restraints excluded: chain A residue 508 ILE Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 518 TYR Chi-restraints excluded: chain A residue 556 THR Chi-restraints excluded: chain A residue 597 ASN Chi-restraints excluded: chain A residue 617 ARG Chi-restraints excluded: chain A residue 625 LEU Chi-restraints excluded: chain A residue 819 ASN Chi-restraints excluded: chain A residue 839 ILE Chi-restraints excluded: chain A residue 840 VAL Chi-restraints excluded: chain A residue 1065 ARG Chi-restraints excluded: chain A residue 1071 LEU Chi-restraints excluded: chain A residue 1136 SER Chi-restraints excluded: chain A residue 1209 ILE Chi-restraints excluded: chain A residue 1223 SER Chi-restraints excluded: chain A residue 1309 LEU Chi-restraints excluded: chain A residue 1333 SER Chi-restraints excluded: chain A residue 1357 ILE Chi-restraints excluded: chain A residue 1363 HIS Chi-restraints excluded: chain A residue 1365 LEU Chi-restraints excluded: chain A residue 1407 LEU Chi-restraints excluded: chain A residue 1414 LEU Chi-restraints excluded: chain A residue 1435 GLN Chi-restraints excluded: chain A residue 1452 LEU Chi-restraints excluded: chain A residue 1480 VAL Chi-restraints excluded: chain A residue 1498 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 115 optimal weight: 0.0970 chunk 36 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 47 optimal weight: 0.8980 chunk 121 optimal weight: 0.1980 chunk 91 optimal weight: 0.9980 chunk 59 optimal weight: 5.9990 chunk 75 optimal weight: 2.9990 chunk 46 optimal weight: 0.9980 chunk 51 optimal weight: 0.6980 chunk 83 optimal weight: 0.0370 overall best weight: 0.3856 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 834 GLN ** A1420 HIS ** 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 = 0.4161 r_free = 0.4161 target = 0.179580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.134651 restraints weight = 13055.442| |-----------------------------------------------------------------------------| r_work (start): 0.3659 rms_B_bonded: 2.13 r_work: 0.3446 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3300 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.4422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10866 Z= 0.117 Angle : 0.561 11.506 14741 Z= 0.276 Chirality : 0.039 0.156 1717 Planarity : 0.004 0.054 1825 Dihedral : 8.001 114.287 1467 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 3.16 % Allowed : 23.55 % Favored : 73.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.64 (0.23), residues: 1310 helix: 2.02 (0.18), residues: 870 sheet: 0.15 (0.56), residues: 87 loop : -1.06 (0.32), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 775 TYR 0.021 0.001 TYR A1032 PHE 0.025 0.001 PHE A 558 TRP 0.020 0.001 TRP A 47 HIS 0.012 0.001 HIS A 985 Details of bonding type rmsd covalent geometry : bond 0.00260 (10866) covalent geometry : angle 0.56096 (14741) hydrogen bonds : bond 0.03749 ( 670) hydrogen bonds : angle 3.87096 ( 1986) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3009.47 seconds wall clock time: 52 minutes 18.32 seconds (3138.32 seconds total)