Starting phenix.real_space_refine on Tue Jun 24 20:08:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5ojs_3824/06_2025/5ojs_3824.cif Found real_map, /net/cci-nas-00/data/ceres_data/5ojs_3824/06_2025/5ojs_3824.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/5ojs_3824/06_2025/5ojs_3824.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5ojs_3824/06_2025/5ojs_3824.map" model { file = "/net/cci-nas-00/data/ceres_data/5ojs_3824/06_2025/5ojs_3824.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5ojs_3824/06_2025/5ojs_3824.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.006 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 120 5.16 5 C 18391 2.51 5 N 4718 2.21 5 O 5178 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 51 residue(s): 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 28407 Number of models: 1 Model: "" Number of chains: 1 Chain: "T" Number of atoms: 28407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3473, 28407 Classifications: {'peptide': 3473} Link IDs: {'CIS': 4, 'PTRANS': 146, 'TRANS': 3322} Chain breaks: 14 Time building chain proxies: 16.51, per 1000 atoms: 0.58 Number of scatterers: 28407 At special positions: 0 Unit cell: (134.62, 204.58, 139.92, 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 120 16.00 O 5178 8.00 N 4718 7.00 C 18391 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: 7.81 Conformation dependent library (CDL) restraints added in 3.4 seconds 6886 Ramachandran restraints generated. 3443 Oldfield, 0 Emsley, 3443 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6780 Finding SS restraints... Secondary structure from input PDB file: 194 helices and 4 sheets defined 64.5% alpha, 1.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.67 Creating SS restraints... Processing helix chain 'T' and resid 3 through 8 removed outlier: 4.196A pdb=" N ILE T 7 " --> pdb=" O LEU T 3 " (cutoff:3.500A) Processing helix chain 'T' and resid 9 through 14 removed outlier: 4.391A pdb=" N SER T 12 " --> pdb=" O GLN T 9 " (cutoff:3.500A) Processing helix chain 'T' and resid 19 through 26 removed outlier: 3.699A pdb=" N SER T 23 " --> pdb=" O THR T 20 " (cutoff:3.500A) removed outlier: 5.395A pdb=" N ARG T 24 " --> pdb=" O LEU T 21 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N TYR T 25 " --> pdb=" O GLN T 22 " (cutoff:3.500A) Processing helix chain 'T' and resid 29 through 34 Processing helix chain 'T' and resid 43 through 59 removed outlier: 3.989A pdb=" N PHE T 47 " --> pdb=" O ASP T 43 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N GLN T 49 " --> pdb=" O HIS T 45 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N ALA T 50 " --> pdb=" O PHE T 46 " (cutoff:3.500A) Proline residue: T 53 - end of helix Processing helix chain 'T' and resid 73 through 84 removed outlier: 3.924A pdb=" N ASN T 77 " --> pdb=" O GLN T 73 " (cutoff:3.500A) Processing helix chain 'T' and resid 92 through 100 removed outlier: 5.199A pdb=" N GLU T 98 " --> pdb=" O PRO T 94 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N LEU T 100 " --> pdb=" O ALA T 96 " (cutoff:3.500A) Processing helix chain 'T' and resid 116 through 131 removed outlier: 3.970A pdb=" N THR T 124 " --> pdb=" O LYS T 120 " (cutoff:3.500A) Processing helix chain 'T' and resid 141 through 158 Proline residue: T 152 - end of helix removed outlier: 3.531A pdb=" N THR T 158 " --> pdb=" O LEU T 154 " (cutoff:3.500A) Processing helix chain 'T' and resid 217 through 221 removed outlier: 3.944A pdb=" N SER T 220 " --> pdb=" O SER T 217 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N PHE T 221 " --> pdb=" O MET T 218 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 217 through 221' Processing helix chain 'T' and resid 231 through 240 Processing helix chain 'T' and resid 248 through 254 removed outlier: 3.966A pdb=" N LEU T 252 " --> pdb=" O GLU T 248 " (cutoff:3.500A) Processing helix chain 'T' and resid 292 through 309 Processing helix chain 'T' and resid 324 through 335 removed outlier: 3.753A pdb=" N LEU T 328 " --> pdb=" O PHE T 324 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ASP T 335 " --> pdb=" O ARG T 331 " (cutoff:3.500A) Processing helix chain 'T' and resid 341 through 357 removed outlier: 3.512A pdb=" N LYS T 345 " --> pdb=" O SER T 341 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N GLU T 346 " --> pdb=" O SER T 342 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ILE T 354 " --> pdb=" O ALA T 350 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N THR T 357 " --> pdb=" O HIS T 353 " (cutoff:3.500A) Processing helix chain 'T' and resid 362 through 368 removed outlier: 3.598A pdb=" N LYS T 366 " --> pdb=" O LEU T 362 " (cutoff:3.500A) Processing helix chain 'T' and resid 374 through 379 removed outlier: 4.132A pdb=" N ASN T 379 " --> pdb=" O LEU T 376 " (cutoff:3.500A) Processing helix chain 'T' and resid 387 through 403 removed outlier: 3.566A pdb=" N TYR T 392 " --> pdb=" O ARG T 388 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N THR T 394 " --> pdb=" O LEU T 390 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N VAL T 395 " --> pdb=" O ALA T 391 " (cutoff:3.500A) Processing helix chain 'T' and resid 407 through 424 removed outlier: 4.742A pdb=" N GLY T 420 " --> pdb=" O LYS T 416 " (cutoff:3.500A) Processing helix chain 'T' and resid 429 through 442 Processing helix chain 'T' and resid 442 through 453 removed outlier: 3.791A pdb=" N ASN T 453 " --> pdb=" O LEU T 449 " (cutoff:3.500A) Processing helix chain 'T' and resid 454 through 456 No H-bonds generated for 'chain 'T' and resid 454 through 456' Processing helix chain 'T' and resid 457 through 497 removed outlier: 4.139A pdb=" N ILE T 467 " --> pdb=" O LEU T 463 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N ILE T 468 " --> pdb=" O LEU T 464 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N LEU T 478 " --> pdb=" O ARG T 474 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N ASN T 479 " --> pdb=" O PHE T 475 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ARG T 480 " --> pdb=" O LYS T 476 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N ASP T 483 " --> pdb=" O ASN T 479 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N THR T 484 " --> pdb=" O ARG T 480 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N LYS T 487 " --> pdb=" O ASP T 483 " (cutoff:3.500A) Processing helix chain 'T' and resid 501 through 506 removed outlier: 3.648A pdb=" N ASN T 505 " --> pdb=" O LYS T 502 " (cutoff:3.500A) Processing helix chain 'T' and resid 511 through 522 removed outlier: 3.630A pdb=" N PHE T 517 " --> pdb=" O GLU T 513 " (cutoff:3.500A) Processing helix chain 'T' and resid 563 through 567 removed outlier: 3.847A pdb=" N ALA T 567 " --> pdb=" O LYS T 564 " (cutoff:3.500A) Processing helix chain 'T' and resid 578 through 601 removed outlier: 4.532A pdb=" N THR T 596 " --> pdb=" O SER T 592 " (cutoff:3.500A) Processing helix chain 'T' and resid 602 through 605 removed outlier: 4.207A pdb=" N ASN T 605 " --> pdb=" O LYS T 602 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 602 through 605' Processing helix chain 'T' and resid 607 through 612 removed outlier: 3.855A pdb=" N TYR T 611 " --> pdb=" O PRO T 607 " (cutoff:3.500A) Processing helix chain 'T' and resid 615 through 619 Processing helix chain 'T' and resid 627 through 643 removed outlier: 4.654A pdb=" N VAL T 633 " --> pdb=" O GLU T 629 " (cutoff:3.500A) Processing helix chain 'T' and resid 644 through 648 removed outlier: 3.667A pdb=" N PHE T 647 " --> pdb=" O GLY T 644 " (cutoff:3.500A) Processing helix chain 'T' and resid 677 through 690 removed outlier: 3.796A pdb=" N LEU T 682 " --> pdb=" O ASP T 678 " (cutoff:3.500A) Processing helix chain 'T' and resid 698 through 714 removed outlier: 3.721A pdb=" N GLN T 704 " --> pdb=" O GLU T 700 " (cutoff:3.500A) Proline residue: T 707 - end of helix Processing helix chain 'T' and resid 719 through 728 Processing helix chain 'T' and resid 732 through 747 removed outlier: 4.730A pdb=" N GLY T 738 " --> pdb=" O PRO T 734 " (cutoff:3.500A) Processing helix chain 'T' and resid 755 through 771 removed outlier: 3.760A pdb=" N LYS T 767 " --> pdb=" O ILE T 763 " (cutoff:3.500A) Processing helix chain 'T' and resid 780 through 784 Processing helix chain 'T' and resid 788 through 801 removed outlier: 3.678A pdb=" N SER T 799 " --> pdb=" O SER T 795 " (cutoff:3.500A) Processing helix chain 'T' and resid 805 through 817 removed outlier: 4.210A pdb=" N PHE T 809 " --> pdb=" O PRO T 805 " (cutoff:3.500A) Processing helix chain 'T' and resid 823 through 827 removed outlier: 3.752A pdb=" N ASN T 826 " --> pdb=" O ARG T 823 " (cutoff:3.500A) Processing helix chain 'T' and resid 831 through 841 removed outlier: 3.906A pdb=" N LEU T 838 " --> pdb=" O ILE T 834 " (cutoff:3.500A) Processing helix chain 'T' and resid 855 through 864 removed outlier: 3.594A pdb=" N THR T 864 " --> pdb=" O GLU T 860 " (cutoff:3.500A) Processing helix chain 'T' and resid 879 through 890 removed outlier: 3.755A pdb=" N VAL T 884 " --> pdb=" O MET T 880 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N PHE T 885 " --> pdb=" O LYS T 881 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEU T 887 " --> pdb=" O LEU T 883 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N TYR T 890 " --> pdb=" O ALA T 886 " (cutoff:3.500A) Processing helix chain 'T' and resid 893 through 903 removed outlier: 3.943A pdb=" N LEU T 903 " --> pdb=" O ARG T 899 " (cutoff:3.500A) Processing helix chain 'T' and resid 917 through 919 No H-bonds generated for 'chain 'T' and resid 917 through 919' Processing helix chain 'T' and resid 920 through 932 removed outlier: 3.913A pdb=" N LYS T 926 " --> pdb=" O ASP T 922 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N PHE T 929 " --> pdb=" O SER T 925 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N LEU T 932 " --> pdb=" O LEU T 928 " (cutoff:3.500A) Processing helix chain 'T' and resid 940 through 952 Processing helix chain 'T' and resid 998 through 1006 removed outlier: 3.739A pdb=" N GLN T1005 " --> pdb=" O LEU T1001 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N SER T1006 " --> pdb=" O ASN T1002 " (cutoff:3.500A) Processing helix chain 'T' and resid 1010 through 1029 removed outlier: 3.965A pdb=" N TYR T1020 " --> pdb=" O SER T1016 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N THR T1022 " --> pdb=" O TYR T1018 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N CYS T1023 " --> pdb=" O LYS T1019 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N VAL T1024 " --> pdb=" O TYR T1020 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N LEU T1025 " --> pdb=" O LEU T1021 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N THR T1029 " --> pdb=" O LEU T1025 " (cutoff:3.500A) Processing helix chain 'T' and resid 1030 through 1033 Processing helix chain 'T' and resid 1041 through 1048 removed outlier: 3.660A pdb=" N THR T1045 " --> pdb=" O GLU T1041 " (cutoff:3.500A) Processing helix chain 'T' and resid 1068 through 1090 removed outlier: 4.732A pdb=" N ASN T1074 " --> pdb=" O ARG T1070 " (cutoff:3.500A) Processing helix chain 'T' and resid 1095 through 1110 Processing helix chain 'T' and resid 1112 through 1121 removed outlier: 4.097A pdb=" N ASN T1116 " --> pdb=" O LEU T1112 " (cutoff:3.500A) Processing helix chain 'T' and resid 1144 through 1148 Processing helix chain 'T' and resid 1159 through 1179 removed outlier: 3.960A pdb=" N VAL T1163 " --> pdb=" O GLU T1159 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N TYR T1179 " --> pdb=" O SER T1175 " (cutoff:3.500A) Processing helix chain 'T' and resid 1183 through 1188 Processing helix chain 'T' and resid 1188 through 1200 removed outlier: 4.050A pdb=" N GLU T1192 " --> pdb=" O SER T1188 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N GLN T1196 " --> pdb=" O GLU T1192 " (cutoff:3.500A) Processing helix chain 'T' and resid 1201 through 1203 No H-bonds generated for 'chain 'T' and resid 1201 through 1203' Processing helix chain 'T' and resid 1206 through 1221 removed outlier: 3.696A pdb=" N LEU T1214 " --> pdb=" O ARG T1210 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ASP T1221 " --> pdb=" O LYS T1217 " (cutoff:3.500A) Processing helix chain 'T' and resid 1228 through 1233 removed outlier: 3.707A pdb=" N LYS T1232 " --> pdb=" O VAL T1228 " (cutoff:3.500A) Processing helix chain 'T' and resid 1233 through 1247 removed outlier: 3.646A pdb=" N LEU T1237 " --> pdb=" O TYR T1233 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASN T1239 " --> pdb=" O TYR T1235 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N LEU T1245 " --> pdb=" O LEU T1241 " (cutoff:3.500A) Processing helix chain 'T' and resid 1260 through 1271 Processing helix chain 'T' and resid 1283 through 1294 Processing helix chain 'T' and resid 1301 through 1314 Processing helix chain 'T' and resid 1334 through 1340 removed outlier: 4.606A pdb=" N LYS T1340 " --> pdb=" O PRO T1336 " (cutoff:3.500A) Processing helix chain 'T' and resid 1346 through 1355 removed outlier: 3.895A pdb=" N GLN T1350 " --> pdb=" O PRO T1346 " (cutoff:3.500A) Processing helix chain 'T' and resid 1355 through 1362 removed outlier: 4.204A pdb=" N PHE T1359 " --> pdb=" O ASP T1355 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N CYS T1360 " --> pdb=" O ALA T1356 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N LEU T1361 " --> pdb=" O ILE T1357 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N SER T1362 " --> pdb=" O THR T1358 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 1355 through 1362' Processing helix chain 'T' and resid 1372 through 1384 Processing helix chain 'T' and resid 1403 through 1425 removed outlier: 4.105A pdb=" N ALA T1420 " --> pdb=" O ILE T1416 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ILE T1421 " --> pdb=" O LYS T1417 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ASN T1425 " --> pdb=" O ILE T1421 " (cutoff:3.500A) Processing helix chain 'T' and resid 1436 through 1447 removed outlier: 3.906A pdb=" N VAL T1443 " --> pdb=" O ARG T1439 " (cutoff:3.500A) Processing helix chain 'T' and resid 1448 through 1450 No H-bonds generated for 'chain 'T' and resid 1448 through 1450' Processing helix chain 'T' and resid 1452 through 1467 removed outlier: 3.614A pdb=" N ILE T1456 " --> pdb=" O SER T1452 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N THR T1458 " --> pdb=" O GLU T1454 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N GLY T1465 " --> pdb=" O GLU T1461 " (cutoff:3.500A) Processing helix chain 'T' and resid 1476 through 1481 removed outlier: 3.915A pdb=" N ASN T1480 " --> pdb=" O GLU T1476 " (cutoff:3.500A) Processing helix chain 'T' and resid 1482 through 1488 Processing helix chain 'T' and resid 1497 through 1507 removed outlier: 3.860A pdb=" N LEU T1503 " --> pdb=" O GLY T1499 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LYS T1505 " --> pdb=" O ASP T1501 " (cutoff:3.500A) Processing helix chain 'T' and resid 1517 through 1529 Processing helix chain 'T' and resid 1531 through 1537 removed outlier: 3.760A pdb=" N LEU T1535 " --> pdb=" O ARG T1531 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N THR T1537 " --> pdb=" O GLU T1533 " (cutoff:3.500A) Processing helix chain 'T' and resid 1546 through 1557 Processing helix chain 'T' and resid 1570 through 1584 removed outlier: 3.926A pdb=" N LEU T1574 " --> pdb=" O LEU T1570 " (cutoff:3.500A) Processing helix chain 'T' and resid 1593 through 1601 Processing helix chain 'T' and resid 1604 through 1614 removed outlier: 3.526A pdb=" N THR T1608 " --> pdb=" O HIS T1604 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLU T1609 " --> pdb=" O ASN T1605 " (cutoff:3.500A) Processing helix chain 'T' and resid 1617 through 1629 removed outlier: 3.754A pdb=" N ASN T1626 " --> pdb=" O LEU T1622 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ILE T1627 " --> pdb=" O PHE T1623 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N VAL T1628 " --> pdb=" O MET T1624 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLN T1629 " --> pdb=" O CYS T1625 " (cutoff:3.500A) Processing helix chain 'T' and resid 1639 through 1642 removed outlier: 3.757A pdb=" N LYS T1642 " --> pdb=" O ASP T1639 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 1639 through 1642' Processing helix chain 'T' and resid 1643 through 1654 removed outlier: 3.699A pdb=" N TYR T1648 " --> pdb=" O LEU T1644 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N ASP T1649 " --> pdb=" O ASP T1645 " (cutoff:3.500A) Processing helix chain 'T' and resid 1662 through 1679 removed outlier: 4.152A pdb=" N ASN T1668 " --> pdb=" O SER T1664 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N MET T1669 " --> pdb=" O PHE T1665 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ILE T1678 " --> pdb=" O ASN T1674 " (cutoff:3.500A) Processing helix chain 'T' and resid 1692 through 1709 removed outlier: 3.505A pdb=" N ASN T1709 " --> pdb=" O THR T1705 " (cutoff:3.500A) Processing helix chain 'T' and resid 1715 through 1734 removed outlier: 4.075A pdb=" N ALA T1723 " --> pdb=" O ASN T1719 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ALA T1727 " --> pdb=" O ALA T1723 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N GLU T1734 " --> pdb=" O LEU T1730 " (cutoff:3.500A) Processing helix chain 'T' and resid 1741 through 1750 removed outlier: 3.867A pdb=" N LEU T1745 " --> pdb=" O ASN T1741 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ASP T1746 " --> pdb=" O PRO T1742 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N PHE T1747 " --> pdb=" O LEU T1743 " (cutoff:3.500A) Processing helix chain 'T' and resid 1762 through 1769 removed outlier: 3.802A pdb=" N ILE T1766 " --> pdb=" O LEU T1762 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N HIS T1768 " --> pdb=" O LYS T1764 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ASN T1769 " --> pdb=" O PHE T1765 " (cutoff:3.500A) Processing helix chain 'T' and resid 1778 through 1791 removed outlier: 3.518A pdb=" N LEU T1791 " --> pdb=" O THR T1787 " (cutoff:3.500A) Processing helix chain 'T' and resid 1796 through 1817 Processing helix chain 'T' and resid 1833 through 1842 Processing helix chain 'T' and resid 1858 through 1875 removed outlier: 4.232A pdb=" N PHE T1862 " --> pdb=" O ASP T1858 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N PHE T1871 " --> pdb=" O LEU T1867 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ILE T1872 " --> pdb=" O SER T1868 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LYS T1873 " --> pdb=" O ALA T1869 " (cutoff:3.500A) Processing helix chain 'T' and resid 1879 through 1891 removed outlier: 3.569A pdb=" N LYS T1883 " --> pdb=" O ILE T1879 " (cutoff:3.500A) Processing helix chain 'T' and resid 1892 through 1896 Processing helix chain 'T' and resid 1901 through 1913 Processing helix chain 'T' and resid 1922 through 1929 Processing helix chain 'T' and resid 1938 through 1956 Proline residue: T1951 - end of helix Processing helix chain 'T' and resid 1964 through 1977 removed outlier: 4.151A pdb=" N VAL T1970 " --> pdb=" O TRP T1966 " (cutoff:3.500A) Processing helix chain 'T' and resid 1980 through 1988 removed outlier: 3.559A pdb=" N TYR T1986 " --> pdb=" O ASN T1982 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N PHE T1988 " --> pdb=" O ILE T1984 " (cutoff:3.500A) Processing helix chain 'T' and resid 1989 through 1991 No H-bonds generated for 'chain 'T' and resid 1989 through 1991' Processing helix chain 'T' and resid 2001 through 2014 removed outlier: 4.730A pdb=" N SER T2005 " --> pdb=" O ASP T2001 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N ASN T2006 " --> pdb=" O LEU T2002 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ILE T2007 " --> pdb=" O PHE T2003 " (cutoff:3.500A) Processing helix chain 'T' and resid 2024 through 2042 removed outlier: 3.560A pdb=" N ALA T2028 " --> pdb=" O SER T2024 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ALA T2032 " --> pdb=" O ALA T2028 " (cutoff:3.500A) Processing helix chain 'T' and resid 2090 through 2107 Processing helix chain 'T' and resid 2116 through 2128 removed outlier: 3.587A pdb=" N ILE T2128 " --> pdb=" O LEU T2124 " (cutoff:3.500A) Processing helix chain 'T' and resid 2140 through 2145 removed outlier: 3.520A pdb=" N PHE T2143 " --> pdb=" O LEU T2140 " (cutoff:3.500A) Processing helix chain 'T' and resid 2157 through 2174 removed outlier: 3.572A pdb=" N LYS T2173 " --> pdb=" O TYR T2169 " (cutoff:3.500A) Processing helix chain 'T' and resid 2183 through 2192 removed outlier: 3.734A pdb=" N ILE T2187 " --> pdb=" O ASN T2183 " (cutoff:3.500A) Processing helix chain 'T' and resid 2196 through 2200 removed outlier: 3.861A pdb=" N HIS T2199 " --> pdb=" O LYS T2196 " (cutoff:3.500A) Processing helix chain 'T' and resid 2203 through 2218 removed outlier: 5.346A pdb=" N GLN T2211 " --> pdb=" O GLN T2207 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N VAL T2212 " --> pdb=" O LYS T2208 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LYS T2218 " --> pdb=" O MET T2214 " (cutoff:3.500A) Processing helix chain 'T' and resid 2229 through 2244 removed outlier: 3.982A pdb=" N MET T2238 " --> pdb=" O THR T2234 " (cutoff:3.500A) Processing helix chain 'T' and resid 2249 through 2252 removed outlier: 3.642A pdb=" N SER T2252 " --> pdb=" O GLU T2249 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 2249 through 2252' Processing helix chain 'T' and resid 2253 through 2265 removed outlier: 3.705A pdb=" N VAL T2257 " --> pdb=" O VAL T2253 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N THR T2258 " --> pdb=" O THR T2254 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ALA T2260 " --> pdb=" O GLY T2256 " (cutoff:3.500A) Processing helix chain 'T' and resid 2275 through 2287 removed outlier: 3.714A pdb=" N MET T2279 " --> pdb=" O LEU T2275 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LYS T2287 " --> pdb=" O SER T2283 " (cutoff:3.500A) Processing helix chain 'T' and resid 2289 through 2294 Processing helix chain 'T' and resid 2302 through 2321 removed outlier: 4.369A pdb=" N THR T2308 " --> pdb=" O ALA T2304 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N SER T2319 " --> pdb=" O LEU T2315 " (cutoff:3.500A) Processing helix chain 'T' and resid 2328 through 2342 removed outlier: 3.809A pdb=" N VAL T2336 " --> pdb=" O PHE T2332 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N HIS T2342 " --> pdb=" O LEU T2338 " (cutoff:3.500A) Processing helix chain 'T' and resid 2346 through 2361 removed outlier: 3.708A pdb=" N LYS T2351 " --> pdb=" O ASN T2347 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N ILE T2352 " --> pdb=" O PHE T2348 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N PHE T2361 " --> pdb=" O ARG T2357 " (cutoff:3.500A) Processing helix chain 'T' and resid 2368 through 2377 removed outlier: 4.393A pdb=" N LYS T2372 " --> pdb=" O THR T2368 " (cutoff:3.500A) Processing helix chain 'T' and resid 2380 through 2386 removed outlier: 4.227A pdb=" N ILE T2384 " --> pdb=" O LEU T2380 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N GLY T2386 " --> pdb=" O PHE T2382 " (cutoff:3.500A) Processing helix chain 'T' and resid 2390 through 2404 removed outlier: 3.947A pdb=" N PHE T2394 " --> pdb=" O LEU T2390 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLN T2404 " --> pdb=" O LYS T2400 " (cutoff:3.500A) Processing helix chain 'T' and resid 2428 through 2441 Processing helix chain 'T' and resid 2447 through 2456 removed outlier: 4.496A pdb=" N TYR T2453 " --> pdb=" O GLU T2449 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ILE T2455 " --> pdb=" O LEU T2451 " (cutoff:3.500A) Processing helix chain 'T' and resid 2468 through 2478 removed outlier: 3.708A pdb=" N ALA T2472 " --> pdb=" O TRP T2468 " (cutoff:3.500A) Processing helix chain 'T' and resid 2498 through 2502 removed outlier: 3.517A pdb=" N GLU T2502 " --> pdb=" O ILE T2499 " (cutoff:3.500A) Processing helix chain 'T' and resid 2518 through 2534 removed outlier: 4.980A pdb=" N LYS T2524 " --> pdb=" O SER T2520 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N GLY T2525 " --> pdb=" O ASN T2521 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N HIS T2526 " --> pdb=" O PHE T2522 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ILE T2527 " --> pdb=" O VAL T2523 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N GLY T2532 " --> pdb=" O ALA T2528 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N CYS T2534 " --> pdb=" O MET T2530 " (cutoff:3.500A) Processing helix chain 'T' and resid 2537 through 2543 Processing helix chain 'T' and resid 2545 through 2550 removed outlier: 3.603A pdb=" N PHE T2549 " --> pdb=" O LEU T2545 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N TYR T2550 " --> pdb=" O ILE T2546 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 2545 through 2550' Processing helix chain 'T' and resid 2554 through 2568 removed outlier: 3.703A pdb=" N ARG T2558 " --> pdb=" O LYS T2554 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N THR T2562 " --> pdb=" O ARG T2558 " (cutoff:3.500A) Proline residue: T2565 - end of helix Processing helix chain 'T' and resid 2569 through 2571 No H-bonds generated for 'chain 'T' and resid 2569 through 2571' Processing helix chain 'T' and resid 2575 through 2588 removed outlier: 3.685A pdb=" N PHE T2579 " --> pdb=" O GLU T2575 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N THR T2585 " --> pdb=" O ARG T2581 " (cutoff:3.500A) Processing helix chain 'T' and resid 2604 through 2612 removed outlier: 3.554A pdb=" N SER T2609 " --> pdb=" O MET T2605 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N ILE T2610 " --> pdb=" O LEU T2606 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N SER T2611 " --> pdb=" O LEU T2607 " (cutoff:3.500A) Processing helix chain 'T' and resid 2622 through 2627 removed outlier: 3.597A pdb=" N ALA T2627 " --> pdb=" O VAL T2623 " (cutoff:3.500A) Processing helix chain 'T' and resid 2636 through 2642 Processing helix chain 'T' and resid 2643 through 2646 Processing helix chain 'T' and resid 2651 through 2670 removed outlier: 3.907A pdb=" N ILE T2655 " --> pdb=" O ASN T2651 " (cutoff:3.500A) Processing helix chain 'T' and resid 2672 through 2681 removed outlier: 4.217A pdb=" N GLY T2677 " --> pdb=" O ASP T2673 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N LEU T2678 " --> pdb=" O MET T2674 " (cutoff:3.500A) Processing helix chain 'T' and resid 2685 through 2696 removed outlier: 4.175A pdb=" N ASN T2689 " --> pdb=" O TYR T2685 " (cutoff:3.500A) Processing helix chain 'T' and resid 2699 through 2714 removed outlier: 3.759A pdb=" N VAL T2712 " --> pdb=" O GLU T2708 " (cutoff:3.500A) Processing helix chain 'T' and resid 2720 through 2723 removed outlier: 3.630A pdb=" N GLN T2723 " --> pdb=" O PRO T2720 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 2720 through 2723' Processing helix chain 'T' and resid 2724 through 2741 removed outlier: 4.192A pdb=" N LEU T2740 " --> pdb=" O CYS T2736 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLN T2741 " --> pdb=" O ALA T2737 " (cutoff:3.500A) Processing helix chain 'T' and resid 2744 through 2747 removed outlier: 3.845A pdb=" N THR T2747 " --> pdb=" O ASP T2744 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 2744 through 2747' Processing helix chain 'T' and resid 2748 through 2753 removed outlier: 3.512A pdb=" N GLU T2753 " --> pdb=" O LEU T2749 " (cutoff:3.500A) Processing helix chain 'T' and resid 2754 through 2759 removed outlier: 4.311A pdb=" N LEU T2759 " --> pdb=" O PHE T2755 " (cutoff:3.500A) Processing helix chain 'T' and resid 2776 through 2781 Processing helix chain 'T' and resid 2788 through 2806 removed outlier: 3.881A pdb=" N ALA T2799 " --> pdb=" O LYS T2795 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ALA T2804 " --> pdb=" O LEU T2800 " (cutoff:3.500A) Processing helix chain 'T' and resid 2812 through 2816 removed outlier: 3.590A pdb=" N LYS T2815 " --> pdb=" O GLU T2812 " (cutoff:3.500A) Processing helix chain 'T' and resid 2817 through 2831 removed outlier: 3.583A pdb=" N SER T2824 " --> pdb=" O GLY T2820 " (cutoff:3.500A) Processing helix chain 'T' and resid 2837 through 2859 removed outlier: 4.268A pdb=" N TRP T2841 " --> pdb=" O PRO T2837 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N LEU T2842 " --> pdb=" O ALA T2838 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N GLU T2851 " --> pdb=" O GLN T2847 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N GLU T2854 " --> pdb=" O MET T2850 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N TYR T2859 " --> pdb=" O ALA T2855 " (cutoff:3.500A) Processing helix chain 'T' and resid 2859 through 2864 Processing helix chain 'T' and resid 2875 through 2883 Processing helix chain 'T' and resid 2884 through 2886 No H-bonds generated for 'chain 'T' and resid 2884 through 2886' Processing helix chain 'T' and resid 2894 through 2915 Processing helix chain 'T' and resid 2943 through 2957 Processing helix chain 'T' and resid 2959 through 2966 removed outlier: 3.752A pdb=" N CYS T2963 " --> pdb=" O MET T2959 " (cutoff:3.500A) Processing helix chain 'T' and resid 2979 through 2991 Processing helix chain 'T' and resid 2992 through 2994 No H-bonds generated for 'chain 'T' and resid 2992 through 2994' Processing helix chain 'T' and resid 2995 through 3001 removed outlier: 3.978A pdb=" N THR T3000 " --> pdb=" O ASN T2997 " (cutoff:3.500A) Processing helix chain 'T' and resid 3015 through 3018 removed outlier: 4.651A pdb=" N GLN T3018 " --> pdb=" O GLY T3015 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 3015 through 3018' Processing helix chain 'T' and resid 3019 through 3033 removed outlier: 4.274A pdb=" N GLY T3027 " --> pdb=" O PHE T3023 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LEU T3033 " --> pdb=" O PHE T3029 " (cutoff:3.500A) Processing helix chain 'T' and resid 3037 through 3051 removed outlier: 4.131A pdb=" N GLN T3048 " --> pdb=" O ALA T3044 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N ASP T3050 " --> pdb=" O ALA T3046 " (cutoff:3.500A) Processing helix chain 'T' and resid 3054 through 3069 removed outlier: 3.963A pdb=" N TRP T3060 " --> pdb=" O ALA T3056 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLY T3061 " --> pdb=" O TRP T3057 " (cutoff:3.500A) Processing helix chain 'T' and resid 3075 through 3077 No H-bonds generated for 'chain 'T' and resid 3075 through 3077' Processing helix chain 'T' and resid 3078 through 3087 Processing helix chain 'T' and resid 3097 through 3108 removed outlier: 3.666A pdb=" N TRP T3106 " --> pdb=" O CYS T3102 " (cutoff:3.500A) Processing helix chain 'T' and resid 3115 through 3123 Processing helix chain 'T' and resid 3133 through 3135 No H-bonds generated for 'chain 'T' and resid 3133 through 3135' Processing helix chain 'T' and resid 3136 through 3142 Processing helix chain 'T' and resid 3151 through 3162 removed outlier: 4.015A pdb=" N ILE T3155 " --> pdb=" O MET T3151 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N ARG T3158 " --> pdb=" O HIS T3154 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ILE T3159 " --> pdb=" O ILE T3155 " (cutoff:3.500A) Processing helix chain 'T' and resid 3164 through 3182 removed outlier: 4.807A pdb=" N PHE T3169 " --> pdb=" O GLN T3165 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N GLN T3170 " --> pdb=" O ALA T3166 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N THR T3173 " --> pdb=" O PHE T3169 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N VAL T3180 " --> pdb=" O GLU T3176 " (cutoff:3.500A) Processing helix chain 'T' and resid 3203 through 3218 removed outlier: 3.808A pdb=" N GLU T3210 " --> pdb=" O GLU T3206 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU T3211 " --> pdb=" O TYR T3207 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ASN T3212 " --> pdb=" O LEU T3208 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA T3218 " --> pdb=" O ILE T3214 " (cutoff:3.500A) Processing helix chain 'T' and resid 3219 through 3237 removed outlier: 3.506A pdb=" N ALA T3223 " --> pdb=" O TYR T3219 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LEU T3229 " --> pdb=" O SER T3225 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N PHE T3237 " --> pdb=" O ILE T3233 " (cutoff:3.500A) Processing helix chain 'T' and resid 3242 through 3261 removed outlier: 3.617A pdb=" N LEU T3258 " --> pdb=" O ILE T3254 " (cutoff:3.500A) Processing helix chain 'T' and resid 3273 through 3283 removed outlier: 3.759A pdb=" N GLU T3277 " --> pdb=" O PRO T3273 " (cutoff:3.500A) Processing helix chain 'T' and resid 3284 through 3287 Processing helix chain 'T' and resid 3292 through 3298 Processing helix chain 'T' and resid 3308 through 3325 removed outlier: 3.692A pdb=" N LYS T3312 " --> pdb=" O GLU T3308 " (cutoff:3.500A) Processing helix chain 'T' and resid 3333 through 3338 Processing helix chain 'T' and resid 3412 through 3423 removed outlier: 3.642A pdb=" N GLU T3416 " --> pdb=" O HIS T3412 " (cutoff:3.500A) Processing helix chain 'T' and resid 3426 through 3433 removed outlier: 3.708A pdb=" N ASN T3433 " --> pdb=" O SER T3429 " (cutoff:3.500A) Processing helix chain 'T' and resid 3467 through 3478 Processing helix chain 'T' and resid 3482 through 3496 removed outlier: 4.089A pdb=" N GLN T3486 " --> pdb=" O PRO T3482 " (cutoff:3.500A) Processing helix chain 'T' and resid 3506 through 3521 removed outlier: 3.672A pdb=" N GLU T3512 " --> pdb=" O ILE T3508 " (cutoff:3.500A) Processing helix chain 'T' and resid 3525 through 3532 Processing helix chain 'T' and resid 3538 through 3561 removed outlier: 3.531A pdb=" N PHE T3544 " --> pdb=" O ASP T3540 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLN T3547 " --> pdb=" O LEU T3543 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N SER T3550 " --> pdb=" O LYS T3546 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N SER T3553 " --> pdb=" O ALA T3549 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N MET T3558 " --> pdb=" O SER T3554 " (cutoff:3.500A) Processing helix chain 'T' and resid 3625 through 3633 removed outlier: 4.741A pdb=" N LEU T3631 " --> pdb=" O ASN T3627 " (cutoff:3.500A) Processing helix chain 'T' and resid 3635 through 3640 Processing helix chain 'T' and resid 3640 through 3653 removed outlier: 4.219A pdb=" N SER T3649 " --> pdb=" O LEU T3645 " (cutoff:3.500A) Processing helix chain 'T' and resid 3657 through 3678 removed outlier: 3.571A pdb=" N THR T3661 " --> pdb=" O ASN T3657 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N LEU T3665 " --> pdb=" O THR T3661 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N GLU T3670 " --> pdb=" O PHE T3666 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N LEU T3678 " --> pdb=" O TRP T3674 " (cutoff:3.500A) Processing helix chain 'T' and resid 3686 through 3703 removed outlier: 4.529A pdb=" N GLU T3690 " --> pdb=" O PRO T3686 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N ASN T3695 " --> pdb=" O MET T3691 " (cutoff:3.500A) Processing helix chain 'T' and resid 3717 through 3728 Processing helix chain 'T' and resid 3729 through 3735 removed outlier: 3.913A pdb=" N ARG T3735 " --> pdb=" O ARG T3731 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'T' and resid 3331 through 3332 Processing sheet with id=AA2, first strand: chain 'T' and resid 3371 through 3374 Processing sheet with id=AA3, first strand: chain 'T' and resid 3371 through 3374 removed outlier: 3.575A pdb=" N ARG T3389 " --> pdb=" O VAL T3405 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLN T3406 " --> pdb=" O ARG T3456 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ARG T3456 " --> pdb=" O GLN T3406 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ILE T3449 " --> pdb=" O ILE T3457 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'T' and resid 3572 through 3574 1254 hydrogen bonds defined for protein. 3666 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: 14.69 Time building geometry restraints manager: 9.14 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: 7393 1.33 - 1.45: 5388 1.45 - 1.57: 16041 1.57 - 1.69: 1 1.69 - 1.81: 203 Bond restraints: 29026 Sorted by residual: bond pdb=" C VAL T 325 " pdb=" N PRO T 326 " ideal model delta sigma weight residual 1.334 1.417 -0.083 2.34e-02 1.83e+03 1.25e+01 bond pdb=" CB LYS T1804 " pdb=" CG LYS T1804 " ideal model delta sigma weight residual 1.520 1.434 0.086 3.00e-02 1.11e+03 8.26e+00 bond pdb=" C ILE T3137 " pdb=" N PRO T3138 " ideal model delta sigma weight residual 1.334 1.400 -0.066 2.34e-02 1.83e+03 8.07e+00 bond pdb=" CA MET T 254 " pdb=" C MET T 254 " ideal model delta sigma weight residual 1.523 1.557 -0.034 1.34e-02 5.57e+03 6.26e+00 bond pdb=" CB ASN T2163 " pdb=" CG ASN T2163 " ideal model delta sigma weight residual 1.516 1.577 -0.061 2.50e-02 1.60e+03 5.98e+00 ... (remaining 29021 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.06: 38725 5.06 - 10.12: 540 10.12 - 15.18: 46 15.18 - 20.24: 10 20.24 - 25.30: 2 Bond angle restraints: 39323 Sorted by residual: angle pdb=" C ILE T1157 " pdb=" N PRO T1158 " pdb=" CA PRO T1158 " ideal model delta sigma weight residual 119.84 139.17 -19.33 1.25e+00 6.40e-01 2.39e+02 angle pdb=" C LEU T2888 " pdb=" N PRO T2889 " pdb=" CA PRO T2889 " ideal model delta sigma weight residual 119.84 131.82 -11.98 1.25e+00 6.40e-01 9.19e+01 angle pdb=" CA LEU T3053 " pdb=" CB LEU T3053 " pdb=" CG LEU T3053 " ideal model delta sigma weight residual 116.30 141.60 -25.30 3.50e+00 8.16e-02 5.22e+01 angle pdb=" C VAL T3715 " pdb=" N THR T3716 " pdb=" CA THR T3716 " ideal model delta sigma weight residual 121.54 135.07 -13.53 1.91e+00 2.74e-01 5.01e+01 angle pdb=" CA LEU T1825 " pdb=" CB LEU T1825 " pdb=" CG LEU T1825 " ideal model delta sigma weight residual 116.30 140.90 -24.60 3.50e+00 8.16e-02 4.94e+01 ... (remaining 39318 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.84: 15947 16.84 - 33.67: 1351 33.67 - 50.51: 306 50.51 - 67.35: 14 67.35 - 84.18: 26 Dihedral angle restraints: 17644 sinusoidal: 7278 harmonic: 10366 Sorted by residual: dihedral pdb=" CA LEU T2888 " pdb=" C LEU T2888 " pdb=" N PRO T2889 " pdb=" CA PRO T2889 " ideal model delta harmonic sigma weight residual -180.00 -108.71 -71.29 0 5.00e+00 4.00e-02 2.03e+02 dihedral pdb=" CA ILE T1157 " pdb=" C ILE T1157 " pdb=" N PRO T1158 " pdb=" CA PRO T1158 " ideal model delta harmonic sigma weight residual -180.00 -111.71 -68.29 0 5.00e+00 4.00e-02 1.87e+02 dihedral pdb=" CA GLU T3618 " pdb=" C GLU T3618 " pdb=" N PRO T3619 " pdb=" CA PRO T3619 " ideal model delta harmonic sigma weight residual -180.00 -119.83 -60.17 0 5.00e+00 4.00e-02 1.45e+02 ... (remaining 17641 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.102: 3969 0.102 - 0.205: 483 0.205 - 0.307: 40 0.307 - 0.410: 6 0.410 - 0.512: 3 Chirality restraints: 4501 Sorted by residual: chirality pdb=" CG LEU T1825 " pdb=" CB LEU T1825 " pdb=" CD1 LEU T1825 " pdb=" CD2 LEU T1825 " both_signs ideal model delta sigma weight residual False -2.59 -2.08 -0.51 2.00e-01 2.50e+01 6.55e+00 chirality pdb=" CG LEU T 876 " pdb=" CB LEU T 876 " pdb=" CD1 LEU T 876 " pdb=" CD2 LEU T 876 " both_signs ideal model delta sigma weight residual False -2.59 -2.11 -0.48 2.00e-01 2.50e+01 5.71e+00 chirality pdb=" CG LEU T 440 " pdb=" CB LEU T 440 " pdb=" CD1 LEU T 440 " pdb=" CD2 LEU T 440 " both_signs ideal model delta sigma weight residual False -2.59 -2.17 -0.42 2.00e-01 2.50e+01 4.38e+00 ... (remaining 4498 not shown) Planarity restraints: 4969 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU T 246 " 0.093 5.00e-02 4.00e+02 1.42e-01 3.23e+01 pdb=" N PRO T 247 " -0.246 5.00e-02 4.00e+02 pdb=" CA PRO T 247 " 0.078 5.00e-02 4.00e+02 pdb=" CD PRO T 247 " 0.075 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS T 227 " 0.075 5.00e-02 4.00e+02 1.15e-01 2.11e+01 pdb=" N PRO T 228 " -0.199 5.00e-02 4.00e+02 pdb=" CA PRO T 228 " 0.061 5.00e-02 4.00e+02 pdb=" CD PRO T 228 " 0.063 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU T 851 " 0.075 5.00e-02 4.00e+02 1.15e-01 2.10e+01 pdb=" N PRO T 852 " -0.198 5.00e-02 4.00e+02 pdb=" CA PRO T 852 " 0.061 5.00e-02 4.00e+02 pdb=" CD PRO T 852 " 0.062 5.00e-02 4.00e+02 ... (remaining 4966 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 3570 2.75 - 3.29: 28916 3.29 - 3.82: 46176 3.82 - 4.36: 55314 4.36 - 4.90: 88734 Nonbonded interactions: 222710 Sorted by model distance: nonbonded pdb=" O GLU T2303 " pdb=" OG1 THR T2307 " model vdw 2.211 3.040 nonbonded pdb=" O VAL T3643 " pdb=" OG1 THR T3647 " model vdw 2.242 3.040 nonbonded pdb=" O LEU T2168 " pdb=" NZ LYS T2215 " model vdw 2.273 3.120 nonbonded pdb=" OG SER T2693 " pdb=" O VAL T3715 " model vdw 2.273 3.040 nonbonded pdb=" O TYR T 585 " pdb=" OG1 THR T 589 " model vdw 2.278 3.040 ... (remaining 222705 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 1.310 Check model and map are aligned: 0.220 Set scattering table: 0.250 Process input model: 70.380 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 77.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7465 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 0.092 29026 Z= 0.318 Angle : 1.429 25.298 39323 Z= 0.714 Chirality : 0.071 0.512 4501 Planarity : 0.009 0.142 4969 Dihedral : 13.414 84.182 10864 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.64 % Allowed : 14.75 % Favored : 84.61 % Rotamer: Outliers : 2.09 % Allowed : 9.66 % Favored : 88.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 10.96 % Twisted General : 1.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.58 (0.11), residues: 3443 helix: -3.55 (0.07), residues: 1969 sheet: -2.88 (0.70), residues: 33 loop : -3.82 (0.15), residues: 1441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.004 TRP T3060 HIS 0.010 0.003 HIS T3346 PHE 0.045 0.004 PHE T3614 TYR 0.055 0.004 TYR T2316 ARG 0.012 0.001 ARG T1161 Details of bonding type rmsd hydrogen bonds : bond 0.16868 ( 1252) hydrogen bonds : angle 10.70719 ( 3666) covalent geometry : bond 0.00727 (29026) covalent geometry : angle 1.42889 (39323) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6886 Ramachandran restraints generated. 3443 Oldfield, 0 Emsley, 3443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6886 Ramachandran restraints generated. 3443 Oldfield, 0 Emsley, 3443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 685 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 618 time to evaluate : 3.179 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: T 38 LEU cc_start: 0.6668 (OUTLIER) cc_final: 0.4704 (mt) REVERT: T 58 GLN cc_start: 0.7676 (tt0) cc_final: 0.7468 (pt0) REVERT: T 119 MET cc_start: 0.5347 (tpt) cc_final: 0.4574 (mpp) REVERT: T 421 TYR cc_start: 0.7899 (m-10) cc_final: 0.7633 (m-80) REVERT: T 453 ASN cc_start: 0.8061 (p0) cc_final: 0.7567 (p0) REVERT: T 459 ARG cc_start: 0.7694 (tmm-80) cc_final: 0.7458 (mtp180) REVERT: T 504 LYS cc_start: 0.7093 (mptt) cc_final: 0.6497 (mmmt) REVERT: T 565 ASN cc_start: 0.7079 (m-40) cc_final: 0.6626 (t0) REVERT: T 838 LEU cc_start: 0.8332 (mp) cc_final: 0.8097 (mp) REVERT: T 965 ASP cc_start: 0.8169 (p0) cc_final: 0.7934 (p0) REVERT: T 1196 GLN cc_start: 0.7489 (mm-40) cc_final: 0.7181 (mm-40) REVERT: T 1373 GLU cc_start: 0.6953 (mp0) cc_final: 0.6650 (mp0) REVERT: T 1377 LEU cc_start: 0.6745 (OUTLIER) cc_final: 0.6397 (pp) REVERT: T 1439 ARG cc_start: 0.8181 (tmt170) cc_final: 0.7962 (tpt170) REVERT: T 1478 LEU cc_start: 0.9171 (mm) cc_final: 0.8811 (mt) REVERT: T 1516 VAL cc_start: 0.7896 (t) cc_final: 0.7683 (t) REVERT: T 1517 GLU cc_start: 0.7010 (pp20) cc_final: 0.6630 (mp0) REVERT: T 1639 ASP cc_start: 0.8481 (t70) cc_final: 0.8240 (t0) REVERT: T 1669 MET cc_start: 0.8276 (tpp) cc_final: 0.7994 (tpp) REVERT: T 1686 LYS cc_start: 0.7442 (mppt) cc_final: 0.7155 (mmmt) REVERT: T 1879 ILE cc_start: 0.7153 (pt) cc_final: 0.6754 (mm) REVERT: T 1882 ILE cc_start: 0.7826 (mm) cc_final: 0.7345 (tt) REVERT: T 2123 ILE cc_start: 0.8951 (mt) cc_final: 0.8740 (mt) REVERT: T 2208 LYS cc_start: 0.7045 (mmmm) cc_final: 0.6509 (mttt) REVERT: T 2228 GLU cc_start: 0.7827 (tp30) cc_final: 0.6912 (mp0) REVERT: T 2238 MET cc_start: 0.8093 (tpt) cc_final: 0.7868 (tpp) REVERT: T 2261 TRP cc_start: 0.7883 (t60) cc_final: 0.7203 (t60) REVERT: T 2270 ASN cc_start: 0.8273 (t0) cc_final: 0.7943 (t0) REVERT: T 2330 ARG cc_start: 0.7861 (ppp-140) cc_final: 0.7658 (mmt180) REVERT: T 2350 ARG cc_start: 0.7721 (tmt-80) cc_final: 0.7461 (ttm110) REVERT: T 2416 MET cc_start: 0.4355 (mpt) cc_final: 0.2417 (tmm) REVERT: T 2494 LEU cc_start: 0.6173 (OUTLIER) cc_final: 0.5855 (pt) REVERT: T 2506 GLU cc_start: 0.5655 (tt0) cc_final: 0.5337 (tt0) REVERT: T 2552 ASP cc_start: 0.7091 (t70) cc_final: 0.6875 (t0) REVERT: T 2678 LEU cc_start: 0.8152 (OUTLIER) cc_final: 0.7866 (tm) REVERT: T 2694 TYR cc_start: 0.7306 (m-80) cc_final: 0.6819 (m-80) REVERT: T 3022 PHE cc_start: 0.7361 (m-80) cc_final: 0.6774 (m-80) REVERT: T 3028 MET cc_start: 0.8341 (ptp) cc_final: 0.7589 (ptp) REVERT: T 3209 GLN cc_start: 0.7425 (mt0) cc_final: 0.6626 (tm-30) REVERT: T 3321 LEU cc_start: 0.7984 (OUTLIER) cc_final: 0.7765 (tt) REVERT: T 3516 SER cc_start: 0.8429 (m) cc_final: 0.8205 (t) REVERT: T 3624 LEU cc_start: 0.8287 (tt) cc_final: 0.8075 (tt) outliers start: 67 outliers final: 20 residues processed: 672 average time/residue: 0.4555 time to fit residues: 477.7484 Evaluate side-chains 408 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 383 time to evaluate : 3.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain T residue 37 LEU Chi-restraints excluded: chain T residue 38 LEU Chi-restraints excluded: chain T residue 246 LEU Chi-restraints excluded: chain T residue 340 LEU Chi-restraints excluded: chain T residue 594 LEU Chi-restraints excluded: chain T residue 694 ASP Chi-restraints excluded: chain T residue 783 VAL Chi-restraints excluded: chain T residue 788 LEU Chi-restraints excluded: chain T residue 876 LEU Chi-restraints excluded: chain T residue 1082 LEU Chi-restraints excluded: chain T residue 1368 LEU Chi-restraints excluded: chain T residue 1377 LEU Chi-restraints excluded: chain T residue 1574 LEU Chi-restraints excluded: chain T residue 1802 VAL Chi-restraints excluded: chain T residue 1825 LEU Chi-restraints excluded: chain T residue 1865 LEU Chi-restraints excluded: chain T residue 2278 LEU Chi-restraints excluded: chain T residue 2324 LEU Chi-restraints excluded: chain T residue 2494 LEU Chi-restraints excluded: chain T residue 2500 LEU Chi-restraints excluded: chain T residue 2662 LEU Chi-restraints excluded: chain T residue 2678 LEU Chi-restraints excluded: chain T residue 3053 LEU Chi-restraints excluded: chain T residue 3321 LEU Chi-restraints excluded: chain T residue 3706 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 347 random chunks: chunk 293 optimal weight: 2.9990 chunk 263 optimal weight: 4.9990 chunk 145 optimal weight: 0.9990 chunk 89 optimal weight: 1.9990 chunk 177 optimal weight: 9.9990 chunk 140 optimal weight: 0.9990 chunk 271 optimal weight: 1.9990 chunk 105 optimal weight: 0.0870 chunk 165 optimal weight: 1.9990 chunk 202 optimal weight: 20.0000 chunk 315 optimal weight: 0.6980 overall best weight: 0.9564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: T 400 HIS T 401 ASN T 565 ASN T 639 HIS ** T 735 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 836 GLN ** T 840 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 956 ASN T1002 ASN T1114 GLN T1126 ASN T1365 ASN ** T1379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T1488 ASN T1619 GLN T1626 ASN T1654 ASN T1680 ASN T1690 ASN ** T1726 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T1740 GLN T1775 ASN T1784 ASN ** T1983 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T2183 ASN ** T2289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T2294 GLN T2418 GLN T2474 GLN T2490 ASN T2501 GLN T2526 HIS T2646 ASN T2741 GLN T2752 HIS ** T2822 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T2839 HIS T2847 GLN T2861 ASN T2863 HIS T2869 ASN T2896 ASN T2899 ASN T2907 HIS T3073 ASN T3080 ASN T3154 HIS T3297 ASN T3346 HIS T3361 ASN T3385 HIS T3406 GLN T3497 HIS ** T3537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T3547 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 46 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.136318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.115304 restraints weight = 70323.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.116251 restraints weight = 43135.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.117360 restraints weight = 31534.755| |-----------------------------------------------------------------------------| r_work (final): 0.3844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7475 moved from start: 0.2291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 29026 Z= 0.177 Angle : 0.934 20.394 39323 Z= 0.466 Chirality : 0.050 0.294 4501 Planarity : 0.007 0.112 4969 Dihedral : 8.807 67.454 3791 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 13.76 Ramachandran Plot: Outliers : 0.17 % Allowed : 13.42 % Favored : 86.41 % Rotamer: Outliers : 4.53 % Allowed : 13.38 % Favored : 82.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 8.90 % Twisted General : 0.48 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.12 (0.12), residues: 3443 helix: -2.10 (0.10), residues: 2066 sheet: -2.46 (0.75), residues: 33 loop : -3.70 (0.16), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.003 TRP T1684 HIS 0.012 0.001 HIS T2752 PHE 0.028 0.002 PHE T 10 TYR 0.040 0.002 TYR T2169 ARG 0.007 0.001 ARG T3267 Details of bonding type rmsd hydrogen bonds : bond 0.05291 ( 1252) hydrogen bonds : angle 6.28826 ( 3666) covalent geometry : bond 0.00378 (29026) covalent geometry : angle 0.93408 (39323) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6886 Ramachandran restraints generated. 3443 Oldfield, 0 Emsley, 3443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6886 Ramachandran restraints generated. 3443 Oldfield, 0 Emsley, 3443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 600 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 145 poor density : 455 time to evaluate : 3.277 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: T 35 MET cc_start: 0.7672 (tpp) cc_final: 0.7220 (mmt) REVERT: T 38 LEU cc_start: 0.6143 (OUTLIER) cc_final: 0.4279 (mt) REVERT: T 421 TYR cc_start: 0.7662 (m-10) cc_final: 0.7457 (m-80) REVERT: T 449 LEU cc_start: 0.8876 (OUTLIER) cc_final: 0.8657 (tm) REVERT: T 565 ASN cc_start: 0.7159 (m110) cc_final: 0.6859 (t0) REVERT: T 683 MET cc_start: 0.8482 (mpt) cc_final: 0.8234 (mpt) REVERT: T 1390 GLU cc_start: 0.7504 (mm-30) cc_final: 0.7209 (tp30) REVERT: T 1439 ARG cc_start: 0.8075 (tmt170) cc_final: 0.7798 (ptt90) REVERT: T 1478 LEU cc_start: 0.9192 (mm) cc_final: 0.8800 (mt) REVERT: T 1517 GLU cc_start: 0.6700 (pp20) cc_final: 0.6471 (mp0) REVERT: T 1639 ASP cc_start: 0.8406 (t70) cc_final: 0.8068 (t0) REVERT: T 1674 ASN cc_start: 0.7582 (t0) cc_final: 0.7335 (t0) REVERT: T 1686 LYS cc_start: 0.7338 (mppt) cc_final: 0.6853 (mmmt) REVERT: T 1691 MET cc_start: 0.7941 (mtt) cc_final: 0.7582 (mtt) REVERT: T 1785 ASP cc_start: 0.8307 (m-30) cc_final: 0.7787 (m-30) REVERT: T 1873 LYS cc_start: 0.6538 (mttt) cc_final: 0.6242 (mmtt) REVERT: T 2168 LEU cc_start: 0.7378 (OUTLIER) cc_final: 0.7116 (tt) REVERT: T 2208 LYS cc_start: 0.7044 (mmmm) cc_final: 0.6408 (mttt) REVERT: T 2228 GLU cc_start: 0.7593 (tp30) cc_final: 0.6810 (mp0) REVERT: T 2261 TRP cc_start: 0.7778 (t60) cc_final: 0.7560 (t-100) REVERT: T 2350 ARG cc_start: 0.7765 (tmt-80) cc_final: 0.7505 (ttm110) REVERT: T 2416 MET cc_start: 0.4873 (mpt) cc_final: 0.2774 (tmm) REVERT: T 2552 ASP cc_start: 0.7090 (t70) cc_final: 0.6564 (t0) REVERT: T 2678 LEU cc_start: 0.8098 (OUTLIER) cc_final: 0.7824 (tm) REVERT: T 2685 TYR cc_start: 0.7213 (m-10) cc_final: 0.6861 (m-10) REVERT: T 2694 TYR cc_start: 0.7414 (m-80) cc_final: 0.7098 (m-80) REVERT: T 2793 MET cc_start: 0.7368 (tmm) cc_final: 0.6811 (ttm) REVERT: T 2980 GLU cc_start: 0.6993 (mp0) cc_final: 0.6705 (pm20) REVERT: T 3022 PHE cc_start: 0.7471 (m-80) cc_final: 0.7152 (m-80) REVERT: T 3029 PHE cc_start: 0.8006 (OUTLIER) cc_final: 0.7364 (t80) REVERT: T 3209 GLN cc_start: 0.7180 (mt0) cc_final: 0.6705 (tm-30) REVERT: T 3363 ASP cc_start: 0.7123 (m-30) cc_final: 0.6915 (m-30) REVERT: T 3421 GLN cc_start: 0.8089 (tt0) cc_final: 0.7886 (tt0) REVERT: T 3458 MET cc_start: 0.7861 (pp-130) cc_final: 0.7562 (ptt) REVERT: T 3567 ARG cc_start: 0.8536 (mmm160) cc_final: 0.8161 (mmm160) REVERT: T 3691 MET cc_start: 0.8290 (ttt) cc_final: 0.8039 (ttt) REVERT: T 3706 LEU cc_start: 0.7079 (OUTLIER) cc_final: 0.6788 (pp) outliers start: 145 outliers final: 57 residues processed: 562 average time/residue: 0.4599 time to fit residues: 418.7295 Evaluate side-chains 411 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 348 time to evaluate : 3.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain T residue 37 LEU Chi-restraints excluded: chain T residue 38 LEU Chi-restraints excluded: chain T residue 107 LEU Chi-restraints excluded: chain T residue 241 LEU Chi-restraints excluded: chain T residue 246 LEU Chi-restraints excluded: chain T residue 332 LEU Chi-restraints excluded: chain T residue 340 LEU Chi-restraints excluded: chain T residue 401 ASN Chi-restraints excluded: chain T residue 423 LEU Chi-restraints excluded: chain T residue 433 ILE Chi-restraints excluded: chain T residue 439 LEU Chi-restraints excluded: chain T residue 449 LEU Chi-restraints excluded: chain T residue 609 ASN Chi-restraints excluded: chain T residue 694 ASP Chi-restraints excluded: chain T residue 763 ILE Chi-restraints excluded: chain T residue 773 VAL Chi-restraints excluded: chain T residue 783 VAL Chi-restraints excluded: chain T residue 811 LEU Chi-restraints excluded: chain T residue 827 LEU Chi-restraints excluded: chain T residue 876 LEU Chi-restraints excluded: chain T residue 1052 LEU Chi-restraints excluded: chain T residue 1066 THR Chi-restraints excluded: chain T residue 1082 LEU Chi-restraints excluded: chain T residue 1100 MET Chi-restraints excluded: chain T residue 1155 TYR Chi-restraints excluded: chain T residue 1178 ILE Chi-restraints excluded: chain T residue 1263 LEU Chi-restraints excluded: chain T residue 1313 THR Chi-restraints excluded: chain T residue 1348 THR Chi-restraints excluded: chain T residue 1368 LEU Chi-restraints excluded: chain T residue 1400 THR Chi-restraints excluded: chain T residue 1418 LEU Chi-restraints excluded: chain T residue 1466 SER Chi-restraints excluded: chain T residue 1574 LEU Chi-restraints excluded: chain T residue 1596 LEU Chi-restraints excluded: chain T residue 1715 HIS Chi-restraints excluded: chain T residue 1752 PHE Chi-restraints excluded: chain T residue 1825 LEU Chi-restraints excluded: chain T residue 1865 LEU Chi-restraints excluded: chain T residue 1922 VAL Chi-restraints excluded: chain T residue 1927 PHE Chi-restraints excluded: chain T residue 2168 LEU Chi-restraints excluded: chain T residue 2272 VAL Chi-restraints excluded: chain T residue 2315 LEU Chi-restraints excluded: chain T residue 2324 LEU Chi-restraints excluded: chain T residue 2490 ASN Chi-restraints excluded: chain T residue 2500 LEU Chi-restraints excluded: chain T residue 2587 LEU Chi-restraints excluded: chain T residue 2622 LEU Chi-restraints excluded: chain T residue 2626 LEU Chi-restraints excluded: chain T residue 2662 LEU Chi-restraints excluded: chain T residue 2678 LEU Chi-restraints excluded: chain T residue 2752 HIS Chi-restraints excluded: chain T residue 2959 MET Chi-restraints excluded: chain T residue 3029 PHE Chi-restraints excluded: chain T residue 3053 LEU Chi-restraints excluded: chain T residue 3211 LEU Chi-restraints excluded: chain T residue 3280 LEU Chi-restraints excluded: chain T residue 3283 PHE Chi-restraints excluded: chain T residue 3392 MET Chi-restraints excluded: chain T residue 3400 VAL Chi-restraints excluded: chain T residue 3637 LEU Chi-restraints excluded: chain T residue 3706 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 347 random chunks: chunk 192 optimal weight: 5.9990 chunk 92 optimal weight: 2.9990 chunk 203 optimal weight: 0.7980 chunk 217 optimal weight: 0.9990 chunk 84 optimal weight: 0.6980 chunk 110 optimal weight: 0.9990 chunk 227 optimal weight: 6.9990 chunk 98 optimal weight: 0.5980 chunk 330 optimal weight: 6.9990 chunk 139 optimal weight: 10.0000 chunk 237 optimal weight: 0.3980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: T 45 HIS ** T 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 753 ASN ** T 840 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 956 ASN T1234 GLN ** T1379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T1601 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T1726 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T1784 ASN ** T1805 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T1866 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T1944 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T1983 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T2289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T2418 GLN T2490 ASN T2741 GLN T2752 HIS ** T2822 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T2975 ASN ** T3139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T3346 HIS T3468 HIS ** T3537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T3547 GLN T3551 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.136626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.114874 restraints weight = 70341.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.117056 restraints weight = 43832.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.117736 restraints weight = 33066.073| |-----------------------------------------------------------------------------| r_work (final): 0.3846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7462 moved from start: 0.2911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 29026 Z= 0.159 Angle : 0.884 20.590 39323 Z= 0.435 Chirality : 0.049 0.316 4501 Planarity : 0.006 0.119 4969 Dihedral : 8.166 66.266 3778 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 12.99 Ramachandran Plot: Outliers : 0.20 % Allowed : 13.13 % Favored : 86.67 % Rotamer: Outliers : 4.75 % Allowed : 15.53 % Favored : 79.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 8.22 % Twisted General : 0.30 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.41 (0.13), residues: 3443 helix: -1.44 (0.10), residues: 2101 sheet: -1.95 (0.82), residues: 33 loop : -3.62 (0.16), residues: 1309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.002 TRP T1684 HIS 0.014 0.001 HIS T2621 PHE 0.045 0.002 PHE T1782 TYR 0.041 0.002 TYR T 482 ARG 0.006 0.000 ARG T 829 Details of bonding type rmsd hydrogen bonds : bond 0.04641 ( 1252) hydrogen bonds : angle 5.64898 ( 3666) covalent geometry : bond 0.00344 (29026) covalent geometry : angle 0.88414 (39323) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6886 Ramachandran restraints generated. 3443 Oldfield, 0 Emsley, 3443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6886 Ramachandran restraints generated. 3443 Oldfield, 0 Emsley, 3443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 558 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 152 poor density : 406 time to evaluate : 3.635 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: T 38 LEU cc_start: 0.5801 (OUTLIER) cc_final: 0.4102 (mt) REVERT: T 229 ILE cc_start: 0.5292 (OUTLIER) cc_final: 0.4756 (pt) REVERT: T 421 TYR cc_start: 0.7604 (m-10) cc_final: 0.7216 (m-10) REVERT: T 518 MET cc_start: 0.7746 (mmm) cc_final: 0.7379 (mmm) REVERT: T 565 ASN cc_start: 0.7049 (m110) cc_final: 0.6816 (t0) REVERT: T 683 MET cc_start: 0.8362 (OUTLIER) cc_final: 0.7986 (mpt) REVERT: T 827 LEU cc_start: 0.8444 (OUTLIER) cc_final: 0.7764 (tt) REVERT: T 1369 THR cc_start: 0.7465 (t) cc_final: 0.7162 (p) REVERT: T 1390 GLU cc_start: 0.7501 (mm-30) cc_final: 0.7192 (tp30) REVERT: T 1517 GLU cc_start: 0.6446 (pp20) cc_final: 0.6243 (mp0) REVERT: T 1639 ASP cc_start: 0.8372 (t70) cc_final: 0.7977 (t0) REVERT: T 1686 LYS cc_start: 0.7090 (mppt) cc_final: 0.6614 (mmmt) REVERT: T 1691 MET cc_start: 0.7881 (mtt) cc_final: 0.7657 (mtt) REVERT: T 1698 MET cc_start: 0.7754 (tpp) cc_final: 0.7552 (ttt) REVERT: T 1785 ASP cc_start: 0.8414 (m-30) cc_final: 0.7839 (m-30) REVERT: T 2208 LYS cc_start: 0.7053 (mmmm) cc_final: 0.6490 (mttt) REVERT: T 2228 GLU cc_start: 0.7509 (tp30) cc_final: 0.6850 (mp0) REVERT: T 2330 ARG cc_start: 0.7851 (ppp-140) cc_final: 0.7599 (mmt180) REVERT: T 2350 ARG cc_start: 0.7767 (tmt-80) cc_final: 0.7517 (ttm110) REVERT: T 2416 MET cc_start: 0.4851 (mpt) cc_final: 0.2715 (ttm) REVERT: T 2571 ILE cc_start: 0.8035 (mm) cc_final: 0.7802 (mm) REVERT: T 2674 MET cc_start: 0.7926 (mmm) cc_final: 0.7292 (mpp) REVERT: T 2685 TYR cc_start: 0.7170 (m-10) cc_final: 0.6854 (m-10) REVERT: T 2793 MET cc_start: 0.7265 (tmm) cc_final: 0.6722 (ttm) REVERT: T 2816 LEU cc_start: 0.7701 (OUTLIER) cc_final: 0.7478 (tm) REVERT: T 3022 PHE cc_start: 0.7633 (m-80) cc_final: 0.7201 (m-80) REVERT: T 3029 PHE cc_start: 0.8064 (m-80) cc_final: 0.7370 (t80) REVERT: T 3209 GLN cc_start: 0.7065 (mt0) cc_final: 0.6667 (tm-30) REVERT: T 3489 MET cc_start: 0.7961 (ptm) cc_final: 0.7608 (ptm) REVERT: T 3706 LEU cc_start: 0.7048 (OUTLIER) cc_final: 0.6669 (pp) outliers start: 152 outliers final: 75 residues processed: 524 average time/residue: 0.3846 time to fit residues: 335.3413 Evaluate side-chains 416 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 335 time to evaluate : 3.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain T residue 37 LEU Chi-restraints excluded: chain T residue 38 LEU Chi-restraints excluded: chain T residue 107 LEU Chi-restraints excluded: chain T residue 157 GLN Chi-restraints excluded: chain T residue 229 ILE Chi-restraints excluded: chain T residue 246 LEU Chi-restraints excluded: chain T residue 332 LEU Chi-restraints excluded: chain T residue 340 LEU Chi-restraints excluded: chain T residue 423 LEU Chi-restraints excluded: chain T residue 433 ILE Chi-restraints excluded: chain T residue 447 LEU Chi-restraints excluded: chain T residue 594 LEU Chi-restraints excluded: chain T residue 609 ASN Chi-restraints excluded: chain T residue 683 MET Chi-restraints excluded: chain T residue 694 ASP Chi-restraints excluded: chain T residue 763 ILE Chi-restraints excluded: chain T residue 773 VAL Chi-restraints excluded: chain T residue 783 VAL Chi-restraints excluded: chain T residue 811 LEU Chi-restraints excluded: chain T residue 826 ASN Chi-restraints excluded: chain T residue 827 LEU Chi-restraints excluded: chain T residue 847 LEU Chi-restraints excluded: chain T residue 848 THR Chi-restraints excluded: chain T residue 876 LEU Chi-restraints excluded: chain T residue 961 LYS Chi-restraints excluded: chain T residue 1042 LEU Chi-restraints excluded: chain T residue 1049 SER Chi-restraints excluded: chain T residue 1052 LEU Chi-restraints excluded: chain T residue 1066 THR Chi-restraints excluded: chain T residue 1082 LEU Chi-restraints excluded: chain T residue 1100 MET Chi-restraints excluded: chain T residue 1102 LEU Chi-restraints excluded: chain T residue 1146 LEU Chi-restraints excluded: chain T residue 1155 TYR Chi-restraints excluded: chain T residue 1178 ILE Chi-restraints excluded: chain T residue 1263 LEU Chi-restraints excluded: chain T residue 1313 THR Chi-restraints excluded: chain T residue 1368 LEU Chi-restraints excluded: chain T residue 1400 THR Chi-restraints excluded: chain T residue 1418 LEU Chi-restraints excluded: chain T residue 1437 ARG Chi-restraints excluded: chain T residue 1574 LEU Chi-restraints excluded: chain T residue 1596 LEU Chi-restraints excluded: chain T residue 1685 LEU Chi-restraints excluded: chain T residue 1715 HIS Chi-restraints excluded: chain T residue 1752 PHE Chi-restraints excluded: chain T residue 1788 LEU Chi-restraints excluded: chain T residue 1812 ILE Chi-restraints excluded: chain T residue 1825 LEU Chi-restraints excluded: chain T residue 1865 LEU Chi-restraints excluded: chain T residue 1907 LEU Chi-restraints excluded: chain T residue 1927 PHE Chi-restraints excluded: chain T residue 2039 GLU Chi-restraints excluded: chain T residue 2186 THR Chi-restraints excluded: chain T residue 2272 VAL Chi-restraints excluded: chain T residue 2324 LEU Chi-restraints excluded: chain T residue 2380 LEU Chi-restraints excluded: chain T residue 2510 MET Chi-restraints excluded: chain T residue 2596 ILE Chi-restraints excluded: chain T residue 2607 LEU Chi-restraints excluded: chain T residue 2662 LEU Chi-restraints excluded: chain T residue 2816 LEU Chi-restraints excluded: chain T residue 2958 ASN Chi-restraints excluded: chain T residue 2959 MET Chi-restraints excluded: chain T residue 2985 LEU Chi-restraints excluded: chain T residue 2996 MET Chi-restraints excluded: chain T residue 3053 LEU Chi-restraints excluded: chain T residue 3105 LEU Chi-restraints excluded: chain T residue 3171 LEU Chi-restraints excluded: chain T residue 3211 LEU Chi-restraints excluded: chain T residue 3226 LEU Chi-restraints excluded: chain T residue 3280 LEU Chi-restraints excluded: chain T residue 3283 PHE Chi-restraints excluded: chain T residue 3286 THR Chi-restraints excluded: chain T residue 3351 ASP Chi-restraints excluded: chain T residue 3392 MET Chi-restraints excluded: chain T residue 3400 VAL Chi-restraints excluded: chain T residue 3543 LEU Chi-restraints excluded: chain T residue 3628 ILE Chi-restraints excluded: chain T residue 3706 LEU Chi-restraints excluded: chain T residue 3716 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 347 random chunks: chunk 239 optimal weight: 0.0030 chunk 289 optimal weight: 3.9990 chunk 260 optimal weight: 0.6980 chunk 346 optimal weight: 0.2980 chunk 274 optimal weight: 2.9990 chunk 234 optimal weight: 5.9990 chunk 266 optimal weight: 0.5980 chunk 67 optimal weight: 2.9990 chunk 258 optimal weight: 0.0870 chunk 25 optimal weight: 6.9990 chunk 55 optimal weight: 2.9990 overall best weight: 0.3368 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: T 6 GLN T 58 GLN T1135 ASN ** T1379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T1546 GLN T1601 ASN T1700 ASN ** T1726 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T1903 GLN ** T1935 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T1944 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T1983 ASN T2183 ASN ** T2270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T2289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T2342 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T2418 GLN ** T2621 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T2822 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T3064 ASN ** T3139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T3168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T3537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T3573 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T3615 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.138520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.117404 restraints weight = 71213.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.118758 restraints weight = 44129.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.119755 restraints weight = 31221.437| |-----------------------------------------------------------------------------| r_work (final): 0.3872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7423 moved from start: 0.3444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 29026 Z= 0.148 Angle : 0.845 20.451 39323 Z= 0.412 Chirality : 0.047 0.316 4501 Planarity : 0.006 0.114 4969 Dihedral : 7.736 66.014 3774 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 12.78 Ramachandran Plot: Outliers : 0.20 % Allowed : 12.75 % Favored : 87.05 % Rotamer: Outliers : 4.69 % Allowed : 16.72 % Favored : 78.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 6.85 % Twisted General : 0.21 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.89 (0.14), residues: 3443 helix: -0.98 (0.11), residues: 2096 sheet: -1.54 (0.88), residues: 33 loop : -3.50 (0.16), residues: 1314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.002 TRP T2179 HIS 0.026 0.001 HIS T2621 PHE 0.026 0.002 PHE T 10 TYR 0.038 0.001 TYR T2169 ARG 0.007 0.000 ARG T3262 Details of bonding type rmsd hydrogen bonds : bond 0.04190 ( 1252) hydrogen bonds : angle 5.21292 ( 3666) covalent geometry : bond 0.00313 (29026) covalent geometry : angle 0.84529 (39323) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6886 Ramachandran restraints generated. 3443 Oldfield, 0 Emsley, 3443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6886 Ramachandran restraints generated. 3443 Oldfield, 0 Emsley, 3443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 557 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 150 poor density : 407 time to evaluate : 3.178 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: T 38 LEU cc_start: 0.5721 (OUTLIER) cc_final: 0.4069 (mt) REVERT: T 229 ILE cc_start: 0.5187 (OUTLIER) cc_final: 0.4594 (pt) REVERT: T 309 PHE cc_start: 0.7852 (p90) cc_final: 0.7554 (p90) REVERT: T 508 GLN cc_start: 0.7116 (OUTLIER) cc_final: 0.6594 (pt0) REVERT: T 518 MET cc_start: 0.7893 (mmm) cc_final: 0.7614 (mmp) REVERT: T 683 MET cc_start: 0.8266 (OUTLIER) cc_final: 0.7999 (mpt) REVERT: T 693 MET cc_start: 0.6272 (mmm) cc_final: 0.5768 (tpt) REVERT: T 985 MET cc_start: 0.7031 (ptp) cc_final: 0.6798 (mtp) REVERT: T 1390 GLU cc_start: 0.7372 (mm-30) cc_final: 0.7035 (tp30) REVERT: T 1639 ASP cc_start: 0.8400 (t70) cc_final: 0.7942 (t0) REVERT: T 1686 LYS cc_start: 0.7052 (mppt) cc_final: 0.6612 (mmmt) REVERT: T 1785 ASP cc_start: 0.8441 (m-30) cc_final: 0.7830 (m-30) REVERT: T 1800 ILE cc_start: 0.6634 (mt) cc_final: 0.6390 (mm) REVERT: T 1828 ASP cc_start: 0.6039 (t0) cc_final: 0.5834 (t70) REVERT: T 1989 LEU cc_start: 0.8303 (OUTLIER) cc_final: 0.7985 (tt) REVERT: T 2091 HIS cc_start: 0.7281 (m90) cc_final: 0.7019 (m90) REVERT: T 2208 LYS cc_start: 0.6908 (mmmm) cc_final: 0.6581 (mttt) REVERT: T 2228 GLU cc_start: 0.7304 (tp30) cc_final: 0.6668 (mp0) REVERT: T 2330 ARG cc_start: 0.7742 (ppp-140) cc_final: 0.7486 (mmt180) REVERT: T 2350 ARG cc_start: 0.7728 (tmt-80) cc_final: 0.7467 (ttm110) REVERT: T 2416 MET cc_start: 0.4855 (mpt) cc_final: 0.2639 (ttm) REVERT: T 2552 ASP cc_start: 0.7155 (OUTLIER) cc_final: 0.6944 (m-30) REVERT: T 2628 ILE cc_start: 0.6468 (OUTLIER) cc_final: 0.5870 (tp) REVERT: T 2685 TYR cc_start: 0.7064 (m-10) cc_final: 0.6732 (m-10) REVERT: T 2793 MET cc_start: 0.7287 (tmm) cc_final: 0.6733 (ttm) REVERT: T 2816 LEU cc_start: 0.7709 (OUTLIER) cc_final: 0.7473 (tm) REVERT: T 2959 MET cc_start: 0.6294 (OUTLIER) cc_final: 0.5693 (pmt) REVERT: T 3068 LEU cc_start: 0.6815 (OUTLIER) cc_final: 0.6587 (tt) REVERT: T 3209 GLN cc_start: 0.7037 (mt0) cc_final: 0.6641 (tm-30) REVERT: T 3706 LEU cc_start: 0.6999 (OUTLIER) cc_final: 0.6657 (pp) REVERT: T 3724 ILE cc_start: 0.8687 (pt) cc_final: 0.8182 (mt) REVERT: T 3741 MET cc_start: 0.7916 (ttm) cc_final: 0.7501 (mtp) outliers start: 150 outliers final: 77 residues processed: 519 average time/residue: 0.4312 time to fit residues: 377.2726 Evaluate side-chains 428 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 340 time to evaluate : 3.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain T residue 37 LEU Chi-restraints excluded: chain T residue 38 LEU Chi-restraints excluded: chain T residue 107 LEU Chi-restraints excluded: chain T residue 157 GLN Chi-restraints excluded: chain T residue 229 ILE Chi-restraints excluded: chain T residue 246 LEU Chi-restraints excluded: chain T residue 332 LEU Chi-restraints excluded: chain T residue 340 LEU Chi-restraints excluded: chain T residue 423 LEU Chi-restraints excluded: chain T residue 433 ILE Chi-restraints excluded: chain T residue 508 GLN Chi-restraints excluded: chain T residue 594 LEU Chi-restraints excluded: chain T residue 609 ASN Chi-restraints excluded: chain T residue 683 MET Chi-restraints excluded: chain T residue 694 ASP Chi-restraints excluded: chain T residue 763 ILE Chi-restraints excluded: chain T residue 773 VAL Chi-restraints excluded: chain T residue 783 VAL Chi-restraints excluded: chain T residue 784 LEU Chi-restraints excluded: chain T residue 826 ASN Chi-restraints excluded: chain T residue 848 THR Chi-restraints excluded: chain T residue 876 LEU Chi-restraints excluded: chain T residue 993 VAL Chi-restraints excluded: chain T residue 1042 LEU Chi-restraints excluded: chain T residue 1052 LEU Chi-restraints excluded: chain T residue 1066 THR Chi-restraints excluded: chain T residue 1082 LEU Chi-restraints excluded: chain T residue 1155 TYR Chi-restraints excluded: chain T residue 1263 LEU Chi-restraints excluded: chain T residue 1313 THR Chi-restraints excluded: chain T residue 1368 LEU Chi-restraints excluded: chain T residue 1400 THR Chi-restraints excluded: chain T residue 1418 LEU Chi-restraints excluded: chain T residue 1437 ARG Chi-restraints excluded: chain T residue 1449 LEU Chi-restraints excluded: chain T residue 1503 LEU Chi-restraints excluded: chain T residue 1510 LEU Chi-restraints excluded: chain T residue 1586 LEU Chi-restraints excluded: chain T residue 1596 LEU Chi-restraints excluded: chain T residue 1685 LEU Chi-restraints excluded: chain T residue 1715 HIS Chi-restraints excluded: chain T residue 1752 PHE Chi-restraints excluded: chain T residue 1788 LEU Chi-restraints excluded: chain T residue 1812 ILE Chi-restraints excluded: chain T residue 1825 LEU Chi-restraints excluded: chain T residue 1853 VAL Chi-restraints excluded: chain T residue 1865 LEU Chi-restraints excluded: chain T residue 1903 GLN Chi-restraints excluded: chain T residue 1927 PHE Chi-restraints excluded: chain T residue 1989 LEU Chi-restraints excluded: chain T residue 2039 GLU Chi-restraints excluded: chain T residue 2272 VAL Chi-restraints excluded: chain T residue 2276 THR Chi-restraints excluded: chain T residue 2324 LEU Chi-restraints excluded: chain T residue 2380 LEU Chi-restraints excluded: chain T residue 2500 LEU Chi-restraints excluded: chain T residue 2510 MET Chi-restraints excluded: chain T residue 2552 ASP Chi-restraints excluded: chain T residue 2587 LEU Chi-restraints excluded: chain T residue 2593 THR Chi-restraints excluded: chain T residue 2596 ILE Chi-restraints excluded: chain T residue 2607 LEU Chi-restraints excluded: chain T residue 2622 LEU Chi-restraints excluded: chain T residue 2628 ILE Chi-restraints excluded: chain T residue 2679 TRP Chi-restraints excluded: chain T residue 2816 LEU Chi-restraints excluded: chain T residue 2958 ASN Chi-restraints excluded: chain T residue 2959 MET Chi-restraints excluded: chain T residue 2985 LEU Chi-restraints excluded: chain T residue 3028 MET Chi-restraints excluded: chain T residue 3053 LEU Chi-restraints excluded: chain T residue 3068 LEU Chi-restraints excluded: chain T residue 3105 LEU Chi-restraints excluded: chain T residue 3171 LEU Chi-restraints excluded: chain T residue 3211 LEU Chi-restraints excluded: chain T residue 3226 LEU Chi-restraints excluded: chain T residue 3241 THR Chi-restraints excluded: chain T residue 3280 LEU Chi-restraints excluded: chain T residue 3283 PHE Chi-restraints excluded: chain T residue 3286 THR Chi-restraints excluded: chain T residue 3351 ASP Chi-restraints excluded: chain T residue 3392 MET Chi-restraints excluded: chain T residue 3400 VAL Chi-restraints excluded: chain T residue 3405 VAL Chi-restraints excluded: chain T residue 3487 ASP Chi-restraints excluded: chain T residue 3543 LEU Chi-restraints excluded: chain T residue 3706 LEU Chi-restraints excluded: chain T residue 3716 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 347 random chunks: chunk 185 optimal weight: 7.9990 chunk 36 optimal weight: 0.9990 chunk 258 optimal weight: 7.9990 chunk 318 optimal weight: 0.8980 chunk 186 optimal weight: 1.9990 chunk 267 optimal weight: 0.9990 chunk 321 optimal weight: 2.9990 chunk 6 optimal weight: 10.0000 chunk 167 optimal weight: 8.9990 chunk 39 optimal weight: 1.9990 chunk 59 optimal weight: 0.5980 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** T 735 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 896 GLN ** T1379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T1726 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T1935 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T1944 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T2270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T2289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T2342 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T2418 GLN ** T2621 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T2670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T2696 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T2822 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T2847 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T3139 GLN ** T3165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T3168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T3537 GLN T3573 HIS T3615 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.136635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.114996 restraints weight = 70518.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.116739 restraints weight = 45231.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.117613 restraints weight = 31812.629| |-----------------------------------------------------------------------------| r_work (final): 0.3839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7468 moved from start: 0.3719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 29026 Z= 0.156 Angle : 0.846 20.122 39323 Z= 0.413 Chirality : 0.048 0.323 4501 Planarity : 0.006 0.119 4969 Dihedral : 7.463 66.124 3770 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 13.04 Ramachandran Plot: Outliers : 0.17 % Allowed : 12.92 % Favored : 86.90 % Rotamer: Outliers : 4.56 % Allowed : 17.84 % Favored : 77.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 6.85 % Twisted General : 0.21 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.57 (0.14), residues: 3443 helix: -0.69 (0.11), residues: 2090 sheet: -1.33 (0.77), residues: 43 loop : -3.44 (0.16), residues: 1310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP T2179 HIS 0.009 0.001 HIS T2621 PHE 0.033 0.002 PHE T1782 TYR 0.037 0.002 TYR T2169 ARG 0.005 0.000 ARG T3262 Details of bonding type rmsd hydrogen bonds : bond 0.04129 ( 1252) hydrogen bonds : angle 5.12052 ( 3666) covalent geometry : bond 0.00350 (29026) covalent geometry : angle 0.84617 (39323) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6886 Ramachandran restraints generated. 3443 Oldfield, 0 Emsley, 3443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6886 Ramachandran restraints generated. 3443 Oldfield, 0 Emsley, 3443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 520 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 374 time to evaluate : 3.610 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: T 35 MET cc_start: 0.7548 (mmt) cc_final: 0.7154 (mmt) REVERT: T 38 LEU cc_start: 0.5653 (OUTLIER) cc_final: 0.4026 (mt) REVERT: T 229 ILE cc_start: 0.5174 (OUTLIER) cc_final: 0.4585 (pt) REVERT: T 508 GLN cc_start: 0.7205 (OUTLIER) cc_final: 0.6645 (pt0) REVERT: T 518 MET cc_start: 0.7991 (mmm) cc_final: 0.7625 (mmp) REVERT: T 683 MET cc_start: 0.8343 (OUTLIER) cc_final: 0.7974 (mpt) REVERT: T 693 MET cc_start: 0.6264 (mmm) cc_final: 0.5628 (tpt) REVERT: T 1051 LYS cc_start: 0.6848 (pttm) cc_final: 0.5905 (mmmt) REVERT: T 1155 TYR cc_start: 0.7567 (OUTLIER) cc_final: 0.7008 (m-80) REVERT: T 1377 LEU cc_start: 0.6769 (OUTLIER) cc_final: 0.6546 (tm) REVERT: T 1547 MET cc_start: 0.7194 (tmm) cc_final: 0.6958 (ptt) REVERT: T 1639 ASP cc_start: 0.8458 (t70) cc_final: 0.7987 (t0) REVERT: T 1686 LYS cc_start: 0.7114 (mppt) cc_final: 0.6652 (mmmt) REVERT: T 1785 ASP cc_start: 0.8423 (m-30) cc_final: 0.7702 (m-30) REVERT: T 1800 ILE cc_start: 0.6678 (mt) cc_final: 0.6448 (mm) REVERT: T 2123 ILE cc_start: 0.9093 (mt) cc_final: 0.8826 (mt) REVERT: T 2208 LYS cc_start: 0.6997 (mmmm) cc_final: 0.6684 (mttt) REVERT: T 2228 GLU cc_start: 0.7194 (tp30) cc_final: 0.6771 (mp0) REVERT: T 2330 ARG cc_start: 0.7821 (ppp-140) cc_final: 0.7594 (mmt180) REVERT: T 2416 MET cc_start: 0.4982 (mpt) cc_final: 0.2194 (ttm) REVERT: T 2474 GLN cc_start: 0.8804 (mm110) cc_final: 0.8228 (tp-100) REVERT: T 2552 ASP cc_start: 0.7255 (OUTLIER) cc_final: 0.7019 (m-30) REVERT: T 2685 TYR cc_start: 0.7120 (m-10) cc_final: 0.6784 (m-10) REVERT: T 2793 MET cc_start: 0.7261 (tmm) cc_final: 0.6955 (ttt) REVERT: T 2816 LEU cc_start: 0.7729 (OUTLIER) cc_final: 0.7476 (tm) REVERT: T 2850 MET cc_start: 0.7771 (mmm) cc_final: 0.7444 (tpp) REVERT: T 3068 LEU cc_start: 0.6820 (OUTLIER) cc_final: 0.6603 (tt) REVERT: T 3209 GLN cc_start: 0.7066 (mt0) cc_final: 0.6660 (tm-30) REVERT: T 3489 MET cc_start: 0.7889 (ptm) cc_final: 0.7627 (ptm) REVERT: T 3613 ILE cc_start: 0.0329 (OUTLIER) cc_final: 0.0125 (mt) REVERT: T 3706 LEU cc_start: 0.7160 (OUTLIER) cc_final: 0.6649 (pp) REVERT: T 3741 MET cc_start: 0.7896 (ttm) cc_final: 0.7647 (mtp) outliers start: 146 outliers final: 90 residues processed: 483 average time/residue: 0.3808 time to fit residues: 307.9965 Evaluate side-chains 423 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 322 time to evaluate : 3.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain T residue 28 LEU Chi-restraints excluded: chain T residue 37 LEU Chi-restraints excluded: chain T residue 38 LEU Chi-restraints excluded: chain T residue 107 LEU Chi-restraints excluded: chain T residue 157 GLN Chi-restraints excluded: chain T residue 229 ILE Chi-restraints excluded: chain T residue 246 LEU Chi-restraints excluded: chain T residue 249 PHE Chi-restraints excluded: chain T residue 332 LEU Chi-restraints excluded: chain T residue 340 LEU Chi-restraints excluded: chain T residue 390 LEU Chi-restraints excluded: chain T residue 423 LEU Chi-restraints excluded: chain T residue 433 ILE Chi-restraints excluded: chain T residue 508 GLN Chi-restraints excluded: chain T residue 594 LEU Chi-restraints excluded: chain T residue 609 ASN Chi-restraints excluded: chain T residue 683 MET Chi-restraints excluded: chain T residue 694 ASP Chi-restraints excluded: chain T residue 751 LEU Chi-restraints excluded: chain T residue 763 ILE Chi-restraints excluded: chain T residue 773 VAL Chi-restraints excluded: chain T residue 783 VAL Chi-restraints excluded: chain T residue 826 ASN Chi-restraints excluded: chain T residue 848 THR Chi-restraints excluded: chain T residue 876 LEU Chi-restraints excluded: chain T residue 961 LYS Chi-restraints excluded: chain T residue 993 VAL Chi-restraints excluded: chain T residue 1042 LEU Chi-restraints excluded: chain T residue 1052 LEU Chi-restraints excluded: chain T residue 1066 THR Chi-restraints excluded: chain T residue 1102 LEU Chi-restraints excluded: chain T residue 1155 TYR Chi-restraints excluded: chain T residue 1263 LEU Chi-restraints excluded: chain T residue 1313 THR Chi-restraints excluded: chain T residue 1368 LEU Chi-restraints excluded: chain T residue 1377 LEU Chi-restraints excluded: chain T residue 1400 THR Chi-restraints excluded: chain T residue 1418 LEU Chi-restraints excluded: chain T residue 1437 ARG Chi-restraints excluded: chain T residue 1449 LEU Chi-restraints excluded: chain T residue 1510 LEU Chi-restraints excluded: chain T residue 1543 LEU Chi-restraints excluded: chain T residue 1586 LEU Chi-restraints excluded: chain T residue 1596 LEU Chi-restraints excluded: chain T residue 1630 ARG Chi-restraints excluded: chain T residue 1685 LEU Chi-restraints excluded: chain T residue 1715 HIS Chi-restraints excluded: chain T residue 1752 PHE Chi-restraints excluded: chain T residue 1788 LEU Chi-restraints excluded: chain T residue 1812 ILE Chi-restraints excluded: chain T residue 1825 LEU Chi-restraints excluded: chain T residue 1853 VAL Chi-restraints excluded: chain T residue 1903 GLN Chi-restraints excluded: chain T residue 1907 LEU Chi-restraints excluded: chain T residue 1927 PHE Chi-restraints excluded: chain T residue 1953 LEU Chi-restraints excluded: chain T residue 2039 GLU Chi-restraints excluded: chain T residue 2121 ILE Chi-restraints excluded: chain T residue 2186 THR Chi-restraints excluded: chain T residue 2272 VAL Chi-restraints excluded: chain T residue 2276 THR Chi-restraints excluded: chain T residue 2324 LEU Chi-restraints excluded: chain T residue 2380 LEU Chi-restraints excluded: chain T residue 2500 LEU Chi-restraints excluded: chain T residue 2514 VAL Chi-restraints excluded: chain T residue 2552 ASP Chi-restraints excluded: chain T residue 2593 THR Chi-restraints excluded: chain T residue 2596 ILE Chi-restraints excluded: chain T residue 2607 LEU Chi-restraints excluded: chain T residue 2659 GLU Chi-restraints excluded: chain T residue 2679 TRP Chi-restraints excluded: chain T residue 2690 ILE Chi-restraints excluded: chain T residue 2741 GLN Chi-restraints excluded: chain T residue 2816 LEU Chi-restraints excluded: chain T residue 2958 ASN Chi-restraints excluded: chain T residue 2959 MET Chi-restraints excluded: chain T residue 2985 LEU Chi-restraints excluded: chain T residue 3028 MET Chi-restraints excluded: chain T residue 3053 LEU Chi-restraints excluded: chain T residue 3068 LEU Chi-restraints excluded: chain T residue 3105 LEU Chi-restraints excluded: chain T residue 3107 LEU Chi-restraints excluded: chain T residue 3137 ILE Chi-restraints excluded: chain T residue 3171 LEU Chi-restraints excluded: chain T residue 3211 LEU Chi-restraints excluded: chain T residue 3226 LEU Chi-restraints excluded: chain T residue 3280 LEU Chi-restraints excluded: chain T residue 3283 PHE Chi-restraints excluded: chain T residue 3286 THR Chi-restraints excluded: chain T residue 3392 MET Chi-restraints excluded: chain T residue 3400 VAL Chi-restraints excluded: chain T residue 3405 VAL Chi-restraints excluded: chain T residue 3487 ASP Chi-restraints excluded: chain T residue 3522 VAL Chi-restraints excluded: chain T residue 3563 MET Chi-restraints excluded: chain T residue 3572 ILE Chi-restraints excluded: chain T residue 3613 ILE Chi-restraints excluded: chain T residue 3628 ILE Chi-restraints excluded: chain T residue 3697 ASP Chi-restraints excluded: chain T residue 3706 LEU Chi-restraints excluded: chain T residue 3716 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 347 random chunks: chunk 205 optimal weight: 3.9990 chunk 79 optimal weight: 4.9990 chunk 141 optimal weight: 0.7980 chunk 164 optimal weight: 1.9990 chunk 156 optimal weight: 1.9990 chunk 120 optimal weight: 7.9990 chunk 336 optimal weight: 0.0870 chunk 17 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 37 optimal weight: 6.9990 chunk 28 optimal weight: 0.4980 overall best weight: 1.0762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: T 432 GLN ** T 735 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T1379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T1726 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T1935 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T1944 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T1983 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T2270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T2289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T2342 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T2696 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T2847 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T3048 GLN ** T3165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T3168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T3617 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.136536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.115503 restraints weight = 70738.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.116378 restraints weight = 46065.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.117285 restraints weight = 33321.491| |-----------------------------------------------------------------------------| r_work (final): 0.3835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7474 moved from start: 0.3913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 29026 Z= 0.154 Angle : 0.840 19.837 39323 Z= 0.409 Chirality : 0.048 0.322 4501 Planarity : 0.006 0.115 4969 Dihedral : 7.249 66.300 3766 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 12.90 Ramachandran Plot: Outliers : 0.15 % Allowed : 13.30 % Favored : 86.55 % Rotamer: Outliers : 4.56 % Allowed : 18.09 % Favored : 77.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 6.85 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.37 (0.14), residues: 3443 helix: -0.52 (0.11), residues: 2085 sheet: -1.22 (0.92), residues: 33 loop : -3.34 (0.17), residues: 1325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.002 TRP T2179 HIS 0.006 0.001 HIS T1560 PHE 0.033 0.002 PHE T1782 TYR 0.037 0.002 TYR T2169 ARG 0.014 0.000 ARG T3262 Details of bonding type rmsd hydrogen bonds : bond 0.04078 ( 1252) hydrogen bonds : angle 5.00004 ( 3666) covalent geometry : bond 0.00345 (29026) covalent geometry : angle 0.83978 (39323) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6886 Ramachandran restraints generated. 3443 Oldfield, 0 Emsley, 3443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6886 Ramachandran restraints generated. 3443 Oldfield, 0 Emsley, 3443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 523 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 377 time to evaluate : 3.709 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: T 35 MET cc_start: 0.7511 (mmt) cc_final: 0.7275 (mmt) REVERT: T 38 LEU cc_start: 0.5645 (OUTLIER) cc_final: 0.4070 (mt) REVERT: T 229 ILE cc_start: 0.5121 (OUTLIER) cc_final: 0.4494 (pt) REVERT: T 508 GLN cc_start: 0.7263 (OUTLIER) cc_final: 0.6727 (pt0) REVERT: T 518 MET cc_start: 0.8033 (mmm) cc_final: 0.7567 (mmp) REVERT: T 683 MET cc_start: 0.8292 (OUTLIER) cc_final: 0.7911 (mpt) REVERT: T 693 MET cc_start: 0.6165 (mmm) cc_final: 0.5613 (tpt) REVERT: T 1155 TYR cc_start: 0.7595 (OUTLIER) cc_final: 0.7089 (m-80) REVERT: T 1377 LEU cc_start: 0.6751 (OUTLIER) cc_final: 0.6545 (tm) REVERT: T 1639 ASP cc_start: 0.8485 (t70) cc_final: 0.8046 (t0) REVERT: T 1686 LYS cc_start: 0.7055 (mppt) cc_final: 0.6697 (mmmt) REVERT: T 1785 ASP cc_start: 0.8372 (m-30) cc_final: 0.7707 (m-30) REVERT: T 2039 GLU cc_start: 0.7410 (OUTLIER) cc_final: 0.7156 (tp30) REVERT: T 2123 ILE cc_start: 0.9092 (mt) cc_final: 0.8834 (mt) REVERT: T 2208 LYS cc_start: 0.7050 (mmmm) cc_final: 0.6793 (mttt) REVERT: T 2228 GLU cc_start: 0.7128 (tp30) cc_final: 0.6729 (mp0) REVERT: T 2416 MET cc_start: 0.5011 (mpt) cc_final: 0.2133 (ttm) REVERT: T 2436 MET cc_start: 0.8019 (mmm) cc_final: 0.7661 (mmm) REVERT: T 2474 GLN cc_start: 0.8794 (mm110) cc_final: 0.8290 (tp-100) REVERT: T 2552 ASP cc_start: 0.7167 (OUTLIER) cc_final: 0.6936 (m-30) REVERT: T 2659 GLU cc_start: 0.7589 (OUTLIER) cc_final: 0.7381 (mp0) REVERT: T 2685 TYR cc_start: 0.7148 (m-10) cc_final: 0.6833 (m-10) REVERT: T 2694 TYR cc_start: 0.7324 (m-80) cc_final: 0.7082 (m-80) REVERT: T 2764 TRP cc_start: 0.5717 (p90) cc_final: 0.5081 (p90) REVERT: T 2793 MET cc_start: 0.7248 (tmm) cc_final: 0.6963 (ttt) REVERT: T 2816 LEU cc_start: 0.7763 (OUTLIER) cc_final: 0.7528 (tm) REVERT: T 2850 MET cc_start: 0.7830 (mmm) cc_final: 0.7510 (tpp) REVERT: T 3068 LEU cc_start: 0.6864 (OUTLIER) cc_final: 0.6651 (tt) REVERT: T 3209 GLN cc_start: 0.7052 (mt0) cc_final: 0.6625 (tm-30) REVERT: T 3494 ASN cc_start: 0.7616 (t0) cc_final: 0.7132 (m110) REVERT: T 3653 ILE cc_start: 0.7451 (OUTLIER) cc_final: 0.7239 (pt) REVERT: T 3706 LEU cc_start: 0.6946 (OUTLIER) cc_final: 0.6481 (pp) REVERT: T 3741 MET cc_start: 0.7867 (ttm) cc_final: 0.7423 (mtp) outliers start: 146 outliers final: 89 residues processed: 484 average time/residue: 0.3935 time to fit residues: 319.3668 Evaluate side-chains 435 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 333 time to evaluate : 3.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain T residue 37 LEU Chi-restraints excluded: chain T residue 38 LEU Chi-restraints excluded: chain T residue 141 ILE Chi-restraints excluded: chain T residue 157 GLN Chi-restraints excluded: chain T residue 229 ILE Chi-restraints excluded: chain T residue 246 LEU Chi-restraints excluded: chain T residue 249 PHE Chi-restraints excluded: chain T residue 332 LEU Chi-restraints excluded: chain T residue 340 LEU Chi-restraints excluded: chain T residue 390 LEU Chi-restraints excluded: chain T residue 433 ILE Chi-restraints excluded: chain T residue 508 GLN Chi-restraints excluded: chain T residue 594 LEU Chi-restraints excluded: chain T residue 609 ASN Chi-restraints excluded: chain T residue 683 MET Chi-restraints excluded: chain T residue 694 ASP Chi-restraints excluded: chain T residue 751 LEU Chi-restraints excluded: chain T residue 763 ILE Chi-restraints excluded: chain T residue 773 VAL Chi-restraints excluded: chain T residue 783 VAL Chi-restraints excluded: chain T residue 826 ASN Chi-restraints excluded: chain T residue 848 THR Chi-restraints excluded: chain T residue 876 LEU Chi-restraints excluded: chain T residue 961 LYS Chi-restraints excluded: chain T residue 993 VAL Chi-restraints excluded: chain T residue 1042 LEU Chi-restraints excluded: chain T residue 1052 LEU Chi-restraints excluded: chain T residue 1063 LEU Chi-restraints excluded: chain T residue 1066 THR Chi-restraints excluded: chain T residue 1102 LEU Chi-restraints excluded: chain T residue 1155 TYR Chi-restraints excluded: chain T residue 1214 LEU Chi-restraints excluded: chain T residue 1263 LEU Chi-restraints excluded: chain T residue 1264 LEU Chi-restraints excluded: chain T residue 1313 THR Chi-restraints excluded: chain T residue 1368 LEU Chi-restraints excluded: chain T residue 1377 LEU Chi-restraints excluded: chain T residue 1400 THR Chi-restraints excluded: chain T residue 1418 LEU Chi-restraints excluded: chain T residue 1437 ARG Chi-restraints excluded: chain T residue 1466 SER Chi-restraints excluded: chain T residue 1507 LEU Chi-restraints excluded: chain T residue 1543 LEU Chi-restraints excluded: chain T residue 1575 LEU Chi-restraints excluded: chain T residue 1586 LEU Chi-restraints excluded: chain T residue 1596 LEU Chi-restraints excluded: chain T residue 1685 LEU Chi-restraints excluded: chain T residue 1715 HIS Chi-restraints excluded: chain T residue 1752 PHE Chi-restraints excluded: chain T residue 1812 ILE Chi-restraints excluded: chain T residue 1825 LEU Chi-restraints excluded: chain T residue 1853 VAL Chi-restraints excluded: chain T residue 1865 LEU Chi-restraints excluded: chain T residue 1903 GLN Chi-restraints excluded: chain T residue 1907 LEU Chi-restraints excluded: chain T residue 1927 PHE Chi-restraints excluded: chain T residue 1953 LEU Chi-restraints excluded: chain T residue 2039 GLU Chi-restraints excluded: chain T residue 2121 ILE Chi-restraints excluded: chain T residue 2186 THR Chi-restraints excluded: chain T residue 2272 VAL Chi-restraints excluded: chain T residue 2276 THR Chi-restraints excluded: chain T residue 2315 LEU Chi-restraints excluded: chain T residue 2324 LEU Chi-restraints excluded: chain T residue 2380 LEU Chi-restraints excluded: chain T residue 2422 VAL Chi-restraints excluded: chain T residue 2500 LEU Chi-restraints excluded: chain T residue 2514 VAL Chi-restraints excluded: chain T residue 2552 ASP Chi-restraints excluded: chain T residue 2593 THR Chi-restraints excluded: chain T residue 2596 ILE Chi-restraints excluded: chain T residue 2607 LEU Chi-restraints excluded: chain T residue 2659 GLU Chi-restraints excluded: chain T residue 2679 TRP Chi-restraints excluded: chain T residue 2741 GLN Chi-restraints excluded: chain T residue 2816 LEU Chi-restraints excluded: chain T residue 2958 ASN Chi-restraints excluded: chain T residue 2959 MET Chi-restraints excluded: chain T residue 2985 LEU Chi-restraints excluded: chain T residue 3028 MET Chi-restraints excluded: chain T residue 3053 LEU Chi-restraints excluded: chain T residue 3068 LEU Chi-restraints excluded: chain T residue 3105 LEU Chi-restraints excluded: chain T residue 3107 LEU Chi-restraints excluded: chain T residue 3137 ILE Chi-restraints excluded: chain T residue 3171 LEU Chi-restraints excluded: chain T residue 3211 LEU Chi-restraints excluded: chain T residue 3226 LEU Chi-restraints excluded: chain T residue 3280 LEU Chi-restraints excluded: chain T residue 3283 PHE Chi-restraints excluded: chain T residue 3286 THR Chi-restraints excluded: chain T residue 3392 MET Chi-restraints excluded: chain T residue 3400 VAL Chi-restraints excluded: chain T residue 3405 VAL Chi-restraints excluded: chain T residue 3487 ASP Chi-restraints excluded: chain T residue 3522 VAL Chi-restraints excluded: chain T residue 3572 ILE Chi-restraints excluded: chain T residue 3628 ILE Chi-restraints excluded: chain T residue 3653 ILE Chi-restraints excluded: chain T residue 3697 ASP Chi-restraints excluded: chain T residue 3706 LEU Chi-restraints excluded: chain T residue 3716 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 347 random chunks: chunk 294 optimal weight: 10.0000 chunk 4 optimal weight: 0.0020 chunk 128 optimal weight: 0.5980 chunk 323 optimal weight: 1.9990 chunk 310 optimal weight: 2.9990 chunk 268 optimal weight: 1.9990 chunk 266 optimal weight: 2.9990 chunk 322 optimal weight: 0.1980 chunk 180 optimal weight: 9.9990 chunk 126 optimal weight: 0.8980 chunk 211 optimal weight: 4.9990 overall best weight: 0.7390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: T1109 HIS ** T1379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T1726 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T1935 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T1944 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T1983 ASN ** T2289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T2342 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T2696 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T2847 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T3165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T3168 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 = 0.4134 r_free = 0.4134 target = 0.137126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.115707 restraints weight = 70095.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.117381 restraints weight = 43867.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.118744 restraints weight = 30379.782| |-----------------------------------------------------------------------------| r_work (final): 0.3860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7440 moved from start: 0.4137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 29026 Z= 0.145 Angle : 0.831 19.495 39323 Z= 0.402 Chirality : 0.048 0.335 4501 Planarity : 0.006 0.121 4969 Dihedral : 7.116 66.247 3766 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 12.67 Ramachandran Plot: Outliers : 0.15 % Allowed : 12.90 % Favored : 86.96 % Rotamer: Outliers : 4.31 % Allowed : 19.09 % Favored : 76.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 6.85 % Twisted General : 0.21 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.19 (0.14), residues: 3443 helix: -0.38 (0.11), residues: 2080 sheet: -1.22 (0.91), residues: 33 loop : -3.27 (0.17), residues: 1330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.061 0.002 TRP T2179 HIS 0.007 0.001 HIS T1560 PHE 0.034 0.002 PHE T1782 TYR 0.036 0.002 TYR T2169 ARG 0.013 0.000 ARG T3262 Details of bonding type rmsd hydrogen bonds : bond 0.03971 ( 1252) hydrogen bonds : angle 4.89990 ( 3666) covalent geometry : bond 0.00322 (29026) covalent geometry : angle 0.83073 (39323) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6886 Ramachandran restraints generated. 3443 Oldfield, 0 Emsley, 3443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6886 Ramachandran restraints generated. 3443 Oldfield, 0 Emsley, 3443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 509 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 371 time to evaluate : 4.524 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: T 35 MET cc_start: 0.7493 (mmt) cc_final: 0.7275 (mmt) REVERT: T 38 LEU cc_start: 0.5628 (OUTLIER) cc_final: 0.4033 (mt) REVERT: T 508 GLN cc_start: 0.7129 (OUTLIER) cc_final: 0.6668 (pt0) REVERT: T 518 MET cc_start: 0.7980 (mmm) cc_final: 0.7563 (mmp) REVERT: T 683 MET cc_start: 0.8312 (OUTLIER) cc_final: 0.7939 (mpt) REVERT: T 693 MET cc_start: 0.6082 (mmm) cc_final: 0.5437 (tpt) REVERT: T 827 LEU cc_start: 0.8605 (OUTLIER) cc_final: 0.7945 (tt) REVERT: T 985 MET cc_start: 0.7117 (ptp) cc_final: 0.6799 (mtp) REVERT: T 1051 LYS cc_start: 0.6773 (pttm) cc_final: 0.5905 (mmmt) REVERT: T 1155 TYR cc_start: 0.7562 (OUTLIER) cc_final: 0.7094 (m-80) REVERT: T 1639 ASP cc_start: 0.8491 (t70) cc_final: 0.8096 (t0) REVERT: T 1676 MET cc_start: 0.7884 (mmt) cc_final: 0.7679 (mmt) REVERT: T 1686 LYS cc_start: 0.6987 (mppt) cc_final: 0.6650 (mmmt) REVERT: T 1740 GLN cc_start: 0.7337 (OUTLIER) cc_final: 0.6998 (mt0) REVERT: T 1785 ASP cc_start: 0.8379 (m-30) cc_final: 0.7814 (m-30) REVERT: T 2039 GLU cc_start: 0.7394 (OUTLIER) cc_final: 0.7164 (tp30) REVERT: T 2123 ILE cc_start: 0.9122 (mt) cc_final: 0.8850 (mt) REVERT: T 2208 LYS cc_start: 0.7038 (mmmm) cc_final: 0.6815 (mttt) REVERT: T 2228 GLU cc_start: 0.7096 (tp30) cc_final: 0.6758 (mp0) REVERT: T 2261 TRP cc_start: 0.7564 (t60) cc_final: 0.7339 (t-100) REVERT: T 2416 MET cc_start: 0.4636 (mpt) cc_final: 0.3509 (mtt) REVERT: T 2436 MET cc_start: 0.8178 (mmm) cc_final: 0.7910 (mmm) REVERT: T 2474 GLN cc_start: 0.8899 (mm110) cc_final: 0.8422 (tp-100) REVERT: T 2552 ASP cc_start: 0.7139 (OUTLIER) cc_final: 0.6903 (m-30) REVERT: T 2685 TYR cc_start: 0.7156 (m-10) cc_final: 0.6868 (m-10) REVERT: T 2694 TYR cc_start: 0.7334 (m-80) cc_final: 0.7096 (m-80) REVERT: T 2696 GLN cc_start: 0.8075 (pt0) cc_final: 0.7780 (tm-30) REVERT: T 2764 TRP cc_start: 0.5737 (p90) cc_final: 0.5107 (p90) REVERT: T 2793 MET cc_start: 0.7322 (tmm) cc_final: 0.7056 (ttt) REVERT: T 2816 LEU cc_start: 0.7794 (OUTLIER) cc_final: 0.7518 (tm) REVERT: T 2850 MET cc_start: 0.7783 (mmm) cc_final: 0.7491 (tpp) REVERT: T 3205 TRP cc_start: 0.7283 (p-90) cc_final: 0.6961 (p-90) REVERT: T 3209 GLN cc_start: 0.6978 (mt0) cc_final: 0.6461 (tm-30) REVERT: T 3494 ASN cc_start: 0.7639 (t0) cc_final: 0.7124 (m110) REVERT: T 3706 LEU cc_start: 0.6991 (OUTLIER) cc_final: 0.6489 (pp) REVERT: T 3741 MET cc_start: 0.7981 (ttm) cc_final: 0.7515 (mtp) outliers start: 138 outliers final: 93 residues processed: 474 average time/residue: 0.4589 time to fit residues: 369.3688 Evaluate side-chains 444 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 341 time to evaluate : 3.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain T residue 37 LEU Chi-restraints excluded: chain T residue 38 LEU Chi-restraints excluded: chain T residue 107 LEU Chi-restraints excluded: chain T residue 154 LEU Chi-restraints excluded: chain T residue 157 GLN Chi-restraints excluded: chain T residue 246 LEU Chi-restraints excluded: chain T residue 249 PHE Chi-restraints excluded: chain T residue 332 LEU Chi-restraints excluded: chain T residue 340 LEU Chi-restraints excluded: chain T residue 433 ILE Chi-restraints excluded: chain T residue 508 GLN Chi-restraints excluded: chain T residue 594 LEU Chi-restraints excluded: chain T residue 609 ASN Chi-restraints excluded: chain T residue 683 MET Chi-restraints excluded: chain T residue 694 ASP Chi-restraints excluded: chain T residue 763 ILE Chi-restraints excluded: chain T residue 773 VAL Chi-restraints excluded: chain T residue 783 VAL Chi-restraints excluded: chain T residue 826 ASN Chi-restraints excluded: chain T residue 827 LEU Chi-restraints excluded: chain T residue 848 THR Chi-restraints excluded: chain T residue 876 LEU Chi-restraints excluded: chain T residue 961 LYS Chi-restraints excluded: chain T residue 993 VAL Chi-restraints excluded: chain T residue 1001 LEU Chi-restraints excluded: chain T residue 1042 LEU Chi-restraints excluded: chain T residue 1063 LEU Chi-restraints excluded: chain T residue 1066 THR Chi-restraints excluded: chain T residue 1102 LEU Chi-restraints excluded: chain T residue 1155 TYR Chi-restraints excluded: chain T residue 1178 ILE Chi-restraints excluded: chain T residue 1214 LEU Chi-restraints excluded: chain T residue 1230 LEU Chi-restraints excluded: chain T residue 1263 LEU Chi-restraints excluded: chain T residue 1264 LEU Chi-restraints excluded: chain T residue 1313 THR Chi-restraints excluded: chain T residue 1368 LEU Chi-restraints excluded: chain T residue 1400 THR Chi-restraints excluded: chain T residue 1418 LEU Chi-restraints excluded: chain T residue 1437 ARG Chi-restraints excluded: chain T residue 1466 SER Chi-restraints excluded: chain T residue 1467 LEU Chi-restraints excluded: chain T residue 1510 LEU Chi-restraints excluded: chain T residue 1543 LEU Chi-restraints excluded: chain T residue 1575 LEU Chi-restraints excluded: chain T residue 1586 LEU Chi-restraints excluded: chain T residue 1596 LEU Chi-restraints excluded: chain T residue 1630 ARG Chi-restraints excluded: chain T residue 1715 HIS Chi-restraints excluded: chain T residue 1740 GLN Chi-restraints excluded: chain T residue 1752 PHE Chi-restraints excluded: chain T residue 1812 ILE Chi-restraints excluded: chain T residue 1825 LEU Chi-restraints excluded: chain T residue 1853 VAL Chi-restraints excluded: chain T residue 1865 LEU Chi-restraints excluded: chain T residue 1907 LEU Chi-restraints excluded: chain T residue 1927 PHE Chi-restraints excluded: chain T residue 1953 LEU Chi-restraints excluded: chain T residue 1990 ILE Chi-restraints excluded: chain T residue 2039 GLU Chi-restraints excluded: chain T residue 2121 ILE Chi-restraints excluded: chain T residue 2186 THR Chi-restraints excluded: chain T residue 2272 VAL Chi-restraints excluded: chain T residue 2276 THR Chi-restraints excluded: chain T residue 2315 LEU Chi-restraints excluded: chain T residue 2324 LEU Chi-restraints excluded: chain T residue 2380 LEU Chi-restraints excluded: chain T residue 2422 VAL Chi-restraints excluded: chain T residue 2500 LEU Chi-restraints excluded: chain T residue 2514 VAL Chi-restraints excluded: chain T residue 2552 ASP Chi-restraints excluded: chain T residue 2593 THR Chi-restraints excluded: chain T residue 2596 ILE Chi-restraints excluded: chain T residue 2607 LEU Chi-restraints excluded: chain T residue 2679 TRP Chi-restraints excluded: chain T residue 2741 GLN Chi-restraints excluded: chain T residue 2816 LEU Chi-restraints excluded: chain T residue 2958 ASN Chi-restraints excluded: chain T residue 2959 MET Chi-restraints excluded: chain T residue 2985 LEU Chi-restraints excluded: chain T residue 3028 MET Chi-restraints excluded: chain T residue 3053 LEU Chi-restraints excluded: chain T residue 3100 LEU Chi-restraints excluded: chain T residue 3105 LEU Chi-restraints excluded: chain T residue 3107 LEU Chi-restraints excluded: chain T residue 3137 ILE Chi-restraints excluded: chain T residue 3171 LEU Chi-restraints excluded: chain T residue 3226 LEU Chi-restraints excluded: chain T residue 3280 LEU Chi-restraints excluded: chain T residue 3283 PHE Chi-restraints excluded: chain T residue 3286 THR Chi-restraints excluded: chain T residue 3392 MET Chi-restraints excluded: chain T residue 3400 VAL Chi-restraints excluded: chain T residue 3405 VAL Chi-restraints excluded: chain T residue 3487 ASP Chi-restraints excluded: chain T residue 3522 VAL Chi-restraints excluded: chain T residue 3568 THR Chi-restraints excluded: chain T residue 3572 ILE Chi-restraints excluded: chain T residue 3628 ILE Chi-restraints excluded: chain T residue 3697 ASP Chi-restraints excluded: chain T residue 3706 LEU Chi-restraints excluded: chain T residue 3712 THR Chi-restraints excluded: chain T residue 3716 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 347 random chunks: chunk 20 optimal weight: 10.0000 chunk 55 optimal weight: 0.7980 chunk 306 optimal weight: 4.9990 chunk 2 optimal weight: 7.9990 chunk 173 optimal weight: 2.9990 chunk 127 optimal weight: 8.9990 chunk 198 optimal weight: 0.8980 chunk 47 optimal weight: 3.9990 chunk 228 optimal weight: 0.9990 chunk 28 optimal weight: 2.9990 chunk 246 optimal weight: 6.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: T 400 HIS ** T 735 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T1379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T1726 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T1768 HIS ** T1935 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T1944 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T2289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T2342 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T2696 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T2847 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T3018 GLN ** T3165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.134651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.113638 restraints weight = 71258.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.114688 restraints weight = 45327.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.115013 restraints weight = 33010.356| |-----------------------------------------------------------------------------| r_work (final): 0.3804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7531 moved from start: 0.4210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 29026 Z= 0.178 Angle : 0.859 18.364 39323 Z= 0.419 Chirality : 0.049 0.361 4501 Planarity : 0.006 0.121 4969 Dihedral : 7.186 65.960 3766 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 13.55 Ramachandran Plot: Outliers : 0.17 % Allowed : 13.53 % Favored : 86.29 % Rotamer: Outliers : 4.06 % Allowed : 19.78 % Favored : 76.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 6.85 % Twisted General : 0.21 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.18 (0.14), residues: 3443 helix: -0.35 (0.11), residues: 2086 sheet: -1.28 (0.91), residues: 33 loop : -3.30 (0.17), residues: 1324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.068 0.002 TRP T2179 HIS 0.007 0.001 HIS T1768 PHE 0.040 0.002 PHE T1750 TYR 0.035 0.002 TYR T2169 ARG 0.011 0.001 ARG T3262 Details of bonding type rmsd hydrogen bonds : bond 0.04183 ( 1252) hydrogen bonds : angle 4.96483 ( 3666) covalent geometry : bond 0.00411 (29026) covalent geometry : angle 0.85894 (39323) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6886 Ramachandran restraints generated. 3443 Oldfield, 0 Emsley, 3443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6886 Ramachandran restraints generated. 3443 Oldfield, 0 Emsley, 3443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 492 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 362 time to evaluate : 3.281 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: T 38 LEU cc_start: 0.5723 (OUTLIER) cc_final: 0.4172 (mt) REVERT: T 508 GLN cc_start: 0.7248 (OUTLIER) cc_final: 0.6790 (pt0) REVERT: T 683 MET cc_start: 0.8314 (OUTLIER) cc_final: 0.7896 (mpt) REVERT: T 827 LEU cc_start: 0.8652 (OUTLIER) cc_final: 0.7969 (tt) REVERT: T 985 MET cc_start: 0.7277 (ptp) cc_final: 0.6648 (mtp) REVERT: T 1051 LYS cc_start: 0.6973 (pttm) cc_final: 0.6031 (mmmt) REVERT: T 1052 LEU cc_start: 0.5870 (OUTLIER) cc_final: 0.5572 (tm) REVERT: T 1155 TYR cc_start: 0.7647 (OUTLIER) cc_final: 0.7082 (m-80) REVERT: T 1639 ASP cc_start: 0.8425 (t70) cc_final: 0.8106 (t0) REVERT: T 1686 LYS cc_start: 0.7058 (mppt) cc_final: 0.6692 (mmmt) REVERT: T 1691 MET cc_start: 0.7663 (mtt) cc_final: 0.7453 (mtt) REVERT: T 1785 ASP cc_start: 0.8362 (m-30) cc_final: 0.7687 (m-30) REVERT: T 1935 HIS cc_start: 0.7548 (OUTLIER) cc_final: 0.7104 (p-80) REVERT: T 2123 ILE cc_start: 0.9144 (mt) cc_final: 0.8858 (mt) REVERT: T 2228 GLU cc_start: 0.7128 (tp30) cc_final: 0.6701 (mp0) REVERT: T 2261 TRP cc_start: 0.7517 (t60) cc_final: 0.7315 (t-100) REVERT: T 2330 ARG cc_start: 0.7551 (mmt180) cc_final: 0.7328 (mmt180) REVERT: T 2416 MET cc_start: 0.4860 (mpt) cc_final: 0.3816 (mtt) REVERT: T 2474 GLN cc_start: 0.8850 (mm110) cc_final: 0.8373 (tp-100) REVERT: T 2552 ASP cc_start: 0.7257 (OUTLIER) cc_final: 0.7034 (m-30) REVERT: T 2685 TYR cc_start: 0.7245 (m-10) cc_final: 0.6916 (m-10) REVERT: T 2694 TYR cc_start: 0.7289 (m-80) cc_final: 0.7077 (m-80) REVERT: T 2793 MET cc_start: 0.7218 (tmm) cc_final: 0.6951 (ttt) REVERT: T 2816 LEU cc_start: 0.7825 (OUTLIER) cc_final: 0.7572 (tm) REVERT: T 3022 PHE cc_start: 0.7462 (m-80) cc_final: 0.6986 (m-80) REVERT: T 3063 PHE cc_start: 0.6724 (t80) cc_final: 0.6017 (t80) REVERT: T 3092 TYR cc_start: 0.6884 (t80) cc_final: 0.6267 (t80) REVERT: T 3102 CYS cc_start: 0.9118 (OUTLIER) cc_final: 0.8619 (t) REVERT: T 3205 TRP cc_start: 0.7304 (p-90) cc_final: 0.6984 (p-90) REVERT: T 3209 GLN cc_start: 0.7007 (mt0) cc_final: 0.6452 (tm-30) REVERT: T 3278 LYS cc_start: 0.7663 (pttp) cc_final: 0.7420 (pttm) REVERT: T 3494 ASN cc_start: 0.7690 (t0) cc_final: 0.7137 (m110) REVERT: T 3706 LEU cc_start: 0.7077 (OUTLIER) cc_final: 0.6602 (pp) REVERT: T 3741 MET cc_start: 0.8056 (ttm) cc_final: 0.7585 (mtp) outliers start: 130 outliers final: 100 residues processed: 461 average time/residue: 0.3872 time to fit residues: 298.3569 Evaluate side-chains 453 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 342 time to evaluate : 3.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain T residue 37 LEU Chi-restraints excluded: chain T residue 38 LEU Chi-restraints excluded: chain T residue 107 LEU Chi-restraints excluded: chain T residue 154 LEU Chi-restraints excluded: chain T residue 157 GLN Chi-restraints excluded: chain T residue 246 LEU Chi-restraints excluded: chain T residue 249 PHE Chi-restraints excluded: chain T residue 332 LEU Chi-restraints excluded: chain T residue 340 LEU Chi-restraints excluded: chain T residue 433 ILE Chi-restraints excluded: chain T residue 508 GLN Chi-restraints excluded: chain T residue 594 LEU Chi-restraints excluded: chain T residue 609 ASN Chi-restraints excluded: chain T residue 683 MET Chi-restraints excluded: chain T residue 694 ASP Chi-restraints excluded: chain T residue 748 LEU Chi-restraints excluded: chain T residue 753 ASN Chi-restraints excluded: chain T residue 763 ILE Chi-restraints excluded: chain T residue 773 VAL Chi-restraints excluded: chain T residue 783 VAL Chi-restraints excluded: chain T residue 826 ASN Chi-restraints excluded: chain T residue 827 LEU Chi-restraints excluded: chain T residue 848 THR Chi-restraints excluded: chain T residue 876 LEU Chi-restraints excluded: chain T residue 961 LYS Chi-restraints excluded: chain T residue 993 VAL Chi-restraints excluded: chain T residue 1042 LEU Chi-restraints excluded: chain T residue 1052 LEU Chi-restraints excluded: chain T residue 1063 LEU Chi-restraints excluded: chain T residue 1066 THR Chi-restraints excluded: chain T residue 1102 LEU Chi-restraints excluded: chain T residue 1155 TYR Chi-restraints excluded: chain T residue 1230 LEU Chi-restraints excluded: chain T residue 1263 LEU Chi-restraints excluded: chain T residue 1264 LEU Chi-restraints excluded: chain T residue 1265 ILE Chi-restraints excluded: chain T residue 1313 THR Chi-restraints excluded: chain T residue 1368 LEU Chi-restraints excluded: chain T residue 1400 THR Chi-restraints excluded: chain T residue 1418 LEU Chi-restraints excluded: chain T residue 1437 ARG Chi-restraints excluded: chain T residue 1466 SER Chi-restraints excluded: chain T residue 1467 LEU Chi-restraints excluded: chain T residue 1510 LEU Chi-restraints excluded: chain T residue 1543 LEU Chi-restraints excluded: chain T residue 1586 LEU Chi-restraints excluded: chain T residue 1596 LEU Chi-restraints excluded: chain T residue 1630 ARG Chi-restraints excluded: chain T residue 1715 HIS Chi-restraints excluded: chain T residue 1718 LEU Chi-restraints excluded: chain T residue 1768 HIS Chi-restraints excluded: chain T residue 1788 LEU Chi-restraints excluded: chain T residue 1812 ILE Chi-restraints excluded: chain T residue 1825 LEU Chi-restraints excluded: chain T residue 1853 VAL Chi-restraints excluded: chain T residue 1865 LEU Chi-restraints excluded: chain T residue 1907 LEU Chi-restraints excluded: chain T residue 1927 PHE Chi-restraints excluded: chain T residue 1935 HIS Chi-restraints excluded: chain T residue 1953 LEU Chi-restraints excluded: chain T residue 1996 PHE Chi-restraints excluded: chain T residue 2035 ILE Chi-restraints excluded: chain T residue 2039 GLU Chi-restraints excluded: chain T residue 2121 ILE Chi-restraints excluded: chain T residue 2186 THR Chi-restraints excluded: chain T residue 2272 VAL Chi-restraints excluded: chain T residue 2276 THR Chi-restraints excluded: chain T residue 2315 LEU Chi-restraints excluded: chain T residue 2324 LEU Chi-restraints excluded: chain T residue 2380 LEU Chi-restraints excluded: chain T residue 2422 VAL Chi-restraints excluded: chain T residue 2442 SER Chi-restraints excluded: chain T residue 2500 LEU Chi-restraints excluded: chain T residue 2514 VAL Chi-restraints excluded: chain T residue 2552 ASP Chi-restraints excluded: chain T residue 2593 THR Chi-restraints excluded: chain T residue 2596 ILE Chi-restraints excluded: chain T residue 2607 LEU Chi-restraints excluded: chain T residue 2613 ILE Chi-restraints excluded: chain T residue 2679 TRP Chi-restraints excluded: chain T residue 2741 GLN Chi-restraints excluded: chain T residue 2816 LEU Chi-restraints excluded: chain T residue 2958 ASN Chi-restraints excluded: chain T residue 2959 MET Chi-restraints excluded: chain T residue 2985 LEU Chi-restraints excluded: chain T residue 3028 MET Chi-restraints excluded: chain T residue 3053 LEU Chi-restraints excluded: chain T residue 3102 CYS Chi-restraints excluded: chain T residue 3105 LEU Chi-restraints excluded: chain T residue 3107 LEU Chi-restraints excluded: chain T residue 3137 ILE Chi-restraints excluded: chain T residue 3171 LEU Chi-restraints excluded: chain T residue 3181 ILE Chi-restraints excluded: chain T residue 3211 LEU Chi-restraints excluded: chain T residue 3226 LEU Chi-restraints excluded: chain T residue 3280 LEU Chi-restraints excluded: chain T residue 3283 PHE Chi-restraints excluded: chain T residue 3286 THR Chi-restraints excluded: chain T residue 3392 MET Chi-restraints excluded: chain T residue 3400 VAL Chi-restraints excluded: chain T residue 3405 VAL Chi-restraints excluded: chain T residue 3487 ASP Chi-restraints excluded: chain T residue 3506 MET Chi-restraints excluded: chain T residue 3522 VAL Chi-restraints excluded: chain T residue 3568 THR Chi-restraints excluded: chain T residue 3572 ILE Chi-restraints excluded: chain T residue 3628 ILE Chi-restraints excluded: chain T residue 3697 ASP Chi-restraints excluded: chain T residue 3706 LEU Chi-restraints excluded: chain T residue 3712 THR Chi-restraints excluded: chain T residue 3716 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 347 random chunks: chunk 333 optimal weight: 0.9980 chunk 174 optimal weight: 6.9990 chunk 74 optimal weight: 0.9980 chunk 62 optimal weight: 0.5980 chunk 300 optimal weight: 4.9990 chunk 64 optimal weight: 0.0070 chunk 89 optimal weight: 7.9990 chunk 301 optimal weight: 6.9990 chunk 67 optimal weight: 4.9990 chunk 232 optimal weight: 3.9990 chunk 167 optimal weight: 4.9990 overall best weight: 1.3200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** T 735 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T1234 GLN ** T1379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T1726 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T1935 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T1944 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T2289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T2342 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T2696 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T2847 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T3064 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T3165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.135323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.113837 restraints weight = 70565.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.115348 restraints weight = 45191.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.116469 restraints weight = 31333.055| |-----------------------------------------------------------------------------| r_work (final): 0.3825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7504 moved from start: 0.4294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 29026 Z= 0.161 Angle : 0.855 17.208 39323 Z= 0.415 Chirality : 0.049 0.359 4501 Planarity : 0.006 0.125 4969 Dihedral : 7.145 66.428 3766 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 13.13 Ramachandran Plot: Outliers : 0.15 % Allowed : 13.33 % Favored : 86.52 % Rotamer: Outliers : 4.00 % Allowed : 20.19 % Favored : 75.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 6.85 % Twisted General : 0.21 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.12 (0.14), residues: 3443 helix: -0.30 (0.11), residues: 2085 sheet: -1.22 (0.92), residues: 33 loop : -3.27 (0.17), residues: 1325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.075 0.002 TRP T2179 HIS 0.019 0.001 HIS T1768 PHE 0.033 0.002 PHE T 317 TYR 0.034 0.002 TYR T2169 ARG 0.018 0.000 ARG T3067 Details of bonding type rmsd hydrogen bonds : bond 0.04056 ( 1252) hydrogen bonds : angle 4.91221 ( 3666) covalent geometry : bond 0.00368 (29026) covalent geometry : angle 0.85483 (39323) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6886 Ramachandran restraints generated. 3443 Oldfield, 0 Emsley, 3443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6886 Ramachandran restraints generated. 3443 Oldfield, 0 Emsley, 3443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 485 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 357 time to evaluate : 3.828 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: T 35 MET cc_start: 0.7609 (mmt) cc_final: 0.7351 (mmt) REVERT: T 38 LEU cc_start: 0.5717 (OUTLIER) cc_final: 0.4189 (mt) REVERT: T 508 GLN cc_start: 0.7164 (OUTLIER) cc_final: 0.6744 (pt0) REVERT: T 683 MET cc_start: 0.8343 (OUTLIER) cc_final: 0.7930 (mpt) REVERT: T 693 MET cc_start: 0.6150 (mmm) cc_final: 0.5580 (tpt) REVERT: T 985 MET cc_start: 0.7224 (ptp) cc_final: 0.6762 (mtp) REVERT: T 1051 LYS cc_start: 0.7001 (pttm) cc_final: 0.6067 (mmmt) REVERT: T 1052 LEU cc_start: 0.5821 (OUTLIER) cc_final: 0.5508 (tm) REVERT: T 1155 TYR cc_start: 0.7662 (OUTLIER) cc_final: 0.7090 (m-80) REVERT: T 1639 ASP cc_start: 0.8581 (t70) cc_final: 0.8135 (t0) REVERT: T 1785 ASP cc_start: 0.8399 (m-30) cc_final: 0.8022 (m-30) REVERT: T 1935 HIS cc_start: 0.7522 (OUTLIER) cc_final: 0.7055 (p-80) REVERT: T 2123 ILE cc_start: 0.9157 (mt) cc_final: 0.8876 (mt) REVERT: T 2228 GLU cc_start: 0.7186 (tp30) cc_final: 0.6626 (mp0) REVERT: T 2416 MET cc_start: 0.4764 (mpt) cc_final: 0.3780 (mtt) REVERT: T 2474 GLN cc_start: 0.8813 (mm110) cc_final: 0.8349 (tp-100) REVERT: T 2552 ASP cc_start: 0.7274 (OUTLIER) cc_final: 0.7052 (m-30) REVERT: T 2607 LEU cc_start: 0.8639 (OUTLIER) cc_final: 0.8329 (tp) REVERT: T 2685 TYR cc_start: 0.7260 (m-10) cc_final: 0.6928 (m-10) REVERT: T 2793 MET cc_start: 0.7217 (tmm) cc_final: 0.6997 (ttt) REVERT: T 2816 LEU cc_start: 0.7935 (OUTLIER) cc_final: 0.7680 (tm) REVERT: T 2850 MET cc_start: 0.7810 (mmm) cc_final: 0.7493 (tpp) REVERT: T 3022 PHE cc_start: 0.7503 (m-80) cc_final: 0.6973 (m-80) REVERT: T 3063 PHE cc_start: 0.6755 (t80) cc_final: 0.5970 (t80) REVERT: T 3092 TYR cc_start: 0.6898 (t80) cc_final: 0.6245 (t80) REVERT: T 3102 CYS cc_start: 0.9121 (OUTLIER) cc_final: 0.8562 (t) REVERT: T 3205 TRP cc_start: 0.7313 (p-90) cc_final: 0.7035 (p-90) REVERT: T 3209 GLN cc_start: 0.7005 (mt0) cc_final: 0.6457 (tm-30) REVERT: T 3494 ASN cc_start: 0.7652 (t0) cc_final: 0.7443 (m-40) REVERT: T 3706 LEU cc_start: 0.7096 (OUTLIER) cc_final: 0.6680 (pp) REVERT: T 3741 MET cc_start: 0.8077 (ttm) cc_final: 0.7569 (mtp) outliers start: 128 outliers final: 98 residues processed: 456 average time/residue: 0.3885 time to fit residues: 297.5302 Evaluate side-chains 447 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 338 time to evaluate : 3.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain T residue 37 LEU Chi-restraints excluded: chain T residue 38 LEU Chi-restraints excluded: chain T residue 107 LEU Chi-restraints excluded: chain T residue 133 LEU Chi-restraints excluded: chain T residue 154 LEU Chi-restraints excluded: chain T residue 157 GLN Chi-restraints excluded: chain T residue 246 LEU Chi-restraints excluded: chain T residue 249 PHE Chi-restraints excluded: chain T residue 332 LEU Chi-restraints excluded: chain T residue 340 LEU Chi-restraints excluded: chain T residue 390 LEU Chi-restraints excluded: chain T residue 433 ILE Chi-restraints excluded: chain T residue 508 GLN Chi-restraints excluded: chain T residue 594 LEU Chi-restraints excluded: chain T residue 633 VAL Chi-restraints excluded: chain T residue 683 MET Chi-restraints excluded: chain T residue 694 ASP Chi-restraints excluded: chain T residue 753 ASN Chi-restraints excluded: chain T residue 763 ILE Chi-restraints excluded: chain T residue 773 VAL Chi-restraints excluded: chain T residue 783 VAL Chi-restraints excluded: chain T residue 826 ASN Chi-restraints excluded: chain T residue 848 THR Chi-restraints excluded: chain T residue 876 LEU Chi-restraints excluded: chain T residue 961 LYS Chi-restraints excluded: chain T residue 993 VAL Chi-restraints excluded: chain T residue 1042 LEU Chi-restraints excluded: chain T residue 1052 LEU Chi-restraints excluded: chain T residue 1063 LEU Chi-restraints excluded: chain T residue 1066 THR Chi-restraints excluded: chain T residue 1102 LEU Chi-restraints excluded: chain T residue 1155 TYR Chi-restraints excluded: chain T residue 1230 LEU Chi-restraints excluded: chain T residue 1263 LEU Chi-restraints excluded: chain T residue 1264 LEU Chi-restraints excluded: chain T residue 1265 ILE Chi-restraints excluded: chain T residue 1313 THR Chi-restraints excluded: chain T residue 1368 LEU Chi-restraints excluded: chain T residue 1400 THR Chi-restraints excluded: chain T residue 1418 LEU Chi-restraints excluded: chain T residue 1437 ARG Chi-restraints excluded: chain T residue 1466 SER Chi-restraints excluded: chain T residue 1467 LEU Chi-restraints excluded: chain T residue 1510 LEU Chi-restraints excluded: chain T residue 1543 LEU Chi-restraints excluded: chain T residue 1586 LEU Chi-restraints excluded: chain T residue 1596 LEU Chi-restraints excluded: chain T residue 1630 ARG Chi-restraints excluded: chain T residue 1695 LEU Chi-restraints excluded: chain T residue 1715 HIS Chi-restraints excluded: chain T residue 1718 LEU Chi-restraints excluded: chain T residue 1788 LEU Chi-restraints excluded: chain T residue 1812 ILE Chi-restraints excluded: chain T residue 1825 LEU Chi-restraints excluded: chain T residue 1853 VAL Chi-restraints excluded: chain T residue 1865 LEU Chi-restraints excluded: chain T residue 1907 LEU Chi-restraints excluded: chain T residue 1927 PHE Chi-restraints excluded: chain T residue 1935 HIS Chi-restraints excluded: chain T residue 1953 LEU Chi-restraints excluded: chain T residue 1990 ILE Chi-restraints excluded: chain T residue 2039 GLU Chi-restraints excluded: chain T residue 2121 ILE Chi-restraints excluded: chain T residue 2186 THR Chi-restraints excluded: chain T residue 2272 VAL Chi-restraints excluded: chain T residue 2276 THR Chi-restraints excluded: chain T residue 2315 LEU Chi-restraints excluded: chain T residue 2324 LEU Chi-restraints excluded: chain T residue 2369 VAL Chi-restraints excluded: chain T residue 2380 LEU Chi-restraints excluded: chain T residue 2422 VAL Chi-restraints excluded: chain T residue 2442 SER Chi-restraints excluded: chain T residue 2500 LEU Chi-restraints excluded: chain T residue 2514 VAL Chi-restraints excluded: chain T residue 2552 ASP Chi-restraints excluded: chain T residue 2593 THR Chi-restraints excluded: chain T residue 2596 ILE Chi-restraints excluded: chain T residue 2607 LEU Chi-restraints excluded: chain T residue 2613 ILE Chi-restraints excluded: chain T residue 2679 TRP Chi-restraints excluded: chain T residue 2741 GLN Chi-restraints excluded: chain T residue 2816 LEU Chi-restraints excluded: chain T residue 2958 ASN Chi-restraints excluded: chain T residue 2959 MET Chi-restraints excluded: chain T residue 2985 LEU Chi-restraints excluded: chain T residue 3028 MET Chi-restraints excluded: chain T residue 3053 LEU Chi-restraints excluded: chain T residue 3102 CYS Chi-restraints excluded: chain T residue 3105 LEU Chi-restraints excluded: chain T residue 3107 LEU Chi-restraints excluded: chain T residue 3137 ILE Chi-restraints excluded: chain T residue 3171 LEU Chi-restraints excluded: chain T residue 3181 ILE Chi-restraints excluded: chain T residue 3211 LEU Chi-restraints excluded: chain T residue 3226 LEU Chi-restraints excluded: chain T residue 3280 LEU Chi-restraints excluded: chain T residue 3283 PHE Chi-restraints excluded: chain T residue 3286 THR Chi-restraints excluded: chain T residue 3392 MET Chi-restraints excluded: chain T residue 3400 VAL Chi-restraints excluded: chain T residue 3405 VAL Chi-restraints excluded: chain T residue 3487 ASP Chi-restraints excluded: chain T residue 3522 VAL Chi-restraints excluded: chain T residue 3568 THR Chi-restraints excluded: chain T residue 3572 ILE Chi-restraints excluded: chain T residue 3628 ILE Chi-restraints excluded: chain T residue 3697 ASP Chi-restraints excluded: chain T residue 3706 LEU Chi-restraints excluded: chain T residue 3716 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 347 random chunks: chunk 148 optimal weight: 1.9990 chunk 157 optimal weight: 5.9990 chunk 335 optimal weight: 3.9990 chunk 244 optimal weight: 3.9990 chunk 341 optimal weight: 0.1980 chunk 34 optimal weight: 0.8980 chunk 295 optimal weight: 0.8980 chunk 316 optimal weight: 1.9990 chunk 109 optimal weight: 7.9990 chunk 213 optimal weight: 0.9980 chunk 94 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** T 735 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T1726 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T1740 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T1768 HIS ** T1935 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T1944 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T2289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T2342 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T2526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T2696 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T2847 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T3165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.136184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.114600 restraints weight = 70593.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.116219 restraints weight = 45312.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.117637 restraints weight = 31218.769| |-----------------------------------------------------------------------------| r_work (final): 0.3844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7477 moved from start: 0.4439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 29026 Z= 0.152 Angle : 0.855 16.441 39323 Z= 0.413 Chirality : 0.049 0.372 4501 Planarity : 0.006 0.122 4969 Dihedral : 7.056 66.410 3766 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 13.13 Ramachandran Plot: Outliers : 0.15 % Allowed : 13.24 % Favored : 86.61 % Rotamer: Outliers : 3.56 % Allowed : 20.75 % Favored : 75.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 6.85 % Twisted General : 0.21 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.03 (0.15), residues: 3443 helix: -0.23 (0.12), residues: 2080 sheet: -1.19 (0.92), residues: 33 loop : -3.24 (0.17), residues: 1330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.064 0.002 TRP T2179 HIS 0.010 0.001 HIS T1768 PHE 0.037 0.002 PHE T1750 TYR 0.033 0.002 TYR T2169 ARG 0.010 0.000 ARG T3262 Details of bonding type rmsd hydrogen bonds : bond 0.03988 ( 1252) hydrogen bonds : angle 4.87640 ( 3666) covalent geometry : bond 0.00347 (29026) covalent geometry : angle 0.85508 (39323) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6886 Ramachandran restraints generated. 3443 Oldfield, 0 Emsley, 3443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6886 Ramachandran restraints generated. 3443 Oldfield, 0 Emsley, 3443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 475 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 361 time to evaluate : 3.589 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: T 35 MET cc_start: 0.7604 (mmt) cc_final: 0.7341 (mmt) REVERT: T 38 LEU cc_start: 0.5651 (OUTLIER) cc_final: 0.3846 (mt) REVERT: T 39 ASN cc_start: 0.5235 (OUTLIER) cc_final: 0.4908 (m110) REVERT: T 116 ILE cc_start: 0.5994 (pt) cc_final: 0.5579 (pp) REVERT: T 508 GLN cc_start: 0.7142 (OUTLIER) cc_final: 0.6749 (pt0) REVERT: T 683 MET cc_start: 0.8349 (OUTLIER) cc_final: 0.7975 (mpt) REVERT: T 693 MET cc_start: 0.6038 (mmm) cc_final: 0.5403 (tpt) REVERT: T 961 LYS cc_start: 0.8081 (OUTLIER) cc_final: 0.7613 (pmtt) REVERT: T 985 MET cc_start: 0.7089 (ptp) cc_final: 0.6842 (mtp) REVERT: T 1051 LYS cc_start: 0.6920 (pttm) cc_final: 0.6056 (mmmt) REVERT: T 1052 LEU cc_start: 0.5788 (OUTLIER) cc_final: 0.5520 (tm) REVERT: T 1155 TYR cc_start: 0.7614 (OUTLIER) cc_final: 0.7094 (m-80) REVERT: T 1639 ASP cc_start: 0.8581 (t70) cc_final: 0.8170 (t0) REVERT: T 1669 MET cc_start: 0.7894 (tpp) cc_final: 0.7592 (tpp) REVERT: T 1691 MET cc_start: 0.7604 (mtt) cc_final: 0.7348 (mtt) REVERT: T 1785 ASP cc_start: 0.8274 (m-30) cc_final: 0.7827 (m-30) REVERT: T 1801 PHE cc_start: 0.7165 (t80) cc_final: 0.6905 (t80) REVERT: T 1935 HIS cc_start: 0.7697 (OUTLIER) cc_final: 0.7093 (p-80) REVERT: T 2123 ILE cc_start: 0.9168 (mt) cc_final: 0.8887 (mt) REVERT: T 2169 TYR cc_start: 0.6673 (t80) cc_final: 0.6176 (t80) REVERT: T 2228 GLU cc_start: 0.7174 (tp30) cc_final: 0.6581 (mp0) REVERT: T 2416 MET cc_start: 0.4629 (mpt) cc_final: 0.3740 (mtt) REVERT: T 2474 GLN cc_start: 0.8778 (mm110) cc_final: 0.8139 (mm-40) REVERT: T 2552 ASP cc_start: 0.7246 (OUTLIER) cc_final: 0.7026 (m-30) REVERT: T 2607 LEU cc_start: 0.8628 (OUTLIER) cc_final: 0.8349 (tp) REVERT: T 2685 TYR cc_start: 0.7147 (m-10) cc_final: 0.6875 (m-10) REVERT: T 2793 MET cc_start: 0.7251 (tmm) cc_final: 0.7041 (ttt) REVERT: T 2816 LEU cc_start: 0.7942 (OUTLIER) cc_final: 0.7681 (tm) REVERT: T 2850 MET cc_start: 0.7760 (mmm) cc_final: 0.7453 (tpp) REVERT: T 2959 MET cc_start: 0.6649 (OUTLIER) cc_final: 0.6370 (pmt) REVERT: T 3063 PHE cc_start: 0.6696 (t80) cc_final: 0.6062 (t80) REVERT: T 3092 TYR cc_start: 0.6861 (t80) cc_final: 0.6218 (t80) REVERT: T 3102 CYS cc_start: 0.9116 (OUTLIER) cc_final: 0.8656 (t) REVERT: T 3205 TRP cc_start: 0.7285 (p-90) cc_final: 0.6994 (p-90) REVERT: T 3209 GLN cc_start: 0.6991 (mt0) cc_final: 0.6448 (tm-30) REVERT: T 3494 ASN cc_start: 0.7724 (t0) cc_final: 0.7453 (m-40) REVERT: T 3706 LEU cc_start: 0.7053 (OUTLIER) cc_final: 0.6605 (pp) REVERT: T 3741 MET cc_start: 0.8017 (ttm) cc_final: 0.7510 (mtp) outliers start: 114 outliers final: 90 residues processed: 451 average time/residue: 0.3752 time to fit residues: 284.7355 Evaluate side-chains 450 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 346 time to evaluate : 3.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain T residue 37 LEU Chi-restraints excluded: chain T residue 38 LEU Chi-restraints excluded: chain T residue 39 ASN Chi-restraints excluded: chain T residue 107 LEU Chi-restraints excluded: chain T residue 133 LEU Chi-restraints excluded: chain T residue 154 LEU Chi-restraints excluded: chain T residue 157 GLN Chi-restraints excluded: chain T residue 246 LEU Chi-restraints excluded: chain T residue 249 PHE Chi-restraints excluded: chain T residue 332 LEU Chi-restraints excluded: chain T residue 340 LEU Chi-restraints excluded: chain T residue 433 ILE Chi-restraints excluded: chain T residue 508 GLN Chi-restraints excluded: chain T residue 594 LEU Chi-restraints excluded: chain T residue 683 MET Chi-restraints excluded: chain T residue 694 ASP Chi-restraints excluded: chain T residue 753 ASN Chi-restraints excluded: chain T residue 763 ILE Chi-restraints excluded: chain T residue 773 VAL Chi-restraints excluded: chain T residue 783 VAL Chi-restraints excluded: chain T residue 826 ASN Chi-restraints excluded: chain T residue 848 THR Chi-restraints excluded: chain T residue 876 LEU Chi-restraints excluded: chain T residue 961 LYS Chi-restraints excluded: chain T residue 993 VAL Chi-restraints excluded: chain T residue 1042 LEU Chi-restraints excluded: chain T residue 1052 LEU Chi-restraints excluded: chain T residue 1063 LEU Chi-restraints excluded: chain T residue 1066 THR Chi-restraints excluded: chain T residue 1102 LEU Chi-restraints excluded: chain T residue 1155 TYR Chi-restraints excluded: chain T residue 1230 LEU Chi-restraints excluded: chain T residue 1263 LEU Chi-restraints excluded: chain T residue 1264 LEU Chi-restraints excluded: chain T residue 1265 ILE Chi-restraints excluded: chain T residue 1313 THR Chi-restraints excluded: chain T residue 1368 LEU Chi-restraints excluded: chain T residue 1400 THR Chi-restraints excluded: chain T residue 1418 LEU Chi-restraints excluded: chain T residue 1437 ARG Chi-restraints excluded: chain T residue 1466 SER Chi-restraints excluded: chain T residue 1467 LEU Chi-restraints excluded: chain T residue 1510 LEU Chi-restraints excluded: chain T residue 1543 LEU Chi-restraints excluded: chain T residue 1586 LEU Chi-restraints excluded: chain T residue 1596 LEU Chi-restraints excluded: chain T residue 1630 ARG Chi-restraints excluded: chain T residue 1715 HIS Chi-restraints excluded: chain T residue 1752 PHE Chi-restraints excluded: chain T residue 1788 LEU Chi-restraints excluded: chain T residue 1812 ILE Chi-restraints excluded: chain T residue 1825 LEU Chi-restraints excluded: chain T residue 1853 VAL Chi-restraints excluded: chain T residue 1865 LEU Chi-restraints excluded: chain T residue 1907 LEU Chi-restraints excluded: chain T residue 1927 PHE Chi-restraints excluded: chain T residue 1935 HIS Chi-restraints excluded: chain T residue 1953 LEU Chi-restraints excluded: chain T residue 1990 ILE Chi-restraints excluded: chain T residue 2121 ILE Chi-restraints excluded: chain T residue 2186 THR Chi-restraints excluded: chain T residue 2272 VAL Chi-restraints excluded: chain T residue 2276 THR Chi-restraints excluded: chain T residue 2315 LEU Chi-restraints excluded: chain T residue 2324 LEU Chi-restraints excluded: chain T residue 2369 VAL Chi-restraints excluded: chain T residue 2422 VAL Chi-restraints excluded: chain T residue 2442 SER Chi-restraints excluded: chain T residue 2500 LEU Chi-restraints excluded: chain T residue 2514 VAL Chi-restraints excluded: chain T residue 2552 ASP Chi-restraints excluded: chain T residue 2593 THR Chi-restraints excluded: chain T residue 2596 ILE Chi-restraints excluded: chain T residue 2607 LEU Chi-restraints excluded: chain T residue 2613 ILE Chi-restraints excluded: chain T residue 2679 TRP Chi-restraints excluded: chain T residue 2741 GLN Chi-restraints excluded: chain T residue 2816 LEU Chi-restraints excluded: chain T residue 2958 ASN Chi-restraints excluded: chain T residue 2959 MET Chi-restraints excluded: chain T residue 2985 LEU Chi-restraints excluded: chain T residue 3028 MET Chi-restraints excluded: chain T residue 3053 LEU Chi-restraints excluded: chain T residue 3102 CYS Chi-restraints excluded: chain T residue 3105 LEU Chi-restraints excluded: chain T residue 3107 LEU Chi-restraints excluded: chain T residue 3137 ILE Chi-restraints excluded: chain T residue 3171 LEU Chi-restraints excluded: chain T residue 3226 LEU Chi-restraints excluded: chain T residue 3280 LEU Chi-restraints excluded: chain T residue 3283 PHE Chi-restraints excluded: chain T residue 3286 THR Chi-restraints excluded: chain T residue 3392 MET Chi-restraints excluded: chain T residue 3400 VAL Chi-restraints excluded: chain T residue 3405 VAL Chi-restraints excluded: chain T residue 3487 ASP Chi-restraints excluded: chain T residue 3506 MET Chi-restraints excluded: chain T residue 3522 VAL Chi-restraints excluded: chain T residue 3568 THR Chi-restraints excluded: chain T residue 3572 ILE Chi-restraints excluded: chain T residue 3628 ILE Chi-restraints excluded: chain T residue 3697 ASP Chi-restraints excluded: chain T residue 3706 LEU Chi-restraints excluded: chain T residue 3716 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 347 random chunks: chunk 318 optimal weight: 0.3980 chunk 21 optimal weight: 2.9990 chunk 98 optimal weight: 0.6980 chunk 199 optimal weight: 4.9990 chunk 1 optimal weight: 6.9990 chunk 326 optimal weight: 0.7980 chunk 319 optimal weight: 0.9990 chunk 22 optimal weight: 2.9990 chunk 43 optimal weight: 4.9990 chunk 32 optimal weight: 2.9990 chunk 276 optimal weight: 8.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** T 510 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 735 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T1726 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T1740 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T1768 HIS ** T1935 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T1944 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T2207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T2289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T2342 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T2526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T2696 GLN ** T2847 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T3139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T3165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T3406 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.135844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.114730 restraints weight = 70848.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.115628 restraints weight = 47484.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.116382 restraints weight = 34791.333| |-----------------------------------------------------------------------------| r_work (final): 0.3825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7502 moved from start: 0.4516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 29026 Z= 0.158 Angle : 0.859 16.158 39323 Z= 0.416 Chirality : 0.049 0.347 4501 Planarity : 0.006 0.125 4969 Dihedral : 7.031 66.099 3766 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 13.32 Ramachandran Plot: Outliers : 0.17 % Allowed : 13.10 % Favored : 86.73 % Rotamer: Outliers : 3.56 % Allowed : 20.59 % Favored : 75.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 6.85 % Twisted General : 0.24 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.96 (0.15), residues: 3443 helix: -0.20 (0.12), residues: 2092 sheet: -0.77 (0.88), residues: 43 loop : -3.20 (0.17), residues: 1308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.059 0.002 TRP T2179 HIS 0.015 0.001 HIS T1768 PHE 0.029 0.002 PHE T 309 TYR 0.032 0.002 TYR T2169 ARG 0.011 0.000 ARG T3262 Details of bonding type rmsd hydrogen bonds : bond 0.03978 ( 1252) hydrogen bonds : angle 4.85516 ( 3666) covalent geometry : bond 0.00360 (29026) covalent geometry : angle 0.85862 (39323) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10197.34 seconds wall clock time: 178 minutes 21.81 seconds (10701.81 seconds total)