Starting phenix.real_space_refine on Thu Aug 6 05:38:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vdr_43156/08_2026/8vdr_43156.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vdr_43156/08_2026/8vdr_43156.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 { model { file = "/net/cci-nas-00/data/ceres_data/8vdr_43156/08_2026/8vdr_43156.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vdr_43156/08_2026/8vdr_43156.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8vdr_43156/08_2026/8vdr_43156.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vdr_43156/08_2026/8vdr_43156.map" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.023 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 66 5.16 5 C 8340 2.51 5 N 2412 2.21 5 O 2729 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 68 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13547 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 13547 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1852, 13547 Classifications: {'peptide': 1852} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 70, 'TRANS': 1781} Chain breaks: 1 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 3.03, per 1000 atoms: 0.22 Number of scatterers: 13547 At special positions: 0 Unit cell: (113.76, 146.88, 145.44, 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 66 16.00 O 2729 8.00 N 2412 7.00 C 8340 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.30 Conformation dependent library (CDL) restraints added in 712.6 milliseconds 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3470 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 2 sheets defined 81.4% alpha, 1.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.38 Creating SS restraints... Processing helix chain 'A' and resid 208 through 225 removed outlier: 3.666A pdb=" N LEU A 212 " --> pdb=" O ASP A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 246 Processing helix chain 'A' and resid 275 through 287 Processing helix chain 'A' and resid 290 through 305 removed outlier: 3.636A pdb=" N LEU A 305 " --> pdb=" O LEU A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 356 No H-bonds generated for 'chain 'A' and resid 354 through 356' Processing helix chain 'A' and resid 384 through 403 removed outlier: 3.755A pdb=" N LYS A 403 " --> pdb=" O ILE A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 489 through 514 removed outlier: 3.750A pdb=" N GLN A 493 " --> pdb=" O THR A 489 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N ALA A 494 " --> pdb=" O SER A 490 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU A 513 " --> pdb=" O ALA A 509 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ASP A 514 " --> pdb=" O GLN A 510 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 562 removed outlier: 3.534A pdb=" N MET A 536 " --> pdb=" O ARG A 532 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N GLN A 546 " --> pdb=" O GLU A 542 " (cutoff:3.500A) Processing helix chain 'A' and resid 569 through 601 removed outlier: 3.619A pdb=" N THR A 579 " --> pdb=" O CYS A 575 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLU A 586 " --> pdb=" O SER A 582 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N MET A 587 " --> pdb=" O ASN A 583 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LYS A 592 " --> pdb=" O SER A 588 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLU A 601 " --> pdb=" O LEU A 597 " (cutoff:3.500A) Processing helix chain 'A' and resid 605 through 627 removed outlier: 3.512A pdb=" N LEU A 623 " --> pdb=" O VAL A 619 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N SER A 625 " --> pdb=" O GLU A 621 " (cutoff:3.500A) Processing helix chain 'A' and resid 633 through 656 removed outlier: 4.225A pdb=" N LEU A 637 " --> pdb=" O PRO A 633 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N VAL A 644 " --> pdb=" O ALA A 640 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N GLU A 650 " --> pdb=" O GLN A 646 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LEU A 651 " --> pdb=" O ALA A 647 " (cutoff:3.500A) Processing helix chain 'A' and resid 661 through 693 removed outlier: 3.532A pdb=" N ASP A 666 " --> pdb=" O PRO A 662 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLN A 691 " --> pdb=" O LYS A 687 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ARG A 692 " --> pdb=" O SER A 688 " (cutoff:3.500A) Processing helix chain 'A' and resid 697 through 724 removed outlier: 3.939A pdb=" N VAL A 702 " --> pdb=" O LEU A 698 " (cutoff:3.500A) Processing helix chain 'A' and resid 725 through 727 No H-bonds generated for 'chain 'A' and resid 725 through 727' Processing helix chain 'A' and resid 729 through 756 removed outlier: 3.717A pdb=" N GLN A 733 " --> pdb=" O SER A 729 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLU A 738 " --> pdb=" O GLU A 734 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ALA A 756 " --> pdb=" O SER A 752 " (cutoff:3.500A) Processing helix chain 'A' and resid 760 through 787 removed outlier: 4.167A pdb=" N LEU A 764 " --> pdb=" O ASP A 760 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N THR A 772 " --> pdb=" O GLY A 768 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N ALA A 787 " --> pdb=" O GLN A 783 " (cutoff:3.500A) Processing helix chain 'A' and resid 798 through 815 removed outlier: 3.732A pdb=" N THR A 804 " --> pdb=" O GLN A 800 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ILE A 805 " --> pdb=" O ALA A 801 " (cutoff:3.500A) Processing helix chain 'A' and resid 818 through 847 Processing helix chain 'A' and resid 849 through 880 removed outlier: 3.558A pdb=" N ILE A 862 " --> pdb=" O SER A 858 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU A 863 " --> pdb=" O ALA A 859 " (cutoff:3.500A) Processing helix chain 'A' and resid 883 through 904 removed outlier: 3.571A pdb=" N GLN A 887 " --> pdb=" O SER A 883 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLY A 896 " --> pdb=" O GLU A 892 " (cutoff:3.500A) Processing helix chain 'A' and resid 907 through 930 removed outlier: 4.204A pdb=" N LEU A 913 " --> pdb=" O ILE A 909 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N VAL A 914 " --> pdb=" O LYS A 910 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N LEU A 917 " --> pdb=" O LEU A 913 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N ALA A 920 " --> pdb=" O ARG A 916 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LYS A 922 " --> pdb=" O GLU A 918 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLN A 923 " --> pdb=" O HIS A 919 " (cutoff:3.500A) Processing helix chain 'A' and resid 931 through 940 removed outlier: 4.255A pdb=" N ALA A 938 " --> pdb=" O ALA A 934 " (cutoff:3.500A) Processing helix chain 'A' and resid 948 through 976 removed outlier: 3.710A pdb=" N GLN A 954 " --> pdb=" O PRO A 950 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ALA A 958 " --> pdb=" O GLN A 954 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N VAL A 959 " --> pdb=" O SER A 955 " (cutoff:3.500A) Proline residue: A 964 - end of helix removed outlier: 3.782A pdb=" N GLY A 969 " --> pdb=" O LEU A 965 " (cutoff:3.500A) Processing helix chain 'A' and resid 979 through 1005 removed outlier: 3.748A pdb=" N GLN A 983 " --> pdb=" O SER A 979 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LEU A 994 " --> pdb=" O SER A 990 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N GLN A 995 " --> pdb=" O GLN A 991 " (cutoff:3.500A) Proline residue: A 996 - end of helix removed outlier: 4.049A pdb=" N MET A1000 " --> pdb=" O PRO A 996 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N VAL A1001 " --> pdb=" O GLY A 997 " (cutoff:3.500A) Processing helix chain 'A' and resid 1013 through 1045 removed outlier: 3.654A pdb=" N LEU A1020 " --> pdb=" O SER A1016 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N CYS A1023 " --> pdb=" O GLN A1019 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA A1032 " --> pdb=" O GLY A1028 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LEU A1034 " --> pdb=" O ALA A1030 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ALA A1037 " --> pdb=" O GLU A1033 " (cutoff:3.500A) Processing helix chain 'A' and resid 1051 through 1074 removed outlier: 3.920A pdb=" N ARG A1072 " --> pdb=" O LYS A1068 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ASP A1073 " --> pdb=" O ALA A1069 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLY A1074 " --> pdb=" O ALA A1070 " (cutoff:3.500A) Processing helix chain 'A' and resid 1083 through 1112 removed outlier: 3.716A pdb=" N THR A1088 " --> pdb=" O MET A1084 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N GLN A1089 " --> pdb=" O GLU A1085 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ASP A1090 " --> pdb=" O LYS A1086 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LYS A1096 " --> pdb=" O GLY A1092 " (cutoff:3.500A) Processing helix chain 'A' and resid 1115 through 1142 removed outlier: 3.628A pdb=" N ILE A1119 " --> pdb=" O ASN A1115 " (cutoff:3.500A) Processing helix chain 'A' and resid 1144 through 1174 removed outlier: 4.054A pdb=" N VAL A1151 " --> pdb=" O VAL A1147 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU A1152 " --> pdb=" O GLN A1148 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLY A1174 " --> pdb=" O LYS A1170 " (cutoff:3.500A) Processing helix chain 'A' and resid 1178 through 1203 removed outlier: 3.651A pdb=" N GLN A1182 " --> pdb=" O ASP A1178 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N THR A1193 " --> pdb=" O ALA A1189 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ARG A1198 " --> pdb=" O GLN A1194 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU A1203 " --> pdb=" O CYS A1199 " (cutoff:3.500A) Processing helix chain 'A' and resid 1208 through 1225 removed outlier: 3.884A pdb=" N ARG A1222 " --> pdb=" O ASP A1218 " (cutoff:3.500A) Processing helix chain 'A' and resid 1234 through 1245 removed outlier: 3.566A pdb=" N GLN A1239 " --> pdb=" O PHE A1235 " (cutoff:3.500A) Processing helix chain 'A' and resid 1245 through 1260 removed outlier: 3.714A pdb=" N LEU A1249 " --> pdb=" O ALA A1245 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LEU A1256 " --> pdb=" O ALA A1252 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N VAL A1257 " --> pdb=" O ALA A1253 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLN A1258 " --> pdb=" O THR A1254 " (cutoff:3.500A) Processing helix chain 'A' and resid 1263 through 1288 removed outlier: 3.500A pdb=" N ARG A1269 " --> pdb=" O GLN A1265 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA A1270 " --> pdb=" O ASP A1266 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ALA A1284 " --> pdb=" O THR A1280 " (cutoff:3.500A) Processing helix chain 'A' and resid 1295 through 1323 removed outlier: 3.712A pdb=" N ALA A1299 " --> pdb=" O GLN A1295 " (cutoff:3.500A) Processing helix chain 'A' and resid 1328 through 1353 removed outlier: 3.594A pdb=" N LEU A1349 " --> pdb=" O SER A1345 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ILE A1350 " --> pdb=" O ILE A1346 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N MET A1352 " --> pdb=" O GLN A1348 " (cutoff:3.500A) Processing helix chain 'A' and resid 1360 through 1377 removed outlier: 3.790A pdb=" N ASP A1364 " --> pdb=" O GLN A1360 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ASN A1365 " --> pdb=" O LYS A1361 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ARG A1374 " --> pdb=" O LEU A1370 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N GLU A1375 " --> pdb=" O GLU A1371 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LEU A1376 " --> pdb=" O THR A1372 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU A1377 " --> pdb=" O VAL A1373 " (cutoff:3.500A) Processing helix chain 'A' and resid 1388 through 1417 removed outlier: 3.633A pdb=" N THR A1408 " --> pdb=" O GLY A1404 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ASN A1413 " --> pdb=" O GLY A1409 " (cutoff:3.500A) Processing helix chain 'A' and resid 1418 through 1451 removed outlier: 4.050A pdb=" N ALA A1425 " --> pdb=" O GLU A1421 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N ILE A1426 " --> pdb=" O PHE A1422 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA A1427 " --> pdb=" O GLY A1423 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N THR A1428 " --> pdb=" O ASP A1424 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N VAL A1447 " --> pdb=" O ALA A1443 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ASP A1451 " --> pdb=" O VAL A1447 " (cutoff:3.500A) Processing helix chain 'A' and resid 1463 through 1483 removed outlier: 3.641A pdb=" N ARG A1469 " --> pdb=" O THR A1465 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU A1481 " --> pdb=" O ALA A1477 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N GLU A1483 " --> pdb=" O GLN A1479 " (cutoff:3.500A) Processing helix chain 'A' and resid 1487 through 1514 removed outlier: 4.257A pdb=" N SER A1493 " --> pdb=" O ALA A1489 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ALA A1504 " --> pdb=" O LYS A1500 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N CYS A1509 " --> pdb=" O LEU A1505 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA A1514 " --> pdb=" O ARG A1510 " (cutoff:3.500A) Processing helix chain 'A' and resid 1518 through 1546 removed outlier: 3.656A pdb=" N LYS A1522 " --> pdb=" O ASN A1518 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ARG A1523 " --> pdb=" O PRO A1519 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL A1532 " --> pdb=" O SER A1528 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ALA A1533 " --> pdb=" O ALA A1529 " (cutoff:3.500A) Processing helix chain 'A' and resid 1551 through 1577 removed outlier: 4.040A pdb=" N ALA A1563 " --> pdb=" O ARG A1559 " (cutoff:3.500A) Proline residue: A1564 - end of helix removed outlier: 3.557A pdb=" N SER A1577 " --> pdb=" O SER A1573 " (cutoff:3.500A) Processing helix chain 'A' and resid 1578 through 1582 removed outlier: 3.691A pdb=" N SER A1582 " --> pdb=" O PRO A1579 " (cutoff:3.500A) Processing helix chain 'A' and resid 1589 through 1623 Proline residue: A1598 - end of helix removed outlier: 3.736A pdb=" N LEU A1607 " --> pdb=" O ALA A1603 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLN A1615 " --> pdb=" O GLY A1611 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N THR A1616 " --> pdb=" O GLY A1612 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ALA A1617 " --> pdb=" O LEU A1613 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ARG A1618 " --> pdb=" O ILE A1614 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ALA A1619 " --> pdb=" O GLN A1615 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N VAL A1622 " --> pdb=" O ARG A1618 " (cutoff:3.500A) Processing helix chain 'A' and resid 1626 through 1655 removed outlier: 3.600A pdb=" N ALA A1634 " --> pdb=" O TRP A1630 " (cutoff:3.500A) Processing helix chain 'A' and resid 1659 through 1684 removed outlier: 3.770A pdb=" N LEU A1675 " --> pdb=" O CYS A1671 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N SER A1684 " --> pdb=" O LEU A1680 " (cutoff:3.500A) Processing helix chain 'A' and resid 1694 through 1720 removed outlier: 3.675A pdb=" N LEU A1698 " --> pdb=" O SER A1694 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N HIS A1699 " --> pdb=" O GLN A1695 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N VAL A1706 " --> pdb=" O MET A1702 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N GLU A1714 " --> pdb=" O SER A1710 " (cutoff:3.500A) Proline residue: A1715 - end of helix Processing helix chain 'A' and resid 1723 through 1736 removed outlier: 3.960A pdb=" N LEU A1727 " --> pdb=" O GLU A1723 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N HIS A1729 " --> pdb=" O SER A1725 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL A1731 " --> pdb=" O LEU A1727 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N SER A1732 " --> pdb=" O GLY A1728 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLN A1736 " --> pdb=" O SER A1732 " (cutoff:3.500A) Processing helix chain 'A' and resid 1737 through 1752 removed outlier: 3.888A pdb=" N THR A1752 " --> pdb=" O ALA A1748 " (cutoff:3.500A) Processing helix chain 'A' and resid 1754 through 1783 removed outlier: 3.636A pdb=" N THR A1765 " --> pdb=" O LEU A1761 " (cutoff:3.500A) Processing helix chain 'A' and resid 1789 through 1821 removed outlier: 4.201A pdb=" N ALA A1795 " --> pdb=" O HIS A1791 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N MET A1802 " --> pdb=" O GLU A1798 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N ALA A1821 " --> pdb=" O ALA A1817 " (cutoff:3.500A) Processing helix chain 'A' and resid 1826 through 1835 removed outlier: 3.554A pdb=" N ILE A1831 " --> pdb=" O MET A1827 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N THR A1832 " --> pdb=" O VAL A1828 " (cutoff:3.500A) Processing helix chain 'A' and resid 1850 through 1878 removed outlier: 3.882A pdb=" N THR A1856 " --> pdb=" O ASP A1852 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ARG A1859 " --> pdb=" O THR A1855 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALA A1863 " --> pdb=" O ARG A1859 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N VAL A1868 " --> pdb=" O ILE A1864 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N THR A1873 " --> pdb=" O GLN A1869 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N LYS A1874 " --> pdb=" O GLU A1870 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ASN A1876 " --> pdb=" O VAL A1872 " (cutoff:3.500A) Processing helix chain 'A' and resid 1881 through 1899 removed outlier: 3.684A pdb=" N LEU A1885 " --> pdb=" O GLU A1881 " (cutoff:3.500A) Processing helix chain 'A' and resid 1899 through 1907 Processing helix chain 'A' and resid 1909 through 1939 removed outlier: 3.535A pdb=" N VAL A1920 " --> pdb=" O ILE A1916 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N GLY A1926 " --> pdb=" O GLU A1922 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLN A1938 " --> pdb=" O ALA A1934 " (cutoff:3.500A) Processing helix chain 'A' and resid 1945 through 1969 removed outlier: 3.554A pdb=" N GLU A1949 " --> pdb=" O TYR A1945 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ILE A1951 " --> pdb=" O LYS A1947 " (cutoff:3.500A) Processing helix chain 'A' and resid 1975 through 2002 Processing helix chain 'A' and resid 2012 through 2036 Processing helix chain 'A' and resid 2040 through 2068 removed outlier: 3.835A pdb=" N LEU A2044 " --> pdb=" O SER A2040 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LYS A2063 " --> pdb=" O ALA A2059 " (cutoff:3.500A) Processing helix chain 'A' and resid 2073 through 2101 Processing helix chain 'A' and resid 2108 through 2136 removed outlier: 4.085A pdb=" N TRP A2112 " --> pdb=" O ASP A2108 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLN A2113 " --> pdb=" O PRO A2109 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 311 through 317 removed outlier: 3.595A pdb=" N SER A 311 " --> pdb=" O ILE A 332 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N PHE A 313 " --> pdb=" O LEU A 330 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL A 315 " --> pdb=" O ARG A 328 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N VAL A 340 " --> pdb=" O LEU A 329 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 365 through 368 1103 hydrogen bonds defined for protein. 3300 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.62 Time building geometry restraints manager: 1.71 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: 4306 1.33 - 1.46: 1721 1.46 - 1.58: 7570 1.58 - 1.70: 0 1.70 - 1.82: 102 Bond restraints: 13699 Sorted by residual: bond pdb=" N VAL A1584 " pdb=" CA VAL A1584 " ideal model delta sigma weight residual 1.461 1.507 -0.046 1.23e-02 6.61e+03 1.40e+01 bond pdb=" N GLN A1382 " pdb=" CA GLN A1382 " ideal model delta sigma weight residual 1.452 1.489 -0.036 1.11e-02 8.12e+03 1.07e+01 bond pdb=" N ASN A1379 " pdb=" CA ASN A1379 " ideal model delta sigma weight residual 1.463 1.491 -0.028 8.80e-03 1.29e+04 1.04e+01 bond pdb=" N SER A1582 " pdb=" CA SER A1582 " ideal model delta sigma weight residual 1.455 1.495 -0.040 1.27e-02 6.20e+03 1.01e+01 bond pdb=" N VAL A 774 " pdb=" CA VAL A 774 " ideal model delta sigma weight residual 1.461 1.497 -0.037 1.19e-02 7.06e+03 9.61e+00 ... (remaining 13694 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.05: 17916 2.05 - 4.09: 578 4.09 - 6.14: 66 6.14 - 8.18: 10 8.18 - 10.23: 2 Bond angle restraints: 18572 Sorted by residual: angle pdb=" N SER A1582 " pdb=" CA SER A1582 " pdb=" C SER A1582 " ideal model delta sigma weight residual 109.07 119.30 -10.23 1.52e+00 4.33e-01 4.53e+01 angle pdb=" N SER A1583 " pdb=" CA SER A1583 " pdb=" C SER A1583 " ideal model delta sigma weight residual 113.40 122.39 -8.99 1.47e+00 4.63e-01 3.74e+01 angle pdb=" N PHE A1581 " pdb=" CA PHE A1581 " pdb=" C PHE A1581 " ideal model delta sigma weight residual 111.28 117.38 -6.10 1.09e+00 8.42e-01 3.13e+01 angle pdb=" N GLU A1049 " pdb=" CA GLU A1049 " pdb=" C GLU A1049 " ideal model delta sigma weight residual 113.38 107.67 5.71 1.17e+00 7.31e-01 2.38e+01 angle pdb=" CA PHE A1581 " pdb=" C PHE A1581 " pdb=" O PHE A1581 " ideal model delta sigma weight residual 120.55 115.94 4.61 1.06e+00 8.90e-01 1.90e+01 ... (remaining 18567 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 7648 17.96 - 35.92: 701 35.92 - 53.87: 122 53.87 - 71.83: 40 71.83 - 89.79: 18 Dihedral angle restraints: 8529 sinusoidal: 3191 harmonic: 5338 Sorted by residual: dihedral pdb=" CA THR A 758 " pdb=" C THR A 758 " pdb=" N GLU A 759 " pdb=" CA GLU A 759 " ideal model delta harmonic sigma weight residual 180.00 158.40 21.60 0 5.00e+00 4.00e-02 1.87e+01 dihedral pdb=" CA GLY A1112 " pdb=" C GLY A1112 " pdb=" N ASN A1113 " pdb=" CA ASN A1113 " ideal model delta harmonic sigma weight residual 180.00 159.13 20.87 0 5.00e+00 4.00e-02 1.74e+01 dihedral pdb=" CA SER A 927 " pdb=" C SER A 927 " pdb=" N ALA A 928 " pdb=" CA ALA A 928 " ideal model delta harmonic sigma weight residual 180.00 159.77 20.23 0 5.00e+00 4.00e-02 1.64e+01 ... (remaining 8526 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 2057 0.077 - 0.155: 153 0.155 - 0.232: 11 0.232 - 0.309: 2 0.309 - 0.387: 1 Chirality restraints: 2224 Sorted by residual: chirality pdb=" CA SER A1583 " pdb=" N SER A1583 " pdb=" C SER A1583 " pdb=" CB SER A1583 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.74e+00 chirality pdb=" CB VAL A1381 " pdb=" CA VAL A1381 " pdb=" CG1 VAL A1381 " pdb=" CG2 VAL A1381 " both_signs ideal model delta sigma weight residual False -2.63 -2.38 -0.25 2.00e-01 2.50e+01 1.52e+00 chirality pdb=" CB THR A 518 " pdb=" CA THR A 518 " pdb=" OG1 THR A 518 " pdb=" CG2 THR A 518 " both_signs ideal model delta sigma weight residual False 2.55 2.31 0.24 2.00e-01 2.50e+01 1.45e+00 ... (remaining 2221 not shown) Planarity restraints: 2469 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY A 768 " -0.015 2.00e-02 2.50e+03 2.93e-02 8.57e+00 pdb=" C GLY A 768 " 0.051 2.00e-02 2.50e+03 pdb=" O GLY A 768 " -0.019 2.00e-02 2.50e+03 pdb=" N ALA A 769 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 308 " -0.025 2.00e-02 2.50e+03 2.04e-02 8.36e+00 pdb=" CG TYR A 308 " 0.050 2.00e-02 2.50e+03 pdb=" CD1 TYR A 308 " -0.011 2.00e-02 2.50e+03 pdb=" CD2 TYR A 308 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR A 308 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR A 308 " -0.012 2.00e-02 2.50e+03 pdb=" CZ TYR A 308 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR A 308 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN A 949 " 0.041 5.00e-02 4.00e+02 6.14e-02 6.03e+00 pdb=" N PRO A 950 " -0.106 5.00e-02 4.00e+02 pdb=" CA PRO A 950 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 950 " 0.035 5.00e-02 4.00e+02 ... (remaining 2466 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 894 2.72 - 3.27: 16711 3.27 - 3.81: 23438 3.81 - 4.36: 27599 4.36 - 4.90: 42831 Nonbonded interactions: 111473 Sorted by model distance: nonbonded pdb=" OE1 GLU A 517 " pdb=" OG1 THR A 518 " model vdw 2.179 3.040 nonbonded pdb=" NE2 GLN A 244 " pdb=" O GLY A 287 " model vdw 2.200 3.120 nonbonded pdb=" O GLN A1976 " pdb=" OG1 THR A1980 " model vdw 2.206 3.040 nonbonded pdb=" O GLU A1405 " pdb=" OG1 THR A1408 " model vdw 2.209 3.040 nonbonded pdb=" NZ LYS A 357 " pdb=" O PHE A 370 " model vdw 2.215 3.120 ... (remaining 111468 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 14.050 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 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 : 0.006 0.052 13699 Z= 0.317 Angle : 0.816 10.226 18572 Z= 0.517 Chirality : 0.044 0.387 2224 Planarity : 0.004 0.061 2469 Dihedral : 15.250 89.790 5059 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 14.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.34 % Allowed : 1.55 % Favored : 97.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.40 (0.19), residues: 1848 helix: 0.14 (0.14), residues: 1366 sheet: -0.29 (0.90), residues: 35 loop : -1.18 (0.30), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 220 TYR 0.050 0.003 TYR A 308 PHE 0.023 0.002 PHE A 241 TRP 0.017 0.002 TRP A 351 HIS 0.004 0.001 HIS A 937 Details of bonding type rmsd/Z covalent geometry : bond 0.00570 / 0.32 (13699) covalent geometry : angle 0.81555 / 0.52 (18572) hydrogen bonds : bond 0.27987 / 18.56 ( 1103) hydrogen bonds : angle 8.55701 / 6.18 ( 3300) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 140 time to evaluate : 0.501 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 216 TYR cc_start: 0.6468 (t80) cc_final: 0.5981 (t80) REVERT: A 221 ASP cc_start: 0.8946 (m-30) cc_final: 0.8738 (m-30) REVERT: A 503 MET cc_start: 0.8020 (tpp) cc_final: 0.7562 (tpp) REVERT: A 657 GLU cc_start: 0.6853 (OUTLIER) cc_final: 0.5745 (tm-30) REVERT: A 786 LYS cc_start: 0.8619 (ttpt) cc_final: 0.8224 (ttpt) REVERT: A 1310 MET cc_start: 0.8892 (mpp) cc_final: 0.8570 (mpp) REVERT: A 1344 ASP cc_start: 0.8980 (m-30) cc_final: 0.8744 (p0) REVERT: A 1445 TYR cc_start: 0.9000 (t80) cc_final: 0.8714 (t80) REVERT: A 1992 LEU cc_start: 0.9456 (mt) cc_final: 0.9224 (tt) REVERT: A 2112 TRP cc_start: 0.8553 (m-90) cc_final: 0.8268 (m-90) REVERT: A 2121 MET cc_start: 0.8809 (tpp) cc_final: 0.8264 (tpp) outliers start: 19 outliers final: 5 residues processed: 149 average time/residue: 0.1141 time to fit residues: 25.8437 Evaluate side-chains 105 residues out of total 1425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 99 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 657 GLU Chi-restraints excluded: chain A residue 772 THR Chi-restraints excluded: chain A residue 778 LEU Chi-restraints excluded: chain A residue 909 ILE Chi-restraints excluded: chain A residue 1333 SER Chi-restraints excluded: chain A residue 1997 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 98 optimal weight: 0.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 0.2980 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 6.9990 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 6.9990 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 0.9980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 244 GLN A 733 GLN A 779 ASN A 783 GLN A1413 ASN ** A1475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1695 GLN A1736 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.119242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.088025 restraints weight = 42759.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.090510 restraints weight = 23183.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.092185 restraints weight = 15661.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.092988 restraints weight = 12307.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.093510 restraints weight = 10733.022| |-----------------------------------------------------------------------------| r_work (final): 0.3574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.2019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 13699 Z= 0.173 Angle : 0.687 8.005 18572 Z= 0.360 Chirality : 0.040 0.204 2224 Planarity : 0.004 0.040 2469 Dihedral : 5.648 61.189 1946 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.34 % Allowed : 8.40 % Favored : 90.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.09 (0.19), residues: 1848 helix: 1.31 (0.13), residues: 1435 sheet: -0.03 (0.90), residues: 35 loop : -1.36 (0.34), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1638 TYR 0.024 0.002 TYR A 308 PHE 0.013 0.002 PHE A 280 TRP 0.016 0.002 TRP A 351 HIS 0.007 0.001 HIS A 784 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.17 (13699) covalent geometry : angle 0.68742 / 0.36 (18572) hydrogen bonds : bond 0.06289 / 4.11 ( 1103) hydrogen bonds : angle 4.75387 / 3.43 ( 3300) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 136 time to evaluate : 0.535 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 216 TYR cc_start: 0.6644 (t80) cc_final: 0.6057 (t80) REVERT: A 221 ASP cc_start: 0.8954 (m-30) cc_final: 0.8751 (m-30) REVERT: A 298 TYR cc_start: 0.7159 (t80) cc_final: 0.6742 (t80) REVERT: A 388 ILE cc_start: 0.8982 (mt) cc_final: 0.8774 (mt) REVERT: A 499 ILE cc_start: 0.9131 (OUTLIER) cc_final: 0.8930 (pt) REVERT: A 657 GLU cc_start: 0.7563 (OUTLIER) cc_final: 0.7015 (tm-30) REVERT: A 748 GLU cc_start: 0.7904 (tm-30) cc_final: 0.7703 (tm-30) REVERT: A 786 LYS cc_start: 0.8697 (ttpt) cc_final: 0.8277 (ttpt) REVERT: A 870 MET cc_start: 0.9086 (tmm) cc_final: 0.8840 (tmm) REVERT: A 1606 MET cc_start: 0.9163 (tmm) cc_final: 0.8551 (tmm) REVERT: A 1651 MET cc_start: 0.9264 (mmm) cc_final: 0.8935 (mmm) REVERT: A 1992 LEU cc_start: 0.9531 (mt) cc_final: 0.9327 (tp) REVERT: A 1997 MET cc_start: 0.8878 (mmt) cc_final: 0.8633 (mmt) outliers start: 19 outliers final: 10 residues processed: 147 average time/residue: 0.0938 time to fit residues: 22.3197 Evaluate side-chains 114 residues out of total 1425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 102 time to evaluate : 0.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 268 LYS Chi-restraints excluded: chain A residue 499 ILE Chi-restraints excluded: chain A residue 627 GLN Chi-restraints excluded: chain A residue 657 GLU Chi-restraints excluded: chain A residue 784 HIS Chi-restraints excluded: chain A residue 909 ILE Chi-restraints excluded: chain A residue 911 LYS Chi-restraints excluded: chain A residue 951 LEU Chi-restraints excluded: chain A residue 1025 LYS Chi-restraints excluded: chain A residue 1210 ASP Chi-restraints excluded: chain A residue 1333 SER Chi-restraints excluded: chain A residue 1571 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 67 optimal weight: 1.9990 chunk 23 optimal weight: 0.0670 chunk 86 optimal weight: 0.9990 chunk 43 optimal weight: 0.9990 chunk 149 optimal weight: 2.9990 chunk 164 optimal weight: 1.9990 chunk 151 optimal weight: 0.6980 chunk 21 optimal weight: 0.6980 chunk 24 optimal weight: 0.9980 chunk 19 optimal weight: 20.0000 chunk 182 optimal weight: 4.9990 overall best weight: 0.6920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 733 GLN A1475 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.125411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.093961 restraints weight = 42937.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.096627 restraints weight = 22516.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.098431 restraints weight = 14903.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.099399 restraints weight = 11517.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.100073 restraints weight = 9902.930| |-----------------------------------------------------------------------------| r_work (final): 0.3600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.2640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13699 Z= 0.143 Angle : 0.617 11.019 18572 Z= 0.317 Chirality : 0.039 0.181 2224 Planarity : 0.004 0.038 2469 Dihedral : 5.005 54.511 1940 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 1.83 % Allowed : 11.50 % Favored : 86.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.69 (0.20), residues: 1848 helix: 1.78 (0.13), residues: 1443 sheet: 0.02 (0.87), residues: 35 loop : -1.41 (0.33), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 854 TYR 0.021 0.002 TYR A 308 PHE 0.011 0.001 PHE A1525 TRP 0.018 0.002 TRP A 351 HIS 0.007 0.001 HIS A 283 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.14 (13699) covalent geometry : angle 0.61707 / 0.32 (18572) hydrogen bonds : bond 0.04934 / 3.26 ( 1103) hydrogen bonds : angle 4.19760 / 3.02 ( 3300) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 121 time to evaluate : 0.511 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 221 ASP cc_start: 0.8931 (m-30) cc_final: 0.8713 (m-30) REVERT: A 357 LYS cc_start: 0.8371 (OUTLIER) cc_final: 0.7898 (mtmm) REVERT: A 546 GLN cc_start: 0.7780 (OUTLIER) cc_final: 0.7087 (mm-40) REVERT: A 657 GLU cc_start: 0.7513 (OUTLIER) cc_final: 0.6939 (tm-30) REVERT: A 748 GLU cc_start: 0.7934 (tm-30) cc_final: 0.7674 (tm-30) REVERT: A 786 LYS cc_start: 0.8782 (ttpt) cc_final: 0.8399 (ttpt) REVERT: A 831 GLN cc_start: 0.7803 (tm-30) cc_final: 0.7574 (tm-30) REVERT: A 870 MET cc_start: 0.9145 (tmm) cc_final: 0.8908 (tmm) REVERT: A 1310 MET cc_start: 0.8597 (mmt) cc_final: 0.8253 (mmt) REVERT: A 1407 MET cc_start: 0.7582 (ppp) cc_final: 0.7034 (ppp) REVERT: A 1606 MET cc_start: 0.9078 (tmm) cc_final: 0.8495 (tmm) REVERT: A 1734 MET cc_start: 0.7825 (ttt) cc_final: 0.7560 (ttt) REVERT: A 1803 MET cc_start: 0.7214 (ttt) cc_final: 0.6255 (tmm) REVERT: A 1827 MET cc_start: 0.8204 (mtm) cc_final: 0.7798 (mtm) outliers start: 26 outliers final: 14 residues processed: 142 average time/residue: 0.0915 time to fit residues: 21.1709 Evaluate side-chains 117 residues out of total 1425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 100 time to evaluate : 0.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 268 LYS Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 357 LYS Chi-restraints excluded: chain A residue 546 GLN Chi-restraints excluded: chain A residue 657 GLU Chi-restraints excluded: chain A residue 663 HIS Chi-restraints excluded: chain A residue 784 HIS Chi-restraints excluded: chain A residue 798 TYR Chi-restraints excluded: chain A residue 850 LEU Chi-restraints excluded: chain A residue 951 LEU Chi-restraints excluded: chain A residue 1025 LYS Chi-restraints excluded: chain A residue 1159 LEU Chi-restraints excluded: chain A residue 1210 ASP Chi-restraints excluded: chain A residue 1465 THR Chi-restraints excluded: chain A residue 1571 ASN Chi-restraints excluded: chain A residue 1632 VAL Chi-restraints excluded: chain A residue 1837 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 65 optimal weight: 2.9990 chunk 144 optimal weight: 0.9990 chunk 23 optimal weight: 0.0050 chunk 83 optimal weight: 2.9990 chunk 131 optimal weight: 1.9990 chunk 4 optimal weight: 30.0000 chunk 69 optimal weight: 5.9990 chunk 110 optimal weight: 0.7980 chunk 32 optimal weight: 0.9990 chunk 53 optimal weight: 0.3980 chunk 149 optimal weight: 0.9990 overall best weight: 0.6398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1475 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.125614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.094160 restraints weight = 43005.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.096924 restraints weight = 22504.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.098660 restraints weight = 14840.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.099800 restraints weight = 11410.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.100260 restraints weight = 9786.313| |-----------------------------------------------------------------------------| r_work (final): 0.3576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.3037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13699 Z= 0.130 Angle : 0.600 10.387 18572 Z= 0.307 Chirality : 0.038 0.287 2224 Planarity : 0.004 0.041 2469 Dihedral : 4.833 53.112 1937 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 1.91 % Allowed : 13.83 % Favored : 84.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.95 (0.20), residues: 1848 helix: 1.97 (0.13), residues: 1449 sheet: -0.39 (0.81), residues: 37 loop : -1.37 (0.34), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 220 TYR 0.021 0.002 TYR A1945 PHE 0.011 0.001 PHE A 265 TRP 0.018 0.002 TRP A 351 HIS 0.006 0.001 HIS A 784 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.13 (13699) covalent geometry : angle 0.59977 / 0.31 (18572) hydrogen bonds : bond 0.04318 / 2.85 ( 1103) hydrogen bonds : angle 3.98140 / 2.86 ( 3300) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 120 time to evaluate : 0.526 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 221 ASP cc_start: 0.8937 (m-30) cc_final: 0.8693 (m-30) REVERT: A 298 TYR cc_start: 0.7794 (t80) cc_final: 0.7532 (t80) REVERT: A 357 LYS cc_start: 0.8372 (OUTLIER) cc_final: 0.7910 (mtmm) REVERT: A 546 GLN cc_start: 0.7974 (OUTLIER) cc_final: 0.7427 (mt0) REVERT: A 748 GLU cc_start: 0.7935 (tm-30) cc_final: 0.7629 (tm-30) REVERT: A 786 LYS cc_start: 0.8784 (ttpt) cc_final: 0.8388 (ttpt) REVERT: A 831 GLN cc_start: 0.7832 (tm-30) cc_final: 0.7625 (tm-30) REVERT: A 870 MET cc_start: 0.9153 (tmm) cc_final: 0.8872 (tmm) REVERT: A 1251 GLN cc_start: 0.8870 (tp40) cc_final: 0.8620 (tp40) REVERT: A 1310 MET cc_start: 0.8568 (mmt) cc_final: 0.8230 (mmt) REVERT: A 1407 MET cc_start: 0.7764 (ppp) cc_final: 0.7418 (ppp) REVERT: A 1469 ARG cc_start: 0.8787 (ptp-170) cc_final: 0.8395 (ptp-170) REVERT: A 1492 LEU cc_start: 0.9194 (tt) cc_final: 0.8931 (pp) REVERT: A 1606 MET cc_start: 0.9074 (tmm) cc_final: 0.8496 (tmm) REVERT: A 2021 LYS cc_start: 0.8793 (mppt) cc_final: 0.8486 (mmtt) outliers start: 27 outliers final: 12 residues processed: 141 average time/residue: 0.1012 time to fit residues: 21.9636 Evaluate side-chains 113 residues out of total 1425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 99 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 268 LYS Chi-restraints excluded: chain A residue 357 LYS Chi-restraints excluded: chain A residue 546 GLN Chi-restraints excluded: chain A residue 663 HIS Chi-restraints excluded: chain A residue 784 HIS Chi-restraints excluded: chain A residue 850 LEU Chi-restraints excluded: chain A residue 951 LEU Chi-restraints excluded: chain A residue 1025 LYS Chi-restraints excluded: chain A residue 1210 ASP Chi-restraints excluded: chain A residue 1433 LEU Chi-restraints excluded: chain A residue 1465 THR Chi-restraints excluded: chain A residue 1571 ASN Chi-restraints excluded: chain A residue 1632 VAL Chi-restraints excluded: chain A residue 1742 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 139 optimal weight: 0.9980 chunk 69 optimal weight: 5.9990 chunk 170 optimal weight: 0.9990 chunk 55 optimal weight: 0.6980 chunk 151 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 chunk 59 optimal weight: 0.8980 chunk 92 optimal weight: 0.9990 chunk 162 optimal weight: 0.7980 chunk 91 optimal weight: 2.9990 chunk 26 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2124 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.125226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.093806 restraints weight = 43024.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.096521 restraints weight = 22502.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.098255 restraints weight = 14857.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.099133 restraints weight = 11481.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.099979 restraints weight = 9965.927| |-----------------------------------------------------------------------------| r_work (final): 0.3608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.3259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13699 Z= 0.133 Angle : 0.614 12.774 18572 Z= 0.307 Chirality : 0.039 0.279 2224 Planarity : 0.004 0.041 2469 Dihedral : 4.390 23.541 1934 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.91 % Allowed : 15.81 % Favored : 82.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.15 (0.20), residues: 1848 helix: 2.13 (0.14), residues: 1449 sheet: -0.56 (0.79), residues: 37 loop : -1.35 (0.34), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 220 TYR 0.015 0.001 TYR A 216 PHE 0.015 0.001 PHE A 241 TRP 0.016 0.002 TRP A 351 HIS 0.006 0.001 HIS A 784 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.13 (13699) covalent geometry : angle 0.61357 / 0.31 (18572) hydrogen bonds : bond 0.04107 / 2.71 ( 1103) hydrogen bonds : angle 3.88120 / 2.78 ( 3300) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 112 time to evaluate : 0.504 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 221 ASP cc_start: 0.8920 (m-30) cc_final: 0.8629 (m-30) REVERT: A 241 PHE cc_start: 0.7739 (m-80) cc_final: 0.7310 (m-80) REVERT: A 357 LYS cc_start: 0.8409 (OUTLIER) cc_final: 0.7927 (mtmm) REVERT: A 546 GLN cc_start: 0.7892 (OUTLIER) cc_final: 0.7057 (mm-40) REVERT: A 748 GLU cc_start: 0.7929 (tm-30) cc_final: 0.7599 (tm-30) REVERT: A 786 LYS cc_start: 0.8766 (ttpt) cc_final: 0.8377 (ttpt) REVERT: A 831 GLN cc_start: 0.7845 (tm-30) cc_final: 0.7598 (tm-30) REVERT: A 870 MET cc_start: 0.9149 (tmm) cc_final: 0.8867 (tmm) REVERT: A 1251 GLN cc_start: 0.8862 (tp40) cc_final: 0.8618 (tp40) REVERT: A 1310 MET cc_start: 0.8596 (mmt) cc_final: 0.8189 (mmt) REVERT: A 1407 MET cc_start: 0.7673 (ppp) cc_final: 0.7328 (ppp) REVERT: A 1606 MET cc_start: 0.8999 (tmm) cc_final: 0.8615 (tmm) REVERT: A 1684 SER cc_start: 0.9403 (OUTLIER) cc_final: 0.9172 (p) REVERT: A 1803 MET cc_start: 0.6961 (ttt) cc_final: 0.6718 (ttt) REVERT: A 2021 LYS cc_start: 0.8835 (mtpt) cc_final: 0.8630 (mmtt) outliers start: 27 outliers final: 18 residues processed: 131 average time/residue: 0.1013 time to fit residues: 20.7003 Evaluate side-chains 124 residues out of total 1425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 103 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 268 LYS Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 357 LYS Chi-restraints excluded: chain A residue 546 GLN Chi-restraints excluded: chain A residue 571 THR Chi-restraints excluded: chain A residue 663 HIS Chi-restraints excluded: chain A residue 750 CYS Chi-restraints excluded: chain A residue 784 HIS Chi-restraints excluded: chain A residue 798 TYR Chi-restraints excluded: chain A residue 850 LEU Chi-restraints excluded: chain A residue 1025 LYS Chi-restraints excluded: chain A residue 1210 ASP Chi-restraints excluded: chain A residue 1392 CYS Chi-restraints excluded: chain A residue 1433 LEU Chi-restraints excluded: chain A residue 1465 THR Chi-restraints excluded: chain A residue 1571 ASN Chi-restraints excluded: chain A residue 1632 VAL Chi-restraints excluded: chain A residue 1684 SER Chi-restraints excluded: chain A residue 1742 THR Chi-restraints excluded: chain A residue 1837 GLN Chi-restraints excluded: chain A residue 1994 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 149 optimal weight: 0.9990 chunk 48 optimal weight: 0.9980 chunk 90 optimal weight: 0.7980 chunk 122 optimal weight: 0.2980 chunk 43 optimal weight: 0.6980 chunk 151 optimal weight: 0.5980 chunk 35 optimal weight: 2.9990 chunk 153 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 79 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 70.7894 > 50:) chunk 7 optimal weight: 8.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 281 GLN ** A1300 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 = 0.4056 r_free = 0.4056 target = 0.123750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.092995 restraints weight = 42666.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.094563 restraints weight = 25083.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.095314 restraints weight = 16684.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.095528 restraints weight = 16137.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.095850 restraints weight = 14447.687| |-----------------------------------------------------------------------------| r_work (final): 0.3567 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.3466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 13699 Z= 0.126 Angle : 0.595 12.333 18572 Z= 0.299 Chirality : 0.038 0.258 2224 Planarity : 0.004 0.041 2469 Dihedral : 4.315 23.221 1934 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 2.05 % Allowed : 17.01 % Favored : 80.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.31 (0.20), residues: 1848 helix: 2.27 (0.14), residues: 1447 sheet: -0.57 (0.78), residues: 37 loop : -1.37 (0.34), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 297 TYR 0.016 0.001 TYR A 216 PHE 0.011 0.001 PHE A 241 TRP 0.015 0.001 TRP A 351 HIS 0.006 0.001 HIS A 784 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.13 (13699) covalent geometry : angle 0.59527 / 0.30 (18572) hydrogen bonds : bond 0.03933 / 2.61 ( 1103) hydrogen bonds : angle 3.79841 / 2.72 ( 3300) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 108 time to evaluate : 0.524 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 216 TYR cc_start: 0.6519 (t80) cc_final: 0.6215 (t80) REVERT: A 221 ASP cc_start: 0.8911 (m-30) cc_final: 0.8608 (m-30) REVERT: A 357 LYS cc_start: 0.8556 (OUTLIER) cc_final: 0.8158 (mtmm) REVERT: A 748 GLU cc_start: 0.7869 (tm-30) cc_final: 0.7544 (tm-30) REVERT: A 786 LYS cc_start: 0.8846 (ttpt) cc_final: 0.8430 (ttpt) REVERT: A 831 GLN cc_start: 0.7845 (tm-30) cc_final: 0.7586 (tm-30) REVERT: A 870 MET cc_start: 0.9109 (tmm) cc_final: 0.8835 (tmm) REVERT: A 1251 GLN cc_start: 0.8869 (tp40) cc_final: 0.8655 (tp40) REVERT: A 1310 MET cc_start: 0.8647 (mmt) cc_final: 0.8202 (mmt) REVERT: A 1353 CYS cc_start: 0.3902 (OUTLIER) cc_final: 0.3367 (m) REVERT: A 1407 MET cc_start: 0.7555 (ppp) cc_final: 0.7244 (ppp) REVERT: A 1606 MET cc_start: 0.8978 (tmm) cc_final: 0.8582 (tmm) REVERT: A 1651 MET cc_start: 0.9217 (mmm) cc_final: 0.8639 (mmm) REVERT: A 1684 SER cc_start: 0.9439 (OUTLIER) cc_final: 0.9232 (p) REVERT: A 1803 MET cc_start: 0.6614 (ttt) cc_final: 0.6327 (ttt) REVERT: A 2021 LYS cc_start: 0.8970 (mtpt) cc_final: 0.8710 (mmtt) outliers start: 29 outliers final: 18 residues processed: 131 average time/residue: 0.1025 time to fit residues: 21.2253 Evaluate side-chains 119 residues out of total 1425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 98 time to evaluate : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 268 LYS Chi-restraints excluded: chain A residue 281 GLN Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 357 LYS Chi-restraints excluded: chain A residue 546 GLN Chi-restraints excluded: chain A residue 571 THR Chi-restraints excluded: chain A residue 663 HIS Chi-restraints excluded: chain A residue 750 CYS Chi-restraints excluded: chain A residue 784 HIS Chi-restraints excluded: chain A residue 850 LEU Chi-restraints excluded: chain A residue 1025 LYS Chi-restraints excluded: chain A residue 1210 ASP Chi-restraints excluded: chain A residue 1353 CYS Chi-restraints excluded: chain A residue 1392 CYS Chi-restraints excluded: chain A residue 1433 LEU Chi-restraints excluded: chain A residue 1465 THR Chi-restraints excluded: chain A residue 1571 ASN Chi-restraints excluded: chain A residue 1632 VAL Chi-restraints excluded: chain A residue 1684 SER Chi-restraints excluded: chain A residue 1742 THR Chi-restraints excluded: chain A residue 1837 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 53 optimal weight: 0.0010 chunk 174 optimal weight: 2.9990 chunk 51 optimal weight: 0.7980 chunk 104 optimal weight: 1.9990 chunk 157 optimal weight: 0.9980 chunk 85 optimal weight: 0.8980 chunk 147 optimal weight: 0.6980 chunk 110 optimal weight: 1.9990 chunk 55 optimal weight: 0.4980 chunk 37 optimal weight: 1.9990 chunk 122 optimal weight: 0.0670 overall best weight: 0.4124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 281 GLN ** A1300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1475 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.124730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.092802 restraints weight = 42665.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.095488 restraints weight = 22746.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.097262 restraints weight = 15260.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.098215 restraints weight = 11858.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.098932 restraints weight = 10243.455| |-----------------------------------------------------------------------------| r_work (final): 0.3596 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.3651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 13699 Z= 0.122 Angle : 0.605 12.382 18572 Z= 0.302 Chirality : 0.038 0.315 2224 Planarity : 0.004 0.038 2469 Dihedral : 4.248 24.128 1934 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.98 % Allowed : 18.00 % Favored : 80.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.39 (0.20), residues: 1848 helix: 2.33 (0.14), residues: 1453 sheet: -0.51 (0.77), residues: 37 loop : -1.42 (0.34), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 220 TYR 0.017 0.001 TYR A 216 PHE 0.009 0.001 PHE A 280 TRP 0.015 0.002 TRP A 351 HIS 0.006 0.001 HIS A 283 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.12 (13699) covalent geometry : angle 0.60503 / 0.30 (18572) hydrogen bonds : bond 0.03815 / 2.53 ( 1103) hydrogen bonds : angle 3.74444 / 2.67 ( 3300) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 112 time to evaluate : 0.527 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 216 TYR cc_start: 0.6514 (t80) cc_final: 0.6227 (t80) REVERT: A 221 ASP cc_start: 0.9002 (m-30) cc_final: 0.8787 (m-30) REVERT: A 357 LYS cc_start: 0.8431 (OUTLIER) cc_final: 0.8031 (mtmm) REVERT: A 546 GLN cc_start: 0.7905 (OUTLIER) cc_final: 0.7167 (mm-40) REVERT: A 748 GLU cc_start: 0.7861 (tm-30) cc_final: 0.7527 (tm-30) REVERT: A 786 LYS cc_start: 0.8814 (ttpt) cc_final: 0.8394 (ttpt) REVERT: A 831 GLN cc_start: 0.7831 (tm-30) cc_final: 0.7570 (tm-30) REVERT: A 870 MET cc_start: 0.9151 (tmm) cc_final: 0.8896 (tmm) REVERT: A 1310 MET cc_start: 0.8665 (mmt) cc_final: 0.8258 (mmt) REVERT: A 1393 LEU cc_start: 0.9443 (OUTLIER) cc_final: 0.9027 (tt) REVERT: A 1407 MET cc_start: 0.7645 (ppp) cc_final: 0.7274 (ppp) REVERT: A 1469 ARG cc_start: 0.8690 (ptp-170) cc_final: 0.8369 (ptp-110) REVERT: A 1606 MET cc_start: 0.8959 (tmm) cc_final: 0.8569 (tmm) REVERT: A 1651 MET cc_start: 0.9220 (mmm) cc_final: 0.8637 (mmm) outliers start: 28 outliers final: 17 residues processed: 135 average time/residue: 0.1076 time to fit residues: 22.6153 Evaluate side-chains 123 residues out of total 1425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 103 time to evaluate : 0.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 268 LYS Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 357 LYS Chi-restraints excluded: chain A residue 546 GLN Chi-restraints excluded: chain A residue 571 THR Chi-restraints excluded: chain A residue 663 HIS Chi-restraints excluded: chain A residue 784 HIS Chi-restraints excluded: chain A residue 850 LEU Chi-restraints excluded: chain A residue 1025 LYS Chi-restraints excluded: chain A residue 1099 SER Chi-restraints excluded: chain A residue 1159 LEU Chi-restraints excluded: chain A residue 1210 ASP Chi-restraints excluded: chain A residue 1392 CYS Chi-restraints excluded: chain A residue 1393 LEU Chi-restraints excluded: chain A residue 1433 LEU Chi-restraints excluded: chain A residue 1465 THR Chi-restraints excluded: chain A residue 1571 ASN Chi-restraints excluded: chain A residue 1632 VAL Chi-restraints excluded: chain A residue 1633 LEU Chi-restraints excluded: chain A residue 1868 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 103 optimal weight: 2.9990 chunk 62 optimal weight: 0.4980 chunk 176 optimal weight: 0.6980 chunk 74 optimal weight: 0.9980 chunk 26 optimal weight: 0.9980 chunk 108 optimal weight: 1.9990 chunk 164 optimal weight: 0.8980 chunk 12 optimal weight: 10.0000 chunk 50 optimal weight: 6.9990 chunk 124 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 288 GLN ** A1300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1475 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.124079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.093301 restraints weight = 42374.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.094980 restraints weight = 24021.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.095857 restraints weight = 16140.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.096035 restraints weight = 15346.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.096179 restraints weight = 13927.423| |-----------------------------------------------------------------------------| r_work (final): 0.3572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.3720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 13699 Z= 0.132 Angle : 0.612 13.165 18572 Z= 0.309 Chirality : 0.039 0.315 2224 Planarity : 0.004 0.040 2469 Dihedral : 4.221 24.305 1934 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.76 % Allowed : 18.98 % Favored : 79.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.44 (0.20), residues: 1848 helix: 2.37 (0.14), residues: 1451 sheet: -0.37 (0.89), residues: 31 loop : -1.43 (0.33), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 220 TYR 0.017 0.001 TYR A 216 PHE 0.010 0.001 PHE A 280 TRP 0.013 0.002 TRP A 351 HIS 0.006 0.001 HIS A 784 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.13 (13699) covalent geometry : angle 0.61196 / 0.31 (18572) hydrogen bonds : bond 0.03830 / 2.54 ( 1103) hydrogen bonds : angle 3.77277 / 2.70 ( 3300) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 104 time to evaluate : 0.509 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 216 TYR cc_start: 0.6541 (t80) cc_final: 0.6257 (t80) REVERT: A 221 ASP cc_start: 0.9003 (m-30) cc_final: 0.8777 (m-30) REVERT: A 289 MET cc_start: 0.4422 (ppp) cc_final: 0.4199 (ppp) REVERT: A 300 LYS cc_start: 0.9254 (tppt) cc_final: 0.8729 (mptt) REVERT: A 357 LYS cc_start: 0.8548 (OUTLIER) cc_final: 0.8127 (mtmm) REVERT: A 748 GLU cc_start: 0.7881 (tm-30) cc_final: 0.7561 (tm-30) REVERT: A 786 LYS cc_start: 0.8884 (ttpt) cc_final: 0.8467 (ttpt) REVERT: A 831 GLN cc_start: 0.7851 (tm-30) cc_final: 0.7561 (tm-30) REVERT: A 1310 MET cc_start: 0.8702 (mmt) cc_final: 0.8282 (mmt) REVERT: A 1393 LEU cc_start: 0.9440 (OUTLIER) cc_final: 0.9018 (tt) REVERT: A 1407 MET cc_start: 0.7568 (ppp) cc_final: 0.7238 (ppp) REVERT: A 1606 MET cc_start: 0.8955 (tmm) cc_final: 0.8658 (tmm) REVERT: A 1651 MET cc_start: 0.9253 (mmm) cc_final: 0.8633 (mmm) REVERT: A 1997 MET cc_start: 0.8680 (mmm) cc_final: 0.8410 (mpp) REVERT: A 2021 LYS cc_start: 0.8954 (mtpt) cc_final: 0.8709 (mmtt) outliers start: 25 outliers final: 20 residues processed: 124 average time/residue: 0.1053 time to fit residues: 20.6058 Evaluate side-chains 119 residues out of total 1425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 97 time to evaluate : 0.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 268 LYS Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 357 LYS Chi-restraints excluded: chain A residue 546 GLN Chi-restraints excluded: chain A residue 571 THR Chi-restraints excluded: chain A residue 663 HIS Chi-restraints excluded: chain A residue 784 HIS Chi-restraints excluded: chain A residue 850 LEU Chi-restraints excluded: chain A residue 1025 LYS Chi-restraints excluded: chain A residue 1099 SER Chi-restraints excluded: chain A residue 1159 LEU Chi-restraints excluded: chain A residue 1210 ASP Chi-restraints excluded: chain A residue 1392 CYS Chi-restraints excluded: chain A residue 1393 LEU Chi-restraints excluded: chain A residue 1433 LEU Chi-restraints excluded: chain A residue 1465 THR Chi-restraints excluded: chain A residue 1571 ASN Chi-restraints excluded: chain A residue 1581 PHE Chi-restraints excluded: chain A residue 1632 VAL Chi-restraints excluded: chain A residue 1633 LEU Chi-restraints excluded: chain A residue 1868 VAL Chi-restraints excluded: chain A residue 1998 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 163 optimal weight: 0.5980 chunk 144 optimal weight: 0.9980 chunk 170 optimal weight: 0.9980 chunk 164 optimal weight: 0.8980 chunk 47 optimal weight: 6.9990 chunk 81 optimal weight: 0.7980 chunk 110 optimal weight: 0.7980 chunk 1 optimal weight: 5.9990 chunk 140 optimal weight: 0.0670 chunk 32 optimal weight: 0.9980 chunk 27 optimal weight: 0.0770 overall best weight: 0.4676 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.125189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.093169 restraints weight = 42719.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.095893 restraints weight = 22838.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.097663 restraints weight = 15263.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.098588 restraints weight = 11849.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.099314 restraints weight = 10257.126| |-----------------------------------------------------------------------------| r_work (final): 0.3638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.3922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 13699 Z= 0.122 Angle : 0.620 14.589 18572 Z= 0.311 Chirality : 0.038 0.293 2224 Planarity : 0.004 0.040 2469 Dihedral : 4.190 25.381 1934 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 1.69 % Allowed : 19.48 % Favored : 78.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.48 (0.20), residues: 1848 helix: 2.41 (0.14), residues: 1450 sheet: -0.32 (0.90), residues: 31 loop : -1.48 (0.33), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 297 TYR 0.017 0.001 TYR A 216 PHE 0.008 0.001 PHE A1467 TRP 0.015 0.002 TRP A 351 HIS 0.006 0.001 HIS A 784 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 (13699) covalent geometry : angle 0.62005 / 0.31 (18572) hydrogen bonds : bond 0.03691 / 2.44 ( 1103) hydrogen bonds : angle 3.71302 / 2.65 ( 3300) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 114 time to evaluate : 0.534 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 216 TYR cc_start: 0.6540 (t80) cc_final: 0.6184 (t80) REVERT: A 221 ASP cc_start: 0.9005 (m-30) cc_final: 0.8790 (m-30) REVERT: A 298 TYR cc_start: 0.7522 (t80) cc_final: 0.7216 (t80) REVERT: A 300 LYS cc_start: 0.9197 (tppt) cc_final: 0.8694 (mptt) REVERT: A 357 LYS cc_start: 0.8418 (OUTLIER) cc_final: 0.8000 (mtmm) REVERT: A 503 MET cc_start: 0.7731 (tpp) cc_final: 0.7418 (tpp) REVERT: A 546 GLN cc_start: 0.8138 (OUTLIER) cc_final: 0.7454 (mm-40) REVERT: A 748 GLU cc_start: 0.7865 (tm-30) cc_final: 0.7540 (tm-30) REVERT: A 786 LYS cc_start: 0.8751 (ttpt) cc_final: 0.8365 (ttpt) REVERT: A 831 GLN cc_start: 0.7832 (tm-30) cc_final: 0.7547 (tm-30) REVERT: A 1084 MET cc_start: 0.8981 (mmm) cc_final: 0.8770 (mmm) REVERT: A 1168 GLU cc_start: 0.8274 (tp30) cc_final: 0.7839 (tp30) REVERT: A 1310 MET cc_start: 0.8619 (mmt) cc_final: 0.8182 (mmt) REVERT: A 1393 LEU cc_start: 0.9443 (OUTLIER) cc_final: 0.8999 (tt) REVERT: A 1407 MET cc_start: 0.7647 (ppp) cc_final: 0.7284 (ppp) REVERT: A 1469 ARG cc_start: 0.8669 (ptp-170) cc_final: 0.8384 (ptp-110) REVERT: A 1606 MET cc_start: 0.8961 (tmm) cc_final: 0.8660 (tmm) REVERT: A 1651 MET cc_start: 0.9276 (mmm) cc_final: 0.8673 (mmm) REVERT: A 1803 MET cc_start: 0.6936 (ttt) cc_final: 0.6170 (tmm) REVERT: A 1892 ASP cc_start: 0.8062 (m-30) cc_final: 0.7799 (m-30) outliers start: 24 outliers final: 17 residues processed: 133 average time/residue: 0.1136 time to fit residues: 23.1749 Evaluate side-chains 125 residues out of total 1425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 105 time to evaluate : 0.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 268 LYS Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 357 LYS Chi-restraints excluded: chain A residue 546 GLN Chi-restraints excluded: chain A residue 571 THR Chi-restraints excluded: chain A residue 663 HIS Chi-restraints excluded: chain A residue 784 HIS Chi-restraints excluded: chain A residue 850 LEU Chi-restraints excluded: chain A residue 1025 LYS Chi-restraints excluded: chain A residue 1099 SER Chi-restraints excluded: chain A residue 1210 ASP Chi-restraints excluded: chain A residue 1392 CYS Chi-restraints excluded: chain A residue 1393 LEU Chi-restraints excluded: chain A residue 1433 LEU Chi-restraints excluded: chain A residue 1465 THR Chi-restraints excluded: chain A residue 1571 ASN Chi-restraints excluded: chain A residue 1581 PHE Chi-restraints excluded: chain A residue 1632 VAL Chi-restraints excluded: chain A residue 1633 LEU Chi-restraints excluded: chain A residue 1868 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 59 optimal weight: 2.9990 chunk 124 optimal weight: 0.9990 chunk 10 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 117 optimal weight: 0.4980 chunk 171 optimal weight: 1.9990 chunk 101 optimal weight: 3.9990 chunk 119 optimal weight: 1.9990 chunk 102 optimal weight: 0.9990 chunk 113 optimal weight: 0.1980 chunk 169 optimal weight: 0.0980 overall best weight: 0.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1479 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.124207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.094291 restraints weight = 42958.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.096065 restraints weight = 25636.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.096519 restraints weight = 16215.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.096805 restraints weight = 16047.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.097283 restraints weight = 14271.175| |-----------------------------------------------------------------------------| r_work (final): 0.3603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.4011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 13699 Z= 0.127 Angle : 0.660 19.854 18572 Z= 0.327 Chirality : 0.039 0.285 2224 Planarity : 0.003 0.042 2469 Dihedral : 4.138 25.104 1934 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 1.62 % Allowed : 20.40 % Favored : 77.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.51 (0.20), residues: 1848 helix: 2.44 (0.14), residues: 1450 sheet: -0.31 (0.90), residues: 31 loop : -1.46 (0.33), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 297 TYR 0.017 0.001 TYR A 216 PHE 0.020 0.001 PHE A 241 TRP 0.016 0.002 TRP A2112 HIS 0.006 0.001 HIS A 784 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.13 (13699) covalent geometry : angle 0.66037 / 0.33 (18572) hydrogen bonds : bond 0.03692 / 2.45 ( 1103) hydrogen bonds : angle 3.73015 / 2.66 ( 3300) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 111 time to evaluate : 0.534 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 216 TYR cc_start: 0.6549 (t80) cc_final: 0.6174 (t80) REVERT: A 221 ASP cc_start: 0.8925 (m-30) cc_final: 0.8633 (m-30) REVERT: A 297 ARG cc_start: 0.8796 (ttp-110) cc_final: 0.8593 (ttp-170) REVERT: A 298 TYR cc_start: 0.7287 (t80) cc_final: 0.6938 (t80) REVERT: A 300 LYS cc_start: 0.9289 (tppt) cc_final: 0.8440 (pttp) REVERT: A 357 LYS cc_start: 0.8538 (OUTLIER) cc_final: 0.8113 (mtmm) REVERT: A 546 GLN cc_start: 0.7936 (OUTLIER) cc_final: 0.7443 (mm-40) REVERT: A 748 GLU cc_start: 0.7846 (tm-30) cc_final: 0.7516 (tm-30) REVERT: A 786 LYS cc_start: 0.8812 (ttpt) cc_final: 0.8404 (ttpt) REVERT: A 831 GLN cc_start: 0.7825 (tm-30) cc_final: 0.7544 (tm-30) REVERT: A 1084 MET cc_start: 0.9008 (mmm) cc_final: 0.8799 (mmm) REVERT: A 1168 GLU cc_start: 0.8279 (tp30) cc_final: 0.7836 (tp30) REVERT: A 1310 MET cc_start: 0.8615 (mmt) cc_final: 0.8174 (mmt) REVERT: A 1393 LEU cc_start: 0.9458 (OUTLIER) cc_final: 0.9004 (tt) REVERT: A 1407 MET cc_start: 0.7608 (ppp) cc_final: 0.7266 (ppp) REVERT: A 1469 ARG cc_start: 0.8678 (ptp-170) cc_final: 0.8344 (ptp-110) REVERT: A 1606 MET cc_start: 0.8931 (tmm) cc_final: 0.8641 (tmm) REVERT: A 1651 MET cc_start: 0.9290 (mmm) cc_final: 0.8679 (mmm) REVERT: A 1803 MET cc_start: 0.6957 (ttt) cc_final: 0.6313 (tmm) REVERT: A 1892 ASP cc_start: 0.8138 (m-30) cc_final: 0.7852 (m-30) outliers start: 23 outliers final: 18 residues processed: 129 average time/residue: 0.1065 time to fit residues: 21.4452 Evaluate side-chains 127 residues out of total 1425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 106 time to evaluate : 0.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 268 LYS Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 357 LYS Chi-restraints excluded: chain A residue 546 GLN Chi-restraints excluded: chain A residue 571 THR Chi-restraints excluded: chain A residue 663 HIS Chi-restraints excluded: chain A residue 784 HIS Chi-restraints excluded: chain A residue 850 LEU Chi-restraints excluded: chain A residue 1025 LYS Chi-restraints excluded: chain A residue 1090 ASP Chi-restraints excluded: chain A residue 1099 SER Chi-restraints excluded: chain A residue 1210 ASP Chi-restraints excluded: chain A residue 1392 CYS Chi-restraints excluded: chain A residue 1393 LEU Chi-restraints excluded: chain A residue 1433 LEU Chi-restraints excluded: chain A residue 1465 THR Chi-restraints excluded: chain A residue 1571 ASN Chi-restraints excluded: chain A residue 1581 PHE Chi-restraints excluded: chain A residue 1632 VAL Chi-restraints excluded: chain A residue 1633 LEU Chi-restraints excluded: chain A residue 1868 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 107 optimal weight: 0.4980 chunk 161 optimal weight: 0.9990 chunk 11 optimal weight: 0.2980 chunk 31 optimal weight: 6.9990 chunk 60 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 177 optimal weight: 5.9990 chunk 181 optimal weight: 0.0470 chunk 116 optimal weight: 0.0670 chunk 36 optimal weight: 0.6980 chunk 67 optimal weight: 0.5980 overall best weight: 0.3016 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.120668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.091131 restraints weight = 42775.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.092574 restraints weight = 24766.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.093120 restraints weight = 16365.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.093417 restraints weight = 15597.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.093931 restraints weight = 13923.057| |-----------------------------------------------------------------------------| r_work (final): 0.3630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.4226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 13699 Z= 0.124 Angle : 0.659 19.298 18572 Z= 0.326 Chirality : 0.039 0.314 2224 Planarity : 0.004 0.043 2469 Dihedral : 4.102 25.562 1934 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.48 % Allowed : 20.89 % Favored : 77.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.54 (0.20), residues: 1848 helix: 2.46 (0.14), residues: 1450 sheet: -0.31 (0.89), residues: 31 loop : -1.48 (0.33), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 297 TYR 0.017 0.001 TYR A 216 PHE 0.016 0.001 PHE A 241 TRP 0.017 0.002 TRP A2112 HIS 0.008 0.001 HIS A 283 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 (13699) covalent geometry : angle 0.65855 / 0.33 (18572) hydrogen bonds : bond 0.03635 / 2.40 ( 1103) hydrogen bonds : angle 3.68002 / 2.63 ( 3300) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2407.92 seconds wall clock time: 42 minutes 35.24 seconds (2555.24 seconds total)