Starting phenix.real_space_refine on Thu Jul 31 20:05:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vdr_43156/07_2025/8vdr_43156.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vdr_43156/07_2025/8vdr_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8vdr_43156/07_2025/8vdr_43156.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vdr_43156/07_2025/8vdr_43156.map" model { file = "/net/cci-nas-00/data/ceres_data/8vdr_43156/07_2025/8vdr_43156.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vdr_43156/07_2025/8vdr_43156.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 7.91, per 1000 atoms: 0.58 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: 4.01 Conformation dependent library (CDL) restraints added in 2.0 seconds 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: 1.54 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: 4.95 Time building geometry restraints manager: 4.53 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: 0.860 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: 0.570 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 34.120 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.017 0.002 TRP A 351 HIS 0.004 0.001 HIS A 937 PHE 0.023 0.002 PHE A 241 TYR 0.050 0.003 TYR A 308 ARG 0.012 0.001 ARG A 220 Details of bonding type rmsd hydrogen bonds : bond 0.27987 ( 1103) hydrogen bonds : angle 8.55701 ( 3300) covalent geometry : bond 0.00570 (13699) covalent geometry : angle 0.81555 (18572) *********************** 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 : 1.484 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: 0.2561 time to fit residues: 58.0070 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 : 1.651 ------------------------------------------------------------------------------- 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 156 optimal weight: 0.9990 chunk 140 optimal weight: 0.8980 chunk 77 optimal weight: 0.9980 chunk 47 optimal weight: 0.0470 chunk 94 optimal weight: 20.0000 chunk 74 optimal weight: 0.6980 chunk 145 optimal weight: 0.9980 chunk 56 optimal weight: 7.9990 chunk 88 optimal weight: 7.9990 chunk 107 optimal weight: 3.9990 chunk 168 optimal weight: 0.0570 overall best weight: 0.5396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 244 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.122949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.092593 restraints weight = 43125.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.094774 restraints weight = 27045.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.095687 restraints weight = 15760.361| |-----------------------------------------------------------------------------| r_work (final): 0.3544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.1973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13699 Z= 0.173 Angle : 0.687 8.446 18572 Z= 0.359 Chirality : 0.040 0.204 2224 Planarity : 0.004 0.040 2469 Dihedral : 5.668 61.497 1946 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.27 % Allowed : 8.61 % Favored : 90.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.19), residues: 1848 helix: 1.27 (0.13), residues: 1436 sheet: -0.08 (0.89), residues: 35 loop : -1.33 (0.34), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 351 HIS 0.007 0.001 HIS A 784 PHE 0.016 0.002 PHE A 280 TYR 0.025 0.002 TYR A 308 ARG 0.003 0.000 ARG A 220 Details of bonding type rmsd hydrogen bonds : bond 0.06381 ( 1103) hydrogen bonds : angle 4.76349 ( 3300) covalent geometry : bond 0.00342 (13699) covalent geometry : angle 0.68692 (18572) *********************** 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 153 residues out of total 1425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 135 time to evaluate : 1.716 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 216 TYR cc_start: 0.6656 (t80) cc_final: 0.6082 (t80) REVERT: A 221 ASP cc_start: 0.8933 (m-30) cc_final: 0.8674 (m-30) REVERT: A 298 TYR cc_start: 0.7146 (t80) cc_final: 0.6780 (t80) REVERT: A 388 ILE cc_start: 0.9000 (mt) cc_final: 0.8785 (mt) REVERT: A 657 GLU cc_start: 0.7359 (OUTLIER) cc_final: 0.7007 (tm-30) REVERT: A 786 LYS cc_start: 0.8714 (ttpt) cc_final: 0.8260 (ttpt) REVERT: A 870 MET cc_start: 0.9082 (tmm) cc_final: 0.8850 (tmm) REVERT: A 1606 MET cc_start: 0.9152 (tmm) cc_final: 0.8549 (tmm) REVERT: A 1651 MET cc_start: 0.9251 (mmm) cc_final: 0.8979 (mmm) REVERT: A 1997 MET cc_start: 0.8891 (mmt) cc_final: 0.8647 (mmt) outliers start: 18 outliers final: 10 residues processed: 145 average time/residue: 0.2228 time to fit residues: 52.0650 Evaluate side-chains 113 residues out of total 1425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 102 time to evaluate : 1.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 268 LYS 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 88 optimal weight: 0.9990 chunk 0 optimal weight: 30.0000 chunk 103 optimal weight: 2.9990 chunk 43 optimal weight: 0.8980 chunk 151 optimal weight: 0.9990 chunk 166 optimal weight: 0.9990 chunk 6 optimal weight: 0.0870 chunk 122 optimal weight: 10.0000 chunk 169 optimal weight: 0.9990 chunk 126 optimal weight: 7.9990 chunk 12 optimal weight: 6.9990 overall best weight: 0.7964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1475 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 = 0.125117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.095055 restraints weight = 42795.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.096884 restraints weight = 23285.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.097245 restraints weight = 15875.088| |-----------------------------------------------------------------------------| r_work (final): 0.3537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.2580 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= 0.147 Angle : 0.618 11.566 18572 Z= 0.318 Chirality : 0.039 0.188 2224 Planarity : 0.004 0.040 2469 Dihedral : 4.995 52.776 1940 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 1.83 % Allowed : 11.71 % Favored : 86.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.65 (0.20), residues: 1848 helix: 1.75 (0.13), residues: 1440 sheet: -0.07 (0.84), residues: 35 loop : -1.37 (0.33), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 351 HIS 0.007 0.001 HIS A 283 PHE 0.011 0.001 PHE A1525 TYR 0.019 0.002 TYR A1945 ARG 0.006 0.000 ARG A 854 Details of bonding type rmsd hydrogen bonds : bond 0.04996 ( 1103) hydrogen bonds : angle 4.25163 ( 3300) covalent geometry : bond 0.00305 (13699) covalent geometry : angle 0.61794 (18572) *********************** 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 146 residues out of total 1425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 120 time to evaluate : 1.453 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 221 ASP cc_start: 0.8920 (m-30) cc_final: 0.8686 (m-30) REVERT: A 357 LYS cc_start: 0.8442 (OUTLIER) cc_final: 0.7974 (mtmm) REVERT: A 546 GLN cc_start: 0.7772 (OUTLIER) cc_final: 0.7297 (mt0) REVERT: A 657 GLU cc_start: 0.7510 (OUTLIER) cc_final: 0.6942 (tm-30) REVERT: A 786 LYS cc_start: 0.8827 (ttpt) cc_final: 0.8426 (ttpt) REVERT: A 831 GLN cc_start: 0.7739 (tm-30) cc_final: 0.7517 (tm-30) REVERT: A 870 MET cc_start: 0.9124 (tmm) cc_final: 0.8889 (tmm) REVERT: A 1310 MET cc_start: 0.8719 (mpp) cc_final: 0.8462 (mmt) REVERT: A 1606 MET cc_start: 0.9101 (tmm) cc_final: 0.8517 (tmm) REVERT: A 1651 MET cc_start: 0.9286 (mmm) cc_final: 0.8947 (mmm) REVERT: A 1734 MET cc_start: 0.7811 (ttt) cc_final: 0.7465 (ttt) REVERT: A 1803 MET cc_start: 0.7094 (ttt) cc_final: 0.6181 (tmm) REVERT: A 1997 MET cc_start: 0.8943 (mmt) cc_final: 0.8716 (mmt) outliers start: 26 outliers final: 13 residues processed: 140 average time/residue: 0.2119 time to fit residues: 47.5839 Evaluate side-chains 115 residues out of total 1425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 99 time to evaluate : 1.457 ------------------------------------------------------------------------------- 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 657 GLU 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 909 ILE 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 44 optimal weight: 0.0070 chunk 138 optimal weight: 2.9990 chunk 123 optimal weight: 3.9990 chunk 28 optimal weight: 0.7980 chunk 176 optimal weight: 0.8980 chunk 31 optimal weight: 6.9990 chunk 94 optimal weight: 0.0870 chunk 56 optimal weight: 7.9990 chunk 1 optimal weight: 2.9990 chunk 109 optimal weight: 3.9990 chunk 17 optimal weight: 4.9990 overall best weight: 0.9578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1475 GLN A2124 ASN 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 = 0.120756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.090745 restraints weight = 42773.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.093004 restraints weight = 22631.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.093137 restraints weight = 15106.982| |-----------------------------------------------------------------------------| r_work (final): 0.3536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.2922 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= 0.143 Angle : 0.608 10.414 18572 Z= 0.313 Chirality : 0.039 0.266 2224 Planarity : 0.004 0.041 2469 Dihedral : 4.883 51.843 1939 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 1.98 % Allowed : 14.18 % Favored : 83.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.86 (0.20), residues: 1848 helix: 1.90 (0.13), residues: 1450 sheet: -0.38 (0.81), residues: 37 loop : -1.39 (0.34), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 351 HIS 0.006 0.001 HIS A 784 PHE 0.011 0.001 PHE A 265 TYR 0.022 0.002 TYR A1945 ARG 0.008 0.000 ARG A 220 Details of bonding type rmsd hydrogen bonds : bond 0.04441 ( 1103) hydrogen bonds : angle 4.06670 ( 3300) covalent geometry : bond 0.00307 (13699) covalent geometry : angle 0.60830 (18572) *********************** 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 139 residues out of total 1425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 111 time to evaluate : 1.528 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 221 ASP cc_start: 0.8936 (m-30) cc_final: 0.8697 (m-30) REVERT: A 298 TYR cc_start: 0.7803 (t80) cc_final: 0.7541 (t80) REVERT: A 357 LYS cc_start: 0.8483 (OUTLIER) cc_final: 0.8032 (mtmm) REVERT: A 546 GLN cc_start: 0.7844 (OUTLIER) cc_final: 0.7377 (mt0) REVERT: A 786 LYS cc_start: 0.8857 (ttpt) cc_final: 0.8457 (ttpt) REVERT: A 831 GLN cc_start: 0.7888 (tm-30) cc_final: 0.7646 (tm-30) REVERT: A 870 MET cc_start: 0.9142 (tmm) cc_final: 0.8853 (tmm) REVERT: A 1310 MET cc_start: 0.8730 (mpp) cc_final: 0.8459 (mmt) REVERT: A 1407 MET cc_start: 0.7665 (ppp) cc_final: 0.7359 (ppp) REVERT: A 1606 MET cc_start: 0.9112 (tmm) cc_final: 0.8530 (tmm) REVERT: A 1734 MET cc_start: 0.7897 (ttt) cc_final: 0.7649 (ttt) REVERT: A 2021 LYS cc_start: 0.8859 (mppt) cc_final: 0.8513 (mmtt) outliers start: 28 outliers final: 13 residues processed: 132 average time/residue: 0.2214 time to fit residues: 46.4893 Evaluate side-chains 114 residues out of total 1425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 99 time to evaluate : 1.509 ------------------------------------------------------------------------------- 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 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 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 Chi-restraints excluded: chain A residue 1837 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 43 optimal weight: 0.7980 chunk 51 optimal weight: 0.9990 chunk 106 optimal weight: 0.8980 chunk 59 optimal weight: 0.7980 chunk 39 optimal weight: 0.9980 chunk 17 optimal weight: 3.9990 chunk 16 optimal weight: 7.9990 chunk 8 optimal weight: 7.9990 chunk 82 optimal weight: 3.9990 chunk 115 optimal weight: 1.9990 chunk 182 optimal weight: 5.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1475 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 = 0.4086 r_free = 0.4086 target = 0.125011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.093432 restraints weight = 42810.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.096116 restraints weight = 22494.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.097851 restraints weight = 14947.156| |-----------------------------------------------------------------------------| r_work (final): 0.3560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.3163 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= 0.137 Angle : 0.609 13.031 18572 Z= 0.308 Chirality : 0.038 0.279 2224 Planarity : 0.004 0.042 2469 Dihedral : 4.444 23.035 1934 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 1.91 % Allowed : 15.88 % Favored : 82.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.08 (0.20), residues: 1848 helix: 2.08 (0.14), residues: 1449 sheet: -0.47 (0.79), residues: 37 loop : -1.37 (0.34), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 351 HIS 0.006 0.001 HIS A 784 PHE 0.015 0.001 PHE A 241 TYR 0.015 0.001 TYR A 216 ARG 0.009 0.000 ARG A 220 Details of bonding type rmsd hydrogen bonds : bond 0.04189 ( 1103) hydrogen bonds : angle 3.95566 ( 3300) covalent geometry : bond 0.00293 (13699) covalent geometry : angle 0.60860 (18572) *********************** 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 : 1.614 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 221 ASP cc_start: 0.8928 (m-30) cc_final: 0.8648 (m-30) REVERT: A 241 PHE cc_start: 0.7740 (m-80) cc_final: 0.7100 (m-80) REVERT: A 289 MET cc_start: 0.5668 (ppp) cc_final: 0.5339 (ppp) REVERT: A 357 LYS cc_start: 0.8445 (OUTLIER) cc_final: 0.7963 (mtmm) REVERT: A 546 GLN cc_start: 0.7834 (OUTLIER) cc_final: 0.7162 (mt0) REVERT: A 669 MET cc_start: 0.8123 (mpp) cc_final: 0.7789 (mtm) REVERT: A 786 LYS cc_start: 0.8818 (ttpt) cc_final: 0.8399 (ttpt) REVERT: A 831 GLN cc_start: 0.7950 (tm-30) cc_final: 0.7678 (tm-30) REVERT: A 870 MET cc_start: 0.9150 (tmm) cc_final: 0.8874 (tmm) REVERT: A 1251 GLN cc_start: 0.8882 (tp40) cc_final: 0.8626 (tp40) REVERT: A 1407 MET cc_start: 0.7661 (ppp) cc_final: 0.7339 (ppp) REVERT: A 1492 LEU cc_start: 0.9175 (tt) cc_final: 0.8905 (pp) REVERT: A 1606 MET cc_start: 0.9008 (tmm) cc_final: 0.8632 (tmm) REVERT: A 2021 LYS cc_start: 0.8945 (mtpt) cc_final: 0.8660 (mmtt) outliers start: 27 outliers final: 16 residues processed: 131 average time/residue: 0.2595 time to fit residues: 51.4089 Evaluate side-chains 118 residues out of total 1425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 100 time to evaluate : 1.489 ------------------------------------------------------------------------------- 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 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 1159 LEU 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 1742 THR Chi-restraints excluded: chain A residue 1837 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 132 optimal weight: 3.9990 chunk 9 optimal weight: 0.9990 chunk 44 optimal weight: 0.4980 chunk 1 optimal weight: 6.9990 chunk 172 optimal weight: 0.9980 chunk 36 optimal weight: 0.6980 chunk 63 optimal weight: 0.8980 chunk 170 optimal weight: 1.9990 chunk 167 optimal weight: 2.9990 chunk 108 optimal weight: 2.9990 chunk 84 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4090 r_free = 0.4090 target = 0.125397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.093978 restraints weight = 43385.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.096649 restraints weight = 22610.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.098413 restraints weight = 14966.637| |-----------------------------------------------------------------------------| r_work (final): 0.3536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.3380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 13699 Z= 0.133 Angle : 0.605 12.778 18572 Z= 0.305 Chirality : 0.038 0.257 2224 Planarity : 0.004 0.040 2469 Dihedral : 4.380 23.429 1934 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 1.91 % Allowed : 17.15 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.22 (0.20), residues: 1848 helix: 2.19 (0.14), residues: 1449 sheet: -0.53 (0.78), residues: 37 loop : -1.38 (0.34), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 351 HIS 0.006 0.001 HIS A 784 PHE 0.010 0.001 PHE A 241 TYR 0.016 0.002 TYR A 216 ARG 0.006 0.000 ARG A 297 Details of bonding type rmsd hydrogen bonds : bond 0.04023 ( 1103) hydrogen bonds : angle 3.87813 ( 3300) covalent geometry : bond 0.00289 (13699) covalent geometry : angle 0.60527 (18572) *********************** 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 138 residues out of total 1425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 111 time to evaluate : 1.481 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 216 TYR cc_start: 0.6515 (t80) cc_final: 0.6223 (t80) REVERT: A 221 ASP cc_start: 0.8915 (m-30) cc_final: 0.8627 (m-30) REVERT: A 289 MET cc_start: 0.5289 (ppp) cc_final: 0.4862 (ppp) REVERT: A 357 LYS cc_start: 0.8535 (OUTLIER) cc_final: 0.8119 (mtmm) REVERT: A 546 GLN cc_start: 0.7830 (OUTLIER) cc_final: 0.7178 (mt0) REVERT: A 786 LYS cc_start: 0.8801 (ttpt) cc_final: 0.8389 (ttpt) REVERT: A 831 GLN cc_start: 0.7910 (tm-30) cc_final: 0.7615 (tm-30) REVERT: A 870 MET cc_start: 0.9168 (tmm) cc_final: 0.8882 (tmm) REVERT: A 1251 GLN cc_start: 0.8860 (tp40) cc_final: 0.8645 (tp40) REVERT: A 1407 MET cc_start: 0.7610 (ppp) cc_final: 0.7279 (ppp) REVERT: A 1469 ARG cc_start: 0.8745 (ptp-170) cc_final: 0.8287 (ptp-170) REVERT: A 1606 MET cc_start: 0.8988 (tmm) cc_final: 0.8593 (tmm) REVERT: A 1997 MET cc_start: 0.8655 (mmm) cc_final: 0.8368 (mpp) REVERT: A 2021 LYS cc_start: 0.8873 (mtpt) cc_final: 0.8652 (mmtt) outliers start: 27 outliers final: 17 residues processed: 132 average time/residue: 0.2378 time to fit residues: 48.4298 Evaluate side-chains 118 residues out of total 1425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 99 time to evaluate : 1.561 ------------------------------------------------------------------------------- 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 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 1742 THR Chi-restraints excluded: chain A residue 1868 VAL Chi-restraints excluded: chain A residue 1871 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 39 optimal weight: 1.9990 chunk 40 optimal weight: 6.9990 chunk 23 optimal weight: 0.8980 chunk 184 optimal weight: 4.9990 chunk 35 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 28 optimal weight: 0.9990 chunk 62 optimal weight: 0.0770 chunk 33 optimal weight: 0.9990 chunk 11 optimal weight: 0.8980 chunk 163 optimal weight: 0.9980 overall best weight: 0.7740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4037 r_free = 0.4037 target = 0.119308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.087547 restraints weight = 42766.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.090182 restraints weight = 22793.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.091878 restraints weight = 15265.596| |-----------------------------------------------------------------------------| r_work (final): 0.3534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.3522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 13699 Z= 0.130 Angle : 0.604 12.183 18572 Z= 0.303 Chirality : 0.039 0.357 2224 Planarity : 0.003 0.037 2469 Dihedral : 4.309 23.642 1934 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 1.83 % Allowed : 18.07 % Favored : 80.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.29 (0.20), residues: 1848 helix: 2.25 (0.14), residues: 1453 sheet: -0.46 (0.78), residues: 37 loop : -1.43 (0.34), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 351 HIS 0.007 0.001 HIS A 283 PHE 0.015 0.001 PHE A 280 TYR 0.017 0.001 TYR A 216 ARG 0.007 0.000 ARG A 220 Details of bonding type rmsd hydrogen bonds : bond 0.03934 ( 1103) hydrogen bonds : angle 3.83233 ( 3300) covalent geometry : bond 0.00286 (13699) covalent geometry : angle 0.60402 (18572) *********************** 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 133 residues out of total 1425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 107 time to evaluate : 1.474 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 216 TYR cc_start: 0.6525 (t80) cc_final: 0.6250 (t80) REVERT: A 221 ASP cc_start: 0.8968 (m-30) cc_final: 0.8738 (m-30) REVERT: A 289 MET cc_start: 0.5260 (ppp) cc_final: 0.4798 (ppp) REVERT: A 357 LYS cc_start: 0.8547 (OUTLIER) cc_final: 0.8134 (mtmm) REVERT: A 546 GLN cc_start: 0.7941 (OUTLIER) cc_final: 0.7428 (mm-40) REVERT: A 786 LYS cc_start: 0.8875 (ttpt) cc_final: 0.8457 (ttpt) REVERT: A 831 GLN cc_start: 0.8058 (tm-30) cc_final: 0.7761 (tm-30) REVERT: A 870 MET cc_start: 0.9225 (tmm) cc_final: 0.8925 (tmm) REVERT: A 1251 GLN cc_start: 0.8861 (tp40) cc_final: 0.8644 (tp40) REVERT: A 1393 LEU cc_start: 0.9372 (OUTLIER) cc_final: 0.8920 (tt) REVERT: A 1407 MET cc_start: 0.7630 (ppp) cc_final: 0.7270 (ppp) REVERT: A 1469 ARG cc_start: 0.8731 (ptp-170) cc_final: 0.8398 (ptp-110) REVERT: A 1606 MET cc_start: 0.8983 (tmm) cc_final: 0.8592 (tmm) REVERT: A 1803 MET cc_start: 0.6613 (ttt) cc_final: 0.6364 (ttt) outliers start: 26 outliers final: 18 residues processed: 127 average time/residue: 0.2460 time to fit residues: 47.9873 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 : 1.606 ------------------------------------------------------------------------------- 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 784 HIS Chi-restraints excluded: chain A residue 850 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 1392 CYS Chi-restraints excluded: chain A residue 1393 LEU Chi-restraints excluded: chain A residue 1397 MET 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 1871 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 32 optimal weight: 1.9990 chunk 119 optimal weight: 10.0000 chunk 157 optimal weight: 0.7980 chunk 66 optimal weight: 0.0970 chunk 174 optimal weight: 0.9980 chunk 40 optimal weight: 4.9990 chunk 38 optimal weight: 0.6980 chunk 46 optimal weight: 0.4980 chunk 34 optimal weight: 0.7980 chunk 139 optimal weight: 0.7980 chunk 71 optimal weight: 0.5980 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4099 r_free = 0.4099 target = 0.124225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.094395 restraints weight = 43191.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.096470 restraints weight = 22861.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.097325 restraints weight = 14590.505| |-----------------------------------------------------------------------------| r_work (final): 0.3552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.3725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 13699 Z= 0.122 Angle : 0.601 13.607 18572 Z= 0.302 Chirality : 0.038 0.319 2224 Planarity : 0.003 0.040 2469 Dihedral : 4.228 24.840 1934 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 1.76 % Allowed : 19.05 % Favored : 79.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.41 (0.20), residues: 1848 helix: 2.33 (0.14), residues: 1455 sheet: -0.36 (0.89), residues: 31 loop : -1.37 (0.34), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 351 HIS 0.006 0.001 HIS A 784 PHE 0.009 0.001 PHE A 280 TYR 0.017 0.001 TYR A 216 ARG 0.007 0.000 ARG A 220 Details of bonding type rmsd hydrogen bonds : bond 0.03762 ( 1103) hydrogen bonds : angle 3.74956 ( 3300) covalent geometry : bond 0.00265 (13699) covalent geometry : angle 0.60137 (18572) *********************** 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 142 residues out of total 1425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 117 time to evaluate : 1.538 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 216 TYR cc_start: 0.6549 (t80) cc_final: 0.6257 (t80) REVERT: A 221 ASP cc_start: 0.8988 (m-30) cc_final: 0.8761 (m-30) REVERT: A 289 MET cc_start: 0.5211 (ppp) cc_final: 0.4775 (ppp) REVERT: A 300 LYS cc_start: 0.9246 (tppt) cc_final: 0.8752 (mptt) REVERT: A 357 LYS cc_start: 0.8561 (OUTLIER) cc_final: 0.8164 (mtmm) REVERT: A 397 ASP cc_start: 0.9229 (t0) cc_final: 0.9008 (m-30) REVERT: A 546 GLN cc_start: 0.7915 (OUTLIER) cc_final: 0.7182 (mm-40) REVERT: A 786 LYS cc_start: 0.8808 (ttpt) cc_final: 0.8392 (ttpt) REVERT: A 831 GLN cc_start: 0.7965 (tm-30) cc_final: 0.7668 (tm-30) REVERT: A 870 MET cc_start: 0.9194 (tmm) cc_final: 0.8908 (tmm) REVERT: A 1251 GLN cc_start: 0.8796 (tp40) cc_final: 0.8566 (tp40) REVERT: A 1393 LEU cc_start: 0.9443 (OUTLIER) cc_final: 0.9009 (tt) REVERT: A 1407 MET cc_start: 0.7574 (ppp) cc_final: 0.7237 (ppp) REVERT: A 1469 ARG cc_start: 0.8701 (ptp-170) cc_final: 0.8369 (ptp-110) REVERT: A 1606 MET cc_start: 0.8963 (tmm) cc_final: 0.8575 (tmm) REVERT: A 1651 MET cc_start: 0.9124 (mtp) cc_final: 0.8791 (mmm) REVERT: A 1734 MET cc_start: 0.8121 (ttt) cc_final: 0.7906 (ttt) REVERT: A 1892 ASP cc_start: 0.8247 (m-30) cc_final: 0.7912 (m-30) outliers start: 25 outliers final: 15 residues processed: 136 average time/residue: 0.2409 time to fit residues: 51.3381 Evaluate side-chains 120 residues out of total 1425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 102 time to evaluate : 1.498 ------------------------------------------------------------------------------- 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 571 THR 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 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 1868 VAL Chi-restraints excluded: chain A residue 1871 MET 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 165 optimal weight: 1.9990 chunk 152 optimal weight: 0.9990 chunk 151 optimal weight: 1.9990 chunk 135 optimal weight: 0.8980 chunk 118 optimal weight: 0.5980 chunk 104 optimal weight: 0.7980 chunk 17 optimal weight: 0.7980 chunk 15 optimal weight: 0.9980 chunk 129 optimal weight: 0.3980 chunk 139 optimal weight: 0.8980 chunk 177 optimal weight: 3.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 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 = 0.4102 r_free = 0.4102 target = 0.126203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.094865 restraints weight = 42789.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.097598 restraints weight = 22519.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.099405 restraints weight = 14922.199| |-----------------------------------------------------------------------------| r_work (final): 0.3559 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.3837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 13699 Z= 0.130 Angle : 0.645 19.879 18572 Z= 0.321 Chirality : 0.039 0.311 2224 Planarity : 0.004 0.039 2469 Dihedral : 4.194 24.700 1934 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.91 % Allowed : 19.83 % Favored : 78.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.46 (0.20), residues: 1848 helix: 2.39 (0.14), residues: 1449 sheet: -0.34 (0.90), residues: 31 loop : -1.42 (0.34), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A2112 HIS 0.006 0.001 HIS A 784 PHE 0.020 0.001 PHE A 241 TYR 0.017 0.001 TYR A 216 ARG 0.007 0.000 ARG A 220 Details of bonding type rmsd hydrogen bonds : bond 0.03787 ( 1103) hydrogen bonds : angle 3.78109 ( 3300) covalent geometry : bond 0.00288 (13699) covalent geometry : angle 0.64492 (18572) *********************** 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 132 residues out of total 1425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 105 time to evaluate : 1.549 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 216 TYR cc_start: 0.6553 (t80) cc_final: 0.6238 (t80) REVERT: A 221 ASP cc_start: 0.8966 (m-30) cc_final: 0.8702 (m-30) REVERT: A 289 MET cc_start: 0.5184 (ppp) cc_final: 0.4906 (ppp) REVERT: A 300 LYS cc_start: 0.9203 (tppt) cc_final: 0.8708 (mptt) REVERT: A 357 LYS cc_start: 0.8485 (OUTLIER) cc_final: 0.8047 (mtmm) REVERT: A 546 GLN cc_start: 0.7883 (OUTLIER) cc_final: 0.7461 (mm-40) REVERT: A 786 LYS cc_start: 0.8751 (ttpt) cc_final: 0.8357 (ttpt) REVERT: A 831 GLN cc_start: 0.7894 (tm-30) cc_final: 0.7569 (tm-30) REVERT: A 870 MET cc_start: 0.9155 (tmm) cc_final: 0.8860 (tmm) REVERT: A 1251 GLN cc_start: 0.8799 (tp40) cc_final: 0.8585 (tp40) REVERT: A 1393 LEU cc_start: 0.9435 (OUTLIER) cc_final: 0.8994 (tt) REVERT: A 1407 MET cc_start: 0.7635 (ppp) cc_final: 0.7281 (ppp) REVERT: A 1606 MET cc_start: 0.8943 (tmm) cc_final: 0.8649 (tmm) REVERT: A 1803 MET cc_start: 0.7152 (ttt) cc_final: 0.6291 (tmm) REVERT: A 1892 ASP cc_start: 0.8091 (m-30) cc_final: 0.7836 (m-30) outliers start: 27 outliers final: 20 residues processed: 124 average time/residue: 0.2259 time to fit residues: 44.0792 Evaluate side-chains 124 residues out of total 1425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 101 time to evaluate : 1.555 ------------------------------------------------------------------------------- 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 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 1871 MET Chi-restraints excluded: chain A residue 1994 THR Chi-restraints excluded: chain A residue 1998 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 132 optimal weight: 7.9990 chunk 179 optimal weight: 0.0030 chunk 65 optimal weight: 2.9990 chunk 158 optimal weight: 0.8980 chunk 18 optimal weight: 6.9990 chunk 138 optimal weight: 1.9990 chunk 147 optimal weight: 0.8980 chunk 56 optimal weight: 9.9990 chunk 53 optimal weight: 0.9980 chunk 0 optimal weight: 30.0000 chunk 4 optimal weight: 9.9990 overall best weight: 0.9592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4095 r_free = 0.4095 target = 0.125830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.094247 restraints weight = 42933.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.097032 restraints weight = 22564.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.098828 restraints weight = 14924.179| |-----------------------------------------------------------------------------| r_work (final): 0.3579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.3884 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= 0.145 Angle : 0.649 18.458 18572 Z= 0.328 Chirality : 0.039 0.312 2224 Planarity : 0.004 0.040 2469 Dihedral : 4.191 24.565 1934 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.76 % Allowed : 20.04 % Favored : 78.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.42 (0.20), residues: 1848 helix: 2.36 (0.14), residues: 1449 sheet: -0.33 (0.90), residues: 31 loop : -1.44 (0.33), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A2112 HIS 0.008 0.001 HIS A 283 PHE 0.012 0.001 PHE A 241 TYR 0.019 0.002 TYR A 298 ARG 0.008 0.000 ARG A2016 Details of bonding type rmsd hydrogen bonds : bond 0.03842 ( 1103) hydrogen bonds : angle 3.82941 ( 3300) covalent geometry : bond 0.00328 (13699) covalent geometry : angle 0.64878 (18572) ********************** 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 126 residues out of total 1425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 101 time to evaluate : 1.509 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 216 TYR cc_start: 0.6594 (t80) cc_final: 0.6241 (t80) REVERT: A 221 ASP cc_start: 0.8967 (m-30) cc_final: 0.8698 (m-30) REVERT: A 241 PHE cc_start: 0.6983 (OUTLIER) cc_final: 0.6620 (t80) REVERT: A 289 MET cc_start: 0.5349 (ppp) cc_final: 0.5105 (ppp) REVERT: A 298 TYR cc_start: 0.7359 (t80) cc_final: 0.7019 (t80) REVERT: A 300 LYS cc_start: 0.9280 (tppt) cc_final: 0.8754 (mptt) REVERT: A 357 LYS cc_start: 0.8529 (OUTLIER) cc_final: 0.8076 (mtmm) REVERT: A 546 GLN cc_start: 0.7947 (OUTLIER) cc_final: 0.7603 (mm-40) REVERT: A 786 LYS cc_start: 0.8779 (ttpt) cc_final: 0.8379 (ttpt) REVERT: A 831 GLN cc_start: 0.7923 (tm-30) cc_final: 0.7601 (tm-30) REVERT: A 870 MET cc_start: 0.9166 (tmm) cc_final: 0.8857 (tmm) REVERT: A 1251 GLN cc_start: 0.8802 (tp40) cc_final: 0.8583 (tp40) REVERT: A 1393 LEU cc_start: 0.9431 (OUTLIER) cc_final: 0.8988 (tt) REVERT: A 1407 MET cc_start: 0.7653 (ppp) cc_final: 0.7300 (ppp) REVERT: A 1606 MET cc_start: 0.8942 (tmm) cc_final: 0.8648 (tmm) REVERT: A 1651 MET cc_start: 0.9210 (mmm) cc_final: 0.8781 (mmm) REVERT: A 1998 PHE cc_start: 0.9480 (OUTLIER) cc_final: 0.8686 (t80) outliers start: 25 outliers final: 19 residues processed: 119 average time/residue: 0.2180 time to fit residues: 41.9922 Evaluate side-chains 121 residues out of total 1425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 97 time to evaluate : 1.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 PHE 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 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 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 1397 MET 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 1871 MET Chi-restraints excluded: chain A residue 1998 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 171 optimal weight: 3.9990 chunk 28 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 chunk 92 optimal weight: 0.9980 chunk 72 optimal weight: 0.0070 chunk 134 optimal weight: 5.9990 chunk 48 optimal weight: 0.9990 chunk 147 optimal weight: 0.5980 chunk 66 optimal weight: 0.9990 chunk 132 optimal weight: 10.0000 chunk 96 optimal weight: 2.9990 overall best weight: 0.7200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4061 r_free = 0.4061 target = 0.124309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.093292 restraints weight = 42914.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.095257 restraints weight = 25000.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.096561 restraints weight = 15340.902| |-----------------------------------------------------------------------------| r_work (final): 0.3574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.4003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 13699 Z= 0.134 Angle : 0.651 18.258 18572 Z= 0.325 Chirality : 0.039 0.305 2224 Planarity : 0.004 0.040 2469 Dihedral : 4.183 24.950 1934 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.55 % Allowed : 20.82 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.45 (0.20), residues: 1848 helix: 2.38 (0.14), residues: 1447 sheet: -0.34 (0.90), residues: 31 loop : -1.39 (0.33), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A2112 HIS 0.007 0.001 HIS A 283 PHE 0.007 0.001 PHE A1467 TYR 0.017 0.002 TYR A 216 ARG 0.007 0.000 ARG A 220 Details of bonding type rmsd hydrogen bonds : bond 0.03786 ( 1103) hydrogen bonds : angle 3.78752 ( 3300) covalent geometry : bond 0.00299 (13699) covalent geometry : angle 0.65118 (18572) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4399.55 seconds wall clock time: 77 minutes 17.89 seconds (4637.89 seconds total)