Starting phenix.real_space_refine on Sat Aug 23 18:00:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vdr_43156/08_2025/8vdr_43156.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vdr_43156/08_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_43156/08_2025/8vdr_43156.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vdr_43156/08_2025/8vdr_43156.map" model { file = "/net/cci-nas-00/data/ceres_data/8vdr_43156/08_2025/8vdr_43156.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vdr_43156/08_2025/8vdr_43156.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.023 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 66 5.16 5 C 8340 2.51 5 N 2412 2.21 5 O 2729 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 68 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13547 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 13547 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1852, 13547 Classifications: {'peptide': 1852} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 70, 'TRANS': 1781} Chain breaks: 1 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 3.04, per 1000 atoms: 0.22 Number of scatterers: 13547 At special positions: 0 Unit cell: (113.76, 146.88, 145.44, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 66 16.00 O 2729 8.00 N 2412 7.00 C 8340 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.04 Conformation dependent library (CDL) restraints added in 615.6 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3470 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 2 sheets defined 81.4% alpha, 1.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.43 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: 1.67 Time building geometry restraints manager: 1.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4306 1.33 - 1.46: 1721 1.46 - 1.58: 7570 1.58 - 1.70: 0 1.70 - 1.82: 102 Bond restraints: 13699 Sorted by residual: bond pdb=" N VAL A1584 " pdb=" CA VAL A1584 " ideal model delta sigma weight residual 1.461 1.507 -0.046 1.23e-02 6.61e+03 1.40e+01 bond pdb=" N GLN A1382 " pdb=" CA GLN A1382 " ideal model delta sigma weight residual 1.452 1.489 -0.036 1.11e-02 8.12e+03 1.07e+01 bond pdb=" N ASN A1379 " pdb=" CA ASN A1379 " ideal model delta sigma weight residual 1.463 1.491 -0.028 8.80e-03 1.29e+04 1.04e+01 bond pdb=" N SER A1582 " pdb=" CA SER A1582 " ideal model delta sigma weight residual 1.455 1.495 -0.040 1.27e-02 6.20e+03 1.01e+01 bond pdb=" N VAL A 774 " pdb=" CA VAL A 774 " ideal model delta sigma weight residual 1.461 1.497 -0.037 1.19e-02 7.06e+03 9.61e+00 ... (remaining 13694 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.05: 17916 2.05 - 4.09: 578 4.09 - 6.14: 66 6.14 - 8.18: 10 8.18 - 10.23: 2 Bond angle restraints: 18572 Sorted by residual: angle pdb=" N SER A1582 " pdb=" CA SER A1582 " pdb=" C SER A1582 " ideal model delta sigma weight residual 109.07 119.30 -10.23 1.52e+00 4.33e-01 4.53e+01 angle pdb=" N SER A1583 " pdb=" CA SER A1583 " pdb=" C SER A1583 " ideal model delta sigma weight residual 113.40 122.39 -8.99 1.47e+00 4.63e-01 3.74e+01 angle pdb=" N PHE A1581 " pdb=" CA PHE A1581 " pdb=" C PHE A1581 " ideal model delta sigma weight residual 111.28 117.38 -6.10 1.09e+00 8.42e-01 3.13e+01 angle pdb=" N GLU A1049 " pdb=" CA GLU A1049 " pdb=" C GLU A1049 " ideal model delta sigma weight residual 113.38 107.67 5.71 1.17e+00 7.31e-01 2.38e+01 angle pdb=" CA PHE A1581 " pdb=" C PHE A1581 " pdb=" O PHE A1581 " ideal model delta sigma weight residual 120.55 115.94 4.61 1.06e+00 8.90e-01 1.90e+01 ... (remaining 18567 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 7648 17.96 - 35.92: 701 35.92 - 53.87: 122 53.87 - 71.83: 40 71.83 - 89.79: 18 Dihedral angle restraints: 8529 sinusoidal: 3191 harmonic: 5338 Sorted by residual: dihedral pdb=" CA THR A 758 " pdb=" C THR A 758 " pdb=" N GLU A 759 " pdb=" CA GLU A 759 " ideal model delta harmonic sigma weight residual 180.00 158.40 21.60 0 5.00e+00 4.00e-02 1.87e+01 dihedral pdb=" CA GLY A1112 " pdb=" C GLY A1112 " pdb=" N ASN A1113 " pdb=" CA ASN A1113 " ideal model delta harmonic sigma weight residual 180.00 159.13 20.87 0 5.00e+00 4.00e-02 1.74e+01 dihedral pdb=" CA SER A 927 " pdb=" C SER A 927 " pdb=" N ALA A 928 " pdb=" CA ALA A 928 " ideal model delta harmonic sigma weight residual 180.00 159.77 20.23 0 5.00e+00 4.00e-02 1.64e+01 ... (remaining 8526 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 2057 0.077 - 0.155: 153 0.155 - 0.232: 11 0.232 - 0.309: 2 0.309 - 0.387: 1 Chirality restraints: 2224 Sorted by residual: chirality pdb=" CA SER A1583 " pdb=" N SER A1583 " pdb=" C SER A1583 " pdb=" CB SER A1583 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.74e+00 chirality pdb=" CB VAL A1381 " pdb=" CA VAL A1381 " pdb=" CG1 VAL A1381 " pdb=" CG2 VAL A1381 " both_signs ideal model delta sigma weight residual False -2.63 -2.38 -0.25 2.00e-01 2.50e+01 1.52e+00 chirality pdb=" CB THR A 518 " pdb=" CA THR A 518 " pdb=" OG1 THR A 518 " pdb=" CG2 THR A 518 " both_signs ideal model delta sigma weight residual False 2.55 2.31 0.24 2.00e-01 2.50e+01 1.45e+00 ... (remaining 2221 not shown) Planarity restraints: 2469 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY A 768 " -0.015 2.00e-02 2.50e+03 2.93e-02 8.57e+00 pdb=" C GLY A 768 " 0.051 2.00e-02 2.50e+03 pdb=" O GLY A 768 " -0.019 2.00e-02 2.50e+03 pdb=" N ALA A 769 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 308 " -0.025 2.00e-02 2.50e+03 2.04e-02 8.36e+00 pdb=" CG TYR A 308 " 0.050 2.00e-02 2.50e+03 pdb=" CD1 TYR A 308 " -0.011 2.00e-02 2.50e+03 pdb=" CD2 TYR A 308 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR A 308 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR A 308 " -0.012 2.00e-02 2.50e+03 pdb=" CZ TYR A 308 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR A 308 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN A 949 " 0.041 5.00e-02 4.00e+02 6.14e-02 6.03e+00 pdb=" N PRO A 950 " -0.106 5.00e-02 4.00e+02 pdb=" CA PRO A 950 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 950 " 0.035 5.00e-02 4.00e+02 ... (remaining 2466 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 894 2.72 - 3.27: 16711 3.27 - 3.81: 23438 3.81 - 4.36: 27599 4.36 - 4.90: 42831 Nonbonded interactions: 111473 Sorted by model distance: nonbonded pdb=" OE1 GLU A 517 " pdb=" OG1 THR A 518 " model vdw 2.179 3.040 nonbonded pdb=" NE2 GLN A 244 " pdb=" O GLY A 287 " model vdw 2.200 3.120 nonbonded pdb=" O GLN A1976 " pdb=" OG1 THR A1980 " model vdw 2.206 3.040 nonbonded pdb=" O GLU A1405 " pdb=" OG1 THR A1408 " model vdw 2.209 3.040 nonbonded pdb=" NZ LYS A 357 " pdb=" O PHE A 370 " model vdw 2.215 3.120 ... (remaining 111468 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.350 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: 0.140 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 11.570 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.460 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.40 (0.19), residues: 1848 helix: 0.14 (0.14), residues: 1366 sheet: -0.29 (0.90), residues: 35 loop : -1.18 (0.30), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 220 TYR 0.050 0.003 TYR A 308 PHE 0.023 0.002 PHE A 241 TRP 0.017 0.002 TRP A 351 HIS 0.004 0.001 HIS A 937 Details of bonding type rmsd covalent geometry : bond 0.00570 (13699) covalent geometry : angle 0.81555 (18572) hydrogen bonds : bond 0.27987 ( 1103) hydrogen bonds : angle 8.55701 ( 3300) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 140 time to evaluate : 0.450 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: 0.0991 time to fit residues: 22.3441 Evaluate side-chains 105 residues out of total 1425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 99 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 657 GLU Chi-restraints excluded: chain A residue 772 THR Chi-restraints excluded: chain A residue 778 LEU Chi-restraints excluded: chain A residue 909 ILE Chi-restraints excluded: chain A residue 1333 SER Chi-restraints excluded: chain A residue 1997 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 98 optimal weight: 0.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 0.2980 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 6.9990 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 6.9990 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 0.9980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 244 GLN A 733 GLN A 779 ASN A 783 GLN A1413 ASN ** A1475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1695 GLN A1736 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.119242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.088025 restraints weight = 42759.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.090510 restraints weight = 23183.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.092185 restraints weight = 15661.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.092988 restraints weight = 12307.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.093510 restraints weight = 10733.022| |-----------------------------------------------------------------------------| r_work (final): 0.3574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.2019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 13699 Z= 0.173 Angle : 0.687 8.005 18572 Z= 0.360 Chirality : 0.040 0.204 2224 Planarity : 0.004 0.040 2469 Dihedral : 5.648 61.189 1946 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.34 % Allowed : 8.40 % Favored : 90.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.09 (0.19), residues: 1848 helix: 1.31 (0.13), residues: 1435 sheet: -0.03 (0.90), residues: 35 loop : -1.36 (0.34), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1638 TYR 0.024 0.002 TYR A 308 PHE 0.013 0.002 PHE A 280 TRP 0.016 0.002 TRP A 351 HIS 0.007 0.001 HIS A 784 Details of bonding type rmsd covalent geometry : bond 0.00355 (13699) covalent geometry : angle 0.68742 (18572) hydrogen bonds : bond 0.06289 ( 1103) hydrogen bonds : angle 4.75387 ( 3300) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 136 time to evaluate : 0.380 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 216 TYR cc_start: 0.6644 (t80) cc_final: 0.6057 (t80) REVERT: A 221 ASP cc_start: 0.8954 (m-30) cc_final: 0.8751 (m-30) REVERT: A 298 TYR cc_start: 0.7159 (t80) cc_final: 0.6742 (t80) REVERT: A 388 ILE cc_start: 0.8982 (mt) cc_final: 0.8774 (mt) REVERT: A 499 ILE cc_start: 0.9131 (OUTLIER) cc_final: 0.8930 (pt) REVERT: A 657 GLU cc_start: 0.7563 (OUTLIER) cc_final: 0.7015 (tm-30) REVERT: A 748 GLU cc_start: 0.7904 (tm-30) cc_final: 0.7703 (tm-30) REVERT: A 786 LYS cc_start: 0.8697 (ttpt) cc_final: 0.8277 (ttpt) REVERT: A 870 MET cc_start: 0.9086 (tmm) cc_final: 0.8840 (tmm) REVERT: A 1606 MET cc_start: 0.9163 (tmm) cc_final: 0.8551 (tmm) REVERT: A 1651 MET cc_start: 0.9264 (mmm) cc_final: 0.8935 (mmm) REVERT: A 1992 LEU cc_start: 0.9531 (mt) cc_final: 0.9327 (tp) REVERT: A 1997 MET cc_start: 0.8878 (mmt) cc_final: 0.8633 (mmt) outliers start: 19 outliers final: 10 residues processed: 147 average time/residue: 0.0822 time to fit residues: 19.2871 Evaluate side-chains 114 residues out of total 1425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 102 time to evaluate : 0.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 268 LYS Chi-restraints excluded: chain A residue 499 ILE Chi-restraints excluded: chain A residue 627 GLN Chi-restraints excluded: chain A residue 657 GLU Chi-restraints excluded: chain A residue 784 HIS Chi-restraints excluded: chain A residue 909 ILE Chi-restraints excluded: chain A residue 911 LYS Chi-restraints excluded: chain A residue 951 LEU Chi-restraints excluded: chain A residue 1025 LYS Chi-restraints excluded: chain A residue 1210 ASP Chi-restraints excluded: chain A residue 1333 SER Chi-restraints excluded: chain A residue 1571 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 67 optimal weight: 1.9990 chunk 23 optimal weight: 0.0670 chunk 86 optimal weight: 0.9990 chunk 43 optimal weight: 0.9990 chunk 149 optimal weight: 2.9990 chunk 164 optimal weight: 1.9990 chunk 151 optimal weight: 0.6980 chunk 21 optimal weight: 0.6980 chunk 24 optimal weight: 0.9980 chunk 19 optimal weight: 20.0000 chunk 182 optimal weight: 4.9990 overall best weight: 0.6920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 733 GLN A1475 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.125411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.093961 restraints weight = 42937.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.096627 restraints weight = 22516.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.098431 restraints weight = 14903.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.099399 restraints weight = 11517.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.100073 restraints weight = 9902.930| |-----------------------------------------------------------------------------| r_work (final): 0.3600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.2640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13699 Z= 0.143 Angle : 0.617 11.019 18572 Z= 0.317 Chirality : 0.039 0.181 2224 Planarity : 0.004 0.038 2469 Dihedral : 5.005 54.511 1940 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 1.83 % Allowed : 11.50 % Favored : 86.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.69 (0.20), residues: 1848 helix: 1.78 (0.13), residues: 1443 sheet: 0.02 (0.87), residues: 35 loop : -1.41 (0.33), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 854 TYR 0.021 0.002 TYR A 308 PHE 0.011 0.001 PHE A1525 TRP 0.018 0.002 TRP A 351 HIS 0.007 0.001 HIS A 283 Details of bonding type rmsd covalent geometry : bond 0.00295 (13699) covalent geometry : angle 0.61707 (18572) hydrogen bonds : bond 0.04934 ( 1103) hydrogen bonds : angle 4.19760 ( 3300) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 121 time to evaluate : 0.533 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 221 ASP cc_start: 0.8931 (m-30) cc_final: 0.8713 (m-30) REVERT: A 357 LYS cc_start: 0.8371 (OUTLIER) cc_final: 0.7898 (mtmm) REVERT: A 546 GLN cc_start: 0.7780 (OUTLIER) cc_final: 0.7087 (mm-40) REVERT: A 657 GLU cc_start: 0.7513 (OUTLIER) cc_final: 0.6939 (tm-30) REVERT: A 748 GLU cc_start: 0.7934 (tm-30) cc_final: 0.7674 (tm-30) REVERT: A 786 LYS cc_start: 0.8782 (ttpt) cc_final: 0.8399 (ttpt) REVERT: A 831 GLN cc_start: 0.7803 (tm-30) cc_final: 0.7574 (tm-30) REVERT: A 870 MET cc_start: 0.9145 (tmm) cc_final: 0.8908 (tmm) REVERT: A 1310 MET cc_start: 0.8597 (mmt) cc_final: 0.8253 (mmt) REVERT: A 1407 MET cc_start: 0.7582 (ppp) cc_final: 0.7034 (ppp) REVERT: A 1606 MET cc_start: 0.9078 (tmm) cc_final: 0.8495 (tmm) REVERT: A 1734 MET cc_start: 0.7825 (ttt) cc_final: 0.7560 (ttt) REVERT: A 1803 MET cc_start: 0.7214 (ttt) cc_final: 0.6255 (tmm) REVERT: A 1827 MET cc_start: 0.8204 (mtm) cc_final: 0.7798 (mtm) outliers start: 26 outliers final: 14 residues processed: 142 average time/residue: 0.0871 time to fit residues: 19.8089 Evaluate side-chains 117 residues out of total 1425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 100 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 268 LYS Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 357 LYS Chi-restraints excluded: chain A residue 546 GLN Chi-restraints excluded: chain A residue 657 GLU Chi-restraints excluded: chain A residue 663 HIS Chi-restraints excluded: chain A residue 784 HIS Chi-restraints excluded: chain A residue 798 TYR Chi-restraints excluded: chain A residue 850 LEU Chi-restraints excluded: chain A residue 951 LEU Chi-restraints excluded: chain A residue 1025 LYS Chi-restraints excluded: chain A residue 1159 LEU Chi-restraints excluded: chain A residue 1210 ASP Chi-restraints excluded: chain A residue 1465 THR Chi-restraints excluded: chain A residue 1571 ASN Chi-restraints excluded: chain A residue 1632 VAL Chi-restraints excluded: chain A residue 1837 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 65 optimal weight: 2.9990 chunk 144 optimal weight: 0.9990 chunk 23 optimal weight: 0.0050 chunk 83 optimal weight: 2.9990 chunk 131 optimal weight: 1.9990 chunk 4 optimal weight: 30.0000 chunk 69 optimal weight: 5.9990 chunk 110 optimal weight: 0.7980 chunk 32 optimal weight: 0.9990 chunk 53 optimal weight: 0.3980 chunk 149 optimal weight: 0.9990 overall best weight: 0.6398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.4095 r_free = 0.4095 target = 0.125614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.094160 restraints weight = 43005.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.096924 restraints weight = 22504.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.098660 restraints weight = 14840.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.099800 restraints weight = 11410.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.100260 restraints weight = 9786.313| |-----------------------------------------------------------------------------| r_work (final): 0.3576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.3037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13699 Z= 0.130 Angle : 0.600 10.387 18572 Z= 0.307 Chirality : 0.038 0.287 2224 Planarity : 0.004 0.041 2469 Dihedral : 4.833 53.112 1937 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 1.91 % Allowed : 13.83 % Favored : 84.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.95 (0.20), residues: 1848 helix: 1.97 (0.13), residues: 1449 sheet: -0.39 (0.81), residues: 37 loop : -1.37 (0.34), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 220 TYR 0.021 0.002 TYR A1945 PHE 0.011 0.001 PHE A 265 TRP 0.018 0.002 TRP A 351 HIS 0.006 0.001 HIS A 784 Details of bonding type rmsd covalent geometry : bond 0.00272 (13699) covalent geometry : angle 0.59977 (18572) hydrogen bonds : bond 0.04318 ( 1103) hydrogen bonds : angle 3.98140 ( 3300) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 120 time to evaluate : 0.310 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 221 ASP cc_start: 0.8937 (m-30) cc_final: 0.8693 (m-30) REVERT: A 298 TYR cc_start: 0.7794 (t80) cc_final: 0.7532 (t80) REVERT: A 357 LYS cc_start: 0.8372 (OUTLIER) cc_final: 0.7910 (mtmm) REVERT: A 546 GLN cc_start: 0.7974 (OUTLIER) cc_final: 0.7427 (mt0) REVERT: A 748 GLU cc_start: 0.7935 (tm-30) cc_final: 0.7629 (tm-30) REVERT: A 786 LYS cc_start: 0.8784 (ttpt) cc_final: 0.8388 (ttpt) REVERT: A 831 GLN cc_start: 0.7832 (tm-30) cc_final: 0.7625 (tm-30) REVERT: A 870 MET cc_start: 0.9153 (tmm) cc_final: 0.8872 (tmm) REVERT: A 1251 GLN cc_start: 0.8870 (tp40) cc_final: 0.8620 (tp40) REVERT: A 1310 MET cc_start: 0.8568 (mmt) cc_final: 0.8230 (mmt) REVERT: A 1407 MET cc_start: 0.7764 (ppp) cc_final: 0.7418 (ppp) REVERT: A 1469 ARG cc_start: 0.8787 (ptp-170) cc_final: 0.8395 (ptp-170) REVERT: A 1492 LEU cc_start: 0.9194 (tt) cc_final: 0.8931 (pp) REVERT: A 1606 MET cc_start: 0.9074 (tmm) cc_final: 0.8496 (tmm) REVERT: A 2021 LYS cc_start: 0.8793 (mppt) cc_final: 0.8486 (mmtt) outliers start: 27 outliers final: 12 residues processed: 141 average time/residue: 0.0887 time to fit residues: 19.1398 Evaluate side-chains 113 residues out of total 1425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 99 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 268 LYS Chi-restraints excluded: chain A residue 357 LYS Chi-restraints excluded: chain A residue 546 GLN Chi-restraints excluded: chain A residue 663 HIS Chi-restraints excluded: chain A residue 784 HIS Chi-restraints excluded: chain A residue 850 LEU Chi-restraints excluded: chain A residue 951 LEU Chi-restraints excluded: chain A residue 1025 LYS Chi-restraints excluded: chain A residue 1210 ASP Chi-restraints excluded: chain A residue 1433 LEU Chi-restraints excluded: chain A residue 1465 THR Chi-restraints excluded: chain A residue 1571 ASN Chi-restraints excluded: chain A residue 1632 VAL Chi-restraints excluded: chain A residue 1742 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 139 optimal weight: 0.9980 chunk 69 optimal weight: 5.9990 chunk 170 optimal weight: 0.9990 chunk 55 optimal weight: 0.6980 chunk 151 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 chunk 59 optimal weight: 0.8980 chunk 92 optimal weight: 0.9990 chunk 162 optimal weight: 0.7980 chunk 91 optimal weight: 2.9990 chunk 26 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2124 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.125226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.093806 restraints weight = 43024.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.096521 restraints weight = 22502.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.098255 restraints weight = 14857.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.099133 restraints weight = 11481.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.099979 restraints weight = 9965.927| |-----------------------------------------------------------------------------| r_work (final): 0.3608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.3259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13699 Z= 0.133 Angle : 0.614 12.774 18572 Z= 0.307 Chirality : 0.039 0.279 2224 Planarity : 0.004 0.041 2469 Dihedral : 4.390 23.541 1934 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.91 % Allowed : 15.81 % Favored : 82.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.15 (0.20), residues: 1848 helix: 2.13 (0.14), residues: 1449 sheet: -0.56 (0.79), residues: 37 loop : -1.35 (0.34), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 220 TYR 0.015 0.001 TYR A 216 PHE 0.015 0.001 PHE A 241 TRP 0.016 0.002 TRP A 351 HIS 0.006 0.001 HIS A 784 Details of bonding type rmsd covalent geometry : bond 0.00284 (13699) covalent geometry : angle 0.61357 (18572) hydrogen bonds : bond 0.04107 ( 1103) hydrogen bonds : angle 3.88120 ( 3300) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 112 time to evaluate : 0.532 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 221 ASP cc_start: 0.8920 (m-30) cc_final: 0.8629 (m-30) REVERT: A 241 PHE cc_start: 0.7739 (m-80) cc_final: 0.7310 (m-80) REVERT: A 357 LYS cc_start: 0.8409 (OUTLIER) cc_final: 0.7927 (mtmm) REVERT: A 546 GLN cc_start: 0.7892 (OUTLIER) cc_final: 0.7057 (mm-40) REVERT: A 748 GLU cc_start: 0.7929 (tm-30) cc_final: 0.7599 (tm-30) REVERT: A 786 LYS cc_start: 0.8766 (ttpt) cc_final: 0.8377 (ttpt) REVERT: A 831 GLN cc_start: 0.7845 (tm-30) cc_final: 0.7598 (tm-30) REVERT: A 870 MET cc_start: 0.9149 (tmm) cc_final: 0.8867 (tmm) REVERT: A 1251 GLN cc_start: 0.8862 (tp40) cc_final: 0.8618 (tp40) REVERT: A 1310 MET cc_start: 0.8596 (mmt) cc_final: 0.8189 (mmt) REVERT: A 1407 MET cc_start: 0.7673 (ppp) cc_final: 0.7328 (ppp) REVERT: A 1606 MET cc_start: 0.8999 (tmm) cc_final: 0.8615 (tmm) REVERT: A 1684 SER cc_start: 0.9403 (OUTLIER) cc_final: 0.9172 (p) REVERT: A 1803 MET cc_start: 0.6961 (ttt) cc_final: 0.6718 (ttt) REVERT: A 2021 LYS cc_start: 0.8835 (mtpt) cc_final: 0.8630 (mmtt) outliers start: 27 outliers final: 18 residues processed: 131 average time/residue: 0.1098 time to fit residues: 22.0139 Evaluate side-chains 124 residues out of total 1425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 103 time to evaluate : 0.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 268 LYS Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 357 LYS Chi-restraints excluded: chain A residue 546 GLN Chi-restraints excluded: chain A residue 571 THR Chi-restraints excluded: chain A residue 663 HIS Chi-restraints excluded: chain A residue 750 CYS Chi-restraints excluded: chain A residue 784 HIS Chi-restraints excluded: chain A residue 798 TYR Chi-restraints excluded: chain A residue 850 LEU Chi-restraints excluded: chain A residue 1025 LYS Chi-restraints excluded: chain A residue 1210 ASP Chi-restraints excluded: chain A residue 1392 CYS Chi-restraints excluded: chain A residue 1433 LEU Chi-restraints excluded: chain A residue 1465 THR Chi-restraints excluded: chain A residue 1571 ASN Chi-restraints excluded: chain A residue 1632 VAL Chi-restraints excluded: chain A residue 1684 SER Chi-restraints excluded: chain A residue 1742 THR Chi-restraints excluded: chain A residue 1837 GLN Chi-restraints excluded: chain A residue 1994 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 70.7894 > 50: distance: 50 - 56: 34.541 distance: 56 - 57: 40.965 distance: 57 - 58: 68.046 distance: 57 - 60: 53.915 distance: 58 - 59: 33.388 distance: 58 - 64: 39.437 distance: 60 - 61: 68.842 distance: 61 - 62: 40.779 distance: 64 - 65: 35.317 distance: 65 - 66: 56.561 distance: 65 - 68: 41.258 distance: 66 - 67: 32.584 distance: 66 - 73: 57.061 distance: 68 - 69: 69.422 distance: 69 - 70: 39.196 distance: 70 - 71: 55.968 distance: 71 - 72: 44.350 distance: 73 - 74: 37.095 distance: 73 - 79: 57.831 distance: 74 - 75: 52.186 distance: 74 - 77: 34.468 distance: 75 - 76: 35.642 distance: 75 - 80: 19.088 distance: 77 - 78: 39.747 distance: 78 - 79: 54.763 distance: 80 - 81: 40.753 distance: 81 - 82: 43.363 distance: 81 - 84: 31.906 distance: 82 - 83: 13.086 distance: 82 - 88: 18.668 distance: 84 - 85: 10.444 distance: 85 - 86: 44.438 distance: 85 - 87: 32.499 distance: 88 - 89: 20.471 distance: 88 - 94: 21.316 distance: 89 - 92: 48.040 distance: 90 - 91: 56.749 distance: 90 - 95: 54.761 distance: 92 - 93: 47.414 distance: 93 - 94: 40.594 distance: 95 - 96: 52.024 distance: 96 - 97: 5.775 distance: 97 - 98: 11.546 distance: 97 - 99: 52.960 distance: 99 - 100: 20.174 distance: 100 - 101: 39.572 distance: 100 - 103: 20.625 distance: 101 - 102: 7.855 distance: 101 - 108: 11.925 distance: 103 - 104: 6.471 distance: 104 - 105: 22.534 distance: 105 - 106: 18.658 distance: 105 - 107: 26.538 distance: 109 - 110: 25.482 distance: 109 - 112: 39.563 distance: 110 - 111: 44.224 distance: 110 - 115: 40.012 distance: 111 - 141: 32.859 distance: 112 - 113: 9.082 distance: 112 - 114: 29.198 distance: 115 - 116: 12.807 distance: 116 - 117: 13.236 distance: 116 - 119: 20.880 distance: 117 - 118: 11.597 distance: 117 - 123: 10.181 distance: 119 - 120: 19.447 distance: 120 - 121: 19.686 distance: 121 - 122: 25.925 distance: 123 - 124: 23.661 distance: 124 - 125: 32.604 distance: 124 - 127: 8.377 distance: 125 - 132: 34.012 distance: 127 - 128: 35.407 distance: 128 - 129: 37.202 distance: 129 - 130: 30.913 distance: 129 - 131: 14.307