Starting phenix.real_space_refine on Tue Dec 31 01:03:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b8k_44348/12_2024/9b8k_44348.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b8k_44348/12_2024/9b8k_44348.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.96 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9b8k_44348/12_2024/9b8k_44348.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b8k_44348/12_2024/9b8k_44348.map" model { file = "/net/cci-nas-00/data/ceres_data/9b8k_44348/12_2024/9b8k_44348.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b8k_44348/12_2024/9b8k_44348.cif" } resolution = 2.96 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= 0.013 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 72 5.16 5 C 9085 2.51 5 N 2426 2.21 5 O 2648 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 14231 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 14231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1761, 14231 Classifications: {'peptide': 1761} Link IDs: {'PCIS': 1, 'PTRANS': 114, 'TRANS': 1645} Chain breaks: 1 Time building chain proxies: 8.42, per 1000 atoms: 0.59 Number of scatterers: 14231 At special positions: 0 Unit cell: (99.792, 99.792, 208.494, 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 72 16.00 O 2648 8.00 N 2426 7.00 C 9085 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: 3.51 Conformation dependent library (CDL) restraints added in 1.9 seconds 3514 Ramachandran restraints generated. 1757 Oldfield, 0 Emsley, 1757 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3310 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 19 sheets defined 17.1% alpha, 26.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.23 Creating SS restraints... Processing helix chain 'A' and resid 273 through 278 Processing helix chain 'A' and resid 304 through 311 removed outlier: 4.127A pdb=" N ILE A 308 " --> pdb=" O ASP A 304 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N GLU A 311 " --> pdb=" O THR A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 398 through 403 Processing helix chain 'A' and resid 404 through 407 Processing helix chain 'A' and resid 540 through 544 Processing helix chain 'A' and resid 576 through 580 Processing helix chain 'A' and resid 583 through 587 Processing helix chain 'A' and resid 622 through 626 removed outlier: 3.805A pdb=" N MET A 626 " --> pdb=" O LYS A 623 " (cutoff:3.500A) Processing helix chain 'A' and resid 668 through 697 removed outlier: 4.879A pdb=" N THR A 674 " --> pdb=" O HIS A 670 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLN A 675 " --> pdb=" O ARG A 671 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N LYS A 697 " --> pdb=" O HIS A 693 " (cutoff:3.500A) Processing helix chain 'A' and resid 701 through 721 Processing helix chain 'A' and resid 734 through 761 removed outlier: 4.736A pdb=" N LEU A 756 " --> pdb=" O THR A 752 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ALA A 757 " --> pdb=" O GLU A 753 " (cutoff:3.500A) removed outlier: 5.909A pdb=" N LYS A 759 " --> pdb=" O ALA A 755 " (cutoff:3.500A) Processing helix chain 'A' and resid 764 through 782 Processing helix chain 'A' and resid 810 through 814 Processing helix chain 'A' and resid 820 through 824 Processing helix chain 'A' and resid 862 through 871 removed outlier: 4.831A pdb=" N LYS A 865 " --> pdb=" O VAL A 862 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASN A 868 " --> pdb=" O LYS A 865 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N GLN A 869 " --> pdb=" O GLU A 866 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ALA A 871 " --> pdb=" O ASN A 868 " (cutoff:3.500A) Processing helix chain 'A' and resid 914 through 918 removed outlier: 3.990A pdb=" N PHE A 918 " --> pdb=" O LYS A 915 " (cutoff:3.500A) Processing helix chain 'A' and resid 982 through 986 removed outlier: 3.830A pdb=" N ILE A 986 " --> pdb=" O LYS A 983 " (cutoff:3.500A) Processing helix chain 'A' and resid 1053 through 1059 removed outlier: 3.563A pdb=" N ARG A1058 " --> pdb=" O ALA A1055 " (cutoff:3.500A) Processing helix chain 'A' and resid 1104 through 1111 removed outlier: 4.154A pdb=" N ALA A1107 " --> pdb=" O THR A1104 " (cutoff:3.500A) Processing helix chain 'A' and resid 1213 through 1218 Processing helix chain 'A' and resid 1348 through 1353 removed outlier: 3.681A pdb=" N SER A1353 " --> pdb=" O ALA A1350 " (cutoff:3.500A) Processing helix chain 'A' and resid 1424 through 1429 Processing helix chain 'A' and resid 1469 through 1474 Processing helix chain 'A' and resid 1477 through 1484 Processing helix chain 'A' and resid 1491 through 1498 removed outlier: 3.574A pdb=" N ASP A1498 " --> pdb=" O LEU A1495 " (cutoff:3.500A) Processing helix chain 'A' and resid 1508 through 1519 removed outlier: 5.743A pdb=" N GLU A1513 " --> pdb=" O GLU A1510 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N ALA A1514 " --> pdb=" O ASN A1511 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N PHE A1515 " --> pdb=" O VAL A1512 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N GLY A1517 " --> pdb=" O ALA A1514 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N SER A1519 " --> pdb=" O GLU A1516 " (cutoff:3.500A) Processing helix chain 'A' and resid 1666 through 1671 Processing helix chain 'A' and resid 1687 through 1691 removed outlier: 4.134A pdb=" N ASN A1690 " --> pdb=" O SER A1687 " (cutoff:3.500A) Processing helix chain 'A' and resid 1697 through 1709 Processing helix chain 'A' and resid 1731 through 1733 No H-bonds generated for 'chain 'A' and resid 1731 through 1733' Processing helix chain 'A' and resid 1745 through 1757 Processing helix chain 'A' and resid 1847 through 1851 Processing helix chain 'A' and resid 1938 through 1942 Processing helix chain 'A' and resid 1943 through 1947 Processing helix chain 'A' and resid 1952 through 1954 No H-bonds generated for 'chain 'A' and resid 1952 through 1954' Processing helix chain 'A' and resid 1958 through 1962 removed outlier: 3.768A pdb=" N GLU A1961 " --> pdb=" O SER A1958 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 261 through 272 removed outlier: 6.832A pdb=" N ILE A 227 " --> pdb=" O PHE A 262 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N GLU A 264 " --> pdb=" O GLN A 225 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N GLN A 225 " --> pdb=" O GLU A 264 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N LEU A 266 " --> pdb=" O ARG A 223 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N ARG A 223 " --> pdb=" O LEU A 266 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N PHE A 268 " --> pdb=" O GLN A 221 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N GLN A 221 " --> pdb=" O PHE A 268 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N LEU A 270 " --> pdb=" O ASP A 219 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N ASP A 219 " --> pdb=" O LEU A 270 " (cutoff:3.500A) removed outlier: 5.770A pdb=" N ILE A 222 " --> pdb=" O LEU A 344 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N LEU A 344 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 5.044A pdb=" N VAL A 224 " --> pdb=" O CYS A 342 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N CYS A 342 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 5.651A pdb=" N VAL A 226 " --> pdb=" O SER A 340 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N SER A 340 " --> pdb=" O VAL A 226 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLU A 228 " --> pdb=" O LYS A 338 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N LEU A 341 " --> pdb=" O LEU A 317 " (cutoff:3.500A) removed outlier: 5.320A pdb=" N LEU A 317 " --> pdb=" O LEU A 341 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N VAL A 343 " --> pdb=" O ALA A 315 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N ALA A 315 " --> pdb=" O VAL A 343 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU A 322 " --> pdb=" O LEU A 368 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 248 through 251 removed outlier: 5.805A pdb=" N ASP A 288 " --> pdb=" O LEU A 297 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N LEU A 297 " --> pdb=" O ASP A 288 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 518 through 527 removed outlier: 6.872A pdb=" N LEU A 558 " --> pdb=" O PRO A 520 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N TYR A 522 " --> pdb=" O LEU A 556 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N LEU A 556 " --> pdb=" O TYR A 522 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N ASN A 524 " --> pdb=" O GLY A 554 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N GLY A 554 " --> pdb=" O ASN A 524 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N TYR A 526 " --> pdb=" O TYR A 552 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N TYR A 552 " --> pdb=" O TYR A 526 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N ARG A 555 " --> pdb=" O ALA A 388 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N ALA A 388 " --> pdb=" O ARG A 555 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N LEU A 557 " --> pdb=" O PHE A 386 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N GLY A 378 " --> pdb=" O VAL A 565 " (cutoff:3.500A) removed outlier: 7.309A pdb=" N ARG A 387 " --> pdb=" O TRP A 442 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N TRP A 442 " --> pdb=" O ARG A 387 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LYS A 571 " --> pdb=" O THR A 447 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 427 through 430 removed outlier: 6.441A pdb=" N MET A 459 " --> pdb=" O TYR A 479 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N TYR A 479 " --> pdb=" O MET A 459 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N ILE A 461 " --> pdb=" O THR A 477 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N THR A 477 " --> pdb=" O ILE A 461 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N ILE A 463 " --> pdb=" O VAL A 475 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 590 through 602 removed outlier: 7.930A pdb=" N SER A 600 " --> pdb=" O VAL A 655 " (cutoff:3.500A) removed outlier: 11.761A pdb=" N VAL A 655 " --> pdb=" O SER A 600 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 655 through 665 current: chain 'A' and resid 851 through 860 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 851 through 860 current: chain 'A' and resid 893 through 895 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 893 through 895 current: chain 'A' and resid 1089 through 1100 Processing sheet with id=AA6, first strand: chain 'A' and resid 611 through 617 removed outlier: 3.629A pdb=" N ALA A 805 " --> pdb=" O MET A 797 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N GLN A 799 " --> pdb=" O ARG A 803 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N ARG A 803 " --> pdb=" O GLN A 799 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 641 through 642 Processing sheet with id=AA8, first strand: chain 'A' and resid 948 through 958 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 972 through 973 current: chain 'A' and resid 1035 through 1048 Processing sheet with id=AA9, first strand: chain 'A' and resid 1148 through 1162 removed outlier: 6.237A pdb=" N ASN A1150 " --> pdb=" O GLU A1209 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N GLU A1209 " --> pdb=" O ASN A1150 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N TYR A1152 " --> pdb=" O GLU A1207 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N GLN A1160 " --> pdb=" O TRP A1199 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N TRP A1199 " --> pdb=" O GLN A1160 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 1198 through 1210 current: chain 'A' and resid 1265 through 1278 Processing sheet with id=AB1, first strand: chain 'A' and resid 1184 through 1187 removed outlier: 3.597A pdb=" N GLY A1241 " --> pdb=" O LEU A1228 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N ASP A1230 " --> pdb=" O PHE A1239 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N PHE A1239 " --> pdb=" O ASP A1230 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 1313 through 1315 removed outlier: 3.534A pdb=" N GLU A1315 " --> pdb=" O ILE A1318 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 1385 through 1392 removed outlier: 7.000A pdb=" N LYS A1546 " --> pdb=" O TRP A1339 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N LEU A1341 " --> pdb=" O GLU A1544 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N GLU A1544 " --> pdb=" O LEU A1341 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N GLY A1543 " --> pdb=" O LEU A1527 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 1364 through 1367 removed outlier: 3.932A pdb=" N GLY A1418 " --> pdb=" O VAL A1405 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N ASP A1407 " --> pdb=" O VAL A1416 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N VAL A1416 " --> pdb=" O ASP A1407 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1503 through 1505 removed outlier: 3.871A pdb=" N SER A1767 " --> pdb=" O TYR A1505 " (cutoff:3.500A) removed outlier: 8.996A pdb=" N HIS A1764 " --> pdb=" O VAL A1787 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N VAL A1787 " --> pdb=" O HIS A1764 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N GLY A1781 " --> pdb=" O LEU A1770 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ARG A1586 " --> pdb=" O GLN A1784 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N TRP A1786 " --> pdb=" O ILE A1584 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N ILE A1584 " --> pdb=" O TRP A1786 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N ASP A1788 " --> pdb=" O ILE A1582 " (cutoff:3.500A) removed outlier: 5.538A pdb=" N ILE A1582 " --> pdb=" O ASP A1788 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N PHE A1790 " --> pdb=" O VAL A1580 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N VAL A1580 " --> pdb=" O PHE A1790 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N ARG A1586 " --> pdb=" O PHE A1627 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N PHE A1627 " --> pdb=" O ARG A1586 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1610 through 1613 removed outlier: 3.989A pdb=" N GLY A1660 " --> pdb=" O LEU A1647 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N ASP A1649 " --> pdb=" O LYS A1658 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N LYS A1658 " --> pdb=" O ASP A1649 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1720 through 1723 Processing sheet with id=AB8, first strand: chain 'A' and resid 1869 through 1877 removed outlier: 3.506A pdb=" N ILE A1817 " --> pdb=" O TRP A1869 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ARG A1814 " --> pdb=" O GLU A1990 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLU A1990 " --> pdb=" O ARG A1814 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N GLU A1986 " --> pdb=" O TRP A1818 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N THR A1820 " --> pdb=" O LYS A1984 " (cutoff:3.500A) removed outlier: 8.017A pdb=" N LYS A1984 " --> pdb=" O THR A1820 " (cutoff:3.500A) removed outlier: 5.972A pdb=" N LEU A1981 " --> pdb=" O ALA A1973 " (cutoff:3.500A) removed outlier: 5.130A pdb=" N ALA A1973 " --> pdb=" O LEU A1981 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N GLY A1983 " --> pdb=" O CYS A1971 " (cutoff:3.500A) removed outlier: 12.978A pdb=" N TRP A1968 " --> pdb=" O ASP A1928 " (cutoff:3.500A) removed outlier: 11.355A pdb=" N ASP A1928 " --> pdb=" O TRP A1968 " (cutoff:3.500A) removed outlier: 5.394A pdb=" N GLN A1926 " --> pdb=" O PRO A1970 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N PHE A1921 " --> pdb=" O ASP A1912 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N ASP A1912 " --> pdb=" O PHE A1921 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 1827 through 1828 removed outlier: 3.582A pdb=" N ASP A1827 " --> pdb=" O MET A1835 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 1932 through 1933 364 hydrogen bonds defined for protein. 882 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: 6.87 Time building geometry restraints manager: 4.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 2662 1.32 - 1.45: 3647 1.45 - 1.57: 8183 1.57 - 1.70: 1 1.70 - 1.82: 108 Bond restraints: 14601 Sorted by residual: bond pdb=" CA GLN A1695 " pdb=" C GLN A1695 " ideal model delta sigma weight residual 1.522 1.582 -0.059 1.40e-02 5.10e+03 1.80e+01 bond pdb=" NE ARG A1905 " pdb=" CZ ARG A1905 " ideal model delta sigma weight residual 1.326 1.359 -0.033 1.10e-02 8.26e+03 9.04e+00 bond pdb=" CB HIS A1997 " pdb=" CG HIS A1997 " ideal model delta sigma weight residual 1.497 1.456 0.041 1.40e-02 5.10e+03 8.60e+00 bond pdb=" CG ASP A 304 " pdb=" OD1 ASP A 304 " ideal model delta sigma weight residual 1.249 1.194 0.055 1.90e-02 2.77e+03 8.27e+00 bond pdb=" NE ARG A1821 " pdb=" CZ ARG A1821 " ideal model delta sigma weight residual 1.326 1.356 -0.030 1.10e-02 8.26e+03 7.25e+00 ... (remaining 14596 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.01: 18311 2.01 - 4.01: 1163 4.01 - 6.02: 156 6.02 - 8.03: 159 8.03 - 10.03: 9 Bond angle restraints: 19798 Sorted by residual: angle pdb=" C CYS A1398 " pdb=" N PRO A1399 " pdb=" CA PRO A1399 " ideal model delta sigma weight residual 119.66 125.85 -6.19 7.20e-01 1.93e+00 7.38e+01 angle pdb=" C PRO A1799 " pdb=" N PRO A1800 " pdb=" CA PRO A1800 " ideal model delta sigma weight residual 120.03 128.11 -8.08 9.90e-01 1.02e+00 6.67e+01 angle pdb=" C GLU A1624 " pdb=" N PRO A1625 " pdb=" CA PRO A1625 " ideal model delta sigma weight residual 119.78 128.18 -8.40 1.03e+00 9.43e-01 6.66e+01 angle pdb=" C GLY A1744 " pdb=" N PRO A1745 " pdb=" CA PRO A1745 " ideal model delta sigma weight residual 119.78 127.99 -8.21 1.03e+00 9.43e-01 6.36e+01 angle pdb=" C LEU A1878 " pdb=" N PRO A1879 " pdb=" CA PRO A1879 " ideal model delta sigma weight residual 119.56 127.67 -8.11 1.02e+00 9.61e-01 6.32e+01 ... (remaining 19793 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 8454 17.92 - 35.85: 248 35.85 - 53.77: 60 53.77 - 71.69: 38 71.69 - 89.61: 16 Dihedral angle restraints: 8816 sinusoidal: 3686 harmonic: 5130 Sorted by residual: dihedral pdb=" CA GLN A1775 " pdb=" C GLN A1775 " pdb=" N PRO A1776 " pdb=" CA PRO A1776 " ideal model delta harmonic sigma weight residual -180.00 -155.60 -24.40 0 5.00e+00 4.00e-02 2.38e+01 dihedral pdb=" CA ALA A1713 " pdb=" C ALA A1713 " pdb=" N PRO A1714 " pdb=" CA PRO A1714 " ideal model delta harmonic sigma weight residual 180.00 160.31 19.69 0 5.00e+00 4.00e-02 1.55e+01 dihedral pdb=" CA HIS A1952 " pdb=" C HIS A1952 " pdb=" N PRO A1953 " pdb=" CA PRO A1953 " ideal model delta harmonic sigma weight residual 180.00 -161.84 -18.16 0 5.00e+00 4.00e-02 1.32e+01 ... (remaining 8813 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 1213 0.040 - 0.079: 566 0.079 - 0.119: 224 0.119 - 0.159: 96 0.159 - 0.198: 4 Chirality restraints: 2103 Sorted by residual: chirality pdb=" CA PHE A 452 " pdb=" N PHE A 452 " pdb=" C PHE A 452 " pdb=" CB PHE A 452 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.83e-01 chirality pdb=" CG LEU A 448 " pdb=" CB LEU A 448 " pdb=" CD1 LEU A 448 " pdb=" CD2 LEU A 448 " both_signs ideal model delta sigma weight residual False -2.59 -2.76 0.17 2.00e-01 2.50e+01 7.01e-01 chirality pdb=" CA ILE A1738 " pdb=" N ILE A1738 " pdb=" C ILE A1738 " pdb=" CB ILE A1738 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 7.00e-01 ... (remaining 2100 not shown) Planarity restraints: 2589 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A1583 " -0.025 2.00e-02 2.50e+03 1.33e-02 3.54e+00 pdb=" CG TYR A1583 " 0.012 2.00e-02 2.50e+03 pdb=" CD1 TYR A1583 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 TYR A1583 " 0.010 2.00e-02 2.50e+03 pdb=" CE1 TYR A1583 " 0.007 2.00e-02 2.50e+03 pdb=" CE2 TYR A1583 " 0.006 2.00e-02 2.50e+03 pdb=" CZ TYR A1583 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR A1583 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO A 418 " 0.009 2.00e-02 2.50e+03 1.87e-02 3.48e+00 pdb=" C PRO A 418 " -0.032 2.00e-02 2.50e+03 pdb=" O PRO A 418 " 0.012 2.00e-02 2.50e+03 pdb=" N PHE A 419 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 315 " -0.008 2.00e-02 2.50e+03 1.55e-02 2.41e+00 pdb=" C ALA A 315 " 0.027 2.00e-02 2.50e+03 pdb=" O ALA A 315 " -0.010 2.00e-02 2.50e+03 pdb=" N TYR A 316 " -0.009 2.00e-02 2.50e+03 ... (remaining 2586 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 92 2.62 - 3.19: 11729 3.19 - 3.76: 19769 3.76 - 4.33: 28989 4.33 - 4.90: 46050 Nonbonded interactions: 106629 Sorted by model distance: nonbonded pdb=" O ARG A1693 " pdb=" OD1 ASP A1694 " model vdw 2.047 3.040 nonbonded pdb=" NE1 TRP A1818 " pdb=" OG1 THR A1988 " model vdw 2.366 3.120 nonbonded pdb=" OD2 ASP A1121 " pdb=" NZ LYS A1123 " model vdw 2.367 3.120 nonbonded pdb=" OH TYR A1684 " pdb=" OE1 GLU A1748 " model vdw 2.384 3.040 nonbonded pdb=" OD2 ASP A 683 " pdb=" NZ LYS A 826 " model vdw 2.407 3.120 ... (remaining 106624 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 22.840 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: 0.000 Extract box with map and model: 4.430 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 34.390 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.080 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:14.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 76.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6267 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 : 0.011 0.061 14601 Z= 0.749 Angle : 1.257 10.033 19798 Z= 0.880 Chirality : 0.055 0.198 2103 Planarity : 0.004 0.019 2589 Dihedral : 11.287 89.613 5506 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 1.95 Ramachandran Plot: Outliers : 0.28 % Allowed : 2.39 % Favored : 97.32 % Rotamer: Outliers : 0.13 % Allowed : 0.77 % Favored : 99.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.88 % 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: 0.90 (0.19), residues: 1757 helix: -1.57 (0.30), residues: 198 sheet: 1.47 (0.22), residues: 521 loop : 0.72 (0.18), residues: 1038 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP A1786 HIS 0.004 0.001 HIS A 380 PHE 0.013 0.002 PHE A 419 TYR 0.025 0.003 TYR A1583 ARG 0.003 0.000 ARG A1749 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3514 Ramachandran restraints generated. 1757 Oldfield, 0 Emsley, 1757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3514 Ramachandran restraints generated. 1757 Oldfield, 0 Emsley, 1757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 263 time to evaluate : 1.524 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 258 ASN cc_start: 0.6342 (m110) cc_final: 0.6105 (t0) REVERT: A 1048 ARG cc_start: 0.6344 (ttm-80) cc_final: 0.6112 (ttm-80) REVERT: A 1067 GLU cc_start: 0.6372 (mp0) cc_final: 0.6146 (mm-30) REVERT: A 1848 GLU cc_start: 0.3673 (mp0) cc_final: 0.2914 (tp30) outliers start: 2 outliers final: 1 residues processed: 265 average time/residue: 1.3570 time to fit residues: 393.4833 Evaluate side-chains 201 residues out of total 1553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 200 time to evaluate : 1.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1284 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 148 optimal weight: 0.9990 chunk 133 optimal weight: 0.7980 chunk 74 optimal weight: 0.9980 chunk 45 optimal weight: 0.7980 chunk 89 optimal weight: 0.6980 chunk 71 optimal weight: 0.1980 chunk 137 optimal weight: 0.0470 chunk 53 optimal weight: 0.5980 chunk 83 optimal weight: 0.8980 chunk 102 optimal weight: 0.5980 chunk 159 optimal weight: 0.7980 overall best weight: 0.4278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 445 ASN A 612 GLN A 746 HIS ** A 868 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1010 GLN A1186 GLN A1367 GLN ** A1682 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1742 HIS A1930 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6354 moved from start: 0.2300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 14601 Z= 0.241 Angle : 0.645 7.781 19798 Z= 0.342 Chirality : 0.046 0.159 2103 Planarity : 0.005 0.060 2589 Dihedral : 4.837 24.946 1929 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.50 % Favored : 97.44 % Rotamer: Outliers : 2.58 % Allowed : 7.53 % Favored : 89.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.88 % 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: 0.73 (0.19), residues: 1757 helix: 0.16 (0.38), residues: 189 sheet: 1.21 (0.23), residues: 518 loop : 0.26 (0.18), residues: 1050 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 992 HIS 0.006 0.001 HIS A1709 PHE 0.020 0.002 PHE A1181 TYR 0.020 0.002 TYR A1206 ARG 0.006 0.001 ARG A1581 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3514 Ramachandran restraints generated. 1757 Oldfield, 0 Emsley, 1757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3514 Ramachandran restraints generated. 1757 Oldfield, 0 Emsley, 1757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 215 time to evaluate : 1.361 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 338 LYS cc_start: 0.7515 (tppp) cc_final: 0.7275 (tppp) REVERT: A 868 ASN cc_start: 0.7472 (m110) cc_final: 0.7234 (m110) REVERT: A 1067 GLU cc_start: 0.6359 (mp0) cc_final: 0.6109 (mm-30) REVERT: A 1386 PHE cc_start: 0.5435 (t80) cc_final: 0.5122 (t80) REVERT: A 1405 VAL cc_start: 0.8263 (t) cc_final: 0.8047 (p) REVERT: A 1481 PHE cc_start: 0.5075 (t80) cc_final: 0.4656 (t80) REVERT: A 1520 ASP cc_start: 0.6880 (p0) cc_final: 0.6640 (p0) REVERT: A 1693 ARG cc_start: 0.5968 (OUTLIER) cc_final: 0.5637 (ptm160) REVERT: A 1748 GLU cc_start: 0.5808 (mt-10) cc_final: 0.5005 (tt0) REVERT: A 1757 GLN cc_start: 0.6125 (mt0) cc_final: 0.5682 (pm20) REVERT: A 1848 GLU cc_start: 0.3384 (mp0) cc_final: 0.2955 (mm-30) REVERT: A 1912 ASP cc_start: 0.3102 (OUTLIER) cc_final: 0.2528 (t0) outliers start: 40 outliers final: 11 residues processed: 232 average time/residue: 1.3818 time to fit residues: 353.0593 Evaluate side-chains 207 residues out of total 1553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 194 time to evaluate : 1.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 ARG Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 482 MET Chi-restraints excluded: chain A residue 1036 THR Chi-restraints excluded: chain A residue 1141 THR Chi-restraints excluded: chain A residue 1143 SER Chi-restraints excluded: chain A residue 1206 TYR Chi-restraints excluded: chain A residue 1284 ILE Chi-restraints excluded: chain A residue 1390 MET Chi-restraints excluded: chain A residue 1693 ARG Chi-restraints excluded: chain A residue 1761 VAL Chi-restraints excluded: chain A residue 1877 TYR Chi-restraints excluded: chain A residue 1912 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 88 optimal weight: 0.9980 chunk 49 optimal weight: 0.9980 chunk 133 optimal weight: 0.9980 chunk 108 optimal weight: 0.9990 chunk 44 optimal weight: 0.6980 chunk 160 optimal weight: 0.3980 chunk 172 optimal weight: 0.4980 chunk 142 optimal weight: 1.9990 chunk 158 optimal weight: 0.9990 chunk 54 optimal weight: 2.9990 chunk 128 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 255 HIS A 722 GLN A 746 HIS A 868 ASN A1196 ASN A1682 GLN A1909 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6466 moved from start: 0.3264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 14601 Z= 0.341 Angle : 0.703 7.974 19798 Z= 0.375 Chirality : 0.048 0.184 2103 Planarity : 0.007 0.076 2589 Dihedral : 5.380 25.691 1929 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.87 % Favored : 96.07 % Rotamer: Outliers : 2.96 % Allowed : 9.79 % Favored : 87.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.88 % 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: -0.28 (0.19), residues: 1757 helix: -0.36 (0.37), residues: 199 sheet: 0.57 (0.22), residues: 525 loop : -0.52 (0.18), residues: 1033 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A1692 HIS 0.009 0.001 HIS A1183 PHE 0.022 0.003 PHE A1258 TYR 0.025 0.003 TYR A1157 ARG 0.008 0.001 ARG A1809 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3514 Ramachandran restraints generated. 1757 Oldfield, 0 Emsley, 1757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3514 Ramachandran restraints generated. 1757 Oldfield, 0 Emsley, 1757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 210 time to evaluate : 1.550 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 253 ARG cc_start: 0.7486 (OUTLIER) cc_final: 0.7188 (mtp85) REVERT: A 338 LYS cc_start: 0.7468 (tppp) cc_final: 0.7216 (tppp) REVERT: A 570 GLN cc_start: 0.7300 (pp30) cc_final: 0.6733 (pp30) REVERT: A 742 GLN cc_start: 0.7460 (mt0) cc_final: 0.7184 (mt0) REVERT: A 847 ARG cc_start: 0.7867 (mmm160) cc_final: 0.7663 (mtt180) REVERT: A 942 MET cc_start: 0.6805 (OUTLIER) cc_final: 0.6592 (tpt) REVERT: A 1167 MET cc_start: 0.4315 (mpp) cc_final: 0.4114 (mpp) REVERT: A 1481 PHE cc_start: 0.5001 (t80) cc_final: 0.4647 (t80) REVERT: A 1520 ASP cc_start: 0.7361 (p0) cc_final: 0.7157 (p0) REVERT: A 1748 GLU cc_start: 0.5924 (mt-10) cc_final: 0.5187 (mt-10) REVERT: A 1757 GLN cc_start: 0.6404 (mt0) cc_final: 0.5949 (pm20) REVERT: A 1848 GLU cc_start: 0.3021 (mp0) cc_final: 0.2739 (tp30) REVERT: A 1851 LYS cc_start: 0.4969 (OUTLIER) cc_final: 0.4695 (tttp) REVERT: A 1912 ASP cc_start: 0.3277 (OUTLIER) cc_final: 0.2821 (t0) outliers start: 46 outliers final: 15 residues processed: 230 average time/residue: 1.4445 time to fit residues: 362.6979 Evaluate side-chains 207 residues out of total 1553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 188 time to evaluate : 1.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 ARG Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 455 MET Chi-restraints excluded: chain A residue 482 MET Chi-restraints excluded: chain A residue 777 LEU Chi-restraints excluded: chain A residue 942 MET Chi-restraints excluded: chain A residue 947 LEU Chi-restraints excluded: chain A residue 1036 THR Chi-restraints excluded: chain A residue 1141 THR Chi-restraints excluded: chain A residue 1143 SER Chi-restraints excluded: chain A residue 1206 TYR Chi-restraints excluded: chain A residue 1284 ILE Chi-restraints excluded: chain A residue 1643 LEU Chi-restraints excluded: chain A residue 1727 GLU Chi-restraints excluded: chain A residue 1761 VAL Chi-restraints excluded: chain A residue 1851 LYS Chi-restraints excluded: chain A residue 1877 TYR Chi-restraints excluded: chain A residue 1912 ASP Chi-restraints excluded: chain A residue 1997 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/phenix/phenix/programs/real_space_refine.py", line 213, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 59.7042 > 50: distance: 19 - 130: 20.950 distance: 29 - 133: 14.106 distance: 106 - 111: 15.210 distance: 111 - 112: 13.111 distance: 112 - 113: 16.011 distance: 112 - 115: 4.391 distance: 113 - 114: 8.694 distance: 113 - 120: 14.997 distance: 115 - 116: 19.616 distance: 116 - 117: 14.254 distance: 117 - 118: 7.450 distance: 117 - 119: 9.131 distance: 120 - 121: 12.186 distance: 121 - 122: 15.620 distance: 121 - 124: 21.065 distance: 122 - 123: 27.915 distance: 122 - 130: 11.700 distance: 124 - 125: 36.604 distance: 125 - 126: 23.508 distance: 125 - 127: 5.985 distance: 126 - 128: 3.486 distance: 127 - 129: 38.694 distance: 128 - 129: 21.882 distance: 130 - 131: 27.515 distance: 131 - 132: 11.970 distance: 131 - 134: 21.511 distance: 132 - 133: 18.504 distance: 132 - 137: 17.904 distance: 134 - 135: 28.707 distance: 134 - 136: 22.523 distance: 137 - 138: 14.408 distance: 137 - 271: 18.469 distance: 138 - 139: 6.117 distance: 138 - 141: 8.593 distance: 139 - 140: 9.603 distance: 139 - 146: 10.499 distance: 140 - 268: 9.336 distance: 141 - 142: 11.934 distance: 142 - 143: 4.547 distance: 143 - 144: 13.789 distance: 143 - 145: 14.014 distance: 146 - 147: 13.632 distance: 147 - 148: 3.772 distance: 147 - 150: 17.633 distance: 148 - 152: 26.991 distance: 150 - 151: 25.866 distance: 152 - 153: 20.876 distance: 152 - 258: 30.989 distance: 153 - 154: 14.585 distance: 153 - 156: 14.712 distance: 154 - 155: 10.250 distance: 155 - 255: 10.084 distance: 156 - 157: 21.772 distance: 157 - 158: 25.382 distance: 158 - 159: 15.256 distance: 159 - 160: 10.076 distance: 160 - 161: 17.836 distance: 160 - 162: 17.246 distance: 163 - 164: 8.469 distance: 163 - 169: 5.374 distance: 164 - 165: 18.015 distance: 164 - 167: 17.746 distance: 165 - 166: 18.098 distance: 165 - 170: 10.792 distance: 167 - 168: 27.042 distance: 168 - 169: 21.271 distance: 170 - 171: 17.449 distance: 170 - 245: 14.106 distance: 171 - 172: 19.047 distance: 171 - 174: 17.173 distance: 172 - 173: 27.143 distance: 172 - 178: 17.901 distance: 174 - 175: 11.680 distance: 175 - 176: 36.036 distance: 175 - 177: 5.932 distance: 178 - 179: 8.138 distance: 179 - 180: 18.228 distance: 179 - 182: 14.194 distance: 180 - 181: 15.464 distance: 180 - 190: 17.661 distance: 182 - 183: 22.099 distance: 183 - 184: 5.964 distance: 183 - 185: 46.051 distance: 184 - 186: 19.745 distance: 185 - 187: 18.358 distance: 186 - 188: 41.918 distance: 187 - 188: 18.769 distance: 188 - 189: 16.262 distance: 190 - 191: 38.295 distance: 191 - 192: 32.831 distance: 191 - 194: 22.064 distance: 192 - 193: 7.929 distance: 192 - 196: 6.932 distance: 194 - 195: 15.219