Starting phenix.real_space_refine on Thu Sep 18 05:38:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b8k_44348/09_2025/9b8k_44348.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b8k_44348/09_2025/9b8k_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_44348/09_2025/9b8k_44348.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b8k_44348/09_2025/9b8k_44348.map" model { file = "/net/cci-nas-00/data/ceres_data/9b8k_44348/09_2025/9b8k_44348.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b8k_44348/09_2025/9b8k_44348.cif" } resolution = 2.96 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= 0.013 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 3.56, per 1000 atoms: 0.25 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: 1.13 Conformation dependent library (CDL) restraints added in 673.1 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.65 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: 3.37 Time building geometry restraints manager: 1.55 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: 12.880 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: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 15.670 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.860 ------------------------------------------------------------------------------- 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= 0.631 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 : 1.91 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 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: 0.90 (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 ARG 0.003 0.000 ARG A1749 TYR 0.025 0.003 TYR A1583 PHE 0.013 0.002 PHE A 419 TRP 0.018 0.003 TRP A1786 HIS 0.004 0.001 HIS A 380 Details of bonding type rmsd covalent geometry : bond 0.01145 (14601) covalent geometry : angle 1.25736 (19798) hydrogen bonds : bond 0.25270 ( 364) hydrogen bonds : angle 8.52317 ( 882) *********************** 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 : 0.544 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 258 ASN cc_start: 0.6342 (m110) cc_final: 0.6105 (t0) REVERT: A 399 MET cc_start: 0.6680 (mmm) cc_final: 0.6480 (mmm) REVERT: A 1048 ARG cc_start: 0.6344 (ttm-80) cc_final: 0.6113 (ttm-80) REVERT: A 1067 GLU cc_start: 0.6372 (mp0) cc_final: 0.6145 (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: 0.7028 time to fit residues: 202.7754 Evaluate side-chains 202 residues out of total 1553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 201 time to evaluate : 0.563 ------------------------------------------------------------------------------- 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 98 optimal weight: 0.8980 chunk 107 optimal weight: 0.0170 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 0.5980 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 9.9990 chunk 149 optimal weight: 0.9990 overall best weight: 0.6418 ------------------------------------------------------------------------------- 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 722 GLN A 746 HIS A 868 ASN A1010 GLN A1186 GLN A1367 GLN A1682 GLN A1742 HIS A1930 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4579 r_free = 0.4579 target = 0.205211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4339 r_free = 0.4339 target = 0.181569 restraints weight = 24656.577| |-----------------------------------------------------------------------------| r_work (start): 0.4314 rms_B_bonded: 2.61 r_work: 0.4187 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.4187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6367 moved from start: 0.2539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 14601 Z= 0.220 Angle : 0.713 7.834 19798 Z= 0.380 Chirality : 0.048 0.185 2103 Planarity : 0.006 0.068 2589 Dihedral : 5.227 26.773 1929 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.68 % Favored : 97.27 % Rotamer: Outliers : 2.51 % Allowed : 7.21 % Favored : 90.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.88 % 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: 0.32 (0.19), residues: 1757 helix: -0.02 (0.38), residues: 189 sheet: 1.03 (0.23), residues: 514 loop : -0.10 (0.18), residues: 1054 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A1809 TYR 0.024 0.002 TYR A1206 PHE 0.025 0.003 PHE A1181 TRP 0.020 0.002 TRP A 999 HIS 0.009 0.001 HIS A1709 Details of bonding type rmsd covalent geometry : bond 0.00501 (14601) covalent geometry : angle 0.71289 (19798) hydrogen bonds : bond 0.06501 ( 364) hydrogen bonds : angle 6.46882 ( 882) *********************** 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 256 residues out of total 1553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 217 time to evaluate : 0.631 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 338 LYS cc_start: 0.7442 (tppp) cc_final: 0.7048 (tppp) REVERT: A 738 GLN cc_start: 0.7816 (OUTLIER) cc_final: 0.7602 (mm-40) REVERT: A 847 ARG cc_start: 0.7833 (OUTLIER) cc_final: 0.6702 (mtm180) REVERT: A 1094 TRP cc_start: 0.7164 (m100) cc_final: 0.6802 (m100) REVERT: A 1360 GLU cc_start: 0.5784 (mp0) cc_final: 0.5477 (mp0) REVERT: A 1386 PHE cc_start: 0.5438 (t80) cc_final: 0.5236 (t80) REVERT: A 1405 VAL cc_start: 0.8242 (t) cc_final: 0.7945 (p) REVERT: A 1481 PHE cc_start: 0.5088 (t80) cc_final: 0.4712 (t80) REVERT: A 1693 ARG cc_start: 0.5787 (OUTLIER) cc_final: 0.5501 (ptm160) REVERT: A 1748 GLU cc_start: 0.5710 (mt-10) cc_final: 0.5188 (mt-10) REVERT: A 1848 GLU cc_start: 0.3772 (mp0) cc_final: 0.3215 (mm-30) REVERT: A 1912 ASP cc_start: 0.3611 (OUTLIER) cc_final: 0.2984 (t0) outliers start: 39 outliers final: 12 residues processed: 237 average time/residue: 0.7018 time to fit residues: 181.6697 Evaluate side-chains 211 residues out of total 1553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 195 time to evaluate : 0.585 ------------------------------------------------------------------------------- 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 738 GLN Chi-restraints excluded: chain A residue 847 ARG 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 1158 MET Chi-restraints excluded: chain A residue 1206 TYR Chi-restraints excluded: chain A residue 1284 ILE 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 Chi-restraints excluded: chain A residue 1930 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 172 optimal weight: 0.9980 chunk 100 optimal weight: 0.7980 chunk 130 optimal weight: 0.3980 chunk 124 optimal weight: 0.5980 chunk 111 optimal weight: 0.6980 chunk 32 optimal weight: 0.9980 chunk 115 optimal weight: 0.5980 chunk 83 optimal weight: 0.6980 chunk 68 optimal weight: 0.0970 chunk 41 optimal weight: 0.2980 chunk 173 optimal weight: 0.0070 overall best weight: 0.2796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 746 HIS A 868 ASN A1196 ASN A1682 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4605 r_free = 0.4605 target = 0.207829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4360 r_free = 0.4360 target = 0.183567 restraints weight = 24944.164| |-----------------------------------------------------------------------------| r_work (start): 0.4340 rms_B_bonded: 2.62 r_work: 0.4222 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.4222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6316 moved from start: 0.2925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 14601 Z= 0.122 Angle : 0.554 8.166 19798 Z= 0.295 Chirality : 0.043 0.183 2103 Planarity : 0.005 0.065 2589 Dihedral : 4.657 22.812 1929 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.96 % Favored : 96.98 % Rotamer: Outliers : 2.45 % Allowed : 10.11 % Favored : 87.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.88 % 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: 0.30 (0.20), residues: 1757 helix: 0.33 (0.39), residues: 189 sheet: 0.86 (0.23), residues: 531 loop : -0.12 (0.18), residues: 1037 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1581 TYR 0.016 0.001 TYR A 336 PHE 0.012 0.001 PHE A 642 TRP 0.012 0.001 TRP A 992 HIS 0.004 0.001 HIS A1753 Details of bonding type rmsd covalent geometry : bond 0.00269 (14601) covalent geometry : angle 0.55382 (19798) hydrogen bonds : bond 0.04986 ( 364) hydrogen bonds : angle 5.87182 ( 882) *********************** 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 237 residues out of total 1553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 199 time to evaluate : 0.536 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 253 ARG cc_start: 0.7505 (OUTLIER) cc_final: 0.7218 (mtp85) REVERT: A 399 MET cc_start: 0.6134 (mmm) cc_final: 0.5824 (tmm) REVERT: A 1323 GLN cc_start: 0.6824 (tp40) cc_final: 0.6543 (mm-40) REVERT: A 1386 PHE cc_start: 0.5278 (t80) cc_final: 0.5077 (t80) REVERT: A 1481 PHE cc_start: 0.5034 (t80) cc_final: 0.4810 (t80) REVERT: A 1542 ILE cc_start: 0.7721 (pt) cc_final: 0.7469 (mp) REVERT: A 1607 ILE cc_start: 0.6133 (mt) cc_final: 0.5850 (pp) REVERT: A 1693 ARG cc_start: 0.5812 (OUTLIER) cc_final: 0.5531 (ptm160) REVERT: A 1748 GLU cc_start: 0.5565 (mt-10) cc_final: 0.5206 (mt-10) REVERT: A 1848 GLU cc_start: 0.3511 (mp0) cc_final: 0.2930 (tp30) outliers start: 38 outliers final: 15 residues processed: 215 average time/residue: 0.6983 time to fit residues: 163.4165 Evaluate side-chains 200 residues out of total 1553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 183 time to evaluate : 0.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 ARG Chi-restraints excluded: chain A residue 317 LEU 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 617 ILE Chi-restraints excluded: chain A residue 740 LEU Chi-restraints excluded: chain A residue 947 LEU Chi-restraints excluded: chain A residue 1112 LEU 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 1693 ARG Chi-restraints excluded: chain A residue 1727 GLU Chi-restraints excluded: chain A residue 1761 VAL Chi-restraints excluded: chain A residue 1877 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 117 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 155 optimal weight: 0.0570 chunk 3 optimal weight: 1.9990 chunk 29 optimal weight: 0.7980 chunk 121 optimal weight: 0.7980 chunk 129 optimal weight: 2.9990 chunk 123 optimal weight: 0.9980 chunk 170 optimal weight: 0.3980 chunk 161 optimal weight: 0.3980 chunk 46 optimal weight: 0.9980 overall best weight: 0.4898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 255 HIS A 746 HIS A1196 ASN A1682 GLN A1691 GLN A1909 GLN A1930 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4584 r_free = 0.4584 target = 0.205143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4349 r_free = 0.4349 target = 0.181708 restraints weight = 24533.785| |-----------------------------------------------------------------------------| r_work (start): 0.4325 rms_B_bonded: 2.35 r_work: 0.4203 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.4203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6365 moved from start: 0.3395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 14601 Z= 0.166 Angle : 0.605 8.009 19798 Z= 0.320 Chirality : 0.045 0.169 2103 Planarity : 0.006 0.070 2589 Dihedral : 4.927 24.472 1929 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.59 % Favored : 96.36 % Rotamer: Outliers : 2.32 % Allowed : 11.85 % Favored : 85.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.88 % 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: -0.19 (0.20), residues: 1757 helix: -0.18 (0.38), residues: 206 sheet: 0.57 (0.22), residues: 545 loop : -0.47 (0.19), residues: 1006 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1581 TYR 0.019 0.002 TYR A1157 PHE 0.018 0.002 PHE A1525 TRP 0.012 0.002 TRP A1692 HIS 0.006 0.001 HIS A1183 Details of bonding type rmsd covalent geometry : bond 0.00380 (14601) covalent geometry : angle 0.60472 (19798) hydrogen bonds : bond 0.05245 ( 364) hydrogen bonds : angle 5.93716 ( 882) *********************** REFINEMENT MACRO_CYCLE 4 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 234 residues out of total 1553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 198 time to evaluate : 0.560 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 338 LYS cc_start: 0.7404 (tppp) cc_final: 0.6980 (tppp) REVERT: A 399 MET cc_start: 0.6037 (mmm) cc_final: 0.5765 (tmm) REVERT: A 803 ARG cc_start: 0.7457 (OUTLIER) cc_final: 0.7083 (mtt180) REVERT: A 1542 ILE cc_start: 0.7772 (pt) cc_final: 0.7504 (mp) REVERT: A 1607 ILE cc_start: 0.6246 (mt) cc_final: 0.6010 (pp) REVERT: A 1693 ARG cc_start: 0.5838 (ttp-170) cc_final: 0.5502 (ptm160) REVERT: A 1748 GLU cc_start: 0.5628 (mt-10) cc_final: 0.5146 (mt-10) REVERT: A 1848 GLU cc_start: 0.3500 (mp0) cc_final: 0.2988 (tp30) REVERT: A 1851 LYS cc_start: 0.5363 (OUTLIER) cc_final: 0.5162 (tttp) REVERT: A 1912 ASP cc_start: 0.3692 (OUTLIER) cc_final: 0.3203 (t0) outliers start: 36 outliers final: 16 residues processed: 218 average time/residue: 0.7117 time to fit residues: 169.2011 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 : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 317 LEU 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 803 ARG Chi-restraints excluded: chain A residue 947 LEU Chi-restraints excluded: chain A residue 1036 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 1930 ASN Chi-restraints excluded: chain A residue 1997 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 63 optimal weight: 0.6980 chunk 117 optimal weight: 0.9980 chunk 85 optimal weight: 3.9990 chunk 133 optimal weight: 0.0980 chunk 101 optimal weight: 0.9990 chunk 173 optimal weight: 0.4980 chunk 44 optimal weight: 0.5980 chunk 51 optimal weight: 0.4980 chunk 121 optimal weight: 0.8980 chunk 79 optimal weight: 0.9980 chunk 162 optimal weight: 0.0000 overall best weight: 0.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 411 ASN A1196 ASN A1682 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4591 r_free = 0.4591 target = 0.206198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4349 r_free = 0.4349 target = 0.182139 restraints weight = 24578.528| |-----------------------------------------------------------------------------| r_work (start): 0.4323 rms_B_bonded: 2.56 r_work: 0.4209 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.4209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6354 moved from start: 0.3621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14601 Z= 0.131 Angle : 0.565 9.372 19798 Z= 0.297 Chirality : 0.043 0.173 2103 Planarity : 0.005 0.065 2589 Dihedral : 4.742 23.598 1929 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.93 % Favored : 96.02 % Rotamer: Outliers : 2.90 % Allowed : 12.23 % Favored : 84.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.88 % 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: -0.21 (0.20), residues: 1757 helix: 0.00 (0.38), residues: 200 sheet: 0.47 (0.22), residues: 545 loop : -0.47 (0.19), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1581 TYR 0.014 0.001 TYR A 336 PHE 0.016 0.001 PHE A1525 TRP 0.010 0.001 TRP A1786 HIS 0.005 0.001 HIS A1753 Details of bonding type rmsd covalent geometry : bond 0.00297 (14601) covalent geometry : angle 0.56506 (19798) hydrogen bonds : bond 0.04639 ( 364) hydrogen bonds : angle 5.70183 ( 882) *********************** REFINEMENT MACRO_CYCLE 5 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 238 residues out of total 1553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 193 time to evaluate : 0.519 Fit side-chains revert: symmetry clash REVERT: A 338 LYS cc_start: 0.7400 (tppp) cc_final: 0.6982 (tppp) REVERT: A 399 MET cc_start: 0.6029 (mmm) cc_final: 0.5751 (mmm) REVERT: A 738 GLN cc_start: 0.7625 (OUTLIER) cc_final: 0.6295 (mm-40) REVERT: A 785 GLU cc_start: 0.7561 (OUTLIER) cc_final: 0.7331 (tp30) REVERT: A 803 ARG cc_start: 0.7452 (OUTLIER) cc_final: 0.7096 (mtt180) REVERT: A 1096 ARG cc_start: 0.6403 (ttt180) cc_final: 0.5855 (ttt180) REVERT: A 1335 GLU cc_start: 0.6605 (mm-30) cc_final: 0.6212 (mm-30) REVERT: A 1542 ILE cc_start: 0.7770 (pt) cc_final: 0.7507 (mp) REVERT: A 1607 ILE cc_start: 0.6173 (mt) cc_final: 0.5921 (pp) REVERT: A 1693 ARG cc_start: 0.5702 (ttp-170) cc_final: 0.5319 (ptm160) REVERT: A 1748 GLU cc_start: 0.5667 (mt-10) cc_final: 0.5287 (mt-10) REVERT: A 1848 GLU cc_start: 0.3361 (mp0) cc_final: 0.2925 (tp30) REVERT: A 1912 ASP cc_start: 0.3585 (OUTLIER) cc_final: 0.3161 (t0) REVERT: A 1987 MET cc_start: 0.1338 (tpp) cc_final: 0.1072 (tmt) outliers start: 45 outliers final: 19 residues processed: 216 average time/residue: 0.7080 time to fit residues: 166.9945 Evaluate side-chains 209 residues out of total 1553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 186 time to evaluate : 0.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 455 MET Chi-restraints excluded: chain A residue 482 MET Chi-restraints excluded: chain A residue 617 ILE Chi-restraints excluded: chain A residue 626 MET Chi-restraints excluded: chain A residue 738 GLN Chi-restraints excluded: chain A residue 777 LEU Chi-restraints excluded: chain A residue 785 GLU Chi-restraints excluded: chain A residue 803 ARG 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 1390 MET 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 1877 TYR Chi-restraints excluded: chain A residue 1912 ASP Chi-restraints excluded: chain A residue 1997 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 82 optimal weight: 0.7980 chunk 134 optimal weight: 0.9980 chunk 121 optimal weight: 0.0050 chunk 95 optimal weight: 0.9980 chunk 78 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 46 optimal weight: 0.8980 chunk 21 optimal weight: 0.6980 chunk 123 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 71 optimal weight: 0.9990 overall best weight: 0.6794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 411 ASN A1153 HIS A1196 ASN A1377 ASN A1682 GLN A1930 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4564 r_free = 0.4564 target = 0.203716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4335 r_free = 0.4335 target = 0.180697 restraints weight = 24256.511| |-----------------------------------------------------------------------------| r_work (start): 0.4309 rms_B_bonded: 2.42 r_work: 0.4175 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.4175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6430 moved from start: 0.4007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 14601 Z= 0.212 Angle : 0.680 11.547 19798 Z= 0.357 Chirality : 0.047 0.184 2103 Planarity : 0.006 0.096 2589 Dihedral : 5.314 25.132 1927 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.89 % Favored : 95.05 % Rotamer: Outliers : 3.16 % Allowed : 12.62 % Favored : 84.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.88 % 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: -0.61 (0.19), residues: 1757 helix: -0.09 (0.38), residues: 190 sheet: 0.24 (0.23), residues: 526 loop : -0.79 (0.18), residues: 1041 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A1581 TYR 0.021 0.002 TYR A1505 PHE 0.026 0.002 PHE A1908 TRP 0.018 0.002 TRP A1692 HIS 0.008 0.001 HIS A1183 Details of bonding type rmsd covalent geometry : bond 0.00493 (14601) covalent geometry : angle 0.68014 (19798) hydrogen bonds : bond 0.05840 ( 364) hydrogen bonds : angle 6.21062 ( 882) *********************** REFINEMENT MACRO_CYCLE 6 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: 49 poor density : 206 time to evaluate : 0.574 Fit side-chains revert: symmetry clash REVERT: A 272 ASP cc_start: 0.6980 (m-30) cc_final: 0.6648 (m-30) REVERT: A 395 ASP cc_start: 0.6282 (OUTLIER) cc_final: 0.5556 (t0) REVERT: A 399 MET cc_start: 0.6110 (mmm) cc_final: 0.5819 (mmm) REVERT: A 411 ASN cc_start: 0.3337 (OUTLIER) cc_final: 0.2811 (t0) REVERT: A 584 GLU cc_start: 0.7165 (OUTLIER) cc_final: 0.6885 (mp0) REVERT: A 742 GLN cc_start: 0.7093 (mt0) cc_final: 0.6835 (mt0) REVERT: A 785 GLU cc_start: 0.7653 (OUTLIER) cc_final: 0.7334 (tp30) REVERT: A 803 ARG cc_start: 0.7469 (OUTLIER) cc_final: 0.7215 (mtt180) REVERT: A 1128 MET cc_start: 0.0676 (ppp) cc_final: -0.0743 (ppp) REVERT: A 1279 ARG cc_start: 0.8134 (OUTLIER) cc_final: 0.7252 (mpt-90) REVERT: A 1335 GLU cc_start: 0.6913 (mm-30) cc_final: 0.6613 (mp0) REVERT: A 1542 ILE cc_start: 0.7826 (pt) cc_final: 0.7613 (mp) REVERT: A 1659 ILE cc_start: 0.7026 (OUTLIER) cc_final: 0.6388 (mp) REVERT: A 1693 ARG cc_start: 0.6026 (ttp-170) cc_final: 0.5751 (ptm160) REVERT: A 1730 ILE cc_start: 0.5036 (OUTLIER) cc_final: 0.4642 (pt) REVERT: A 1737 ARG cc_start: 0.5761 (mmm-85) cc_final: 0.4635 (pmt170) REVERT: A 1783 LEU cc_start: 0.5428 (tm) cc_final: 0.5105 (tt) REVERT: A 1844 MET cc_start: 0.0423 (ttm) cc_final: 0.0142 (ttt) REVERT: A 1848 GLU cc_start: 0.3554 (mp0) cc_final: 0.2883 (tp30) REVERT: A 1905 ARG cc_start: 0.1648 (OUTLIER) cc_final: 0.0841 (ptp-170) REVERT: A 1908 PHE cc_start: 0.0124 (OUTLIER) cc_final: -0.1688 (m-80) REVERT: A 1912 ASP cc_start: 0.3775 (OUTLIER) cc_final: 0.3270 (t0) REVERT: A 1987 MET cc_start: 0.2067 (tpp) cc_final: 0.1681 (tmt) outliers start: 49 outliers final: 20 residues processed: 233 average time/residue: 0.7009 time to fit residues: 178.2636 Evaluate side-chains 229 residues out of total 1553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 198 time to evaluate : 0.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 395 ASP Chi-restraints excluded: chain A residue 411 ASN Chi-restraints excluded: chain A residue 455 MET Chi-restraints excluded: chain A residue 482 MET Chi-restraints excluded: chain A residue 584 GLU Chi-restraints excluded: chain A residue 617 ILE Chi-restraints excluded: chain A residue 626 MET Chi-restraints excluded: chain A residue 740 LEU Chi-restraints excluded: chain A residue 777 LEU Chi-restraints excluded: chain A residue 785 GLU Chi-restraints excluded: chain A residue 803 ARG Chi-restraints excluded: chain A residue 1036 THR Chi-restraints excluded: chain A residue 1206 TYR Chi-restraints excluded: chain A residue 1279 ARG Chi-restraints excluded: chain A residue 1284 ILE Chi-restraints excluded: chain A residue 1405 VAL Chi-restraints excluded: chain A residue 1643 LEU Chi-restraints excluded: chain A residue 1659 ILE Chi-restraints excluded: chain A residue 1727 GLU Chi-restraints excluded: chain A residue 1730 ILE Chi-restraints excluded: chain A residue 1761 VAL Chi-restraints excluded: chain A residue 1854 THR Chi-restraints excluded: chain A residue 1877 TYR Chi-restraints excluded: chain A residue 1905 ARG Chi-restraints excluded: chain A residue 1908 PHE Chi-restraints excluded: chain A residue 1912 ASP Chi-restraints excluded: chain A residue 1930 ASN Chi-restraints excluded: chain A residue 1997 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 14 optimal weight: 0.9990 chunk 131 optimal weight: 0.4980 chunk 60 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 105 optimal weight: 0.6980 chunk 123 optimal weight: 0.9990 chunk 166 optimal weight: 0.6980 chunk 172 optimal weight: 0.7980 chunk 83 optimal weight: 2.9990 chunk 94 optimal weight: 0.6980 chunk 32 optimal weight: 0.1980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 411 ASN A1193 ASN A1196 ASN A1323 GLN A1682 GLN A1930 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4567 r_free = 0.4567 target = 0.203896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4333 r_free = 0.4333 target = 0.181127 restraints weight = 24319.347| |-----------------------------------------------------------------------------| r_work (start): 0.4313 rms_B_bonded: 2.63 r_work: 0.4170 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.4170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6435 moved from start: 0.4132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 14601 Z= 0.183 Angle : 0.654 9.610 19798 Z= 0.341 Chirality : 0.046 0.181 2103 Planarity : 0.006 0.085 2589 Dihedral : 5.208 24.680 1927 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.24 % Favored : 94.71 % Rotamer: Outliers : 3.03 % Allowed : 13.46 % Favored : 83.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.88 % 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: -0.72 (0.19), residues: 1757 helix: -0.06 (0.38), residues: 190 sheet: 0.14 (0.23), residues: 528 loop : -0.88 (0.18), residues: 1039 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A1048 TYR 0.017 0.002 TYR A1505 PHE 0.020 0.002 PHE A1908 TRP 0.022 0.002 TRP A 992 HIS 0.010 0.001 HIS A1753 Details of bonding type rmsd covalent geometry : bond 0.00427 (14601) covalent geometry : angle 0.65404 (19798) hydrogen bonds : bond 0.05380 ( 364) hydrogen bonds : angle 6.08343 ( 882) *********************** REFINEMENT MACRO_CYCLE 7 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 246 residues out of total 1553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 199 time to evaluate : 0.579 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 272 ASP cc_start: 0.7087 (m-30) cc_final: 0.6737 (m-30) REVERT: A 395 ASP cc_start: 0.6272 (OUTLIER) cc_final: 0.5569 (t0) REVERT: A 399 MET cc_start: 0.6137 (mmm) cc_final: 0.5817 (mmm) REVERT: A 411 ASN cc_start: 0.3261 (OUTLIER) cc_final: 0.2737 (t0) REVERT: A 785 GLU cc_start: 0.7512 (OUTLIER) cc_final: 0.7296 (tp30) REVERT: A 1128 MET cc_start: 0.0727 (ppp) cc_final: -0.0604 (ppp) REVERT: A 1335 GLU cc_start: 0.6975 (mm-30) cc_final: 0.6570 (mm-30) REVERT: A 1542 ILE cc_start: 0.7837 (pt) cc_final: 0.7614 (mp) REVERT: A 1659 ILE cc_start: 0.6886 (OUTLIER) cc_final: 0.6248 (mp) REVERT: A 1693 ARG cc_start: 0.6150 (ttp-170) cc_final: 0.5774 (ptm-80) REVERT: A 1737 ARG cc_start: 0.5773 (mmm-85) cc_final: 0.4590 (pmt170) REVERT: A 1844 MET cc_start: 0.0273 (ttm) cc_final: -0.0003 (ttt) REVERT: A 1848 GLU cc_start: 0.3505 (mp0) cc_final: 0.2847 (tp30) REVERT: A 1905 ARG cc_start: 0.1664 (OUTLIER) cc_final: 0.0809 (ptp-170) REVERT: A 1908 PHE cc_start: -0.0055 (OUTLIER) cc_final: -0.1895 (m-80) REVERT: A 1912 ASP cc_start: 0.3491 (OUTLIER) cc_final: 0.3115 (t0) REVERT: A 1987 MET cc_start: 0.1842 (tpp) cc_final: 0.1465 (tmt) outliers start: 47 outliers final: 21 residues processed: 223 average time/residue: 0.7157 time to fit residues: 173.9896 Evaluate side-chains 221 residues out of total 1553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 193 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 395 ASP Chi-restraints excluded: chain A residue 411 ASN Chi-restraints excluded: chain A residue 455 MET Chi-restraints excluded: chain A residue 617 ILE Chi-restraints excluded: chain A residue 626 MET Chi-restraints excluded: chain A residue 740 LEU Chi-restraints excluded: chain A residue 777 LEU Chi-restraints excluded: chain A residue 785 GLU Chi-restraints excluded: chain A residue 984 ASP Chi-restraints excluded: chain A residue 1036 THR Chi-restraints excluded: chain A residue 1206 TYR Chi-restraints excluded: chain A residue 1323 GLN Chi-restraints excluded: chain A residue 1405 VAL Chi-restraints excluded: chain A residue 1554 LEU Chi-restraints excluded: chain A residue 1643 LEU Chi-restraints excluded: chain A residue 1659 ILE Chi-restraints excluded: chain A residue 1727 GLU Chi-restraints excluded: chain A residue 1761 VAL Chi-restraints excluded: chain A residue 1785 MET Chi-restraints excluded: chain A residue 1854 THR Chi-restraints excluded: chain A residue 1877 TYR Chi-restraints excluded: chain A residue 1905 ARG Chi-restraints excluded: chain A residue 1908 PHE Chi-restraints excluded: chain A residue 1912 ASP Chi-restraints excluded: chain A residue 1997 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 90 optimal weight: 3.9990 chunk 64 optimal weight: 0.8980 chunk 71 optimal weight: 0.0980 chunk 32 optimal weight: 0.0370 chunk 65 optimal weight: 0.5980 chunk 33 optimal weight: 0.0000 chunk 4 optimal weight: 0.0870 chunk 52 optimal weight: 0.8980 chunk 82 optimal weight: 0.9990 chunk 158 optimal weight: 0.9980 chunk 63 optimal weight: 0.6980 overall best weight: 0.1640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 411 ASN A 742 GLN A1193 ASN A1323 GLN ** A1682 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4596 r_free = 0.4596 target = 0.206596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4357 r_free = 0.4357 target = 0.182963 restraints weight = 24599.992| |-----------------------------------------------------------------------------| r_work (start): 0.4335 rms_B_bonded: 2.64 r_work: 0.4210 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.4210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6347 moved from start: 0.4158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 14601 Z= 0.111 Angle : 0.582 11.754 19798 Z= 0.299 Chirality : 0.044 0.171 2103 Planarity : 0.005 0.072 2589 Dihedral : 4.666 22.454 1927 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.81 % Favored : 96.13 % Rotamer: Outliers : 1.87 % Allowed : 14.62 % Favored : 83.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.88 % 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: -0.54 (0.20), residues: 1757 helix: 0.03 (0.38), residues: 201 sheet: 0.22 (0.23), residues: 537 loop : -0.73 (0.19), residues: 1019 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A1048 TYR 0.016 0.001 TYR A 336 PHE 0.019 0.001 PHE A1525 TRP 0.017 0.001 TRP A 992 HIS 0.006 0.001 HIS A1753 Details of bonding type rmsd covalent geometry : bond 0.00245 (14601) covalent geometry : angle 0.58247 (19798) hydrogen bonds : bond 0.04048 ( 364) hydrogen bonds : angle 5.59683 ( 882) *********************** REFINEMENT MACRO_CYCLE 8 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 228 residues out of total 1553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 199 time to evaluate : 0.571 Fit side-chains revert: symmetry clash REVERT: A 272 ASP cc_start: 0.7115 (m-30) cc_final: 0.6763 (m-30) REVERT: A 399 MET cc_start: 0.6098 (mmm) cc_final: 0.5774 (mmm) REVERT: A 411 ASN cc_start: 0.3259 (OUTLIER) cc_final: 0.2841 (t0) REVERT: A 1128 MET cc_start: 0.0492 (ppp) cc_final: -0.0683 (ppp) REVERT: A 1335 GLU cc_start: 0.6916 (mm-30) cc_final: 0.6516 (mm-30) REVERT: A 1693 ARG cc_start: 0.5861 (ttp-170) cc_final: 0.5608 (ttp-110) REVERT: A 1737 ARG cc_start: 0.5664 (mmm-85) cc_final: 0.4427 (pmt170) REVERT: A 1848 GLU cc_start: 0.3383 (mp0) cc_final: 0.2849 (tp30) REVERT: A 1864 GLU cc_start: 0.5843 (pm20) cc_final: 0.5510 (pm20) REVERT: A 1905 ARG cc_start: 0.1550 (OUTLIER) cc_final: 0.0425 (ptp-170) REVERT: A 1987 MET cc_start: 0.1560 (tpp) cc_final: 0.1056 (tpp) outliers start: 29 outliers final: 9 residues processed: 211 average time/residue: 0.7147 time to fit residues: 164.3312 Evaluate side-chains 205 residues out of total 1553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 194 time to evaluate : 0.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 411 ASN Chi-restraints excluded: chain A residue 455 MET Chi-restraints excluded: chain A residue 617 ILE Chi-restraints excluded: chain A residue 777 LEU Chi-restraints excluded: chain A residue 1167 MET Chi-restraints excluded: chain A residue 1206 TYR Chi-restraints excluded: chain A residue 1761 VAL Chi-restraints excluded: chain A residue 1854 THR Chi-restraints excluded: chain A residue 1877 TYR Chi-restraints excluded: chain A residue 1905 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 146 optimal weight: 0.0010 chunk 65 optimal weight: 0.6980 chunk 44 optimal weight: 0.0270 chunk 137 optimal weight: 1.9990 chunk 142 optimal weight: 0.9990 chunk 13 optimal weight: 0.8980 chunk 17 optimal weight: 0.4980 chunk 162 optimal weight: 0.9980 chunk 52 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 overall best weight: 0.4244 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 380 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 411 ASN A1193 ASN A1196 ASN A1682 GLN A1930 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4581 r_free = 0.4581 target = 0.205036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4348 r_free = 0.4348 target = 0.181759 restraints weight = 24472.787| |-----------------------------------------------------------------------------| r_work (start): 0.4326 rms_B_bonded: 2.45 r_work: 0.4200 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.4200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6377 moved from start: 0.4303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 14601 Z= 0.152 Angle : 0.626 9.456 19798 Z= 0.324 Chirality : 0.045 0.180 2103 Planarity : 0.006 0.088 2589 Dihedral : 4.855 23.763 1927 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.50 % Favored : 95.45 % Rotamer: Outliers : 1.55 % Allowed : 15.45 % Favored : 83.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.88 % 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: -0.54 (0.20), residues: 1757 helix: 0.18 (0.39), residues: 191 sheet: 0.22 (0.23), residues: 530 loop : -0.75 (0.19), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A1162 TYR 0.015 0.001 TYR A1684 PHE 0.019 0.002 PHE A1525 TRP 0.021 0.002 TRP A1692 HIS 0.007 0.001 HIS A1753 Details of bonding type rmsd covalent geometry : bond 0.00353 (14601) covalent geometry : angle 0.62643 (19798) hydrogen bonds : bond 0.04713 ( 364) hydrogen bonds : angle 5.76880 ( 882) *********************** REFINEMENT MACRO_CYCLE 9 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 224 residues out of total 1553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 200 time to evaluate : 0.554 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 272 ASP cc_start: 0.7099 (m-30) cc_final: 0.6742 (m-30) REVERT: A 399 MET cc_start: 0.6040 (mmm) cc_final: 0.5736 (mmm) REVERT: A 474 ILE cc_start: 0.7923 (tt) cc_final: 0.7713 (tt) REVERT: A 1232 ASP cc_start: 0.6359 (m-30) cc_final: 0.6131 (m-30) REVERT: A 1659 ILE cc_start: 0.6805 (OUTLIER) cc_final: 0.6181 (mp) REVERT: A 1737 ARG cc_start: 0.5667 (mmm-85) cc_final: 0.4515 (pmt170) REVERT: A 1784 GLN cc_start: 0.4287 (pm20) cc_final: 0.3952 (pm20) REVERT: A 1848 GLU cc_start: 0.3493 (mp0) cc_final: 0.2885 (tp30) REVERT: A 1864 GLU cc_start: 0.5950 (pm20) cc_final: 0.5721 (pm20) REVERT: A 1905 ARG cc_start: 0.1769 (OUTLIER) cc_final: 0.0835 (ptp-170) REVERT: A 1912 ASP cc_start: 0.3590 (OUTLIER) cc_final: 0.3203 (t0) REVERT: A 1930 ASN cc_start: 0.4667 (OUTLIER) cc_final: 0.4462 (t0) REVERT: A 1987 MET cc_start: 0.1809 (tpp) cc_final: 0.1344 (tpp) outliers start: 24 outliers final: 12 residues processed: 212 average time/residue: 0.6843 time to fit residues: 157.6495 Evaluate side-chains 210 residues out of total 1553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 194 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 380 HIS Chi-restraints excluded: chain A residue 455 MET Chi-restraints excluded: chain A residue 617 ILE Chi-restraints excluded: chain A residue 777 LEU Chi-restraints excluded: chain A residue 1036 THR Chi-restraints excluded: chain A residue 1167 MET Chi-restraints excluded: chain A residue 1206 TYR Chi-restraints excluded: chain A residue 1659 ILE Chi-restraints excluded: chain A residue 1727 GLU Chi-restraints excluded: chain A residue 1761 VAL Chi-restraints excluded: chain A residue 1854 THR Chi-restraints excluded: chain A residue 1877 TYR Chi-restraints excluded: chain A residue 1905 ARG Chi-restraints excluded: chain A residue 1912 ASP Chi-restraints excluded: chain A residue 1930 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 98 optimal weight: 0.9980 chunk 158 optimal weight: 0.0470 chunk 53 optimal weight: 0.9990 chunk 1 optimal weight: 0.0470 chunk 69 optimal weight: 0.4980 chunk 155 optimal weight: 0.4980 chunk 91 optimal weight: 1.9990 chunk 41 optimal weight: 0.4980 chunk 108 optimal weight: 0.0060 chunk 20 optimal weight: 0.8980 chunk 144 optimal weight: 0.0980 overall best weight: 0.1392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 380 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 742 GLN A1193 ASN ** A1508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1682 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1930 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4603 r_free = 0.4603 target = 0.207226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4362 r_free = 0.4362 target = 0.183355 restraints weight = 24732.769| |-----------------------------------------------------------------------------| r_work (start): 0.4339 rms_B_bonded: 2.83 r_work: 0.4206 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.4206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6353 moved from start: 0.4334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 14601 Z= 0.108 Angle : 0.595 11.141 19798 Z= 0.302 Chirality : 0.044 0.176 2103 Planarity : 0.005 0.079 2589 Dihedral : 4.571 22.704 1927 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.36 % Favored : 96.59 % Rotamer: Outliers : 1.16 % Allowed : 16.10 % Favored : 82.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.88 % 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: -0.44 (0.20), residues: 1757 helix: 0.17 (0.39), residues: 201 sheet: 0.31 (0.23), residues: 531 loop : -0.69 (0.19), residues: 1025 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A1162 TYR 0.013 0.001 TYR A1206 PHE 0.017 0.001 PHE A1525 TRP 0.015 0.001 TRP A 466 HIS 0.005 0.001 HIS A1753 Details of bonding type rmsd covalent geometry : bond 0.00240 (14601) covalent geometry : angle 0.59530 (19798) hydrogen bonds : bond 0.03773 ( 364) hydrogen bonds : angle 5.47143 ( 882) ********************** REFINEMENT MACRO_CYCLE 10 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 212 residues out of total 1553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 194 time to evaluate : 0.606 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 272 ASP cc_start: 0.7047 (m-30) cc_final: 0.6681 (m-30) REVERT: A 338 LYS cc_start: 0.7430 (tppp) cc_final: 0.7011 (tppp) REVERT: A 399 MET cc_start: 0.6120 (mmm) cc_final: 0.5813 (mmm) REVERT: A 465 ASP cc_start: 0.6751 (t0) cc_final: 0.6087 (t0) REVERT: A 1335 GLU cc_start: 0.6917 (mm-30) cc_final: 0.6628 (mp0) REVERT: A 1737 ARG cc_start: 0.5646 (mmm-85) cc_final: 0.4411 (pmt170) REVERT: A 1848 GLU cc_start: 0.3401 (mp0) cc_final: 0.2876 (tp30) REVERT: A 1864 GLU cc_start: 0.5872 (pm20) cc_final: 0.5666 (pm20) REVERT: A 1905 ARG cc_start: 0.1559 (OUTLIER) cc_final: 0.0430 (ptp-170) REVERT: A 1930 ASN cc_start: 0.4678 (OUTLIER) cc_final: 0.4454 (t0) REVERT: A 1987 MET cc_start: 0.1853 (tpp) cc_final: 0.1470 (tpp) outliers start: 18 outliers final: 12 residues processed: 202 average time/residue: 0.7267 time to fit residues: 159.7631 Evaluate side-chains 208 residues out of total 1553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 194 time to evaluate : 0.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 380 HIS Chi-restraints excluded: chain A residue 455 MET Chi-restraints excluded: chain A residue 617 ILE Chi-restraints excluded: chain A residue 777 LEU Chi-restraints excluded: chain A residue 1112 LEU Chi-restraints excluded: chain A residue 1167 MET Chi-restraints excluded: chain A residue 1206 TYR Chi-restraints excluded: chain A residue 1727 GLU Chi-restraints excluded: chain A residue 1761 VAL Chi-restraints excluded: chain A residue 1854 THR Chi-restraints excluded: chain A residue 1877 TYR Chi-restraints excluded: chain A residue 1905 ARG Chi-restraints excluded: chain A residue 1930 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 170 optimal weight: 0.9990 chunk 79 optimal weight: 0.2980 chunk 104 optimal weight: 0.1980 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 0.0370 chunk 14 optimal weight: 0.5980 chunk 103 optimal weight: 0.9990 chunk 168 optimal weight: 0.3980 chunk 169 optimal weight: 7.9990 chunk 31 optimal weight: 0.0370 chunk 17 optimal weight: 0.8980 overall best weight: 0.1936 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 380 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 693 HIS A1193 ASN A1196 ASN A1408 ASN ** A1682 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4602 r_free = 0.4602 target = 0.207129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4360 r_free = 0.4360 target = 0.183006 restraints weight = 24517.410| |-----------------------------------------------------------------------------| r_work (start): 0.4338 rms_B_bonded: 2.59 r_work: 0.4219 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.4219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6332 moved from start: 0.4400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 14601 Z= 0.108 Angle : 0.594 11.767 19798 Z= 0.301 Chirality : 0.043 0.166 2103 Planarity : 0.005 0.067 2589 Dihedral : 4.479 22.123 1927 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.93 % Favored : 96.02 % Rotamer: Outliers : 1.22 % Allowed : 16.03 % Favored : 82.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.88 % 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: -0.45 (0.20), residues: 1757 helix: 0.16 (0.38), residues: 207 sheet: 0.34 (0.23), residues: 532 loop : -0.73 (0.19), residues: 1018 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A1931 TYR 0.016 0.001 TYR A 336 PHE 0.017 0.001 PHE A1525 TRP 0.016 0.001 TRP A 466 HIS 0.011 0.001 HIS A 693 Details of bonding type rmsd covalent geometry : bond 0.00245 (14601) covalent geometry : angle 0.59354 (19798) hydrogen bonds : bond 0.03802 ( 364) hydrogen bonds : angle 5.39509 ( 882) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5848.45 seconds wall clock time: 100 minutes 22.75 seconds (6022.75 seconds total)