Starting phenix.real_space_refine on Sun Aug 9 00:41:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/10gx_75163/08_2026/10gx_75163.cif Found real_map, /net/cci-nas-00/data/ceres_data/10gx_75163/08_2026/10gx_75163.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/10gx_75163/08_2026/10gx_75163.map" default_real_map = "/net/cci-nas-00/data/ceres_data/10gx_75163/08_2026/10gx_75163.map" model { file = "/net/cci-nas-00/data/ceres_data/10gx_75163/08_2026/10gx_75163.cif" } default_model = "/net/cci-nas-00/data/ceres_data/10gx_75163/08_2026/10gx_75163.cif" } resolution = 3.2 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= 0.002 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: 5 Type Number sf(0) Gaussians S 70 5.16 5 C 9679 2.51 5 N 2490 2.21 5 O 2790 1.98 5 H 15071 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 30100 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 30100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1853, 30100 Classifications: {'peptide': 1853} Link IDs: {'PTRANS': 65, 'TRANS': 1787} Chain breaks: 5 Time building chain proxies: 4.41, per 1000 atoms: 0.15 Number of scatterers: 30100 At special positions: 0 Unit cell: (89.25, 123.76, 133.28, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 70 16.00 O 2790 8.00 N 2490 7.00 C 9679 6.00 H 15071 1.00 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: 2.68 Conformation dependent library (CDL) restraints added in 906.2 milliseconds 3682 Ramachandran restraints generated. 1841 Oldfield, 0 Emsley, 1841 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3586 Finding SS restraints... Secondary structure from input PDB file: 108 helices and 3 sheets defined 75.8% alpha, 0.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.57 Creating SS restraints... Processing helix chain 'A' and resid 78 through 89 Processing helix chain 'A' and resid 96 through 104 removed outlier: 3.884A pdb=" N LYS A 102 " --> pdb=" O ALA A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 125 Processing helix chain 'A' and resid 132 through 153 Processing helix chain 'A' and resid 163 through 169 Processing helix chain 'A' and resid 231 through 235 removed outlier: 3.862A pdb=" N ALA A 235 " --> pdb=" O ALA A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 239 through 251 Processing helix chain 'A' and resid 256 through 271 removed outlier: 4.045A pdb=" N SER A 262 " --> pdb=" O ALA A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 291 removed outlier: 3.578A pdb=" N HIS A 283 " --> pdb=" O TYR A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 308 Processing helix chain 'A' and resid 312 through 322 removed outlier: 4.088A pdb=" N MET A 316 " --> pdb=" O ASP A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 356 Processing helix chain 'A' and resid 357 through 359 No H-bonds generated for 'chain 'A' and resid 357 through 359' Processing helix chain 'A' and resid 365 through 377 Processing helix chain 'A' and resid 382 through 394 Proline residue: A 388 - end of helix removed outlier: 3.590A pdb=" N VAL A 394 " --> pdb=" O VAL A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 406 Processing helix chain 'A' and resid 407 through 418 removed outlier: 3.700A pdb=" N SER A 417 " --> pdb=" O SER A 413 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 445 removed outlier: 4.642A pdb=" N HIS A 427 " --> pdb=" O ALA A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 453 removed outlier: 3.887A pdb=" N VAL A 452 " --> pdb=" O HIS A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 464 through 481 Processing helix chain 'A' and resid 487 through 492 Processing helix chain 'A' and resid 492 through 497 Processing helix chain 'A' and resid 504 through 518 Processing helix chain 'A' and resid 530 through 557 Processing helix chain 'A' and resid 567 through 587 removed outlier: 4.881A pdb=" N ASN A 580 " --> pdb=" O GLU A 576 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N ILE A 581 " --> pdb=" O ILE A 577 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N GLN A 587 " --> pdb=" O SER A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 590 through 607 removed outlier: 3.546A pdb=" N TYR A 596 " --> pdb=" O ASP A 592 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N TYR A 597 " --> pdb=" O ILE A 593 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N CYS A 600 " --> pdb=" O TYR A 596 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N PHE A 601 " --> pdb=" O TYR A 597 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N ALA A 602 " --> pdb=" O ILE A 598 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N TYR A 603 " --> pdb=" O SER A 599 " (cutoff:3.500A) Processing helix chain 'A' and resid 611 through 627 removed outlier: 4.309A pdb=" N ILE A 615 " --> pdb=" O ASN A 611 " (cutoff:3.500A) Processing helix chain 'A' and resid 634 through 653 removed outlier: 5.151A pdb=" N ARG A 650 " --> pdb=" O THR A 646 " (cutoff:3.500A) removed outlier: 5.476A pdb=" N PHE A 651 " --> pdb=" O ARG A 647 " (cutoff:3.500A) Processing helix chain 'A' and resid 657 through 660 Processing helix chain 'A' and resid 661 through 673 Processing helix chain 'A' and resid 677 through 695 removed outlier: 3.793A pdb=" N PHE A 694 " --> pdb=" O SER A 690 " (cutoff:3.500A) Processing helix chain 'A' and resid 708 through 726 removed outlier: 4.919A pdb=" N LEU A 714 " --> pdb=" O GLU A 710 " (cutoff:3.500A) Proline residue: A 715 - end of helix Processing helix chain 'A' and resid 729 through 733 Processing helix chain 'A' and resid 736 through 748 removed outlier: 3.836A pdb=" N THR A 748 " --> pdb=" O PHE A 744 " (cutoff:3.500A) Processing helix chain 'A' and resid 750 through 765 Processing helix chain 'A' and resid 766 through 768 No H-bonds generated for 'chain 'A' and resid 766 through 768' Processing helix chain 'A' and resid 771 through 789 Processing helix chain 'A' and resid 790 through 808 removed outlier: 3.660A pdb=" N TYR A 796 " --> pdb=" O LYS A 792 " (cutoff:3.500A) Processing helix chain 'A' and resid 818 through 832 Proline residue: A 824 - end of helix Processing helix chain 'A' and resid 835 through 853 Processing helix chain 'A' and resid 865 through 867 No H-bonds generated for 'chain 'A' and resid 865 through 867' Processing helix chain 'A' and resid 868 through 882 Processing helix chain 'A' and resid 883 through 891 removed outlier: 4.867A pdb=" N HIS A 886 " --> pdb=" O ARG A 883 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N GLU A 887 " --> pdb=" O GLN A 884 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU A 889 " --> pdb=" O HIS A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 892 through 907 Processing helix chain 'A' and resid 909 through 917 Processing helix chain 'A' and resid 917 through 929 removed outlier: 4.275A pdb=" N HIS A 921 " --> pdb=" O SER A 917 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEU A 927 " --> pdb=" O ALA A 923 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 949 Processing helix chain 'A' and resid 956 through 961 removed outlier: 3.577A pdb=" N PHE A 960 " --> pdb=" O PRO A 957 " (cutoff:3.500A) Processing helix chain 'A' and resid 973 through 1000 Processing helix chain 'A' and resid 1005 through 1026 removed outlier: 3.851A pdb=" N GLY A1009 " --> pdb=" O ASP A1005 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ASP A1010 " --> pdb=" O SER A1006 " (cutoff:3.500A) Processing helix chain 'A' and resid 1027 through 1030 Processing helix chain 'A' and resid 1159 through 1165 Processing helix chain 'A' and resid 1166 through 1194 removed outlier: 3.842A pdb=" N LEU A1170 " --> pdb=" O ASN A1166 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N PHE A1189 " --> pdb=" O LYS A1185 " (cutoff:3.500A) Processing helix chain 'A' and resid 1197 through 1214 removed outlier: 3.579A pdb=" N PHE A1201 " --> pdb=" O ASN A1197 " (cutoff:3.500A) Processing helix chain 'A' and resid 1230 through 1239 Processing helix chain 'A' and resid 1248 through 1266 Processing helix chain 'A' and resid 1274 through 1289 Processing helix chain 'A' and resid 1292 through 1310 Proline residue: A1298 - end of helix removed outlier: 3.510A pdb=" N GLN A1309 " --> pdb=" O HIS A1305 " (cutoff:3.500A) Processing helix chain 'A' and resid 1312 through 1331 removed outlier: 3.563A pdb=" N VAL A1316 " --> pdb=" O GLY A1312 " (cutoff:3.500A) Proline residue: A1323 - end of helix Processing helix chain 'A' and resid 1333 through 1345 Processing helix chain 'A' and resid 1346 through 1354 removed outlier: 3.563A pdb=" N LYS A1352 " --> pdb=" O LYS A1348 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N MET A1354 " --> pdb=" O HIS A1350 " (cutoff:3.500A) Processing helix chain 'A' and resid 1356 through 1372 removed outlier: 4.470A pdb=" N GLY A1361 " --> pdb=" O TYR A1357 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N ARG A1362 " --> pdb=" O LYS A1358 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ARG A1372 " --> pdb=" O ILE A1368 " (cutoff:3.500A) Processing helix chain 'A' and resid 1374 through 1376 No H-bonds generated for 'chain 'A' and resid 1374 through 1376' Processing helix chain 'A' and resid 1377 through 1393 Processing helix chain 'A' and resid 1403 through 1411 removed outlier: 3.508A pdb=" N PHE A1407 " --> pdb=" O ASP A1404 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N LEU A1408 " --> pdb=" O GLN A1405 " (cutoff:3.500A) Proline residue: A1409 - end of helix Processing helix chain 'A' and resid 1416 through 1453 removed outlier: 3.961A pdb=" N GLN A1420 " --> pdb=" O THR A1416 " (cutoff:3.500A) Processing helix chain 'A' and resid 1457 through 1473 Processing helix chain 'A' and resid 1480 through 1490 Processing helix chain 'A' and resid 1491 through 1494 Processing helix chain 'A' and resid 1495 through 1520 Processing helix chain 'A' and resid 1522 through 1527 Processing helix chain 'A' and resid 1545 through 1554 removed outlier: 3.583A pdb=" N THR A1551 " --> pdb=" O PRO A1547 " (cutoff:3.500A) Processing helix chain 'A' and resid 1592 through 1606 Processing helix chain 'A' and resid 1607 through 1622 Processing helix chain 'A' and resid 1629 through 1645 removed outlier: 3.645A pdb=" N VAL A1633 " --> pdb=" O SER A1629 " (cutoff:3.500A) Processing helix chain 'A' and resid 1651 through 1663 removed outlier: 3.739A pdb=" N LEU A1655 " --> pdb=" O ASN A1651 " (cutoff:3.500A) Processing helix chain 'A' and resid 1667 through 1684 Processing helix chain 'A' and resid 1685 through 1687 No H-bonds generated for 'chain 'A' and resid 1685 through 1687' Processing helix chain 'A' and resid 1689 through 1709 Processing helix chain 'A' and resid 1713 through 1727 Processing helix chain 'A' and resid 1728 through 1730 No H-bonds generated for 'chain 'A' and resid 1728 through 1730' Processing helix chain 'A' and resid 1732 through 1736 Processing helix chain 'A' and resid 1738 through 1746 removed outlier: 3.612A pdb=" N PHE A1743 " --> pdb=" O PHE A1739 " (cutoff:3.500A) Processing helix chain 'A' and resid 1756 through 1775 Processing helix chain 'A' and resid 1776 through 1778 No H-bonds generated for 'chain 'A' and resid 1776 through 1778' Processing helix chain 'A' and resid 1781 through 1788 Processing helix chain 'A' and resid 1794 through 1813 Processing helix chain 'A' and resid 1819 through 1829 Processing helix chain 'A' and resid 1842 through 1859 Processing helix chain 'A' and resid 1860 through 1864 removed outlier: 3.715A pdb=" N VAL A1863 " --> pdb=" O GLU A1860 " (cutoff:3.500A) Processing helix chain 'A' and resid 1867 through 1872 Processing helix chain 'A' and resid 1874 through 1891 Processing helix chain 'A' and resid 1895 through 1904 Proline residue: A1901 - end of helix removed outlier: 4.406A pdb=" N VAL A1904 " --> pdb=" O VAL A1900 " (cutoff:3.500A) Processing helix chain 'A' and resid 1906 through 1916 removed outlier: 3.670A pdb=" N LYS A1916 " --> pdb=" O ILE A1912 " (cutoff:3.500A) Processing helix chain 'A' and resid 1917 through 1925 Processing helix chain 'A' and resid 1927 through 1935 Processing helix chain 'A' and resid 1936 through 1938 No H-bonds generated for 'chain 'A' and resid 1936 through 1938' Processing helix chain 'A' and resid 1941 through 1954 Processing helix chain 'A' and resid 1960 through 1978 Processing helix chain 'A' and resid 1983 through 1997 Processing helix chain 'A' and resid 1998 through 2000 No H-bonds generated for 'chain 'A' and resid 1998 through 2000' Processing helix chain 'A' and resid 2003 through 2018 removed outlier: 3.687A pdb=" N ARG A2007 " --> pdb=" O PHE A2003 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VAL A2008 " --> pdb=" O VAL A2004 " (cutoff:3.500A) Processing helix chain 'A' and resid 2019 through 2022 Processing helix chain 'A' and resid 2024 through 2036 removed outlier: 3.735A pdb=" N GLU A2032 " --> pdb=" O LEU A2028 " (cutoff:3.500A) Processing helix chain 'A' and resid 2047 through 2055 removed outlier: 4.141A pdb=" N LYS A2053 " --> pdb=" O GLN A2049 " (cutoff:3.500A) Processing helix chain 'A' and resid 2056 through 2072 removed outlier: 3.574A pdb=" N PHE A2072 " --> pdb=" O ILE A2068 " (cutoff:3.500A) Processing helix chain 'A' and resid 2080 through 2094 removed outlier: 4.046A pdb=" N ASN A2088 " --> pdb=" O LYS A2084 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N SER A2091 " --> pdb=" O SER A2087 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N TRP A2092 " --> pdb=" O ASN A2088 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ARG A2094 " --> pdb=" O SER A2090 " (cutoff:3.500A) Processing helix chain 'A' and resid 2097 through 2111 Processing sheet with id=AA1, first strand: chain 'A' and resid 293 through 295 Processing sheet with id=AA2, first strand: chain 'A' and resid 931 through 934 removed outlier: 6.922A pdb=" N GLN A 968 " --> pdb=" O THR A 933 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1536 through 1540 922 hydrogen bonds defined for protein. 2688 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.79 Time building geometry restraints manager: 3.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 15044 1.03 - 1.22: 29 1.22 - 1.42: 6446 1.42 - 1.61: 8798 1.61 - 1.81: 113 Bond restraints: 30430 Sorted by residual: bond pdb=" CG LEU A 623 " pdb=" CD2 LEU A 623 " ideal model delta sigma weight residual 1.521 1.480 0.041 3.30e-02 9.18e+02 1.54e+00 bond pdb=" CB MET A1772 " pdb=" CG MET A1772 " ideal model delta sigma weight residual 1.520 1.490 0.030 3.00e-02 1.11e+03 1.03e+00 bond pdb=" CB GLN A1286 " pdb=" CG GLN A1286 " ideal model delta sigma weight residual 1.520 1.550 -0.030 3.00e-02 1.11e+03 9.78e-01 bond pdb=" CG1 ILE A1719 " pdb=" CD1 ILE A1719 " ideal model delta sigma weight residual 1.513 1.476 0.037 3.90e-02 6.57e+02 8.98e-01 bond pdb=" CG1 ILE A 156 " pdb=" CD1 ILE A 156 " ideal model delta sigma weight residual 1.513 1.477 0.036 3.90e-02 6.57e+02 8.57e-01 ... (remaining 30425 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.37: 52989 1.37 - 2.73: 1886 2.73 - 4.10: 145 4.10 - 5.46: 31 5.46 - 6.83: 2 Bond angle restraints: 55053 Sorted by residual: angle pdb=" CG ARG A1777 " pdb=" CD ARG A1777 " pdb=" NE ARG A1777 " ideal model delta sigma weight residual 112.00 118.83 -6.83 2.20e+00 2.07e-01 9.64e+00 angle pdb=" CA TYR A1296 " pdb=" CB TYR A1296 " pdb=" CG TYR A1296 " ideal model delta sigma weight residual 113.90 118.33 -4.43 1.80e+00 3.09e-01 6.07e+00 angle pdb=" CA TYR A 267 " pdb=" CB TYR A 267 " pdb=" CG TYR A 267 " ideal model delta sigma weight residual 113.90 109.50 4.40 1.80e+00 3.09e-01 5.98e+00 angle pdb=" CA GLN A1286 " pdb=" CB GLN A1286 " pdb=" CG GLN A1286 " ideal model delta sigma weight residual 114.10 118.84 -4.74 2.00e+00 2.50e-01 5.62e+00 angle pdb=" CB GLN A1286 " pdb=" CG GLN A1286 " pdb=" CD GLN A1286 " ideal model delta sigma weight residual 112.60 116.51 -3.91 1.70e+00 3.46e-01 5.29e+00 ... (remaining 55048 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 12989 17.93 - 35.85: 930 35.85 - 53.78: 251 53.78 - 71.71: 93 71.71 - 89.63: 54 Dihedral angle restraints: 14317 sinusoidal: 7706 harmonic: 6611 Sorted by residual: dihedral pdb=" CA ARG A1577 " pdb=" C ARG A1577 " pdb=" N LEU A1578 " pdb=" CA LEU A1578 " ideal model delta harmonic sigma weight residual 180.00 154.13 25.87 0 5.00e+00 4.00e-02 2.68e+01 dihedral pdb=" CA ILE A 695 " pdb=" C ILE A 695 " pdb=" N PRO A 696 " pdb=" CA PRO A 696 " ideal model delta harmonic sigma weight residual 180.00 161.00 19.00 0 5.00e+00 4.00e-02 1.44e+01 dihedral pdb=" CA THR A 908 " pdb=" C THR A 908 " pdb=" N ASN A 909 " pdb=" CA ASN A 909 " ideal model delta harmonic sigma weight residual 180.00 161.41 18.59 0 5.00e+00 4.00e-02 1.38e+01 ... (remaining 14314 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 1589 0.034 - 0.069: 581 0.069 - 0.103: 146 0.103 - 0.137: 52 0.137 - 0.172: 6 Chirality restraints: 2374 Sorted by residual: chirality pdb=" CA TYR A 267 " pdb=" N TYR A 267 " pdb=" C TYR A 267 " pdb=" CB TYR A 267 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.38e-01 chirality pdb=" CG LEU A 623 " pdb=" CB LEU A 623 " pdb=" CD1 LEU A 623 " pdb=" CD2 LEU A 623 " both_signs ideal model delta sigma weight residual False -2.59 -2.42 -0.17 2.00e-01 2.50e+01 7.12e-01 chirality pdb=" CA TRP A 243 " pdb=" N TRP A 243 " pdb=" C TRP A 243 " pdb=" CB TRP A 243 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.08e-01 ... (remaining 2371 not shown) Planarity restraints: 4412 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 441 " -0.044 2.00e-02 2.50e+03 5.41e-02 4.38e+01 pdb=" CG ASN A 441 " 0.036 2.00e-02 2.50e+03 pdb=" OD1 ASN A 441 " 0.002 2.00e-02 2.50e+03 pdb=" ND2 ASN A 441 " 0.085 2.00e-02 2.50e+03 pdb="HD21 ASN A 441 " 0.004 2.00e-02 2.50e+03 pdb="HD22 ASN A 441 " -0.084 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A2092 " 0.013 2.00e-02 2.50e+03 2.18e-02 1.91e+01 pdb=" CG TRP A2092 " -0.006 2.00e-02 2.50e+03 pdb=" CD1 TRP A2092 " 0.004 2.00e-02 2.50e+03 pdb=" CD2 TRP A2092 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP A2092 " -0.065 2.00e-02 2.50e+03 pdb=" CE2 TRP A2092 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP A2092 " 0.007 2.00e-02 2.50e+03 pdb=" CZ2 TRP A2092 " -0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP A2092 " 0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP A2092 " 0.002 2.00e-02 2.50e+03 pdb=" HD1 TRP A2092 " -0.005 2.00e-02 2.50e+03 pdb=" HE1 TRP A2092 " 0.055 2.00e-02 2.50e+03 pdb=" HE3 TRP A2092 " -0.001 2.00e-02 2.50e+03 pdb=" HZ2 TRP A2092 " 0.002 2.00e-02 2.50e+03 pdb=" HZ3 TRP A2092 " -0.003 2.00e-02 2.50e+03 pdb=" HH2 TRP A2092 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C MET A 789 " 0.022 2.00e-02 2.50e+03 4.16e-02 1.73e+01 pdb=" N ASP A 790 " -0.071 2.00e-02 2.50e+03 pdb=" CA ASP A 790 " 0.018 2.00e-02 2.50e+03 pdb=" H ASP A 790 " 0.032 2.00e-02 2.50e+03 ... (remaining 4409 not shown) Histogram of nonbonded interaction distances: 1.75 - 2.32: 7992 2.32 - 2.89: 71095 2.89 - 3.46: 83220 3.46 - 4.03: 112826 4.03 - 4.60: 174087 Nonbonded interactions: 449220 Sorted by model distance: nonbonded pdb=" HG2 ARG A1777 " pdb="HH11 ARG A1777 " model vdw 1.750 2.270 nonbonded pdb=" HE1 TYR A 603 " pdb=" HG SER A1241 " model vdw 1.809 2.100 nonbonded pdb="HH12 ARG A1577 " pdb=" HE1 TYR A1580 " model vdw 1.814 2.100 nonbonded pdb=" HH TYR A 545 " pdb=" HD2 HIS A 571 " model vdw 1.850 2.100 nonbonded pdb=" H ILE A 405 " pdb="HG12 ILE A 405 " model vdw 1.851 2.270 ... (remaining 449215 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: 2.100 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: 0.190 Extract box with map and model: 0.430 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 26.220 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 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 : 0.004 0.041 15359 Z= 0.176 Angle : 0.593 6.831 20804 Z= 0.341 Chirality : 0.040 0.172 2374 Planarity : 0.007 0.078 2630 Dihedral : 14.545 89.635 5679 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 0.94 % Allowed : 7.67 % Favored : 91.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.45 (0.19), residues: 1841 helix: -0.21 (0.14), residues: 1258 sheet: -1.46 (1.35), residues: 10 loop : -0.10 (0.28), residues: 573 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.002 ARG A1734 TYR 0.020 0.002 TYR A1296 PHE 0.019 0.002 PHE A 744 TRP 0.039 0.003 TRP A2092 HIS 0.008 0.001 HIS A 486 Details of bonding type rmsd/Z covalent geometry : bond 0.00393 / 0.18 (15359) covalent geometry : angle 0.59343 / 0.34 (20804) hydrogen bonds : bond 0.12255 / 7.77 ( 922) hydrogen bonds : angle 5.70518 / 3.97 ( 2688) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3682 Ramachandran restraints generated. 1841 Oldfield, 0 Emsley, 1841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3682 Ramachandran restraints generated. 1841 Oldfield, 0 Emsley, 1841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 200 time to evaluate : 0.792 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 ARG cc_start: 0.8243 (ttt90) cc_final: 0.8032 (ttt-90) REVERT: A 285 ASP cc_start: 0.8250 (m-30) cc_final: 0.7642 (m-30) REVERT: A 331 TYR cc_start: 0.8327 (m-80) cc_final: 0.7964 (m-80) REVERT: A 333 ARG cc_start: 0.7815 (mmp-170) cc_final: 0.7416 (mpt180) REVERT: A 450 LYS cc_start: 0.8013 (mmmt) cc_final: 0.7738 (mmmt) REVERT: A 623 LEU cc_start: 0.8380 (OUTLIER) cc_final: 0.8060 (tp) REVERT: A 1306 CYS cc_start: 0.8302 (m) cc_final: 0.8068 (m) REVERT: A 1338 GLN cc_start: 0.8539 (tt0) cc_final: 0.8161 (tt0) REVERT: A 1362 ARG cc_start: 0.8486 (ttp-170) cc_final: 0.8025 (mtm110) REVERT: A 1374 ASN cc_start: 0.7175 (m-40) cc_final: 0.6911 (t0) REVERT: A 1420 GLN cc_start: 0.8000 (mt0) cc_final: 0.7715 (mt0) REVERT: A 1552 GLU cc_start: 0.8232 (tt0) cc_final: 0.7728 (tp30) REVERT: A 1559 ASN cc_start: 0.8591 (t0) cc_final: 0.8130 (t0) REVERT: A 1567 ARG cc_start: 0.7693 (tpp80) cc_final: 0.7365 (mmm-85) REVERT: A 1752 ARG cc_start: 0.7749 (ttt90) cc_final: 0.7487 (ttt-90) REVERT: A 1888 LYS cc_start: 0.8671 (tttt) cc_final: 0.8327 (ttpp) REVERT: A 1892 ARG cc_start: 0.7843 (ttp80) cc_final: 0.7409 (ttp80) REVERT: A 1918 LYS cc_start: 0.7963 (tttp) cc_final: 0.7733 (ptpp) REVERT: A 1930 ARG cc_start: 0.8021 (ttp80) cc_final: 0.7703 (ttt-90) REVERT: A 2009 ARG cc_start: 0.7801 (tpt170) cc_final: 0.7466 (tpt-90) REVERT: A 2032 GLU cc_start: 0.8045 (tp30) cc_final: 0.7821 (tp30) outliers start: 16 outliers final: 14 residues processed: 209 average time/residue: 0.3080 time to fit residues: 91.5303 Evaluate side-chains 198 residues out of total 1707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 183 time to evaluate : 0.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain A residue 330 ASP Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 436 SER Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain A residue 701 THR Chi-restraints excluded: chain A residue 771 GLU Chi-restraints excluded: chain A residue 932 ILE Chi-restraints excluded: chain A residue 1404 ASP Chi-restraints excluded: chain A residue 1534 SER Chi-restraints excluded: chain A residue 1777 ARG Chi-restraints excluded: chain A residue 2015 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 98 optimal weight: 0.9980 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 0.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 486 HIS A 580 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.105815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.086225 restraints weight = 57641.014| |-----------------------------------------------------------------------------| r_work (start): 0.3078 rms_B_bonded: 1.67 r_work: 0.2970 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2840 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.0634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 15359 Z= 0.180 Angle : 0.523 6.659 20804 Z= 0.286 Chirality : 0.038 0.147 2374 Planarity : 0.004 0.043 2630 Dihedral : 5.161 50.414 2020 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 0.82 % Allowed : 7.85 % Favored : 91.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.05 (0.20), residues: 1841 helix: 1.06 (0.14), residues: 1255 sheet: -1.59 (1.31), residues: 12 loop : 0.15 (0.28), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1768 TYR 0.020 0.002 TYR A1296 PHE 0.013 0.002 PHE A1182 TRP 0.010 0.001 TRP A1458 HIS 0.005 0.001 HIS A 313 Details of bonding type rmsd/Z covalent geometry : bond 0.00415 / 0.18 (15359) covalent geometry : angle 0.52261 / 0.29 (20804) hydrogen bonds : bond 0.05243 / 3.43 ( 922) hydrogen bonds : angle 4.48135 / 3.12 ( 2688) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3682 Ramachandran restraints generated. 1841 Oldfield, 0 Emsley, 1841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3682 Ramachandran restraints generated. 1841 Oldfield, 0 Emsley, 1841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 190 time to evaluate : 0.772 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 ARG cc_start: 0.8210 (ttt90) cc_final: 0.7993 (ttt-90) REVERT: A 142 HIS cc_start: 0.7787 (m-70) cc_final: 0.6851 (t70) REVERT: A 285 ASP cc_start: 0.8282 (m-30) cc_final: 0.7685 (m-30) REVERT: A 331 TYR cc_start: 0.8329 (m-80) cc_final: 0.8027 (m-80) REVERT: A 333 ARG cc_start: 0.7875 (mmp-170) cc_final: 0.7511 (mpt180) REVERT: A 618 LYS cc_start: 0.8240 (tmtm) cc_final: 0.7855 (ttmt) REVERT: A 1338 GLN cc_start: 0.8577 (tt0) cc_final: 0.8266 (tt0) REVERT: A 1362 ARG cc_start: 0.8354 (ttp-170) cc_final: 0.7873 (mtm110) REVERT: A 1374 ASN cc_start: 0.7173 (m-40) cc_final: 0.6910 (t0) REVERT: A 1420 GLN cc_start: 0.8013 (mt0) cc_final: 0.7744 (mt0) REVERT: A 1552 GLU cc_start: 0.8261 (tt0) cc_final: 0.7753 (tp30) REVERT: A 1559 ASN cc_start: 0.8645 (t0) cc_final: 0.8151 (t0) REVERT: A 1752 ARG cc_start: 0.7729 (ttt90) cc_final: 0.7361 (ttt-90) REVERT: A 1888 LYS cc_start: 0.8659 (tttt) cc_final: 0.8324 (ttpp) REVERT: A 1892 ARG cc_start: 0.7851 (ttp80) cc_final: 0.7421 (ttp80) REVERT: A 1930 ARG cc_start: 0.7857 (ttp80) cc_final: 0.7618 (ttt-90) REVERT: A 2009 ARG cc_start: 0.7678 (tpt170) cc_final: 0.7447 (tpt-90) REVERT: A 2032 GLU cc_start: 0.7931 (tp30) cc_final: 0.7714 (tp30) outliers start: 14 outliers final: 10 residues processed: 198 average time/residue: 0.2916 time to fit residues: 82.6717 Evaluate side-chains 193 residues out of total 1707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 183 time to evaluate : 0.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 771 GLU Chi-restraints excluded: chain A residue 926 THR Chi-restraints excluded: chain A residue 1266 LEU Chi-restraints excluded: chain A residue 1354 MET Chi-restraints excluded: chain A residue 1487 ILE Chi-restraints excluded: chain A residue 1504 LYS Chi-restraints excluded: chain A residue 1725 TRP Chi-restraints excluded: chain A residue 1883 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 99 optimal weight: 0.1980 chunk 161 optimal weight: 3.9990 chunk 138 optimal weight: 1.9990 chunk 65 optimal weight: 0.9980 chunk 126 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 180 optimal weight: 1.9990 chunk 139 optimal weight: 0.6980 chunk 178 optimal weight: 2.9990 chunk 27 optimal weight: 0.9990 chunk 108 optimal weight: 0.1980 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.106480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.086770 restraints weight = 57034.344| |-----------------------------------------------------------------------------| r_work (start): 0.3088 rms_B_bonded: 1.67 r_work: 0.2981 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2851 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.0948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 15359 Z= 0.133 Angle : 0.478 6.405 20804 Z= 0.257 Chirality : 0.036 0.141 2374 Planarity : 0.004 0.043 2630 Dihedral : 4.381 48.811 2000 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 0.70 % Allowed : 8.20 % Favored : 91.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.60 (0.20), residues: 1841 helix: 1.57 (0.15), residues: 1248 sheet: -1.01 (1.42), residues: 12 loop : 0.12 (0.28), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1752 TYR 0.019 0.001 TYR A1296 PHE 0.013 0.001 PHE A1182 TRP 0.009 0.001 TRP A 243 HIS 0.004 0.001 HIS A1173 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 (15359) covalent geometry : angle 0.47812 / 0.26 (20804) hydrogen bonds : bond 0.04507 / 2.95 ( 922) hydrogen bonds : angle 4.11632 / 2.86 ( 2688) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3682 Ramachandran restraints generated. 1841 Oldfield, 0 Emsley, 1841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3682 Ramachandran restraints generated. 1841 Oldfield, 0 Emsley, 1841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 195 time to evaluate : 0.735 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 ARG cc_start: 0.8156 (ttt90) cc_final: 0.7944 (ttt-90) REVERT: A 285 ASP cc_start: 0.8263 (m-30) cc_final: 0.7700 (m-30) REVERT: A 288 GLU cc_start: 0.7919 (tt0) cc_final: 0.7672 (tt0) REVERT: A 333 ARG cc_start: 0.7877 (mmp-170) cc_final: 0.7509 (mpt180) REVERT: A 618 LYS cc_start: 0.8258 (tmtm) cc_final: 0.7873 (ttmt) REVERT: A 1338 GLN cc_start: 0.8549 (tt0) cc_final: 0.8239 (tt0) REVERT: A 1362 ARG cc_start: 0.8332 (ttp-170) cc_final: 0.7881 (mtm110) REVERT: A 1420 GLN cc_start: 0.7973 (mt0) cc_final: 0.7691 (mt0) REVERT: A 1552 GLU cc_start: 0.8248 (tt0) cc_final: 0.7731 (tp30) REVERT: A 1559 ASN cc_start: 0.8620 (t0) cc_final: 0.8154 (t0) REVERT: A 1752 ARG cc_start: 0.7720 (ttt90) cc_final: 0.7400 (ttt-90) REVERT: A 1888 LYS cc_start: 0.8622 (tttt) cc_final: 0.8318 (ttpp) REVERT: A 1892 ARG cc_start: 0.7816 (ttp80) cc_final: 0.7383 (ttp80) REVERT: A 2009 ARG cc_start: 0.7650 (tpt170) cc_final: 0.7401 (tpt-90) REVERT: A 2032 GLU cc_start: 0.7977 (tp30) cc_final: 0.7706 (tp30) outliers start: 12 outliers final: 10 residues processed: 204 average time/residue: 0.3032 time to fit residues: 89.1509 Evaluate side-chains 195 residues out of total 1707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 185 time to evaluate : 0.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 926 THR Chi-restraints excluded: chain A residue 1266 LEU Chi-restraints excluded: chain A residue 1487 ILE Chi-restraints excluded: chain A residue 1504 LYS Chi-restraints excluded: chain A residue 1725 TRP Chi-restraints excluded: chain A residue 1807 THR Chi-restraints excluded: chain A residue 1883 ILE Chi-restraints excluded: chain A residue 2015 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 3 optimal weight: 0.9990 chunk 24 optimal weight: 0.5980 chunk 116 optimal weight: 0.0770 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 1.9990 chunk 183 optimal weight: 4.9990 chunk 53 optimal weight: 0.9980 chunk 179 optimal weight: 0.8980 chunk 181 optimal weight: 0.3980 chunk 104 optimal weight: 0.5980 chunk 182 optimal weight: 0.7980 overall best weight: 0.4938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1153 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.110489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.092097 restraints weight = 56230.015| |-----------------------------------------------------------------------------| r_work (start): 0.3102 rms_B_bonded: 1.56 r_work: 0.3000 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.2873 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.1190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15359 Z= 0.120 Angle : 0.462 6.354 20804 Z= 0.247 Chirality : 0.036 0.140 2374 Planarity : 0.003 0.043 2630 Dihedral : 4.147 45.264 1997 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 0.94 % Allowed : 8.61 % Favored : 90.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.87 (0.20), residues: 1841 helix: 1.81 (0.15), residues: 1250 sheet: 0.02 (1.55), residues: 10 loop : 0.12 (0.28), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1930 TYR 0.018 0.001 TYR A1296 PHE 0.012 0.001 PHE A1182 TRP 0.008 0.001 TRP A1458 HIS 0.005 0.001 HIS A1173 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 (15359) covalent geometry : angle 0.46200 / 0.25 (20804) hydrogen bonds : bond 0.04079 / 2.68 ( 922) hydrogen bonds : angle 3.93469 / 2.74 ( 2688) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3682 Ramachandran restraints generated. 1841 Oldfield, 0 Emsley, 1841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3682 Ramachandran restraints generated. 1841 Oldfield, 0 Emsley, 1841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 195 time to evaluate : 0.701 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 142 HIS cc_start: 0.7696 (m-70) cc_final: 0.6911 (t-90) REVERT: A 285 ASP cc_start: 0.8240 (m-30) cc_final: 0.7677 (m-30) REVERT: A 288 GLU cc_start: 0.7817 (tt0) cc_final: 0.7560 (tt0) REVERT: A 315 ILE cc_start: 0.8713 (mt) cc_final: 0.8297 (tt) REVERT: A 333 ARG cc_start: 0.7873 (mmp-170) cc_final: 0.7550 (mpt180) REVERT: A 1338 GLN cc_start: 0.8526 (tt0) cc_final: 0.8245 (tt0) REVERT: A 1362 ARG cc_start: 0.8170 (ttp-170) cc_final: 0.7723 (mtm110) REVERT: A 1420 GLN cc_start: 0.8053 (mt0) cc_final: 0.7785 (mt0) REVERT: A 1552 GLU cc_start: 0.8205 (tt0) cc_final: 0.7730 (tp30) REVERT: A 1559 ASN cc_start: 0.8645 (t0) cc_final: 0.8184 (t0) REVERT: A 1752 ARG cc_start: 0.7844 (ttt90) cc_final: 0.7497 (ttt-90) REVERT: A 1840 SER cc_start: 0.8482 (p) cc_final: 0.8276 (t) REVERT: A 1888 LYS cc_start: 0.8607 (tttt) cc_final: 0.8320 (ttpp) REVERT: A 1892 ARG cc_start: 0.7842 (ttp80) cc_final: 0.7373 (ttp80) REVERT: A 1930 ARG cc_start: 0.7746 (ttp80) cc_final: 0.7543 (ttt-90) REVERT: A 2009 ARG cc_start: 0.7674 (tpt170) cc_final: 0.7447 (tpt-90) outliers start: 16 outliers final: 11 residues processed: 206 average time/residue: 0.3034 time to fit residues: 88.7907 Evaluate side-chains 195 residues out of total 1707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 184 time to evaluate : 0.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 330 ASP Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 771 GLU Chi-restraints excluded: chain A residue 926 THR Chi-restraints excluded: chain A residue 1266 LEU Chi-restraints excluded: chain A residue 1487 ILE Chi-restraints excluded: chain A residue 1503 VAL Chi-restraints excluded: chain A residue 1504 LYS Chi-restraints excluded: chain A residue 1725 TRP Chi-restraints excluded: chain A residue 1807 THR Chi-restraints excluded: chain A residue 1883 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 10 optimal weight: 0.0980 chunk 119 optimal weight: 0.9980 chunk 100 optimal weight: 1.9990 chunk 130 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 chunk 108 optimal weight: 0.0470 chunk 175 optimal weight: 0.7980 chunk 19 optimal weight: 0.9980 chunk 106 optimal weight: 0.9980 chunk 25 optimal weight: 0.4980 chunk 71 optimal weight: 0.9990 overall best weight: 0.4878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 83 ASN A 486 HIS A 580 ASN A 683 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.106744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.086996 restraints weight = 56926.717| |-----------------------------------------------------------------------------| r_work (start): 0.3096 rms_B_bonded: 1.69 r_work: 0.2988 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.2855 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.1373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 15359 Z= 0.117 Angle : 0.453 6.176 20804 Z= 0.242 Chirality : 0.036 0.138 2374 Planarity : 0.003 0.042 2630 Dihedral : 4.050 42.590 1997 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 0.94 % Allowed : 8.61 % Favored : 90.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.04 (0.20), residues: 1841 helix: 1.98 (0.15), residues: 1245 sheet: -0.16 (1.54), residues: 10 loop : 0.09 (0.28), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 97 TYR 0.017 0.001 TYR A1296 PHE 0.011 0.001 PHE A1182 TRP 0.008 0.001 TRP A1458 HIS 0.005 0.001 HIS A1173 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.12 (15359) covalent geometry : angle 0.45311 / 0.24 (20804) hydrogen bonds : bond 0.03935 / 2.58 ( 922) hydrogen bonds : angle 3.83377 / 2.67 ( 2688) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3682 Ramachandran restraints generated. 1841 Oldfield, 0 Emsley, 1841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3682 Ramachandran restraints generated. 1841 Oldfield, 0 Emsley, 1841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 192 time to evaluate : 0.757 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: A 142 HIS cc_start: 0.7731 (m-70) cc_final: 0.6925 (t-90) REVERT: A 285 ASP cc_start: 0.8272 (m-30) cc_final: 0.7706 (m-30) REVERT: A 288 GLU cc_start: 0.7840 (tt0) cc_final: 0.7603 (tt0) REVERT: A 333 ARG cc_start: 0.7941 (mmp-170) cc_final: 0.7540 (mpt180) REVERT: A 450 LYS cc_start: 0.7919 (mmmt) cc_final: 0.6915 (mtmm) REVERT: A 1338 GLN cc_start: 0.8530 (tt0) cc_final: 0.8248 (tt0) REVERT: A 1362 ARG cc_start: 0.8236 (ttp-170) cc_final: 0.7827 (mtm110) REVERT: A 1420 GLN cc_start: 0.8058 (mt0) cc_final: 0.7777 (mt0) REVERT: A 1552 GLU cc_start: 0.8211 (tt0) cc_final: 0.7736 (tp30) REVERT: A 1559 ASN cc_start: 0.8647 (t0) cc_final: 0.8189 (t0) REVERT: A 1752 ARG cc_start: 0.7853 (ttt90) cc_final: 0.7468 (ttt90) REVERT: A 1888 LYS cc_start: 0.8608 (tttt) cc_final: 0.8328 (ttpp) REVERT: A 1892 ARG cc_start: 0.7866 (ttp80) cc_final: 0.7335 (ttp80) REVERT: A 2009 ARG cc_start: 0.7684 (tpt170) cc_final: 0.7453 (tpt-90) outliers start: 16 outliers final: 15 residues processed: 202 average time/residue: 0.3181 time to fit residues: 92.4373 Evaluate side-chains 200 residues out of total 1707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 185 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 771 GLU Chi-restraints excluded: chain A residue 926 THR Chi-restraints excluded: chain A residue 932 ILE Chi-restraints excluded: chain A residue 1230 ASP Chi-restraints excluded: chain A residue 1266 LEU Chi-restraints excluded: chain A residue 1271 ARG Chi-restraints excluded: chain A residue 1354 MET Chi-restraints excluded: chain A residue 1487 ILE Chi-restraints excluded: chain A residue 1491 ILE Chi-restraints excluded: chain A residue 1503 VAL Chi-restraints excluded: chain A residue 1504 LYS Chi-restraints excluded: chain A residue 1725 TRP Chi-restraints excluded: chain A residue 1807 THR Chi-restraints excluded: chain A residue 1883 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 181 optimal weight: 3.9990 chunk 140 optimal weight: 0.9990 chunk 24 optimal weight: 0.5980 chunk 25 optimal weight: 0.3980 chunk 113 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 chunk 3 optimal weight: 0.5980 chunk 88 optimal weight: 0.9990 chunk 84 optimal weight: 0.9980 chunk 159 optimal weight: 0.8980 chunk 16 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 580 ASN A1620 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.105922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.086372 restraints weight = 56856.435| |-----------------------------------------------------------------------------| r_work (start): 0.3044 rms_B_bonded: 1.68 r_work: 0.2941 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2812 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.1499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15359 Z= 0.143 Angle : 0.463 6.090 20804 Z= 0.248 Chirality : 0.036 0.137 2374 Planarity : 0.003 0.043 2630 Dihedral : 4.059 42.214 1997 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.23 % Allowed : 8.49 % Favored : 90.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.01 (0.20), residues: 1841 helix: 1.99 (0.15), residues: 1251 sheet: -0.02 (1.50), residues: 10 loop : -0.03 (0.28), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1930 TYR 0.017 0.001 TYR A 267 PHE 0.012 0.001 PHE A 431 TRP 0.009 0.001 TRP A1458 HIS 0.007 0.001 HIS A 486 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.14 (15359) covalent geometry : angle 0.46252 / 0.25 (20804) hydrogen bonds : bond 0.04024 / 2.65 ( 922) hydrogen bonds : angle 3.81015 / 2.65 ( 2688) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3682 Ramachandran restraints generated. 1841 Oldfield, 0 Emsley, 1841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3682 Ramachandran restraints generated. 1841 Oldfield, 0 Emsley, 1841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 184 time to evaluate : 0.819 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 285 ASP cc_start: 0.8277 (m-30) cc_final: 0.7714 (m-30) REVERT: A 288 GLU cc_start: 0.7810 (tt0) cc_final: 0.7592 (tt0) REVERT: A 333 ARG cc_start: 0.7912 (mmp-170) cc_final: 0.7411 (mpt180) REVERT: A 450 LYS cc_start: 0.7914 (mmmt) cc_final: 0.6964 (mtmm) REVERT: A 771 GLU cc_start: 0.7816 (OUTLIER) cc_final: 0.7436 (mm-30) REVERT: A 1338 GLN cc_start: 0.8467 (tt0) cc_final: 0.8169 (tt0) REVERT: A 1362 ARG cc_start: 0.8201 (ttp-170) cc_final: 0.7860 (mtm110) REVERT: A 1420 GLN cc_start: 0.8012 (mt0) cc_final: 0.7761 (mt0) REVERT: A 1552 GLU cc_start: 0.8186 (tt0) cc_final: 0.7662 (tp30) REVERT: A 1559 ASN cc_start: 0.8666 (t0) cc_final: 0.8205 (t0) REVERT: A 1752 ARG cc_start: 0.7859 (ttt90) cc_final: 0.7439 (ttt90) REVERT: A 1888 LYS cc_start: 0.8551 (tttt) cc_final: 0.8266 (ttpp) REVERT: A 1892 ARG cc_start: 0.7859 (ttp80) cc_final: 0.7332 (ttp80) REVERT: A 2009 ARG cc_start: 0.7686 (tpt170) cc_final: 0.7431 (tpt-90) outliers start: 21 outliers final: 17 residues processed: 199 average time/residue: 0.3093 time to fit residues: 88.3230 Evaluate side-chains 201 residues out of total 1707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 183 time to evaluate : 0.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 330 ASP Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 504 LYS Chi-restraints excluded: chain A residue 724 ILE Chi-restraints excluded: chain A residue 771 GLU Chi-restraints excluded: chain A residue 926 THR Chi-restraints excluded: chain A residue 932 ILE Chi-restraints excluded: chain A residue 1271 ARG Chi-restraints excluded: chain A residue 1297 LYS Chi-restraints excluded: chain A residue 1354 MET Chi-restraints excluded: chain A residue 1487 ILE Chi-restraints excluded: chain A residue 1491 ILE Chi-restraints excluded: chain A residue 1503 VAL Chi-restraints excluded: chain A residue 1504 LYS Chi-restraints excluded: chain A residue 1725 TRP Chi-restraints excluded: chain A residue 1807 THR Chi-restraints excluded: chain A residue 1883 ILE Chi-restraints excluded: chain A residue 2015 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 11 optimal weight: 0.5980 chunk 121 optimal weight: 0.9980 chunk 126 optimal weight: 0.9990 chunk 56 optimal weight: 0.8980 chunk 69 optimal weight: 1.9990 chunk 81 optimal weight: 0.3980 chunk 17 optimal weight: 0.9980 chunk 90 optimal weight: 2.9990 chunk 166 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 122 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 580 ASN A1620 GLN A1814 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.112381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.093916 restraints weight = 55738.386| |-----------------------------------------------------------------------------| r_work (start): 0.3079 rms_B_bonded: 1.58 r_work: 0.2979 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.2849 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.2849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.1599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15359 Z= 0.150 Angle : 0.468 5.933 20804 Z= 0.250 Chirality : 0.036 0.141 2374 Planarity : 0.003 0.043 2630 Dihedral : 4.067 40.471 1997 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.17 % Allowed : 8.73 % Favored : 90.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.99 (0.20), residues: 1841 helix: 1.98 (0.15), residues: 1249 sheet: -0.08 (1.51), residues: 10 loop : -0.04 (0.28), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1930 TYR 0.018 0.001 TYR A 267 PHE 0.012 0.001 PHE A 431 TRP 0.009 0.001 TRP A1458 HIS 0.005 0.001 HIS A 486 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.15 (15359) covalent geometry : angle 0.46789 / 0.25 (20804) hydrogen bonds : bond 0.04051 / 2.67 ( 922) hydrogen bonds : angle 3.79736 / 2.65 ( 2688) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3682 Ramachandran restraints generated. 1841 Oldfield, 0 Emsley, 1841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3682 Ramachandran restraints generated. 1841 Oldfield, 0 Emsley, 1841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 185 time to evaluate : 0.774 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 288 GLU cc_start: 0.7803 (tt0) cc_final: 0.7602 (tt0) REVERT: A 333 ARG cc_start: 0.7910 (mmp-170) cc_final: 0.7458 (mpt180) REVERT: A 450 LYS cc_start: 0.7873 (mmmt) cc_final: 0.6951 (mtmm) REVERT: A 771 GLU cc_start: 0.7863 (OUTLIER) cc_final: 0.7505 (mm-30) REVERT: A 948 ASP cc_start: 0.8381 (m-30) cc_final: 0.8171 (m-30) REVERT: A 1235 GLU cc_start: 0.7897 (tt0) cc_final: 0.7619 (tt0) REVERT: A 1338 GLN cc_start: 0.8492 (tt0) cc_final: 0.8198 (tt0) REVERT: A 1362 ARG cc_start: 0.8212 (ttp-170) cc_final: 0.7864 (mtm110) REVERT: A 1420 GLN cc_start: 0.8091 (mt0) cc_final: 0.7860 (mt0) REVERT: A 1552 GLU cc_start: 0.8184 (tt0) cc_final: 0.7688 (tp30) REVERT: A 1559 ASN cc_start: 0.8679 (t0) cc_final: 0.8225 (t0) REVERT: A 1752 ARG cc_start: 0.7944 (ttt90) cc_final: 0.7584 (ttt90) REVERT: A 1888 LYS cc_start: 0.8577 (tttt) cc_final: 0.8308 (ttpp) REVERT: A 1892 ARG cc_start: 0.7795 (ttp80) cc_final: 0.7286 (ttp80) outliers start: 20 outliers final: 16 residues processed: 199 average time/residue: 0.3239 time to fit residues: 92.4982 Evaluate side-chains 197 residues out of total 1707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 180 time to evaluate : 0.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 330 ASP Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 504 LYS Chi-restraints excluded: chain A residue 724 ILE Chi-restraints excluded: chain A residue 771 GLU Chi-restraints excluded: chain A residue 926 THR Chi-restraints excluded: chain A residue 932 ILE Chi-restraints excluded: chain A residue 1271 ARG Chi-restraints excluded: chain A residue 1297 LYS Chi-restraints excluded: chain A residue 1354 MET Chi-restraints excluded: chain A residue 1487 ILE Chi-restraints excluded: chain A residue 1491 ILE Chi-restraints excluded: chain A residue 1503 VAL Chi-restraints excluded: chain A residue 1725 TRP Chi-restraints excluded: chain A residue 1807 THR Chi-restraints excluded: chain A residue 1883 ILE Chi-restraints excluded: chain A residue 2015 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 80 optimal weight: 0.9980 chunk 27 optimal weight: 0.9980 chunk 156 optimal weight: 0.4980 chunk 168 optimal weight: 0.9990 chunk 155 optimal weight: 0.9990 chunk 78 optimal weight: 0.9980 chunk 116 optimal weight: 0.6980 chunk 53 optimal weight: 0.9990 chunk 15 optimal weight: 0.9990 chunk 175 optimal weight: 0.9990 chunk 81 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 580 ASN A1620 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.106424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.087708 restraints weight = 56995.462| |-----------------------------------------------------------------------------| r_work (start): 0.3070 rms_B_bonded: 1.59 r_work: 0.2967 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.2839 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.1684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 15359 Z= 0.161 Angle : 0.474 5.958 20804 Z= 0.254 Chirality : 0.037 0.150 2374 Planarity : 0.004 0.044 2630 Dihedral : 4.089 40.102 1997 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.17 % Allowed : 8.96 % Favored : 89.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.97 (0.20), residues: 1841 helix: 1.98 (0.15), residues: 1249 sheet: -0.13 (1.49), residues: 10 loop : -0.11 (0.28), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1930 TYR 0.019 0.001 TYR A 267 PHE 0.013 0.001 PHE A 431 TRP 0.009 0.001 TRP A1458 HIS 0.005 0.001 HIS A 313 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.16 (15359) covalent geometry : angle 0.47411 / 0.25 (20804) hydrogen bonds : bond 0.04105 / 2.71 ( 922) hydrogen bonds : angle 3.79925 / 2.65 ( 2688) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3682 Ramachandran restraints generated. 1841 Oldfield, 0 Emsley, 1841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3682 Ramachandran restraints generated. 1841 Oldfield, 0 Emsley, 1841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 182 time to evaluate : 0.625 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: A 288 GLU cc_start: 0.7789 (tt0) cc_final: 0.7583 (tt0) REVERT: A 333 ARG cc_start: 0.7915 (mmp-170) cc_final: 0.7459 (mpt180) REVERT: A 450 LYS cc_start: 0.7867 (mmmt) cc_final: 0.6936 (mtmm) REVERT: A 771 GLU cc_start: 0.7725 (OUTLIER) cc_final: 0.7385 (mm-30) REVERT: A 948 ASP cc_start: 0.8359 (m-30) cc_final: 0.8148 (m-30) REVERT: A 1235 GLU cc_start: 0.7933 (tt0) cc_final: 0.7674 (tt0) REVERT: A 1338 GLN cc_start: 0.8500 (tt0) cc_final: 0.8201 (tt0) REVERT: A 1362 ARG cc_start: 0.8213 (ttp-170) cc_final: 0.7853 (mtm110) REVERT: A 1420 GLN cc_start: 0.8109 (mt0) cc_final: 0.7873 (mt0) REVERT: A 1552 GLU cc_start: 0.8198 (tt0) cc_final: 0.7695 (tp30) REVERT: A 1559 ASN cc_start: 0.8681 (t0) cc_final: 0.8228 (t0) REVERT: A 1752 ARG cc_start: 0.7960 (ttt90) cc_final: 0.7592 (ttt90) REVERT: A 1888 LYS cc_start: 0.8583 (tttt) cc_final: 0.8311 (ttpp) REVERT: A 1892 ARG cc_start: 0.7810 (ttp80) cc_final: 0.7306 (ttp80) REVERT: A 2082 ILE cc_start: 0.7745 (mt) cc_final: 0.7489 (mm) outliers start: 20 outliers final: 17 residues processed: 194 average time/residue: 0.3006 time to fit residues: 84.1413 Evaluate side-chains 197 residues out of total 1707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 179 time to evaluate : 0.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 330 ASP Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 504 LYS Chi-restraints excluded: chain A residue 724 ILE Chi-restraints excluded: chain A residue 771 GLU Chi-restraints excluded: chain A residue 926 THR Chi-restraints excluded: chain A residue 1271 ARG Chi-restraints excluded: chain A residue 1297 LYS Chi-restraints excluded: chain A residue 1354 MET Chi-restraints excluded: chain A residue 1487 ILE Chi-restraints excluded: chain A residue 1491 ILE Chi-restraints excluded: chain A residue 1503 VAL Chi-restraints excluded: chain A residue 1725 TRP Chi-restraints excluded: chain A residue 1749 MET Chi-restraints excluded: chain A residue 1807 THR Chi-restraints excluded: chain A residue 1883 ILE Chi-restraints excluded: chain A residue 2015 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 93 optimal weight: 1.9990 chunk 11 optimal weight: 0.6980 chunk 67 optimal weight: 1.9990 chunk 75 optimal weight: 0.5980 chunk 95 optimal weight: 0.5980 chunk 140 optimal weight: 0.9980 chunk 175 optimal weight: 1.9990 chunk 128 optimal weight: 0.4980 chunk 55 optimal weight: 0.9990 chunk 164 optimal weight: 1.9990 chunk 24 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 580 ASN A1620 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.107241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.088625 restraints weight = 56585.442| |-----------------------------------------------------------------------------| r_work (start): 0.3065 rms_B_bonded: 1.58 r_work: 0.2964 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.2835 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.2835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.1764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 15359 Z= 0.129 Angle : 0.457 5.772 20804 Z= 0.244 Chirality : 0.036 0.142 2374 Planarity : 0.003 0.043 2630 Dihedral : 4.014 38.417 1997 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.00 % Allowed : 9.37 % Favored : 89.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.07 (0.20), residues: 1841 helix: 2.07 (0.15), residues: 1249 sheet: -0.03 (1.50), residues: 10 loop : -0.08 (0.28), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1176 TYR 0.017 0.001 TYR A1296 PHE 0.011 0.001 PHE A1877 TRP 0.009 0.001 TRP A1458 HIS 0.005 0.001 HIS A1173 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.13 (15359) covalent geometry : angle 0.45746 / 0.24 (20804) hydrogen bonds : bond 0.03891 / 2.56 ( 922) hydrogen bonds : angle 3.73905 / 2.60 ( 2688) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3682 Ramachandran restraints generated. 1841 Oldfield, 0 Emsley, 1841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3682 Ramachandran restraints generated. 1841 Oldfield, 0 Emsley, 1841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 183 time to evaluate : 0.673 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 288 GLU cc_start: 0.7773 (tt0) cc_final: 0.7571 (tt0) REVERT: A 333 ARG cc_start: 0.7868 (mmp-170) cc_final: 0.7364 (mpt180) REVERT: A 450 LYS cc_start: 0.7848 (mmmt) cc_final: 0.6929 (mtmm) REVERT: A 771 GLU cc_start: 0.7738 (OUTLIER) cc_final: 0.7490 (mm-30) REVERT: A 948 ASP cc_start: 0.8288 (m-30) cc_final: 0.8075 (m-30) REVERT: A 963 GLN cc_start: 0.8168 (mt0) cc_final: 0.7842 (mp10) REVERT: A 1235 GLU cc_start: 0.7938 (tt0) cc_final: 0.7674 (tt0) REVERT: A 1338 GLN cc_start: 0.8488 (tt0) cc_final: 0.8202 (tt0) REVERT: A 1362 ARG cc_start: 0.8203 (ttp-170) cc_final: 0.7854 (mtm110) REVERT: A 1420 GLN cc_start: 0.8112 (mt0) cc_final: 0.7882 (mt0) REVERT: A 1552 GLU cc_start: 0.8229 (tt0) cc_final: 0.7724 (tp30) REVERT: A 1559 ASN cc_start: 0.8682 (t0) cc_final: 0.8228 (t0) REVERT: A 1752 ARG cc_start: 0.7953 (ttt90) cc_final: 0.7739 (ttt90) REVERT: A 1888 LYS cc_start: 0.8586 (tttt) cc_final: 0.8321 (ttpp) REVERT: A 1892 ARG cc_start: 0.7798 (ttp80) cc_final: 0.7299 (ttp80) REVERT: A 2082 ILE cc_start: 0.7692 (mt) cc_final: 0.7426 (mm) outliers start: 17 outliers final: 15 residues processed: 195 average time/residue: 0.3043 time to fit residues: 85.8289 Evaluate side-chains 199 residues out of total 1707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 183 time to evaluate : 0.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 504 LYS Chi-restraints excluded: chain A residue 724 ILE Chi-restraints excluded: chain A residue 771 GLU Chi-restraints excluded: chain A residue 926 THR Chi-restraints excluded: chain A residue 932 ILE Chi-restraints excluded: chain A residue 1271 ARG Chi-restraints excluded: chain A residue 1297 LYS Chi-restraints excluded: chain A residue 1354 MET Chi-restraints excluded: chain A residue 1487 ILE Chi-restraints excluded: chain A residue 1491 ILE Chi-restraints excluded: chain A residue 1503 VAL Chi-restraints excluded: chain A residue 1725 TRP Chi-restraints excluded: chain A residue 1807 THR Chi-restraints excluded: chain A residue 1883 ILE Chi-restraints excluded: chain A residue 2015 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 160 optimal weight: 0.9990 chunk 42 optimal weight: 0.7980 chunk 32 optimal weight: 0.9990 chunk 173 optimal weight: 0.0980 chunk 25 optimal weight: 0.0670 chunk 129 optimal weight: 0.1980 chunk 71 optimal weight: 0.9980 chunk 45 optimal weight: 0.9980 chunk 150 optimal weight: 1.9990 chunk 27 optimal weight: 0.5980 chunk 166 optimal weight: 0.2980 overall best weight: 0.2518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 580 ASN ** A 720 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.112347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.094299 restraints weight = 55321.008| |-----------------------------------------------------------------------------| r_work (start): 0.3121 rms_B_bonded: 1.54 r_work: 0.3022 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.2896 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.1877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 15359 Z= 0.096 Angle : 0.444 6.547 20804 Z= 0.235 Chirality : 0.035 0.137 2374 Planarity : 0.003 0.043 2630 Dihedral : 3.871 36.715 1997 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 0.70 % Allowed : 9.78 % Favored : 89.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.33 (0.21), residues: 1841 helix: 2.24 (0.15), residues: 1252 sheet: 0.14 (1.60), residues: 10 loop : 0.06 (0.28), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1466 TYR 0.016 0.001 TYR A1296 PHE 0.015 0.001 PHE A1485 TRP 0.010 0.001 TRP A 243 HIS 0.006 0.001 HIS A1173 Details of bonding type rmsd/Z covalent geometry : bond 0.00215 / 0.10 (15359) covalent geometry : angle 0.44446 / 0.24 (20804) hydrogen bonds : bond 0.03502 / 2.30 ( 922) hydrogen bonds : angle 3.62898 / 2.53 ( 2688) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3682 Ramachandran restraints generated. 1841 Oldfield, 0 Emsley, 1841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3682 Ramachandran restraints generated. 1841 Oldfield, 0 Emsley, 1841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 190 time to evaluate : 0.812 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: A 285 ASP cc_start: 0.8214 (m-30) cc_final: 0.7656 (m-30) REVERT: A 288 GLU cc_start: 0.7707 (tt0) cc_final: 0.7484 (tt0) REVERT: A 333 ARG cc_start: 0.7893 (mmp-170) cc_final: 0.7443 (mpt180) REVERT: A 450 LYS cc_start: 0.7842 (mmmt) cc_final: 0.6940 (mtmm) REVERT: A 771 GLU cc_start: 0.7709 (OUTLIER) cc_final: 0.7436 (mm-30) REVERT: A 931 GLU cc_start: 0.8322 (pt0) cc_final: 0.8095 (pt0) REVERT: A 963 GLN cc_start: 0.8185 (mt0) cc_final: 0.7922 (mp10) REVERT: A 1235 GLU cc_start: 0.7797 (tt0) cc_final: 0.7509 (tt0) REVERT: A 1338 GLN cc_start: 0.8454 (tt0) cc_final: 0.8166 (tt0) REVERT: A 1358 LYS cc_start: 0.8441 (tptp) cc_final: 0.8030 (mppt) REVERT: A 1362 ARG cc_start: 0.8095 (ttp-170) cc_final: 0.7763 (mtm110) REVERT: A 1420 GLN cc_start: 0.8084 (mt0) cc_final: 0.7849 (mt0) REVERT: A 1552 GLU cc_start: 0.8110 (tt0) cc_final: 0.7665 (tp30) REVERT: A 1559 ASN cc_start: 0.8682 (t0) cc_final: 0.8232 (t0) REVERT: A 1752 ARG cc_start: 0.7887 (ttt90) cc_final: 0.7676 (ttt90) REVERT: A 1888 LYS cc_start: 0.8529 (tttt) cc_final: 0.8281 (ttpp) REVERT: A 1892 ARG cc_start: 0.7731 (ttp80) cc_final: 0.7239 (ttp80) REVERT: A 2082 ILE cc_start: 0.7712 (mt) cc_final: 0.7446 (mm) outliers start: 12 outliers final: 10 residues processed: 199 average time/residue: 0.3052 time to fit residues: 87.1990 Evaluate side-chains 193 residues out of total 1707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 182 time to evaluate : 0.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 504 LYS Chi-restraints excluded: chain A residue 771 GLU Chi-restraints excluded: chain A residue 926 THR Chi-restraints excluded: chain A residue 932 ILE Chi-restraints excluded: chain A residue 1271 ARG Chi-restraints excluded: chain A residue 1297 LYS Chi-restraints excluded: chain A residue 1487 ILE Chi-restraints excluded: chain A residue 1491 ILE Chi-restraints excluded: chain A residue 1883 ILE Chi-restraints excluded: chain A residue 2015 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 7 optimal weight: 0.9980 chunk 136 optimal weight: 0.7980 chunk 129 optimal weight: 0.6980 chunk 135 optimal weight: 0.8980 chunk 70 optimal weight: 0.9980 chunk 60 optimal weight: 0.3980 chunk 23 optimal weight: 0.9990 chunk 179 optimal weight: 4.9990 chunk 116 optimal weight: 0.3980 chunk 151 optimal weight: 1.9990 chunk 174 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 313 HIS A 580 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.110236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.091962 restraints weight = 56099.955| |-----------------------------------------------------------------------------| r_work (start): 0.3100 rms_B_bonded: 1.55 r_work: 0.2998 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.2870 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.1901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15359 Z= 0.133 Angle : 0.461 6.450 20804 Z= 0.245 Chirality : 0.036 0.140 2374 Planarity : 0.003 0.046 2630 Dihedral : 3.900 36.267 1997 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 0.76 % Allowed : 9.61 % Favored : 89.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.24 (0.20), residues: 1841 helix: 2.18 (0.15), residues: 1252 sheet: 0.15 (1.58), residues: 10 loop : 0.02 (0.28), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1466 TYR 0.016 0.001 TYR A1296 PHE 0.012 0.001 PHE A 431 TRP 0.009 0.001 TRP A1458 HIS 0.005 0.001 HIS A1173 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.13 (15359) covalent geometry : angle 0.46136 / 0.25 (20804) hydrogen bonds : bond 0.03720 / 2.45 ( 922) hydrogen bonds : angle 3.68695 / 2.57 ( 2688) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5872.29 seconds wall clock time: 100 minutes 23.70 seconds (6023.70 seconds total)