Starting phenix.real_space_refine on Wed Feb 4 04:24:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9pnq_71768/02_2026/9pnq_71768.cif Found real_map, /net/cci-nas-00/data/ceres_data/9pnq_71768/02_2026/9pnq_71768.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.61 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9pnq_71768/02_2026/9pnq_71768.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9pnq_71768/02_2026/9pnq_71768.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9pnq_71768/02_2026/9pnq_71768.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9pnq_71768/02_2026/9pnq_71768.map" } resolution = 2.61 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= 0.003 sd= 0.008 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 41 5.16 5 C 5304 2.51 5 N 1436 2.21 5 O 1668 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8449 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 8449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1095, 8449 Classifications: {'peptide': 1095} Link IDs: {'PTRANS': 43, 'TRANS': 1051} Time building chain proxies: 2.06, per 1000 atoms: 0.24 Number of scatterers: 8449 At special positions: 0 Unit cell: (94.926, 97.36, 111.964, 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 41 16.00 O 1668 8.00 N 1436 7.00 C 5304 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: 0.63 Conformation dependent library (CDL) restraints added in 339.1 milliseconds 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2050 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 15 sheets defined 64.0% alpha, 6.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.38 Creating SS restraints... Processing helix chain 'A' and resid 1050 through 1059 removed outlier: 3.844A pdb=" N ALA A1056 " --> pdb=" O LEU A1052 " (cutoff:3.500A) Processing helix chain 'A' and resid 1061 through 1070 Processing helix chain 'A' and resid 1079 through 1110 removed outlier: 3.697A pdb=" N GLU A1088 " --> pdb=" O LYS A1084 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLY A1095 " --> pdb=" O GLU A1091 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ALA A1105 " --> pdb=" O ARG A1101 " (cutoff:3.500A) Processing helix chain 'A' and resid 1112 through 1118 Processing helix chain 'A' and resid 1122 through 1126 removed outlier: 3.658A pdb=" N ARG A1125 " --> pdb=" O GLU A1122 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N TRP A1126 " --> pdb=" O ALA A1123 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1122 through 1126' Processing helix chain 'A' and resid 1129 through 1133 removed outlier: 3.861A pdb=" N ASN A1133 " --> pdb=" O LYS A1130 " (cutoff:3.500A) Processing helix chain 'A' and resid 1145 through 1163 removed outlier: 3.520A pdb=" N LEU A1161 " --> pdb=" O LEU A1157 " (cutoff:3.500A) Processing helix chain 'A' and resid 1164 through 1167 removed outlier: 3.656A pdb=" N THR A1167 " --> pdb=" O THR A1164 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1164 through 1167' Processing helix chain 'A' and resid 1171 through 1180 Processing helix chain 'A' and resid 1182 through 1186 Processing helix chain 'A' and resid 1189 through 1195 Processing helix chain 'A' and resid 1200 through 1216 removed outlier: 3.549A pdb=" N LYS A1210 " --> pdb=" O SER A1206 " (cutoff:3.500A) Processing helix chain 'A' and resid 1224 through 1229 Processing helix chain 'A' and resid 1229 through 1246 removed outlier: 3.624A pdb=" N THR A1233 " --> pdb=" O LYS A1229 " (cutoff:3.500A) Processing helix chain 'A' and resid 1256 through 1260 Processing helix chain 'A' and resid 1279 through 1284 Processing helix chain 'A' and resid 1286 through 1293 Processing helix chain 'A' and resid 1322 through 1333 Processing helix chain 'A' and resid 1340 through 1351 Processing helix chain 'A' and resid 1351 through 1360 Processing helix chain 'A' and resid 1365 through 1369 removed outlier: 3.712A pdb=" N LEU A1369 " --> pdb=" O LYS A1366 " (cutoff:3.500A) Processing helix chain 'A' and resid 1370 through 1400 removed outlier: 3.500A pdb=" N LYS A1375 " --> pdb=" O ASP A1371 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N SER A1376 " --> pdb=" O ASN A1372 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N VAL A1384 " --> pdb=" O LYS A1380 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLN A1397 " --> pdb=" O SER A1393 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ALA A1400 " --> pdb=" O GLU A1396 " (cutoff:3.500A) Processing helix chain 'A' and resid 1404 through 1408 removed outlier: 3.902A pdb=" N VAL A1408 " --> pdb=" O ILE A1405 " (cutoff:3.500A) Processing helix chain 'A' and resid 1433 through 1438 removed outlier: 3.530A pdb=" N GLU A1438 " --> pdb=" O LYS A1434 " (cutoff:3.500A) Processing helix chain 'A' and resid 1454 through 1468 removed outlier: 3.511A pdb=" N ALA A1459 " --> pdb=" O GLU A1455 " (cutoff:3.500A) Processing helix chain 'A' and resid 1471 through 1475 removed outlier: 3.884A pdb=" N MET A1475 " --> pdb=" O VAL A1472 " (cutoff:3.500A) Processing helix chain 'A' and resid 1476 through 1490 removed outlier: 3.505A pdb=" N LEU A1487 " --> pdb=" O GLU A1483 " (cutoff:3.500A) Processing helix chain 'A' and resid 1492 through 1506 removed outlier: 3.582A pdb=" N THR A1504 " --> pdb=" O VAL A1500 " (cutoff:3.500A) Processing helix chain 'A' and resid 1511 through 1521 Processing helix chain 'A' and resid 1522 through 1524 No H-bonds generated for 'chain 'A' and resid 1522 through 1524' Processing helix chain 'A' and resid 1525 through 1540 removed outlier: 3.642A pdb=" N LEU A1529 " --> pdb=" O SER A1525 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N MET A1530 " --> pdb=" O PHE A1526 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA A1531 " --> pdb=" O VAL A1527 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N VAL A1540 " --> pdb=" O SER A1536 " (cutoff:3.500A) Processing helix chain 'A' and resid 1543 through 1546 removed outlier: 3.749A pdb=" N ALA A1546 " --> pdb=" O ASP A1543 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1543 through 1546' Processing helix chain 'A' and resid 1559 through 1569 Processing helix chain 'A' and resid 1575 through 1584 removed outlier: 3.958A pdb=" N LYS A1584 " --> pdb=" O ARG A1580 " (cutoff:3.500A) Processing helix chain 'A' and resid 1595 through 1603 Processing helix chain 'A' and resid 1607 through 1627 Processing helix chain 'A' and resid 1630 through 1648 removed outlier: 3.703A pdb=" N PHE A1647 " --> pdb=" O LEU A1643 " (cutoff:3.500A) Processing helix chain 'A' and resid 1663 through 1665 No H-bonds generated for 'chain 'A' and resid 1663 through 1665' Processing helix chain 'A' and resid 1666 through 1675 removed outlier: 3.524A pdb=" N ILE A1674 " --> pdb=" O LEU A1670 " (cutoff:3.500A) Processing helix chain 'A' and resid 1678 through 1708 removed outlier: 3.590A pdb=" N VAL A1690 " --> pdb=" O LEU A1686 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ASP A1700 " --> pdb=" O GLU A1696 " (cutoff:3.500A) Processing helix chain 'A' and resid 1712 through 1719 Processing helix chain 'A' and resid 1724 through 1744 Processing helix chain 'A' and resid 1776 through 1790 Processing helix chain 'A' and resid 1790 through 1803 Processing helix chain 'A' and resid 1803 through 1840 removed outlier: 3.759A pdb=" N VAL A1807 " --> pdb=" O GLY A1803 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLN A1833 " --> pdb=" O LYS A1829 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLU A1834 " --> pdb=" O GLN A1830 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LYS A1835 " --> pdb=" O ARG A1831 " (cutoff:3.500A) Processing helix chain 'A' and resid 1852 through 1862 Processing helix chain 'A' and resid 1863 through 1867 Processing helix chain 'A' and resid 1915 through 1924 Processing helix chain 'A' and resid 1925 through 1936 removed outlier: 3.529A pdb=" N THR A1935 " --> pdb=" O GLN A1931 " (cutoff:3.500A) Processing helix chain 'A' and resid 1956 through 1972 Processing helix chain 'A' and resid 1975 through 1991 removed outlier: 3.605A pdb=" N LYS A1986 " --> pdb=" O GLU A1982 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ASN A1990 " --> pdb=" O LYS A1986 " (cutoff:3.500A) Processing helix chain 'A' and resid 1992 through 1996 removed outlier: 3.544A pdb=" N LYS A1995 " --> pdb=" O ASP A1992 " (cutoff:3.500A) Processing helix chain 'A' and resid 1997 through 2009 removed outlier: 3.808A pdb=" N SER A2007 " --> pdb=" O ALA A2003 " (cutoff:3.500A) Processing helix chain 'A' and resid 2011 through 2015 removed outlier: 3.584A pdb=" N ARG A2014 " --> pdb=" O TYR A2011 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N GLU A2015 " --> pdb=" O ASP A2012 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2011 through 2015' Processing helix chain 'A' and resid 2018 through 2048 removed outlier: 3.800A pdb=" N ILE A2029 " --> pdb=" O ALA A2025 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLU A2030 " --> pdb=" O ALA A2026 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ARG A2031 " --> pdb=" O SER A2027 " (cutoff:3.500A) Processing helix chain 'A' and resid 2076 through 2101 removed outlier: 3.544A pdb=" N ASP A2082 " --> pdb=" O GLU A2078 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 1035 through 1036 Processing sheet with id=AA2, first strand: chain 'A' and resid 1135 through 1138 Processing sheet with id=AA3, first strand: chain 'A' and resid 1198 through 1199 Processing sheet with id=AA4, first strand: chain 'A' and resid 1301 through 1302 removed outlier: 4.531A pdb=" N PHE A1301 " --> pdb=" O HIS A1411 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N HIS A1411 " --> pdb=" O PHE A1301 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 1312 through 1313 removed outlier: 6.686A pdb=" N VAL A1319 " --> pdb=" O GLN A1313 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1338 through 1339 Processing sheet with id=AA7, first strand: chain 'A' and resid 1414 through 1416 Processing sheet with id=AA8, first strand: chain 'A' and resid 1445 through 1447 Processing sheet with id=AA9, first strand: chain 'A' and resid 1552 through 1554 Processing sheet with id=AB1, first strand: chain 'A' and resid 1587 through 1589 Processing sheet with id=AB2, first strand: chain 'A' and resid 1651 through 1653 Processing sheet with id=AB3, first strand: chain 'A' and resid 1745 through 1750 Processing sheet with id=AB4, first strand: chain 'A' and resid 1870 through 1871 Processing sheet with id=AB5, first strand: chain 'A' and resid 1881 through 1884 removed outlier: 3.531A pdb=" N SER A1882 " --> pdb=" O ALA A1908 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1891 through 1893 removed outlier: 6.866A pdb=" N VAL A1902 " --> pdb=" O LEU A1892 " (cutoff:3.500A) 486 hydrogen bonds defined for protein. 1392 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.51 Time building geometry restraints manager: 0.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 2852 1.35 - 1.47: 1751 1.47 - 1.59: 3893 1.59 - 1.70: 0 1.70 - 1.82: 82 Bond restraints: 8578 Sorted by residual: bond pdb=" CB LYS A1766 " pdb=" CG LYS A1766 " ideal model delta sigma weight residual 1.520 1.559 -0.039 3.00e-02 1.11e+03 1.73e+00 bond pdb=" CG LYS A1766 " pdb=" CD LYS A1766 " ideal model delta sigma weight residual 1.520 1.554 -0.034 3.00e-02 1.11e+03 1.32e+00 bond pdb=" CG ARG A1315 " pdb=" CD ARG A1315 " ideal model delta sigma weight residual 1.520 1.545 -0.025 3.00e-02 1.11e+03 7.22e-01 bond pdb=" CG MET A1256 " pdb=" SD MET A1256 " ideal model delta sigma weight residual 1.803 1.823 -0.020 2.50e-02 1.60e+03 6.67e-01 bond pdb=" CB MET A1256 " pdb=" CG MET A1256 " ideal model delta sigma weight residual 1.520 1.543 -0.023 3.00e-02 1.11e+03 6.05e-01 ... (remaining 8573 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.32: 11544 2.32 - 4.64: 50 4.64 - 6.96: 6 6.96 - 9.28: 1 9.28 - 11.59: 1 Bond angle restraints: 11602 Sorted by residual: angle pdb=" CB MET A1256 " pdb=" CG MET A1256 " pdb=" SD MET A1256 " ideal model delta sigma weight residual 112.70 124.29 -11.59 3.00e+00 1.11e-01 1.49e+01 angle pdb=" CB LYS A1766 " pdb=" CG LYS A1766 " pdb=" CD LYS A1766 " ideal model delta sigma weight residual 111.30 119.98 -8.68 2.30e+00 1.89e-01 1.42e+01 angle pdb=" CA LYS A1766 " pdb=" CB LYS A1766 " pdb=" CG LYS A1766 " ideal model delta sigma weight residual 114.10 118.60 -4.50 2.00e+00 2.50e-01 5.05e+00 angle pdb=" CG MET A1256 " pdb=" SD MET A1256 " pdb=" CE MET A1256 " ideal model delta sigma weight residual 100.90 105.81 -4.91 2.20e+00 2.07e-01 4.98e+00 angle pdb=" CG LYS A1766 " pdb=" CD LYS A1766 " pdb=" CE LYS A1766 " ideal model delta sigma weight residual 111.30 116.10 -4.80 2.30e+00 1.89e-01 4.35e+00 ... (remaining 11597 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.00: 4586 16.00 - 32.00: 495 32.00 - 48.00: 151 48.00 - 64.01: 43 64.01 - 80.01: 13 Dihedral angle restraints: 5288 sinusoidal: 2114 harmonic: 3174 Sorted by residual: dihedral pdb=" CG ARG A1537 " pdb=" CD ARG A1537 " pdb=" NE ARG A1537 " pdb=" CZ ARG A1537 " ideal model delta sinusoidal sigma weight residual -90.00 -132.73 42.73 2 1.50e+01 4.44e-03 9.82e+00 dihedral pdb=" CB ARG A1477 " pdb=" CG ARG A1477 " pdb=" CD ARG A1477 " pdb=" NE ARG A1477 " ideal model delta sinusoidal sigma weight residual -180.00 -120.19 -59.81 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" CA LYS A1028 " pdb=" CB LYS A1028 " pdb=" CG LYS A1028 " pdb=" CD LYS A1028 " ideal model delta sinusoidal sigma weight residual 180.00 120.31 59.69 3 1.50e+01 4.44e-03 9.48e+00 ... (remaining 5285 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 833 0.025 - 0.051: 313 0.051 - 0.076: 112 0.076 - 0.101: 44 0.101 - 0.126: 31 Chirality restraints: 1333 Sorted by residual: chirality pdb=" CA ILE A1306 " pdb=" N ILE A1306 " pdb=" C ILE A1306 " pdb=" CB ILE A1306 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.00e-01 chirality pdb=" CA ASN A2067 " pdb=" N ASN A2067 " pdb=" C ASN A2067 " pdb=" CB ASN A2067 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.79e-01 chirality pdb=" CA ILE A1946 " pdb=" N ILE A1946 " pdb=" C ILE A1946 " pdb=" CB ILE A1946 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.56e-01 ... (remaining 1330 not shown) Planarity restraints: 1520 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN A1429 " -0.029 5.00e-02 4.00e+02 4.34e-02 3.01e+00 pdb=" N PRO A1430 " 0.075 5.00e-02 4.00e+02 pdb=" CA PRO A1430 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A1430 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG A1315 " 0.121 9.50e-02 1.11e+02 5.48e-02 2.34e+00 pdb=" NE ARG A1315 " -0.012 2.00e-02 2.50e+03 pdb=" CZ ARG A1315 " 0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG A1315 " -0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG A1315 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A1322 " -0.019 5.00e-02 4.00e+02 2.91e-02 1.35e+00 pdb=" N PRO A1323 " 0.050 5.00e-02 4.00e+02 pdb=" CA PRO A1323 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO A1323 " -0.016 5.00e-02 4.00e+02 ... (remaining 1517 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 630 2.74 - 3.28: 8082 3.28 - 3.82: 12714 3.82 - 4.36: 15730 4.36 - 4.90: 27723 Nonbonded interactions: 64879 Sorted by model distance: nonbonded pdb=" O MET A1920 " pdb=" OG1 THR A1924 " model vdw 2.203 3.040 nonbonded pdb=" N GLU A1039 " pdb=" OE1 GLU A1039 " model vdw 2.235 3.120 nonbonded pdb=" N GLU A1403 " pdb=" OE1 GLU A1403 " model vdw 2.235 3.120 nonbonded pdb=" OH TYR A1969 " pdb=" OD1 ASP A2048 " model vdw 2.263 3.040 nonbonded pdb=" O SER A1744 " pdb=" OG1 THR A1759 " model vdw 2.298 3.040 ... (remaining 64874 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: 2.770 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.790 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 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:7.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8770 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 : 0.002 0.039 8578 Z= 0.073 Angle : 0.397 11.595 11602 Z= 0.201 Chirality : 0.036 0.126 1333 Planarity : 0.003 0.055 1520 Dihedral : 15.553 80.006 3238 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 2.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 0.77 % Allowed : 14.97 % Favored : 84.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.01 (0.24), residues: 1093 helix: 0.16 (0.20), residues: 620 sheet: 1.65 (0.67), residues: 69 loop : -0.37 (0.29), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A1315 TYR 0.005 0.001 TYR A1144 PHE 0.011 0.001 PHE A1987 TRP 0.003 0.000 TRP A1159 HIS 0.001 0.000 HIS A1473 Details of bonding type rmsd covalent geometry : bond 0.00162 ( 8578) covalent geometry : angle 0.39699 (11602) hydrogen bonds : bond 0.30309 ( 486) hydrogen bonds : angle 6.85343 ( 1392) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 53 time to evaluate : 0.377 Fit side-chains REVERT: A 1147 GLN cc_start: 0.8983 (OUTLIER) cc_final: 0.7761 (tm-30) REVERT: A 1289 GLU cc_start: 0.9353 (OUTLIER) cc_final: 0.8678 (tt0) outliers start: 7 outliers final: 4 residues processed: 59 average time/residue: 0.8506 time to fit residues: 52.8137 Evaluate side-chains 59 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 53 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1019 THR Chi-restraints excluded: chain A residue 1067 LEU Chi-restraints excluded: chain A residue 1147 GLN Chi-restraints excluded: chain A residue 1262 ASP Chi-restraints excluded: chain A residue 1289 GLU Chi-restraints excluded: chain A residue 1720 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 108 optimal weight: 1.9990 chunk 49 optimal weight: 0.8980 chunk 97 optimal weight: 0.8980 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 0.5980 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 3.9990 chunk 100 optimal weight: 2.9990 chunk 106 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1119 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.080261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2828 r_free = 0.2828 target = 0.060759 restraints weight = 14974.001| |-----------------------------------------------------------------------------| r_work (start): 0.2822 rms_B_bonded: 2.42 r_work: 0.2671 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2539 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8670 moved from start: 0.1360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8578 Z= 0.160 Angle : 0.507 6.840 11602 Z= 0.276 Chirality : 0.041 0.128 1333 Planarity : 0.004 0.042 1520 Dihedral : 5.083 66.570 1180 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 1.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.75 % Allowed : 13.01 % Favored : 85.25 % 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: 1.18 (0.25), residues: 1093 helix: 1.54 (0.21), residues: 624 sheet: 1.24 (0.63), residues: 72 loop : -0.46 (0.29), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A1315 TYR 0.013 0.001 TYR A2011 PHE 0.017 0.001 PHE A1392 TRP 0.003 0.001 TRP A1578 HIS 0.002 0.001 HIS A1092 Details of bonding type rmsd covalent geometry : bond 0.00339 ( 8578) covalent geometry : angle 0.50671 (11602) hydrogen bonds : bond 0.08255 ( 486) hydrogen bonds : angle 4.57281 ( 1392) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 59 time to evaluate : 0.349 Fit side-chains REVERT: A 1137 GLN cc_start: 0.9200 (tt0) cc_final: 0.8818 (tp40) REVERT: A 1530 MET cc_start: 0.9122 (OUTLIER) cc_final: 0.8883 (ttp) REVERT: A 1946 ILE cc_start: 0.7959 (OUTLIER) cc_final: 0.7744 (mt) outliers start: 16 outliers final: 6 residues processed: 70 average time/residue: 0.7786 time to fit residues: 57.3478 Evaluate side-chains 63 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 55 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1363 THR Chi-restraints excluded: chain A residue 1416 MET Chi-restraints excluded: chain A residue 1418 ARG Chi-restraints excluded: chain A residue 1530 MET Chi-restraints excluded: chain A residue 1558 VAL Chi-restraints excluded: chain A residue 1807 VAL Chi-restraints excluded: chain A residue 1872 THR Chi-restraints excluded: chain A residue 1946 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 66 optimal weight: 6.9990 chunk 102 optimal weight: 0.7980 chunk 41 optimal weight: 2.9990 chunk 70 optimal weight: 4.9990 chunk 27 optimal weight: 0.9980 chunk 105 optimal weight: 0.9980 chunk 26 optimal weight: 3.9990 chunk 17 optimal weight: 0.9980 chunk 78 optimal weight: 1.9990 chunk 57 optimal weight: 0.6980 chunk 48 optimal weight: 0.5980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1119 GLN A2067 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.080527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2833 r_free = 0.2833 target = 0.061010 restraints weight = 15026.102| |-----------------------------------------------------------------------------| r_work (start): 0.2828 rms_B_bonded: 2.41 r_work: 0.2679 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2546 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8663 moved from start: 0.1584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8578 Z= 0.145 Angle : 0.470 5.706 11602 Z= 0.250 Chirality : 0.040 0.134 1333 Planarity : 0.004 0.042 1520 Dihedral : 3.533 22.409 1165 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 1.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 1.97 % Allowed : 12.57 % Favored : 85.46 % 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: 1.51 (0.25), residues: 1093 helix: 1.90 (0.21), residues: 628 sheet: 1.30 (0.64), residues: 70 loop : -0.51 (0.29), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A1315 TYR 0.011 0.001 TYR A1388 PHE 0.017 0.001 PHE A1392 TRP 0.004 0.001 TRP A1159 HIS 0.003 0.001 HIS A1788 Details of bonding type rmsd covalent geometry : bond 0.00323 ( 8578) covalent geometry : angle 0.46989 (11602) hydrogen bonds : bond 0.07008 ( 486) hydrogen bonds : angle 4.20203 ( 1392) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 59 time to evaluate : 0.354 Fit side-chains REVERT: A 1137 GLN cc_start: 0.9180 (tt0) cc_final: 0.8822 (tp40) REVERT: A 1289 GLU cc_start: 0.9280 (OUTLIER) cc_final: 0.8730 (tt0) outliers start: 18 outliers final: 11 residues processed: 73 average time/residue: 0.7431 time to fit residues: 57.2902 Evaluate side-chains 66 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 54 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1067 LEU Chi-restraints excluded: chain A residue 1289 GLU Chi-restraints excluded: chain A residue 1363 THR Chi-restraints excluded: chain A residue 1416 MET Chi-restraints excluded: chain A residue 1418 ARG Chi-restraints excluded: chain A residue 1530 MET Chi-restraints excluded: chain A residue 1558 VAL Chi-restraints excluded: chain A residue 1645 ASP Chi-restraints excluded: chain A residue 1795 ARG Chi-restraints excluded: chain A residue 1807 VAL Chi-restraints excluded: chain A residue 1872 THR Chi-restraints excluded: chain A residue 2073 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 60 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 87 optimal weight: 3.9990 chunk 66 optimal weight: 0.0000 chunk 5 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 chunk 94 optimal weight: 2.9990 chunk 78 optimal weight: 1.9990 chunk 4 optimal weight: 0.5980 overall best weight: 1.5190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1119 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.078110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2788 r_free = 0.2788 target = 0.058813 restraints weight = 15330.444| |-----------------------------------------------------------------------------| r_work (start): 0.2787 rms_B_bonded: 2.41 r_work: 0.2636 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2504 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8698 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 : 0.005 0.042 8578 Z= 0.222 Angle : 0.537 7.192 11602 Z= 0.285 Chirality : 0.043 0.157 1333 Planarity : 0.004 0.043 1520 Dihedral : 3.801 28.181 1165 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 1.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 2.08 % Allowed : 13.66 % Favored : 84.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.30 (0.25), residues: 1093 helix: 1.81 (0.21), residues: 626 sheet: 1.06 (0.63), residues: 72 loop : -0.73 (0.29), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A1315 TYR 0.013 0.002 TYR A1086 PHE 0.020 0.002 PHE A1392 TRP 0.007 0.001 TRP A1159 HIS 0.004 0.001 HIS A1788 Details of bonding type rmsd covalent geometry : bond 0.00541 ( 8578) covalent geometry : angle 0.53707 (11602) hydrogen bonds : bond 0.08039 ( 486) hydrogen bonds : angle 4.30722 ( 1392) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 57 time to evaluate : 0.342 Fit side-chains REVERT: A 1137 GLN cc_start: 0.9181 (tt0) cc_final: 0.8827 (tp40) REVERT: A 1274 GLU cc_start: 0.8386 (mm-30) cc_final: 0.8168 (mm-30) REVERT: A 1289 GLU cc_start: 0.9263 (OUTLIER) cc_final: 0.8695 (tt0) outliers start: 19 outliers final: 15 residues processed: 71 average time/residue: 0.6590 time to fit residues: 49.3432 Evaluate side-chains 72 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 56 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1067 LEU Chi-restraints excluded: chain A residue 1259 ILE Chi-restraints excluded: chain A residue 1289 GLU Chi-restraints excluded: chain A residue 1363 THR Chi-restraints excluded: chain A residue 1416 MET Chi-restraints excluded: chain A residue 1418 ARG Chi-restraints excluded: chain A residue 1530 MET Chi-restraints excluded: chain A residue 1558 VAL Chi-restraints excluded: chain A residue 1645 ASP Chi-restraints excluded: chain A residue 1720 LYS Chi-restraints excluded: chain A residue 1795 ARG Chi-restraints excluded: chain A residue 1807 VAL Chi-restraints excluded: chain A residue 1872 THR Chi-restraints excluded: chain A residue 2027 SER Chi-restraints excluded: chain A residue 2028 LEU Chi-restraints excluded: chain A residue 2073 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 31 optimal weight: 1.9990 chunk 56 optimal weight: 0.7980 chunk 14 optimal weight: 0.9980 chunk 71 optimal weight: 3.9990 chunk 93 optimal weight: 0.1980 chunk 76 optimal weight: 0.1980 chunk 104 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 24 optimal weight: 4.9990 chunk 13 optimal weight: 1.9990 chunk 99 optimal weight: 0.1980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1119 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.081946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.062795 restraints weight = 15038.416| |-----------------------------------------------------------------------------| r_work (start): 0.2865 rms_B_bonded: 2.38 r_work: 0.2718 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2585 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2585 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8606 moved from start: 0.1818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 8578 Z= 0.113 Angle : 0.438 6.686 11602 Z= 0.233 Chirality : 0.039 0.140 1333 Planarity : 0.004 0.043 1520 Dihedral : 3.530 19.914 1165 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 2.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 1.53 % Allowed : 13.77 % Favored : 84.70 % 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: 1.66 (0.25), residues: 1093 helix: 2.12 (0.21), residues: 628 sheet: 1.29 (0.65), residues: 70 loop : -0.62 (0.29), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A1315 TYR 0.009 0.001 TYR A1388 PHE 0.013 0.001 PHE A1392 TRP 0.005 0.001 TRP A1578 HIS 0.002 0.001 HIS A1373 Details of bonding type rmsd covalent geometry : bond 0.00235 ( 8578) covalent geometry : angle 0.43758 (11602) hydrogen bonds : bond 0.05491 ( 486) hydrogen bonds : angle 3.95341 ( 1392) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 58 time to evaluate : 0.427 Fit side-chains REVERT: A 1137 GLN cc_start: 0.9140 (tt0) cc_final: 0.8775 (tp40) REVERT: A 1289 GLU cc_start: 0.9264 (OUTLIER) cc_final: 0.8676 (tt0) REVERT: A 1831 ARG cc_start: 0.8584 (OUTLIER) cc_final: 0.7827 (mtt180) outliers start: 14 outliers final: 7 residues processed: 69 average time/residue: 0.7132 time to fit residues: 51.9625 Evaluate side-chains 65 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 56 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1067 LEU Chi-restraints excluded: chain A residue 1289 GLU Chi-restraints excluded: chain A residue 1416 MET Chi-restraints excluded: chain A residue 1558 VAL Chi-restraints excluded: chain A residue 1645 ASP Chi-restraints excluded: chain A residue 1720 LYS Chi-restraints excluded: chain A residue 1807 VAL Chi-restraints excluded: chain A residue 1831 ARG Chi-restraints excluded: chain A residue 1872 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 21 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 14 optimal weight: 0.9980 chunk 77 optimal weight: 0.8980 chunk 28 optimal weight: 0.6980 chunk 42 optimal weight: 0.6980 chunk 50 optimal weight: 1.9990 chunk 82 optimal weight: 0.9980 chunk 85 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1119 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.080374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2838 r_free = 0.2838 target = 0.061185 restraints weight = 15012.673| |-----------------------------------------------------------------------------| r_work (start): 0.2837 rms_B_bonded: 2.38 r_work: 0.2685 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2551 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8639 moved from start: 0.1792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8578 Z= 0.145 Angle : 0.470 7.268 11602 Z= 0.247 Chirality : 0.040 0.136 1333 Planarity : 0.004 0.043 1520 Dihedral : 3.587 24.132 1165 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 1.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.19 % Allowed : 13.11 % Favored : 84.70 % 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: 1.64 (0.25), residues: 1093 helix: 2.14 (0.21), residues: 628 sheet: 1.09 (0.64), residues: 72 loop : -0.68 (0.29), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A1315 TYR 0.015 0.001 TYR A2011 PHE 0.017 0.001 PHE A1392 TRP 0.005 0.001 TRP A1159 HIS 0.003 0.001 HIS A1788 Details of bonding type rmsd covalent geometry : bond 0.00336 ( 8578) covalent geometry : angle 0.47026 (11602) hydrogen bonds : bond 0.06270 ( 486) hydrogen bonds : angle 3.98694 ( 1392) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 57 time to evaluate : 0.308 Fit side-chains REVERT: A 1137 GLN cc_start: 0.9141 (tt0) cc_final: 0.8817 (tp40) REVERT: A 1147 GLN cc_start: 0.8462 (OUTLIER) cc_final: 0.7864 (tt0) REVERT: A 1289 GLU cc_start: 0.9258 (OUTLIER) cc_final: 0.8669 (tt0) REVERT: A 1651 ILE cc_start: 0.8933 (OUTLIER) cc_final: 0.8603 (mm) outliers start: 20 outliers final: 14 residues processed: 74 average time/residue: 0.7310 time to fit residues: 57.0467 Evaluate side-chains 74 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 57 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1067 LEU Chi-restraints excluded: chain A residue 1147 GLN Chi-restraints excluded: chain A residue 1259 ILE Chi-restraints excluded: chain A residue 1289 GLU Chi-restraints excluded: chain A residue 1363 THR Chi-restraints excluded: chain A residue 1416 MET Chi-restraints excluded: chain A residue 1418 ARG Chi-restraints excluded: chain A residue 1558 VAL Chi-restraints excluded: chain A residue 1625 SER Chi-restraints excluded: chain A residue 1645 ASP Chi-restraints excluded: chain A residue 1651 ILE Chi-restraints excluded: chain A residue 1720 LYS Chi-restraints excluded: chain A residue 1795 ARG Chi-restraints excluded: chain A residue 1807 VAL Chi-restraints excluded: chain A residue 1872 THR Chi-restraints excluded: chain A residue 2019 VAL Chi-restraints excluded: chain A residue 2073 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 13 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 65 optimal weight: 4.9990 chunk 14 optimal weight: 0.8980 chunk 70 optimal weight: 4.9990 chunk 75 optimal weight: 4.9990 chunk 102 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 45 optimal weight: 0.6980 chunk 63 optimal weight: 0.7980 chunk 57 optimal weight: 0.5980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1119 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.080585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.061353 restraints weight = 15131.708| |-----------------------------------------------------------------------------| r_work (start): 0.2838 rms_B_bonded: 2.40 r_work: 0.2686 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2553 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2553 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8659 moved from start: 0.1801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8578 Z= 0.139 Angle : 0.469 7.903 11602 Z= 0.246 Chirality : 0.040 0.133 1333 Planarity : 0.004 0.046 1520 Dihedral : 3.590 23.580 1165 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 2.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 2.08 % Allowed : 14.21 % Favored : 83.72 % 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: 1.69 (0.25), residues: 1093 helix: 2.17 (0.21), residues: 628 sheet: 1.26 (0.65), residues: 70 loop : -0.66 (0.29), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A1315 TYR 0.011 0.001 TYR A1388 PHE 0.016 0.001 PHE A1392 TRP 0.005 0.001 TRP A1159 HIS 0.003 0.001 HIS A1788 Details of bonding type rmsd covalent geometry : bond 0.00317 ( 8578) covalent geometry : angle 0.46927 (11602) hydrogen bonds : bond 0.06114 ( 486) hydrogen bonds : angle 3.96090 ( 1392) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 58 time to evaluate : 0.315 Fit side-chains REVERT: A 1137 GLN cc_start: 0.9138 (tt0) cc_final: 0.8821 (tp40) REVERT: A 1147 GLN cc_start: 0.8476 (OUTLIER) cc_final: 0.7877 (tt0) REVERT: A 1289 GLU cc_start: 0.9265 (OUTLIER) cc_final: 0.8677 (tt0) REVERT: A 1651 ILE cc_start: 0.8930 (OUTLIER) cc_final: 0.8616 (mm) outliers start: 19 outliers final: 14 residues processed: 74 average time/residue: 0.7491 time to fit residues: 58.4096 Evaluate side-chains 73 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 56 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1041 GLN Chi-restraints excluded: chain A residue 1067 LEU Chi-restraints excluded: chain A residue 1147 GLN Chi-restraints excluded: chain A residue 1259 ILE Chi-restraints excluded: chain A residue 1289 GLU Chi-restraints excluded: chain A residue 1416 MET Chi-restraints excluded: chain A residue 1418 ARG Chi-restraints excluded: chain A residue 1558 VAL Chi-restraints excluded: chain A residue 1625 SER Chi-restraints excluded: chain A residue 1645 ASP Chi-restraints excluded: chain A residue 1651 ILE Chi-restraints excluded: chain A residue 1720 LYS Chi-restraints excluded: chain A residue 1795 ARG Chi-restraints excluded: chain A residue 1807 VAL Chi-restraints excluded: chain A residue 1872 THR Chi-restraints excluded: chain A residue 2027 SER Chi-restraints excluded: chain A residue 2073 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 82 optimal weight: 0.9980 chunk 107 optimal weight: 0.7980 chunk 101 optimal weight: 3.9990 chunk 24 optimal weight: 0.8980 chunk 83 optimal weight: 0.9990 chunk 87 optimal weight: 3.9990 chunk 67 optimal weight: 0.6980 chunk 42 optimal weight: 0.9990 chunk 15 optimal weight: 0.0980 chunk 91 optimal weight: 0.7980 chunk 7 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1119 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.081708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2824 r_free = 0.2824 target = 0.061661 restraints weight = 15083.588| |-----------------------------------------------------------------------------| r_work (start): 0.2817 rms_B_bonded: 2.49 r_work: 0.2670 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2536 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.1854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8578 Z= 0.126 Angle : 0.467 8.284 11602 Z= 0.244 Chirality : 0.039 0.136 1333 Planarity : 0.004 0.049 1520 Dihedral : 3.534 20.827 1165 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 1.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.30 % Allowed : 13.99 % Favored : 83.72 % 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: 1.77 (0.26), residues: 1093 helix: 2.26 (0.21), residues: 628 sheet: 1.07 (0.64), residues: 72 loop : -0.62 (0.29), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A1315 TYR 0.015 0.001 TYR A2011 PHE 0.015 0.001 PHE A1392 TRP 0.004 0.001 TRP A1159 HIS 0.002 0.001 HIS A1788 Details of bonding type rmsd covalent geometry : bond 0.00279 ( 8578) covalent geometry : angle 0.46744 (11602) hydrogen bonds : bond 0.05748 ( 486) hydrogen bonds : angle 3.90378 ( 1392) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 59 time to evaluate : 0.251 Fit side-chains REVERT: A 1137 GLN cc_start: 0.9088 (tt0) cc_final: 0.8698 (tp40) REVERT: A 1147 GLN cc_start: 0.8171 (OUTLIER) cc_final: 0.7611 (tt0) REVERT: A 1289 GLU cc_start: 0.9164 (OUTLIER) cc_final: 0.8543 (tt0) REVERT: A 1651 ILE cc_start: 0.8712 (OUTLIER) cc_final: 0.8407 (mm) outliers start: 21 outliers final: 16 residues processed: 77 average time/residue: 0.7769 time to fit residues: 62.8065 Evaluate side-chains 76 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 57 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1041 GLN Chi-restraints excluded: chain A residue 1067 LEU Chi-restraints excluded: chain A residue 1147 GLN Chi-restraints excluded: chain A residue 1259 ILE Chi-restraints excluded: chain A residue 1289 GLU Chi-restraints excluded: chain A residue 1363 THR Chi-restraints excluded: chain A residue 1416 MET Chi-restraints excluded: chain A residue 1418 ARG Chi-restraints excluded: chain A residue 1558 VAL Chi-restraints excluded: chain A residue 1625 SER Chi-restraints excluded: chain A residue 1645 ASP Chi-restraints excluded: chain A residue 1651 ILE Chi-restraints excluded: chain A residue 1720 LYS Chi-restraints excluded: chain A residue 1795 ARG Chi-restraints excluded: chain A residue 1807 VAL Chi-restraints excluded: chain A residue 1872 THR Chi-restraints excluded: chain A residue 2019 VAL Chi-restraints excluded: chain A residue 2027 SER Chi-restraints excluded: chain A residue 2053 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 22 optimal weight: 0.9980 chunk 68 optimal weight: 1.9990 chunk 82 optimal weight: 0.8980 chunk 7 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 95 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 chunk 54 optimal weight: 0.8980 chunk 64 optimal weight: 0.9980 chunk 26 optimal weight: 0.0060 chunk 38 optimal weight: 0.5980 overall best weight: 0.6796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1119 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.081715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2825 r_free = 0.2825 target = 0.061658 restraints weight = 15085.586| |-----------------------------------------------------------------------------| r_work (start): 0.2814 rms_B_bonded: 2.49 r_work: 0.2667 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2534 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.1857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8578 Z= 0.129 Angle : 0.477 8.600 11602 Z= 0.248 Chirality : 0.039 0.131 1333 Planarity : 0.004 0.053 1520 Dihedral : 3.539 21.514 1165 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 1.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.30 % Allowed : 14.32 % Favored : 83.39 % 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: 1.80 (0.26), residues: 1093 helix: 2.28 (0.21), residues: 628 sheet: 1.25 (0.66), residues: 70 loop : -0.63 (0.29), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A1750 TYR 0.011 0.001 TYR A1388 PHE 0.015 0.001 PHE A1392 TRP 0.005 0.001 TRP A1159 HIS 0.003 0.001 HIS A1788 Details of bonding type rmsd covalent geometry : bond 0.00290 ( 8578) covalent geometry : angle 0.47735 (11602) hydrogen bonds : bond 0.05758 ( 486) hydrogen bonds : angle 3.89059 ( 1392) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 57 time to evaluate : 0.336 Fit side-chains REVERT: A 1137 GLN cc_start: 0.9086 (tt0) cc_final: 0.8694 (tp40) REVERT: A 1147 GLN cc_start: 0.8198 (OUTLIER) cc_final: 0.7638 (tt0) REVERT: A 1289 GLU cc_start: 0.9159 (OUTLIER) cc_final: 0.8539 (tt0) outliers start: 21 outliers final: 17 residues processed: 75 average time/residue: 0.6942 time to fit residues: 54.9514 Evaluate side-chains 76 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 57 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1041 GLN Chi-restraints excluded: chain A residue 1067 LEU Chi-restraints excluded: chain A residue 1147 GLN Chi-restraints excluded: chain A residue 1259 ILE Chi-restraints excluded: chain A residue 1289 GLU Chi-restraints excluded: chain A residue 1363 THR Chi-restraints excluded: chain A residue 1416 MET Chi-restraints excluded: chain A residue 1418 ARG Chi-restraints excluded: chain A residue 1558 VAL Chi-restraints excluded: chain A residue 1625 SER Chi-restraints excluded: chain A residue 1645 ASP Chi-restraints excluded: chain A residue 1720 LYS Chi-restraints excluded: chain A residue 1795 ARG Chi-restraints excluded: chain A residue 1807 VAL Chi-restraints excluded: chain A residue 1872 THR Chi-restraints excluded: chain A residue 2019 VAL Chi-restraints excluded: chain A residue 2027 SER Chi-restraints excluded: chain A residue 2053 SER Chi-restraints excluded: chain A residue 2073 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 28 optimal weight: 0.6980 chunk 56 optimal weight: 2.9990 chunk 52 optimal weight: 0.9980 chunk 102 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 chunk 76 optimal weight: 0.0170 chunk 53 optimal weight: 0.7980 chunk 43 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 overall best weight: 0.6418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1119 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.082067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2831 r_free = 0.2831 target = 0.061965 restraints weight = 15003.345| |-----------------------------------------------------------------------------| r_work (start): 0.2827 rms_B_bonded: 2.50 r_work: 0.2678 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2543 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2543 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.1887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8578 Z= 0.125 Angle : 0.482 9.840 11602 Z= 0.250 Chirality : 0.039 0.150 1333 Planarity : 0.004 0.059 1520 Dihedral : 3.521 21.146 1165 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 1.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 2.19 % Allowed : 14.64 % Favored : 83.17 % 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: 1.81 (0.26), residues: 1093 helix: 2.31 (0.21), residues: 626 sheet: 1.10 (0.64), residues: 72 loop : -0.63 (0.29), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A1750 TYR 0.016 0.001 TYR A2011 PHE 0.015 0.001 PHE A1392 TRP 0.004 0.001 TRP A1159 HIS 0.002 0.001 HIS A1788 Details of bonding type rmsd covalent geometry : bond 0.00282 ( 8578) covalent geometry : angle 0.48221 (11602) hydrogen bonds : bond 0.05622 ( 486) hydrogen bonds : angle 3.86897 ( 1392) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 57 time to evaluate : 0.372 Fit side-chains REVERT: A 1137 GLN cc_start: 0.9090 (tt0) cc_final: 0.8697 (tp40) REVERT: A 1147 GLN cc_start: 0.8166 (OUTLIER) cc_final: 0.7604 (tt0) REVERT: A 1289 GLU cc_start: 0.9162 (OUTLIER) cc_final: 0.8542 (tt0) outliers start: 20 outliers final: 16 residues processed: 74 average time/residue: 0.6703 time to fit residues: 52.4486 Evaluate side-chains 75 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 57 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1041 GLN Chi-restraints excluded: chain A residue 1067 LEU Chi-restraints excluded: chain A residue 1147 GLN Chi-restraints excluded: chain A residue 1259 ILE Chi-restraints excluded: chain A residue 1289 GLU Chi-restraints excluded: chain A residue 1363 THR Chi-restraints excluded: chain A residue 1416 MET Chi-restraints excluded: chain A residue 1418 ARG Chi-restraints excluded: chain A residue 1558 VAL Chi-restraints excluded: chain A residue 1625 SER Chi-restraints excluded: chain A residue 1645 ASP Chi-restraints excluded: chain A residue 1795 ARG Chi-restraints excluded: chain A residue 1807 VAL Chi-restraints excluded: chain A residue 1872 THR Chi-restraints excluded: chain A residue 2019 VAL Chi-restraints excluded: chain A residue 2027 SER Chi-restraints excluded: chain A residue 2053 SER Chi-restraints excluded: chain A residue 2073 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 92 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 35 optimal weight: 0.2980 chunk 107 optimal weight: 0.7980 chunk 86 optimal weight: 2.9990 chunk 6 optimal weight: 0.0370 chunk 58 optimal weight: 1.9990 chunk 42 optimal weight: 0.7980 chunk 13 optimal weight: 2.9990 chunk 14 optimal weight: 0.9980 chunk 9 optimal weight: 0.9990 overall best weight: 0.5858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1119 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.082439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2840 r_free = 0.2840 target = 0.062396 restraints weight = 15008.128| |-----------------------------------------------------------------------------| r_work (start): 0.2832 rms_B_bonded: 2.48 r_work: 0.2686 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2551 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.1910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8578 Z= 0.120 Angle : 0.476 10.513 11602 Z= 0.246 Chirality : 0.039 0.155 1333 Planarity : 0.004 0.054 1520 Dihedral : 3.489 20.667 1165 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 1.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 1.97 % Allowed : 14.75 % Favored : 83.28 % 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: 1.89 (0.26), residues: 1093 helix: 2.36 (0.21), residues: 628 sheet: 1.27 (0.66), residues: 70 loop : -0.60 (0.29), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A1750 TYR 0.011 0.001 TYR A1388 PHE 0.014 0.001 PHE A1392 TRP 0.004 0.001 TRP A1159 HIS 0.002 0.001 HIS A1788 Details of bonding type rmsd covalent geometry : bond 0.00266 ( 8578) covalent geometry : angle 0.47645 (11602) hydrogen bonds : bond 0.05414 ( 486) hydrogen bonds : angle 3.83407 ( 1392) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2836.66 seconds wall clock time: 49 minutes 0.55 seconds (2940.55 seconds total)