Starting phenix.real_space_refine on Wed Feb 4 06:27:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9pnv_71773/02_2026/9pnv_71773.cif Found real_map, /net/cci-nas-00/data/ceres_data/9pnv_71773/02_2026/9pnv_71773.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9pnv_71773/02_2026/9pnv_71773.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9pnv_71773/02_2026/9pnv_71773.map" model { file = "/net/cci-nas-00/data/ceres_data/9pnv_71773/02_2026/9pnv_71773.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9pnv_71773/02_2026/9pnv_71773.cif" } resolution = 2.8 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= 0.002 sd= 0.007 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 P 19 5.49 5 S 41 5.16 5 C 5490 2.51 5 N 1514 2.21 5 O 1777 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 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: 8841 Number of models: 1 Model: "" Number of chains: 2 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} Chain: "B" Number of atoms: 392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 392 Classifications: {'DNA': 19} Link IDs: {'rna3p': 18} Time building chain proxies: 2.44, per 1000 atoms: 0.28 Number of scatterers: 8841 At special positions: 0 Unit cell: (96.143, 102.228, 113.181, 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 41 16.00 P 19 15.00 O 1777 8.00 N 1514 7.00 C 5490 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: 0.80 Conformation dependent library (CDL) restraints added in 341.0 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: 53 helices and 15 sheets defined 63.4% alpha, 6.6% beta 1 base pairs and 11 stacking pairs defined. Time for finding SS restraints: 1.11 Creating SS restraints... Processing helix chain 'A' and resid 1050 through 1059 removed outlier: 3.599A 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: 3.634A pdb=" N GLU A1088 " --> pdb=" O LYS A1084 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU A1089 " --> pdb=" O ARG A1085 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLY A1095 " --> pdb=" O GLU A1091 " (cutoff:3.500A) removed outlier: 3.567A 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 1133 removed outlier: 3.723A pdb=" N TRP A1126 " --> pdb=" O ALA A1123 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N VAL A1127 " --> pdb=" O ASN A1124 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N GLY A1128 " --> pdb=" O ARG A1125 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N LYS A1130 " --> pdb=" O VAL A1127 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N LEU A1131 " --> pdb=" O GLY A1128 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ASN A1133 " --> pdb=" O LYS A1130 " (cutoff:3.500A) Processing helix chain 'A' and resid 1145 through 1167 removed outlier: 3.646A pdb=" N LEU A1161 " --> pdb=" O LEU A1157 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N THR A1162 " --> pdb=" O GLN A1158 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N THR A1164 " --> pdb=" O ARG A1160 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N SER A1165 " --> pdb=" O LEU A1161 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ASN A1166 " --> pdb=" O THR A1162 " (cutoff:3.500A) Processing helix chain 'A' and resid 1171 through 1180 Processing helix chain 'A' and resid 1182 through 1186 removed outlier: 3.543A pdb=" N LEU A1186 " --> pdb=" O GLN A1183 " (cutoff:3.500A) Processing helix chain 'A' and resid 1189 through 1197 removed outlier: 4.070A pdb=" N GLY A1197 " --> pdb=" O GLN A1193 " (cutoff:3.500A) Processing helix chain 'A' and resid 1200 through 1216 removed outlier: 3.606A 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: 3.629A pdb=" N THR A1233 " --> pdb=" O LYS A1229 " (cutoff:3.500A) Processing helix chain 'A' and resid 1257 through 1259 No H-bonds generated for 'chain 'A' and resid 1257 through 1259' Processing helix chain 'A' and resid 1279 through 1284 Processing helix chain 'A' and resid 1286 through 1293 removed outlier: 3.600A pdb=" N GLU A1290 " --> pdb=" O THR A1286 " (cutoff:3.500A) Processing helix chain 'A' and resid 1322 through 1333 removed outlier: 3.527A pdb=" N ALA A1328 " --> pdb=" O GLU A1324 " (cutoff:3.500A) 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: 3.666A pdb=" N LEU A1369 " --> pdb=" O LYS A1366 " (cutoff:3.500A) Processing helix chain 'A' and resid 1370 through 1400 removed outlier: 3.547A pdb=" N SER A1376 " --> pdb=" O ASN A1372 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N SER A1383 " --> pdb=" O GLY A1379 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VAL A1384 " --> pdb=" O LYS A1380 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLU A1396 " --> pdb=" O PHE A1392 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLN A1397 " --> pdb=" O SER A1393 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ALA A1400 " --> pdb=" O GLU A1396 " (cutoff:3.500A) Processing helix chain 'A' and resid 1404 through 1408 removed outlier: 3.876A pdb=" N VAL A1408 " --> pdb=" O ILE A1405 " (cutoff:3.500A) Processing helix chain 'A' and resid 1433 through 1438 removed outlier: 3.773A pdb=" N GLU A1438 " --> pdb=" O LYS A1434 " (cutoff:3.500A) Processing helix chain 'A' and resid 1454 through 1468 removed outlier: 3.585A pdb=" N SER A1458 " --> pdb=" O ASN A1454 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ALA A1459 " --> pdb=" O GLU A1455 " (cutoff:3.500A) Processing helix chain 'A' and resid 1476 through 1489 Processing helix chain 'A' and resid 1492 through 1506 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 1541 removed outlier: 3.589A pdb=" N LEU A1529 " --> pdb=" O SER A1525 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N MET A1530 " --> pdb=" O PHE A1526 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N VAL A1540 " --> pdb=" O SER A1536 " (cutoff:3.500A) Processing helix chain 'A' and resid 1543 through 1546 removed outlier: 3.806A 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 1583 Processing helix chain 'A' and resid 1595 through 1603 Processing helix chain 'A' and resid 1607 through 1627 removed outlier: 3.736A pdb=" N TYR A1627 " --> pdb=" O LEU A1623 " (cutoff:3.500A) Processing helix chain 'A' and resid 1630 through 1648 removed outlier: 3.512A pdb=" N LEU A1646 " --> pdb=" O SER A1642 " (cutoff:3.500A) removed outlier: 3.805A 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: 3.595A pdb=" N LEU A1670 " --> pdb=" O ALA A1666 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N TYR A1675 " --> pdb=" O THR A1671 " (cutoff:3.500A) Processing helix chain 'A' and resid 1678 through 1708 removed outlier: 3.545A pdb=" N ILE A1682 " --> pdb=" O GLY A1678 " (cutoff:3.500A) removed outlier: 3.664A 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 1720 through 1722 No H-bonds generated for 'chain 'A' and resid 1720 through 1722' Processing helix chain 'A' and resid 1724 through 1743 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: 3.843A pdb=" N VAL A1807 " --> pdb=" O GLY A1803 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLU A1834 " --> pdb=" O GLN A1830 " (cutoff:3.500A) Processing helix chain 'A' and resid 1852 through 1862 Processing helix chain 'A' and resid 1863 through 1867 removed outlier: 3.517A pdb=" N ALA A1867 " --> pdb=" O ASN A1864 " (cutoff:3.500A) Processing helix chain 'A' and resid 1915 through 1924 Processing helix chain 'A' and resid 1925 through 1936 removed outlier: 3.557A 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: 3.567A pdb=" N SER A1983 " --> pdb=" O ASN A1979 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LYS A1986 " --> pdb=" O GLU A1982 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LYS A1989 " --> pdb=" O ALA A1985 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ASN A1990 " --> pdb=" O LYS A1986 " (cutoff:3.500A) Processing helix chain 'A' and resid 1992 through 1996 removed outlier: 3.549A pdb=" N LYS A1995 " --> pdb=" O ASP A1992 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU A1996 " --> pdb=" O PHE A1993 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1992 through 1996' Processing helix chain 'A' and resid 1997 through 2009 removed outlier: 3.924A pdb=" N SER A2007 " --> pdb=" O ALA A2003 " (cutoff:3.500A) Processing helix chain 'A' and resid 2018 through 2048 removed outlier: 3.502A pdb=" N LEU A2028 " --> pdb=" O ASN A2024 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ILE A2029 " --> pdb=" O ALA A2025 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLU A2030 " --> pdb=" O ALA A2026 " (cutoff:3.500A) Processing helix chain 'A' and resid 2076 through 2101 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: 4.564A pdb=" N PHE A1301 " --> pdb=" O HIS A1411 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1312 through 1313 removed outlier: 6.410A 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 Processing sheet with id=AB6, first strand: chain 'A' and resid 1891 through 1893 removed outlier: 6.914A pdb=" N VAL A1902 " --> pdb=" O LEU A1892 " (cutoff:3.500A) 481 hydrogen bonds defined for protein. 1383 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 2 hydrogen bonds 4 hydrogen bond angles 0 basepair planarities 1 basepair parallelities 11 stacking parallelities Total time for adding SS restraints: 1.65 Time building geometry restraints manager: 1.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2898 1.34 - 1.46: 1648 1.46 - 1.58: 4354 1.58 - 1.70: 37 1.70 - 1.82: 82 Bond restraints: 9019 Sorted by residual: bond pdb=" C PHE A1789 " pdb=" N PHE A1790 " ideal model delta sigma weight residual 1.332 1.315 0.017 1.40e-02 5.10e+03 1.50e+00 bond pdb=" CB GLU A1367 " pdb=" CG GLU A1367 " ideal model delta sigma weight residual 1.520 1.556 -0.036 3.00e-02 1.11e+03 1.46e+00 bond pdb=" N ASP A1948 " pdb=" CA ASP A1948 " ideal model delta sigma weight residual 1.457 1.472 -0.014 1.29e-02 6.01e+03 1.26e+00 bond pdb=" CB GLU A1072 " pdb=" CG GLU A1072 " ideal model delta sigma weight residual 1.520 1.551 -0.031 3.00e-02 1.11e+03 1.06e+00 bond pdb=" CB MET A1631 " pdb=" CG MET A1631 " ideal model delta sigma weight residual 1.520 1.546 -0.026 3.00e-02 1.11e+03 7.24e-01 ... (remaining 9014 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.48: 12210 2.48 - 4.96: 62 4.96 - 7.44: 6 7.44 - 9.92: 1 9.92 - 12.40: 1 Bond angle restraints: 12280 Sorted by residual: angle pdb=" CB MET A1631 " pdb=" CG MET A1631 " pdb=" SD MET A1631 " ideal model delta sigma weight residual 112.70 125.10 -12.40 3.00e+00 1.11e-01 1.71e+01 angle pdb=" C ARG A1750 " pdb=" N LYS A1751 " pdb=" CA LYS A1751 " ideal model delta sigma weight residual 122.61 128.87 -6.26 1.56e+00 4.11e-01 1.61e+01 angle pdb=" CA GLU A1367 " pdb=" CB GLU A1367 " pdb=" CG GLU A1367 " ideal model delta sigma weight residual 114.10 120.48 -6.38 2.00e+00 2.50e-01 1.02e+01 angle pdb=" CB MET A1256 " pdb=" CG MET A1256 " pdb=" SD MET A1256 " ideal model delta sigma weight residual 112.70 121.81 -9.11 3.00e+00 1.11e-01 9.23e+00 angle pdb=" C GLY A1916 " pdb=" N ILE A1917 " pdb=" CA ILE A1917 " ideal model delta sigma weight residual 120.33 122.73 -2.40 8.00e-01 1.56e+00 8.97e+00 ... (remaining 12275 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.63: 4584 16.63 - 33.26: 615 33.26 - 49.89: 235 49.89 - 66.52: 59 66.52 - 83.15: 14 Dihedral angle restraints: 5507 sinusoidal: 2333 harmonic: 3174 Sorted by residual: dihedral pdb=" CA MET A2057 " pdb=" C MET A2057 " pdb=" N ALA A2058 " pdb=" CA ALA A2058 " ideal model delta harmonic sigma weight residual -180.00 -158.51 -21.49 0 5.00e+00 4.00e-02 1.85e+01 dihedral pdb=" CG ARG A1663 " pdb=" CD ARG A1663 " pdb=" NE ARG A1663 " pdb=" CZ ARG A1663 " ideal model delta sinusoidal sigma weight residual 180.00 136.46 43.54 2 1.50e+01 4.44e-03 1.01e+01 dihedral pdb=" CG ARG A1062 " pdb=" CD ARG A1062 " pdb=" NE ARG A1062 " pdb=" CZ ARG A1062 " ideal model delta sinusoidal sigma weight residual -90.00 -133.24 43.24 2 1.50e+01 4.44e-03 1.00e+01 ... (remaining 5504 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 899 0.030 - 0.059: 369 0.059 - 0.089: 77 0.089 - 0.119: 58 0.119 - 0.148: 6 Chirality restraints: 1409 Sorted by residual: 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 2.36 0.15 2.00e-01 2.50e+01 5.49e-01 chirality pdb=" CA ILE A1774 " pdb=" N ILE A1774 " pdb=" C ILE A1774 " pdb=" CB ILE A1774 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.05e-01 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 3.96e-01 ... (remaining 1406 not shown) Planarity restraints: 1539 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU A1367 " -0.010 2.00e-02 2.50e+03 2.06e-02 4.25e+00 pdb=" CD GLU A1367 " 0.036 2.00e-02 2.50e+03 pdb=" OE1 GLU A1367 " -0.013 2.00e-02 2.50e+03 pdb=" OE2 GLU A1367 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN A1429 " -0.030 5.00e-02 4.00e+02 4.46e-02 3.19e+00 pdb=" N PRO A1430 " 0.077 5.00e-02 4.00e+02 pdb=" CA PRO A1430 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO A1430 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A1549 " -0.018 5.00e-02 4.00e+02 2.73e-02 1.19e+00 pdb=" N PRO A1550 " 0.047 5.00e-02 4.00e+02 pdb=" CA PRO A1550 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO A1550 " -0.015 5.00e-02 4.00e+02 ... (remaining 1536 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 271 2.71 - 3.26: 8361 3.26 - 3.81: 12757 3.81 - 4.35: 17167 4.35 - 4.90: 29362 Nonbonded interactions: 67918 Sorted by model distance: nonbonded pdb=" N GLU A1072 " pdb=" OE1 GLU A1072 " model vdw 2.167 3.120 nonbonded pdb=" N GLU A1039 " pdb=" OE1 GLU A1039 " model vdw 2.241 3.120 nonbonded pdb=" OH TYR A1969 " pdb=" OD1 ASP A2048 " model vdw 2.244 3.040 nonbonded pdb=" O PRO A1669 " pdb=" OG1 THR A1673 " model vdw 2.251 3.040 nonbonded pdb=" OD1 ASN A1316 " pdb=" OH TYR A1907 " model vdw 2.253 3.040 ... (remaining 67913 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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: 2.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 11.250 Find NCS groups from input model: 0.040 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:7.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8792 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 : 0.003 0.036 9019 Z= 0.139 Angle : 0.464 12.404 12280 Z= 0.240 Chirality : 0.038 0.148 1409 Planarity : 0.003 0.045 1539 Dihedral : 17.978 83.146 3457 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 3.06 % Allowed : 23.06 % Favored : 73.88 % 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: -0.72 (0.24), residues: 1093 helix: -0.31 (0.19), residues: 615 sheet: 0.35 (0.66), residues: 72 loop : -0.66 (0.28), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A1125 TYR 0.014 0.001 TYR A2011 PHE 0.016 0.001 PHE A1278 TRP 0.003 0.001 TRP A1159 HIS 0.001 0.000 HIS A1411 Details of bonding type rmsd covalent geometry : bond 0.00330 ( 9019) covalent geometry : angle 0.46402 (12280) hydrogen bonds : bond 0.31385 ( 483) hydrogen bonds : angle 7.13825 ( 1387) *********************** 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 100 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 72 time to evaluate : 0.384 Fit side-chains REVERT: A 1192 GLU cc_start: 0.8404 (pt0) cc_final: 0.7981 (pp20) REVERT: A 1345 GLN cc_start: 0.8869 (mt0) cc_final: 0.8628 (mt0) REVERT: A 1757 GLN cc_start: 0.7929 (tt0) cc_final: 0.7626 (pt0) REVERT: A 1869 MET cc_start: 0.9376 (OUTLIER) cc_final: 0.8884 (mtt) REVERT: A 1898 ASP cc_start: 0.8748 (OUTLIER) cc_final: 0.8165 (t0) REVERT: A 1904 MET cc_start: 0.9369 (ttp) cc_final: 0.9135 (ttm) REVERT: A 2075 MET cc_start: 0.8827 (mtp) cc_final: 0.8528 (mtp) REVERT: A 2091 GLU cc_start: 0.9091 (OUTLIER) cc_final: 0.8506 (tt0) outliers start: 28 outliers final: 22 residues processed: 96 average time/residue: 0.6448 time to fit residues: 65.7978 Evaluate side-chains 98 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 73 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1019 THR Chi-restraints excluded: chain A residue 1036 THR Chi-restraints excluded: chain A residue 1045 THR Chi-restraints excluded: chain A residue 1250 VAL Chi-restraints excluded: chain A residue 1254 VAL Chi-restraints excluded: chain A residue 1267 ILE Chi-restraints excluded: chain A residue 1297 THR Chi-restraints excluded: chain A residue 1305 ASP Chi-restraints excluded: chain A residue 1353 ASP Chi-restraints excluded: chain A residue 1472 VAL Chi-restraints excluded: chain A residue 1474 THR Chi-restraints excluded: chain A residue 1558 VAL Chi-restraints excluded: chain A residue 1656 ASN Chi-restraints excluded: chain A residue 1743 THR Chi-restraints excluded: chain A residue 1744 SER Chi-restraints excluded: chain A residue 1849 ASP Chi-restraints excluded: chain A residue 1869 MET Chi-restraints excluded: chain A residue 1872 THR Chi-restraints excluded: chain A residue 1882 SER Chi-restraints excluded: chain A residue 1898 ASP Chi-restraints excluded: chain A residue 1934 SER Chi-restraints excluded: chain A residue 2012 ASP Chi-restraints excluded: chain A residue 2016 ASN Chi-restraints excluded: chain A residue 2031 ARG Chi-restraints excluded: chain A residue 2091 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 108 optimal weight: 0.7980 chunk 49 optimal weight: 0.9990 chunk 97 optimal weight: 0.7980 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 100 optimal weight: 0.1980 chunk 106 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1333 GLN A1511 ASN A1652 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.096031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.071031 restraints weight = 14189.550| |-----------------------------------------------------------------------------| r_work (start): 0.2875 rms_B_bonded: 2.61 r_work: 0.2740 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.2740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.1434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 9019 Z= 0.153 Angle : 0.510 6.736 12280 Z= 0.278 Chirality : 0.040 0.146 1409 Planarity : 0.004 0.045 1539 Dihedral : 13.046 72.862 1424 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 2.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 2.62 % Allowed : 20.00 % Favored : 77.38 % 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: 0.93 (0.25), residues: 1093 helix: 1.47 (0.21), residues: 620 sheet: 0.46 (0.69), residues: 70 loop : -0.65 (0.28), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1624 TYR 0.010 0.001 TYR A2011 PHE 0.013 0.001 PHE A2088 TRP 0.005 0.001 TRP A1159 HIS 0.002 0.001 HIS A1340 Details of bonding type rmsd covalent geometry : bond 0.00320 ( 9019) covalent geometry : angle 0.51033 (12280) hydrogen bonds : bond 0.07824 ( 483) hydrogen bonds : angle 4.46809 ( 1387) *********************** 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 106 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 82 time to evaluate : 0.389 Fit side-chains REVERT: A 1378 GLU cc_start: 0.7750 (mm-30) cc_final: 0.7491 (mt-10) REVERT: A 1447 LEU cc_start: 0.8268 (OUTLIER) cc_final: 0.7787 (mp) REVERT: A 1871 GLU cc_start: 0.8593 (OUTLIER) cc_final: 0.7544 (mm-30) REVERT: A 1898 ASP cc_start: 0.8303 (m-30) cc_final: 0.7387 (t0) REVERT: A 1904 MET cc_start: 0.8900 (ttp) cc_final: 0.8668 (ttm) REVERT: A 1924 THR cc_start: 0.8760 (OUTLIER) cc_final: 0.8452 (p) REVERT: A 2012 ASP cc_start: 0.8225 (OUTLIER) cc_final: 0.7760 (p0) REVERT: A 2013 GLN cc_start: 0.8090 (mm-40) cc_final: 0.7735 (mm110) REVERT: A 2091 GLU cc_start: 0.8311 (OUTLIER) cc_final: 0.7875 (tt0) outliers start: 24 outliers final: 8 residues processed: 102 average time/residue: 0.6100 time to fit residues: 65.8429 Evaluate side-chains 85 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 72 time to evaluate : 0.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1254 VAL Chi-restraints excluded: chain A residue 1319 VAL Chi-restraints excluded: chain A residue 1353 ASP Chi-restraints excluded: chain A residue 1447 LEU Chi-restraints excluded: chain A residue 1608 LEU Chi-restraints excluded: chain A residue 1663 ARG Chi-restraints excluded: chain A residue 1807 VAL Chi-restraints excluded: chain A residue 1871 GLU Chi-restraints excluded: chain A residue 1894 THR Chi-restraints excluded: chain A residue 1924 THR Chi-restraints excluded: chain A residue 2012 ASP Chi-restraints excluded: chain A residue 2031 ARG Chi-restraints excluded: chain A residue 2091 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 86 optimal weight: 2.9990 chunk 65 optimal weight: 0.0980 chunk 39 optimal weight: 0.1980 chunk 12 optimal weight: 1.9990 chunk 52 optimal weight: 0.4980 chunk 94 optimal weight: 1.9990 chunk 96 optimal weight: 0.6980 chunk 46 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 chunk 48 optimal weight: 0.6980 chunk 92 optimal weight: 0.7980 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1340 HIS A1652 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.096488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.070929 restraints weight = 14290.336| |-----------------------------------------------------------------------------| r_work (start): 0.2872 rms_B_bonded: 2.68 r_work: 0.2744 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.2744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.1762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 9019 Z= 0.118 Angle : 0.439 7.229 12280 Z= 0.236 Chirality : 0.038 0.146 1409 Planarity : 0.003 0.050 1539 Dihedral : 12.700 74.351 1396 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 2.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 2.84 % Allowed : 20.55 % Favored : 76.61 % 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: 1.54 (0.26), residues: 1093 helix: 2.09 (0.21), residues: 630 sheet: 0.50 (0.69), residues: 70 loop : -0.65 (0.29), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1624 TYR 0.009 0.001 TYR A1808 PHE 0.013 0.001 PHE A1278 TRP 0.004 0.001 TRP A1578 HIS 0.002 0.001 HIS A1340 Details of bonding type rmsd covalent geometry : bond 0.00240 ( 9019) covalent geometry : angle 0.43900 (12280) hydrogen bonds : bond 0.06049 ( 483) hydrogen bonds : angle 3.92665 ( 1387) *********************** 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 103 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 77 time to evaluate : 0.345 Fit side-chains REVERT: A 1757 GLN cc_start: 0.7232 (OUTLIER) cc_final: 0.6988 (pt0) REVERT: A 1898 ASP cc_start: 0.8323 (m-30) cc_final: 0.7522 (t0) REVERT: A 1924 THR cc_start: 0.8836 (OUTLIER) cc_final: 0.8497 (p) REVERT: A 2013 GLN cc_start: 0.8123 (mm-40) cc_final: 0.7768 (mm110) outliers start: 26 outliers final: 8 residues processed: 97 average time/residue: 0.5892 time to fit residues: 60.6291 Evaluate side-chains 84 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 74 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1254 VAL Chi-restraints excluded: chain A residue 1319 VAL Chi-restraints excluded: chain A residue 1608 LEU Chi-restraints excluded: chain A residue 1663 ARG Chi-restraints excluded: chain A residue 1674 ILE Chi-restraints excluded: chain A residue 1757 GLN Chi-restraints excluded: chain A residue 1807 VAL Chi-restraints excluded: chain A residue 1894 THR Chi-restraints excluded: chain A residue 1924 THR Chi-restraints excluded: chain A residue 2031 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 91 optimal weight: 0.9980 chunk 66 optimal weight: 0.9990 chunk 69 optimal weight: 1.9990 chunk 85 optimal weight: 0.0470 chunk 1 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 82 optimal weight: 0.7980 chunk 81 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 chunk 70 optimal weight: 0.9990 chunk 97 optimal weight: 0.4980 overall best weight: 0.6278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1333 GLN A1652 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.096026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.070383 restraints weight = 14472.636| |-----------------------------------------------------------------------------| r_work (start): 0.2860 rms_B_bonded: 2.69 r_work: 0.2732 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.2732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.1871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 9019 Z= 0.126 Angle : 0.450 8.313 12280 Z= 0.240 Chirality : 0.038 0.148 1409 Planarity : 0.003 0.044 1539 Dihedral : 12.583 72.711 1389 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 2.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 3.28 % Allowed : 19.67 % Favored : 77.05 % 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: 1.63 (0.26), residues: 1093 helix: 2.24 (0.21), residues: 637 sheet: 0.27 (0.66), residues: 72 loop : -0.77 (0.28), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1750 TYR 0.013 0.001 TYR A2011 PHE 0.015 0.001 PHE A1278 TRP 0.005 0.001 TRP A1159 HIS 0.002 0.001 HIS A1092 Details of bonding type rmsd covalent geometry : bond 0.00280 ( 9019) covalent geometry : angle 0.45010 (12280) hydrogen bonds : bond 0.05801 ( 483) hydrogen bonds : angle 3.81271 ( 1387) *********************** 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 107 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 77 time to evaluate : 0.246 Fit side-chains REVERT: A 1243 PHE cc_start: 0.8037 (OUTLIER) cc_final: 0.7828 (m-80) REVERT: A 1757 GLN cc_start: 0.7187 (tt0) cc_final: 0.6882 (pt0) REVERT: A 1871 GLU cc_start: 0.8650 (OUTLIER) cc_final: 0.7626 (mm-30) REVERT: A 1898 ASP cc_start: 0.8369 (m-30) cc_final: 0.7601 (t0) REVERT: A 1924 THR cc_start: 0.8860 (OUTLIER) cc_final: 0.8521 (p) REVERT: A 2013 GLN cc_start: 0.8146 (mm-40) cc_final: 0.7862 (mm110) outliers start: 30 outliers final: 15 residues processed: 103 average time/residue: 0.6109 time to fit residues: 66.6927 Evaluate side-chains 91 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 73 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1243 PHE Chi-restraints excluded: chain A residue 1254 VAL Chi-restraints excluded: chain A residue 1319 VAL Chi-restraints excluded: chain A residue 1353 ASP Chi-restraints excluded: chain A residue 1608 LEU Chi-restraints excluded: chain A residue 1645 ASP Chi-restraints excluded: chain A residue 1663 ARG Chi-restraints excluded: chain A residue 1674 ILE Chi-restraints excluded: chain A residue 1701 VAL Chi-restraints excluded: chain A residue 1715 MET Chi-restraints excluded: chain A residue 1807 VAL Chi-restraints excluded: chain A residue 1830 GLN Chi-restraints excluded: chain A residue 1871 GLU Chi-restraints excluded: chain A residue 1872 THR Chi-restraints excluded: chain A residue 1894 THR Chi-restraints excluded: chain A residue 1924 THR Chi-restraints excluded: chain A residue 2012 ASP Chi-restraints excluded: chain A residue 2031 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 15 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 9 optimal weight: 0.9980 chunk 85 optimal weight: 1.9990 chunk 34 optimal weight: 0.2980 chunk 4 optimal weight: 1.9990 chunk 60 optimal weight: 0.8980 chunk 81 optimal weight: 0.1980 chunk 35 optimal weight: 0.9990 chunk 68 optimal weight: 0.5980 chunk 63 optimal weight: 3.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1333 GLN A1652 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.096324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.070666 restraints weight = 14309.288| |-----------------------------------------------------------------------------| r_work (start): 0.2868 rms_B_bonded: 2.68 r_work: 0.2742 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.2742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.1904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9019 Z= 0.123 Angle : 0.452 9.312 12280 Z= 0.239 Chirality : 0.038 0.150 1409 Planarity : 0.003 0.044 1539 Dihedral : 12.566 72.538 1389 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 2.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 3.50 % Allowed : 19.89 % Favored : 76.61 % 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: 1.73 (0.26), residues: 1093 helix: 2.33 (0.21), residues: 637 sheet: 0.38 (0.67), residues: 70 loop : -0.77 (0.28), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1831 TYR 0.009 0.001 TYR A1808 PHE 0.012 0.001 PHE A1392 TRP 0.005 0.001 TRP A1159 HIS 0.002 0.001 HIS A1092 Details of bonding type rmsd covalent geometry : bond 0.00273 ( 9019) covalent geometry : angle 0.45151 (12280) hydrogen bonds : bond 0.05601 ( 483) hydrogen bonds : angle 3.72536 ( 1387) *********************** 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 108 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 76 time to evaluate : 0.223 Fit side-chains REVERT: A 1243 PHE cc_start: 0.7945 (OUTLIER) cc_final: 0.7697 (m-80) REVERT: A 1289 GLU cc_start: 0.8436 (OUTLIER) cc_final: 0.8219 (tt0) REVERT: A 1757 GLN cc_start: 0.7123 (OUTLIER) cc_final: 0.6847 (pt0) REVERT: A 1871 GLU cc_start: 0.8622 (OUTLIER) cc_final: 0.7589 (mm-30) REVERT: A 1898 ASP cc_start: 0.8336 (m-30) cc_final: 0.7574 (t0) REVERT: A 1924 THR cc_start: 0.8827 (OUTLIER) cc_final: 0.8478 (p) REVERT: A 2013 GLN cc_start: 0.8125 (mm-40) cc_final: 0.7842 (mm110) outliers start: 32 outliers final: 17 residues processed: 104 average time/residue: 0.6165 time to fit residues: 68.0426 Evaluate side-chains 96 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 74 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1243 PHE Chi-restraints excluded: chain A residue 1254 VAL Chi-restraints excluded: chain A residue 1281 ILE Chi-restraints excluded: chain A residue 1289 GLU Chi-restraints excluded: chain A residue 1319 VAL Chi-restraints excluded: chain A residue 1353 ASP Chi-restraints excluded: chain A residue 1608 LEU Chi-restraints excluded: chain A residue 1645 ASP Chi-restraints excluded: chain A residue 1663 ARG Chi-restraints excluded: chain A residue 1674 ILE Chi-restraints excluded: chain A residue 1701 VAL Chi-restraints excluded: chain A residue 1715 MET Chi-restraints excluded: chain A residue 1753 VAL Chi-restraints excluded: chain A residue 1757 GLN Chi-restraints excluded: chain A residue 1807 VAL Chi-restraints excluded: chain A residue 1830 GLN Chi-restraints excluded: chain A residue 1871 GLU Chi-restraints excluded: chain A residue 1872 THR Chi-restraints excluded: chain A residue 1894 THR Chi-restraints excluded: chain A residue 1924 THR Chi-restraints excluded: chain A residue 2012 ASP Chi-restraints excluded: chain A residue 2047 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 88 optimal weight: 0.0980 chunk 102 optimal weight: 1.9990 chunk 22 optimal weight: 0.4980 chunk 48 optimal weight: 1.9990 chunk 79 optimal weight: 0.2980 chunk 52 optimal weight: 0.5980 chunk 54 optimal weight: 1.9990 chunk 90 optimal weight: 0.0870 chunk 66 optimal weight: 2.9990 chunk 95 optimal weight: 0.9980 chunk 28 optimal weight: 0.9980 overall best weight: 0.3158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1333 GLN A1652 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.098066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.072341 restraints weight = 14185.944| |-----------------------------------------------------------------------------| r_work (start): 0.2899 rms_B_bonded: 2.69 r_work: 0.2774 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.2774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.2092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 9019 Z= 0.105 Angle : 0.436 9.851 12280 Z= 0.231 Chirality : 0.037 0.149 1409 Planarity : 0.003 0.044 1539 Dihedral : 12.490 72.298 1385 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 2.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 3.28 % Allowed : 20.44 % Favored : 76.28 % 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: 1.91 (0.26), residues: 1093 helix: 2.49 (0.21), residues: 636 sheet: 0.54 (0.68), residues: 68 loop : -0.72 (0.28), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1831 TYR 0.012 0.001 TYR A2011 PHE 0.015 0.001 PHE A1278 TRP 0.004 0.001 TRP A1159 HIS 0.001 0.000 HIS A1092 Details of bonding type rmsd covalent geometry : bond 0.00216 ( 9019) covalent geometry : angle 0.43604 (12280) hydrogen bonds : bond 0.04887 ( 483) hydrogen bonds : angle 3.58272 ( 1387) *********************** 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 109 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 79 time to evaluate : 0.304 Fit side-chains REVERT: A 1243 PHE cc_start: 0.7937 (OUTLIER) cc_final: 0.7661 (m-80) REVERT: A 1652 ASN cc_start: 0.6729 (OUTLIER) cc_final: 0.6316 (m-40) REVERT: A 1660 GLU cc_start: 0.6848 (OUTLIER) cc_final: 0.6495 (pm20) REVERT: A 1757 GLN cc_start: 0.7054 (tt0) cc_final: 0.6798 (pt0) REVERT: A 1871 GLU cc_start: 0.8615 (OUTLIER) cc_final: 0.7588 (mm-30) REVERT: A 1898 ASP cc_start: 0.8299 (m-30) cc_final: 0.7582 (t0) REVERT: A 1924 THR cc_start: 0.8803 (OUTLIER) cc_final: 0.8475 (p) REVERT: A 2013 GLN cc_start: 0.8111 (mm-40) cc_final: 0.7821 (mm110) outliers start: 30 outliers final: 12 residues processed: 105 average time/residue: 0.5726 time to fit residues: 63.7621 Evaluate side-chains 90 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 73 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1243 PHE Chi-restraints excluded: chain A residue 1254 VAL Chi-restraints excluded: chain A residue 1319 VAL Chi-restraints excluded: chain A residue 1353 ASP Chi-restraints excluded: chain A residue 1608 LEU Chi-restraints excluded: chain A residue 1652 ASN Chi-restraints excluded: chain A residue 1660 GLU Chi-restraints excluded: chain A residue 1663 ARG Chi-restraints excluded: chain A residue 1674 ILE Chi-restraints excluded: chain A residue 1715 MET Chi-restraints excluded: chain A residue 1753 VAL Chi-restraints excluded: chain A residue 1807 VAL Chi-restraints excluded: chain A residue 1871 GLU Chi-restraints excluded: chain A residue 1872 THR Chi-restraints excluded: chain A residue 1894 THR Chi-restraints excluded: chain A residue 1924 THR Chi-restraints excluded: chain A residue 2012 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 44 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 27 optimal weight: 0.6980 chunk 96 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 8 optimal weight: 0.5980 chunk 64 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 45 optimal weight: 0.6980 chunk 41 optimal weight: 3.9990 chunk 82 optimal weight: 0.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1333 GLN A1652 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.095162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2850 r_free = 0.2850 target = 0.069421 restraints weight = 14459.120| |-----------------------------------------------------------------------------| r_work (start): 0.2844 rms_B_bonded: 2.69 r_work: 0.2714 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.2714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.1909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9019 Z= 0.166 Angle : 0.492 10.671 12280 Z= 0.258 Chirality : 0.039 0.149 1409 Planarity : 0.004 0.043 1539 Dihedral : 12.539 74.062 1385 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 2.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 3.17 % Allowed : 20.87 % Favored : 75.96 % 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: 1.75 (0.26), residues: 1093 helix: 2.39 (0.21), residues: 638 sheet: 0.35 (0.66), residues: 70 loop : -0.83 (0.28), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1831 TYR 0.010 0.001 TYR A1030 PHE 0.016 0.001 PHE A1392 TRP 0.007 0.001 TRP A1159 HIS 0.002 0.001 HIS A1092 Details of bonding type rmsd covalent geometry : bond 0.00395 ( 9019) covalent geometry : angle 0.49154 (12280) hydrogen bonds : bond 0.06095 ( 483) hydrogen bonds : angle 3.70308 ( 1387) *********************** 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 104 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 75 time to evaluate : 0.347 Fit side-chains REVERT: A 1243 PHE cc_start: 0.7988 (OUTLIER) cc_final: 0.7761 (m-80) REVERT: A 1757 GLN cc_start: 0.7220 (OUTLIER) cc_final: 0.6939 (pt0) REVERT: A 1871 GLU cc_start: 0.8641 (OUTLIER) cc_final: 0.7606 (mm-30) REVERT: A 1898 ASP cc_start: 0.8399 (OUTLIER) cc_final: 0.7617 (t0) REVERT: A 1924 THR cc_start: 0.8866 (OUTLIER) cc_final: 0.8565 (p) REVERT: A 2013 GLN cc_start: 0.8147 (mm-40) cc_final: 0.7895 (mm110) outliers start: 29 outliers final: 17 residues processed: 101 average time/residue: 0.6126 time to fit residues: 65.6540 Evaluate side-chains 95 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 73 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1084 LYS Chi-restraints excluded: chain A residue 1186 LEU Chi-restraints excluded: chain A residue 1243 PHE Chi-restraints excluded: chain A residue 1254 VAL Chi-restraints excluded: chain A residue 1281 ILE Chi-restraints excluded: chain A residue 1319 VAL Chi-restraints excluded: chain A residue 1353 ASP Chi-restraints excluded: chain A residue 1608 LEU Chi-restraints excluded: chain A residue 1663 ARG Chi-restraints excluded: chain A residue 1674 ILE Chi-restraints excluded: chain A residue 1701 VAL Chi-restraints excluded: chain A residue 1715 MET Chi-restraints excluded: chain A residue 1753 VAL Chi-restraints excluded: chain A residue 1757 GLN Chi-restraints excluded: chain A residue 1807 VAL Chi-restraints excluded: chain A residue 1871 GLU Chi-restraints excluded: chain A residue 1872 THR Chi-restraints excluded: chain A residue 1894 THR Chi-restraints excluded: chain A residue 1898 ASP Chi-restraints excluded: chain A residue 1924 THR Chi-restraints excluded: chain A residue 2012 ASP Chi-restraints excluded: chain A residue 2047 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 71 optimal weight: 4.9990 chunk 35 optimal weight: 2.9990 chunk 42 optimal weight: 0.0970 chunk 75 optimal weight: 5.9990 chunk 83 optimal weight: 0.8980 chunk 36 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 49 optimal weight: 0.6980 chunk 8 optimal weight: 0.9980 chunk 37 optimal weight: 0.1980 chunk 72 optimal weight: 0.8980 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1333 GLN A1652 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.096522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.070750 restraints weight = 14253.212| |-----------------------------------------------------------------------------| r_work (start): 0.2848 rms_B_bonded: 2.69 r_work: 0.2714 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.2714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.2064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9019 Z= 0.120 Angle : 0.458 11.409 12280 Z= 0.241 Chirality : 0.038 0.152 1409 Planarity : 0.003 0.044 1539 Dihedral : 12.503 73.509 1385 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 2.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 2.51 % Allowed : 21.97 % Favored : 75.52 % 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 (0.26), residues: 1093 helix: 2.51 (0.21), residues: 637 sheet: 0.41 (0.66), residues: 68 loop : -0.83 (0.28), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1831 TYR 0.013 0.001 TYR A2011 PHE 0.016 0.001 PHE A1278 TRP 0.005 0.001 TRP A1159 HIS 0.002 0.001 HIS A1092 Details of bonding type rmsd covalent geometry : bond 0.00266 ( 9019) covalent geometry : angle 0.45761 (12280) hydrogen bonds : bond 0.05337 ( 483) hydrogen bonds : angle 3.59586 ( 1387) *********************** 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 98 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 75 time to evaluate : 0.295 Fit side-chains REVERT: A 1040 GLU cc_start: 0.7306 (pm20) cc_final: 0.6692 (pm20) REVERT: A 1243 PHE cc_start: 0.7951 (OUTLIER) cc_final: 0.7722 (m-80) REVERT: A 1705 ARG cc_start: 0.7255 (OUTLIER) cc_final: 0.6995 (ttm170) REVERT: A 1757 GLN cc_start: 0.7140 (tt0) cc_final: 0.6866 (pt0) REVERT: A 1871 GLU cc_start: 0.8631 (OUTLIER) cc_final: 0.7600 (mm-30) REVERT: A 1898 ASP cc_start: 0.8339 (m-30) cc_final: 0.7595 (t0) REVERT: A 1924 THR cc_start: 0.8860 (OUTLIER) cc_final: 0.8518 (p) REVERT: A 2013 GLN cc_start: 0.8125 (mm-40) cc_final: 0.7870 (mm110) outliers start: 23 outliers final: 15 residues processed: 95 average time/residue: 0.5593 time to fit residues: 56.3967 Evaluate side-chains 91 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 72 time to evaluate : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1186 LEU Chi-restraints excluded: chain A residue 1243 PHE Chi-restraints excluded: chain A residue 1254 VAL Chi-restraints excluded: chain A residue 1319 VAL Chi-restraints excluded: chain A residue 1353 ASP Chi-restraints excluded: chain A residue 1608 LEU Chi-restraints excluded: chain A residue 1663 ARG Chi-restraints excluded: chain A residue 1674 ILE Chi-restraints excluded: chain A residue 1701 VAL Chi-restraints excluded: chain A residue 1705 ARG Chi-restraints excluded: chain A residue 1715 MET Chi-restraints excluded: chain A residue 1753 VAL Chi-restraints excluded: chain A residue 1807 VAL Chi-restraints excluded: chain A residue 1871 GLU Chi-restraints excluded: chain A residue 1872 THR Chi-restraints excluded: chain A residue 1894 THR Chi-restraints excluded: chain A residue 1924 THR Chi-restraints excluded: chain A residue 2012 ASP Chi-restraints excluded: chain A residue 2016 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 96 optimal weight: 2.9990 chunk 70 optimal weight: 4.9990 chunk 34 optimal weight: 1.9990 chunk 28 optimal weight: 0.2980 chunk 59 optimal weight: 0.6980 chunk 95 optimal weight: 0.5980 chunk 9 optimal weight: 0.8980 chunk 107 optimal weight: 0.6980 chunk 93 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 chunk 66 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1652 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.097284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.071033 restraints weight = 14386.083| |-----------------------------------------------------------------------------| r_work (start): 0.2839 rms_B_bonded: 2.82 r_work: 0.2701 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.2052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9019 Z= 0.127 Angle : 0.467 12.035 12280 Z= 0.245 Chirality : 0.038 0.149 1409 Planarity : 0.004 0.043 1539 Dihedral : 12.501 73.060 1385 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 2.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 2.73 % Allowed : 21.86 % Favored : 75.41 % 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: 1.86 (0.26), residues: 1093 helix: 2.53 (0.21), residues: 637 sheet: 0.24 (0.65), residues: 70 loop : -0.85 (0.29), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1831 TYR 0.009 0.001 TYR A1808 PHE 0.017 0.001 PHE A1278 TRP 0.006 0.001 TRP A1159 HIS 0.002 0.001 HIS A1092 Details of bonding type rmsd covalent geometry : bond 0.00287 ( 9019) covalent geometry : angle 0.46672 (12280) hydrogen bonds : bond 0.05447 ( 483) hydrogen bonds : angle 3.58702 ( 1387) *********************** 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 97 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 72 time to evaluate : 0.355 Fit side-chains REVERT: A 1040 GLU cc_start: 0.7365 (pm20) cc_final: 0.6732 (pm20) REVERT: A 1652 ASN cc_start: 0.6642 (OUTLIER) cc_final: 0.6354 (m-40) REVERT: A 1660 GLU cc_start: 0.6871 (OUTLIER) cc_final: 0.6613 (pm20) REVERT: A 1705 ARG cc_start: 0.7250 (OUTLIER) cc_final: 0.6982 (ttm170) REVERT: A 1757 GLN cc_start: 0.7068 (tt0) cc_final: 0.6799 (pt0) REVERT: A 1871 GLU cc_start: 0.8642 (OUTLIER) cc_final: 0.7614 (mm-30) REVERT: A 1898 ASP cc_start: 0.8359 (m-30) cc_final: 0.7617 (t0) REVERT: A 1924 THR cc_start: 0.8892 (OUTLIER) cc_final: 0.8554 (p) REVERT: A 2013 GLN cc_start: 0.8149 (mm-40) cc_final: 0.7881 (mm110) outliers start: 25 outliers final: 15 residues processed: 93 average time/residue: 0.5809 time to fit residues: 57.4047 Evaluate side-chains 91 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 71 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1084 LYS Chi-restraints excluded: chain A residue 1186 LEU Chi-restraints excluded: chain A residue 1254 VAL Chi-restraints excluded: chain A residue 1281 ILE Chi-restraints excluded: chain A residue 1319 VAL Chi-restraints excluded: chain A residue 1353 ASP Chi-restraints excluded: chain A residue 1608 LEU Chi-restraints excluded: chain A residue 1652 ASN Chi-restraints excluded: chain A residue 1660 GLU Chi-restraints excluded: chain A residue 1663 ARG Chi-restraints excluded: chain A residue 1674 ILE Chi-restraints excluded: chain A residue 1705 ARG Chi-restraints excluded: chain A residue 1715 MET Chi-restraints excluded: chain A residue 1753 VAL Chi-restraints excluded: chain A residue 1807 VAL Chi-restraints excluded: chain A residue 1871 GLU Chi-restraints excluded: chain A residue 1872 THR Chi-restraints excluded: chain A residue 1894 THR Chi-restraints excluded: chain A residue 1924 THR Chi-restraints excluded: chain A residue 2012 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 28 optimal weight: 0.6980 chunk 6 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 56 optimal weight: 0.7980 chunk 7 optimal weight: 0.5980 chunk 4 optimal weight: 1.9990 chunk 27 optimal weight: 0.0980 chunk 95 optimal weight: 0.9980 chunk 109 optimal weight: 5.9990 chunk 52 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.096798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.070700 restraints weight = 14379.250| |-----------------------------------------------------------------------------| r_work (start): 0.2840 rms_B_bonded: 2.76 r_work: 0.2706 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.2706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.2068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 9019 Z= 0.162 Angle : 0.823 59.198 12280 Z= 0.489 Chirality : 0.040 0.435 1409 Planarity : 0.004 0.043 1539 Dihedral : 12.503 73.058 1385 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 2.30 % Allowed : 22.19 % Favored : 75.52 % 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: 1.86 (0.26), residues: 1093 helix: 2.53 (0.21), residues: 637 sheet: 0.20 (0.65), residues: 70 loop : -0.85 (0.29), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1831 TYR 0.008 0.001 TYR A1030 PHE 0.012 0.001 PHE A1392 TRP 0.006 0.001 TRP A1159 HIS 0.002 0.001 HIS A1092 Details of bonding type rmsd covalent geometry : bond 0.00330 ( 9019) covalent geometry : angle 0.82279 (12280) hydrogen bonds : bond 0.05456 ( 483) hydrogen bonds : angle 3.60412 ( 1387) ********************** 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 92 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 71 time to evaluate : 0.342 Fit side-chains REVERT: A 1040 GLU cc_start: 0.7354 (pm20) cc_final: 0.6715 (pm20) REVERT: A 1705 ARG cc_start: 0.7245 (OUTLIER) cc_final: 0.6978 (ttm170) REVERT: A 1757 GLN cc_start: 0.7035 (tt0) cc_final: 0.6768 (pt0) REVERT: A 1871 GLU cc_start: 0.8632 (OUTLIER) cc_final: 0.7601 (mm-30) REVERT: A 1898 ASP cc_start: 0.8344 (m-30) cc_final: 0.7601 (t0) REVERT: A 1924 THR cc_start: 0.8873 (OUTLIER) cc_final: 0.8530 (p) REVERT: A 2013 GLN cc_start: 0.8145 (mm-40) cc_final: 0.7877 (mm110) outliers start: 21 outliers final: 15 residues processed: 89 average time/residue: 0.5920 time to fit residues: 56.0888 Evaluate side-chains 88 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 70 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1084 LYS Chi-restraints excluded: chain A residue 1186 LEU Chi-restraints excluded: chain A residue 1254 VAL Chi-restraints excluded: chain A residue 1281 ILE Chi-restraints excluded: chain A residue 1319 VAL Chi-restraints excluded: chain A residue 1353 ASP Chi-restraints excluded: chain A residue 1608 LEU Chi-restraints excluded: chain A residue 1663 ARG Chi-restraints excluded: chain A residue 1674 ILE Chi-restraints excluded: chain A residue 1705 ARG Chi-restraints excluded: chain A residue 1715 MET Chi-restraints excluded: chain A residue 1753 VAL Chi-restraints excluded: chain A residue 1807 VAL Chi-restraints excluded: chain A residue 1871 GLU Chi-restraints excluded: chain A residue 1872 THR Chi-restraints excluded: chain A residue 1894 THR Chi-restraints excluded: chain A residue 1924 THR Chi-restraints excluded: chain A residue 2012 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 0.8980 chunk 51 optimal weight: 0.6980 chunk 78 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 3 optimal weight: 0.9980 chunk 4 optimal weight: 0.2980 chunk 24 optimal weight: 3.9990 chunk 32 optimal weight: 0.7980 chunk 2 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1652 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.097526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.071464 restraints weight = 14410.195| |-----------------------------------------------------------------------------| r_work (start): 0.2863 rms_B_bonded: 2.77 r_work: 0.2734 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.2734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.2064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 9019 Z= 0.162 Angle : 0.823 59.198 12280 Z= 0.489 Chirality : 0.040 0.435 1409 Planarity : 0.004 0.043 1539 Dihedral : 12.503 73.058 1385 Min Nonbonded Distance : 1.558 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 1.97 % Allowed : 22.51 % Favored : 75.52 % 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: 1.86 (0.26), residues: 1093 helix: 2.53 (0.21), residues: 637 sheet: 0.20 (0.65), residues: 70 loop : -0.85 (0.29), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1831 TYR 0.008 0.001 TYR A1030 PHE 0.012 0.001 PHE A1392 TRP 0.006 0.001 TRP A1159 HIS 0.002 0.001 HIS A1092 Details of bonding type rmsd covalent geometry : bond 0.00330 ( 9019) covalent geometry : angle 0.82279 (12280) hydrogen bonds : bond 0.05456 ( 483) hydrogen bonds : angle 3.60412 ( 1387) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2255.26 seconds wall clock time: 39 minutes 8.83 seconds (2348.83 seconds total)