Starting phenix.real_space_refine on Thu Jul 2 16:22:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9pnv_71773/07_2026/9pnv_71773.cif Found real_map, /net/cci-nas-00/data/ceres_data/9pnv_71773/07_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_71773/07_2026/9pnv_71773.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9pnv_71773/07_2026/9pnv_71773.map" model { file = "/net/cci-nas-00/data/ceres_data/9pnv_71773/07_2026/9pnv_71773.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9pnv_71773/07_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-dev-6108/lib/python3.11/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: 1.93, per 1000 atoms: 0.22 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: 0.87 Conformation dependent library (CDL) restraints added in 312.4 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: 0.96 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: 1.61 Time building geometry restraints manager: 1.10 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=" C3' DT B 11 " pdb=" C2' DT B 11 " ideal model delta sigma weight residual 1.516 1.532 -0.016 8.00e-03 1.56e+04 4.19e+00 bond pdb=" C3' DT B 12 " pdb=" C2' DT B 12 " ideal model delta sigma weight residual 1.516 1.532 -0.016 8.00e-03 1.56e+04 4.18e+00 bond pdb=" C3' DA B 21 " pdb=" C2' DA B 21 " ideal model delta sigma weight residual 1.516 1.532 -0.016 8.00e-03 1.56e+04 4.08e+00 bond pdb=" C1' DT B 4 " pdb=" N1 DT B 4 " ideal model delta sigma weight residual 1.468 1.495 -0.027 1.40e-02 5.10e+03 3.84e+00 bond pdb=" O4' DT B 11 " pdb=" C1' DT B 11 " ideal model delta sigma weight residual 1.420 1.400 0.020 1.10e-02 8.26e+03 3.38e+00 ... (remaining 9014 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.48: 12207 2.48 - 4.96: 65 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=" N3 DT B 11 " pdb=" C4 DT B 11 " pdb=" O4 DT B 11 " ideal model delta sigma weight residual 119.90 122.38 -2.48 6.00e-01 2.78e+00 1.71e+01 angle pdb=" N3 DT B 12 " pdb=" C4 DT B 12 " pdb=" O4 DT B 12 " ideal model delta sigma weight residual 119.90 122.37 -2.47 6.00e-01 2.78e+00 1.69e+01 angle pdb=" N3 DT B 4 " pdb=" C4 DT B 4 " pdb=" O4 DT B 4 " ideal model delta sigma weight residual 119.90 122.36 -2.46 6.00e-01 2.78e+00 1.68e+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 ... (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: 869 0.030 - 0.059: 383 0.059 - 0.089: 88 0.089 - 0.119: 63 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: 2.110 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: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 9.630 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 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:6.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9011 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9019 Z= 0.198 Angle : 0.485 12.404 12280 Z= 0.287 Chirality : 0.039 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/Z covalent geometry : bond 0.00353 / 0.20 ( 9019) covalent geometry : angle 0.48514 / 0.29 (12280) hydrogen bonds : bond 0.31385 / 20.22 ( 483) hydrogen bonds : angle 7.13825 / 4.92 ( 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 : 0.231 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: 0.5407 time to fit residues: 55.3712 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 : 0.331 ------------------------------------------------------------------------------- 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... A1333 GLN A1511 ASN A1652 ASN A2056 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.094288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2853 r_free = 0.2853 target = 0.069277 restraints weight = 14210.340| |-----------------------------------------------------------------------------| r_work (start): 0.2812 rms_B_bonded: 2.61 r_work: 0.2670 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.2670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.1025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 9019 Z= 0.184 Angle : 0.544 7.411 12280 Z= 0.303 Chirality : 0.041 0.147 1409 Planarity : 0.004 0.045 1539 Dihedral : 13.111 71.510 1424 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 2.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 2.73 % Allowed : 21.53 % Favored : 75.74 % 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: 1.09 (0.25), residues: 1093 helix: 1.69 (0.21), residues: 615 sheet: 0.35 (0.68), residues: 72 loop : -0.69 (0.28), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1624 TYR 0.010 0.001 TYR A1030 PHE 0.015 0.001 PHE A2088 TRP 0.007 0.001 TRP A1159 HIS 0.005 0.001 HIS A1092 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.18 ( 9019) covalent geometry : angle 0.54411 / 0.30 (12280) hydrogen bonds : bond 0.10079 / 6.46 ( 483) hydrogen bonds : angle 4.82654 / 3.35 ( 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 102 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 77 time to evaluate : 0.215 Fit side-chains REVERT: A 1871 GLU cc_start: 0.8600 (OUTLIER) cc_final: 0.7564 (mm-30) REVERT: A 1898 ASP cc_start: 0.8367 (m-30) cc_final: 0.7441 (t0) REVERT: A 1904 MET cc_start: 0.8962 (ttp) cc_final: 0.8743 (ttm) REVERT: A 2013 GLN cc_start: 0.8056 (mm-40) cc_final: 0.7663 (mm110) REVERT: A 2091 GLU cc_start: 0.8308 (OUTLIER) cc_final: 0.7833 (tt0) outliers start: 25 outliers final: 14 residues processed: 99 average time/residue: 0.6298 time to fit residues: 66.0080 Evaluate side-chains 88 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 72 time to evaluate : 0.256 ------------------------------------------------------------------------------- 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 1371 ASP Chi-restraints excluded: chain A residue 1441 LEU Chi-restraints excluded: chain A residue 1540 VAL Chi-restraints excluded: chain A residue 1558 VAL Chi-restraints excluded: chain A residue 1608 LEU Chi-restraints excluded: chain A residue 1663 ARG Chi-restraints excluded: chain A residue 1715 MET 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 2031 ARG Chi-restraints excluded: chain A residue 2056 GLN 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: 1.9990 chunk 39 optimal weight: 0.6980 chunk 12 optimal weight: 1.9990 chunk 52 optimal weight: 0.5980 chunk 94 optimal weight: 0.0170 chunk 96 optimal weight: 0.0970 chunk 46 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 92 optimal weight: 0.6980 overall best weight: 0.4216 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1652 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.096425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.071292 restraints weight = 14163.899| |-----------------------------------------------------------------------------| r_work (start): 0.2875 rms_B_bonded: 2.61 r_work: 0.2740 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.2740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.1427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 9019 Z= 0.132 Angle : 0.465 6.090 12280 Z= 0.256 Chirality : 0.038 0.149 1409 Planarity : 0.003 0.044 1539 Dihedral : 12.841 71.705 1395 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 2.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 3.06 % Allowed : 20.22 % Favored : 76.72 % 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: 1.49 (0.26), residues: 1093 helix: 2.09 (0.21), residues: 622 sheet: 0.44 (0.68), residues: 70 loop : -0.70 (0.28), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1750 TYR 0.008 0.001 TYR A1388 PHE 0.013 0.001 PHE A1278 TRP 0.005 0.001 TRP A1159 HIS 0.003 0.001 HIS A1092 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.13 ( 9019) covalent geometry : angle 0.46522 / 0.26 (12280) hydrogen bonds : bond 0.07469 / 4.74 ( 483) hydrogen bonds : angle 4.24750 / 2.97 ( 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 105 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 77 time to evaluate : 0.331 Fit side-chains REVERT: A 1243 PHE cc_start: 0.7842 (OUTLIER) cc_final: 0.7590 (m-80) REVERT: A 1378 GLU cc_start: 0.7738 (mm-30) cc_final: 0.7466 (mt-10) REVERT: A 1447 LEU cc_start: 0.8304 (OUTLIER) cc_final: 0.7832 (mp) REVERT: A 1871 GLU cc_start: 0.8590 (OUTLIER) cc_final: 0.7562 (mm-30) REVERT: A 1898 ASP cc_start: 0.8297 (OUTLIER) cc_final: 0.7444 (t0) REVERT: A 1924 THR cc_start: 0.8726 (OUTLIER) cc_final: 0.8426 (p) REVERT: A 2013 GLN cc_start: 0.8163 (mm-40) cc_final: 0.7863 (mm110) outliers start: 28 outliers final: 10 residues processed: 100 average time/residue: 0.6323 time to fit residues: 66.9287 Evaluate side-chains 87 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 72 time to evaluate : 0.353 ------------------------------------------------------------------------------- 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 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 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 1898 ASP 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 91 optimal weight: 2.9990 chunk 66 optimal weight: 0.4980 chunk 69 optimal weight: 0.5980 chunk 85 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 50 optimal weight: 0.9990 chunk 82 optimal weight: 1.9990 chunk 81 optimal weight: 0.7980 chunk 16 optimal weight: 0.5980 chunk 70 optimal weight: 4.9990 chunk 97 optimal weight: 0.2980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1652 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.096308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.070962 restraints weight = 14550.533| |-----------------------------------------------------------------------------| r_work (start): 0.2859 rms_B_bonded: 2.69 r_work: 0.2729 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.2729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.1680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 9019 Z= 0.125 Angle : 0.455 7.076 12280 Z= 0.246 Chirality : 0.039 0.147 1409 Planarity : 0.003 0.044 1539 Dihedral : 12.771 74.717 1389 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 2.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 2.95 % Allowed : 20.66 % Favored : 76.39 % 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: 1.69 (0.26), residues: 1093 helix: 2.30 (0.21), residues: 629 sheet: 0.23 (0.67), residues: 72 loop : -0.70 (0.29), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1831 TYR 0.013 0.001 TYR A2011 PHE 0.017 0.001 PHE A1278 TRP 0.004 0.001 TRP A1578 HIS 0.002 0.001 HIS A1092 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.13 ( 9019) covalent geometry : angle 0.45460 / 0.25 (12280) hydrogen bonds : bond 0.06301 / 4.00 ( 483) hydrogen bonds : angle 3.94148 / 2.76 ( 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 100 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 73 time to evaluate : 0.346 Fit side-chains REVERT: A 1652 ASN cc_start: 0.6836 (OUTLIER) cc_final: 0.6394 (m-40) REVERT: A 1660 GLU cc_start: 0.6956 (OUTLIER) cc_final: 0.6607 (pm20) REVERT: A 1898 ASP cc_start: 0.8322 (m-30) cc_final: 0.7558 (t0) REVERT: A 1924 THR cc_start: 0.8808 (OUTLIER) cc_final: 0.8520 (p) REVERT: A 2013 GLN cc_start: 0.8166 (mm-40) cc_final: 0.7900 (mm110) outliers start: 27 outliers final: 14 residues processed: 97 average time/residue: 0.5912 time to fit residues: 61.0530 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 : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 1753 VAL Chi-restraints excluded: chain A residue 1807 VAL Chi-restraints excluded: chain A residue 1830 GLN 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: 0.8980 chunk 85 optimal weight: 1.9990 chunk 34 optimal weight: 0.5980 chunk 4 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 81 optimal weight: 0.0470 chunk 35 optimal weight: 0.9990 chunk 68 optimal weight: 0.6980 chunk 63 optimal weight: 2.9990 overall best weight: 0.6480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3251 r_free = 0.3251 target = 0.095559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.069883 restraints weight = 14377.610| |-----------------------------------------------------------------------------| r_work (start): 0.2830 rms_B_bonded: 2.69 r_work: 0.2696 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.2696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.1736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9019 Z= 0.132 Angle : 0.461 8.424 12280 Z= 0.247 Chirality : 0.039 0.149 1409 Planarity : 0.003 0.044 1539 Dihedral : 12.768 72.768 1389 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 2.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 3.28 % Allowed : 20.22 % Favored : 76.50 % 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: 1.76 (0.26), residues: 1093 helix: 2.39 (0.21), residues: 631 sheet: 0.16 (0.66), residues: 72 loop : -0.73 (0.29), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1831 TYR 0.009 0.001 TYR A1030 PHE 0.014 0.001 PHE A1278 TRP 0.005 0.001 TRP A1159 HIS 0.002 0.001 HIS A1092 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.13 ( 9019) covalent geometry : angle 0.46115 / 0.25 (12280) hydrogen bonds : bond 0.06123 / 3.90 ( 483) hydrogen bonds : angle 3.88629 / 2.72 ( 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 105 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 75 time to evaluate : 0.331 Fit side-chains REVERT: A 1243 PHE cc_start: 0.7978 (OUTLIER) cc_final: 0.7722 (m-80) REVERT: A 1871 GLU cc_start: 0.8638 (OUTLIER) cc_final: 0.7614 (mm-30) REVERT: A 1898 ASP cc_start: 0.8312 (m-30) cc_final: 0.7563 (t0) REVERT: A 1904 MET cc_start: 0.8993 (ttp) cc_final: 0.8785 (ttm) REVERT: A 1924 THR cc_start: 0.8809 (OUTLIER) cc_final: 0.8522 (p) REVERT: A 2013 GLN cc_start: 0.8170 (mm-40) cc_final: 0.7897 (mm110) outliers start: 30 outliers final: 19 residues processed: 102 average time/residue: 0.5951 time to fit residues: 64.5187 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 : 0.333 ------------------------------------------------------------------------------- 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 1305 ASP Chi-restraints excluded: chain A residue 1319 VAL Chi-restraints excluded: chain A residue 1353 ASP Chi-restraints excluded: chain A residue 1441 LEU Chi-restraints excluded: chain A residue 1474 THR 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 88 optimal weight: 3.9990 chunk 102 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 54 optimal weight: 0.9980 chunk 90 optimal weight: 0.8980 chunk 66 optimal weight: 0.9980 chunk 95 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3235 r_free = 0.3235 target = 0.094552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2838 r_free = 0.2838 target = 0.069183 restraints weight = 14422.264| |-----------------------------------------------------------------------------| r_work (start): 0.2826 rms_B_bonded: 2.67 r_work: 0.2695 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.2695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.1708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 9019 Z= 0.186 Angle : 0.503 8.984 12280 Z= 0.267 Chirality : 0.041 0.148 1409 Planarity : 0.004 0.043 1539 Dihedral : 12.819 71.499 1389 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 2.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 3.50 % Allowed : 20.22 % 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: 1.54 (0.26), residues: 1093 helix: 2.21 (0.21), residues: 637 sheet: 0.30 (0.66), residues: 70 loop : -0.91 (0.28), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1831 TYR 0.012 0.001 TYR A2011 PHE 0.016 0.002 PHE A1392 TRP 0.007 0.001 TRP A1159 HIS 0.003 0.001 HIS A2044 Details of bonding type rmsd/Z covalent geometry : bond 0.00442 / 0.19 ( 9019) covalent geometry : angle 0.50322 / 0.27 (12280) hydrogen bonds : bond 0.06917 / 4.41 ( 483) hydrogen bonds : angle 3.93085 / 2.74 ( 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 105 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 73 time to evaluate : 0.350 Fit side-chains REVERT: A 1243 PHE cc_start: 0.8101 (OUTLIER) cc_final: 0.7853 (m-80) REVERT: A 1680 ARG cc_start: 0.8210 (mmm160) cc_final: 0.7920 (mtp85) REVERT: A 1871 GLU cc_start: 0.8659 (OUTLIER) cc_final: 0.7628 (mm-30) REVERT: A 1898 ASP cc_start: 0.8424 (OUTLIER) cc_final: 0.7598 (t0) REVERT: A 1904 MET cc_start: 0.9115 (ttp) cc_final: 0.8900 (ttm) REVERT: A 1924 THR cc_start: 0.8915 (OUTLIER) cc_final: 0.8633 (p) REVERT: A 2013 GLN cc_start: 0.8184 (mm-40) cc_final: 0.7917 (mm110) outliers start: 32 outliers final: 19 residues processed: 102 average time/residue: 0.6171 time to fit residues: 67.0426 Evaluate side-chains 92 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 69 time to evaluate : 0.328 ------------------------------------------------------------------------------- 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 1305 ASP Chi-restraints excluded: chain A residue 1319 VAL Chi-restraints excluded: chain A residue 1353 ASP Chi-restraints excluded: chain A residue 1441 LEU Chi-restraints excluded: chain A residue 1474 THR Chi-restraints excluded: chain A residue 1481 SER 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 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 1898 ASP 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: 0.8980 chunk 87 optimal weight: 1.9990 chunk 27 optimal weight: 0.2980 chunk 96 optimal weight: 0.7980 chunk 0 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 chunk 64 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 chunk 41 optimal weight: 2.9990 chunk 82 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3254 r_free = 0.3254 target = 0.095778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.070371 restraints weight = 14489.601| |-----------------------------------------------------------------------------| r_work (start): 0.2819 rms_B_bonded: 2.69 r_work: 0.2682 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.2682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.1813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9019 Z= 0.135 Angle : 0.468 9.917 12280 Z= 0.250 Chirality : 0.039 0.151 1409 Planarity : 0.003 0.044 1539 Dihedral : 12.764 71.348 1385 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 2.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 3.28 % Allowed : 20.87 % Favored : 75.85 % 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: 1.71 (0.26), residues: 1093 helix: 2.39 (0.21), residues: 631 sheet: 0.26 (0.66), residues: 70 loop : -0.86 (0.28), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1831 TYR 0.009 0.001 TYR A1808 PHE 0.016 0.001 PHE A1278 TRP 0.006 0.001 TRP A1159 HIS 0.002 0.001 HIS A1092 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 ( 9019) covalent geometry : angle 0.46833 / 0.25 (12280) hydrogen bonds : bond 0.06112 / 3.89 ( 483) hydrogen bonds : angle 3.80281 / 2.66 ( 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 103 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 73 time to evaluate : 0.277 Fit side-chains revert: symmetry clash REVERT: A 1243 PHE cc_start: 0.7978 (OUTLIER) cc_final: 0.7727 (m-80) REVERT: A 1680 ARG cc_start: 0.7976 (mmm160) cc_final: 0.7687 (mtp85) REVERT: A 1871 GLU cc_start: 0.8640 (OUTLIER) cc_final: 0.7608 (mm-30) REVERT: A 1898 ASP cc_start: 0.8336 (OUTLIER) cc_final: 0.7558 (t0) REVERT: A 1904 MET cc_start: 0.9045 (ttp) cc_final: 0.8826 (ttm) REVERT: A 1924 THR cc_start: 0.8848 (OUTLIER) cc_final: 0.8568 (p) REVERT: A 2013 GLN cc_start: 0.8150 (mm-40) cc_final: 0.7859 (mm110) REVERT: A 2091 GLU cc_start: 0.8371 (OUTLIER) cc_final: 0.7987 (tt0) outliers start: 30 outliers final: 18 residues processed: 99 average time/residue: 0.5872 time to fit residues: 61.8426 Evaluate side-chains 96 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 73 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1073 THR 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 1305 ASP Chi-restraints excluded: chain A residue 1319 VAL Chi-restraints excluded: chain A residue 1353 ASP Chi-restraints excluded: chain A residue 1474 THR 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 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 1898 ASP Chi-restraints excluded: chain A residue 1924 THR Chi-restraints excluded: chain A residue 2012 ASP Chi-restraints excluded: chain A residue 2015 GLU Chi-restraints excluded: chain A residue 2091 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 71 optimal weight: 0.7980 chunk 35 optimal weight: 2.9990 chunk 42 optimal weight: 0.4980 chunk 75 optimal weight: 6.9990 chunk 83 optimal weight: 0.9990 chunk 36 optimal weight: 0.6980 chunk 48 optimal weight: 1.9990 chunk 49 optimal weight: 0.5980 chunk 8 optimal weight: 0.7980 chunk 37 optimal weight: 0.9980 chunk 72 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3252 r_free = 0.3252 target = 0.095484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.069919 restraints weight = 14323.194| |-----------------------------------------------------------------------------| r_work (start): 0.2830 rms_B_bonded: 2.68 r_work: 0.2694 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.2694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.1906 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= 0.132 Angle : 0.472 10.690 12280 Z= 0.251 Chirality : 0.039 0.150 1409 Planarity : 0.003 0.044 1539 Dihedral : 12.752 71.116 1385 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 2.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 3.28 % Allowed : 21.53 % Favored : 75.19 % 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 (0.26), residues: 1093 helix: 2.38 (0.21), residues: 637 sheet: 0.25 (0.65), residues: 70 loop : -0.91 (0.28), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1831 TYR 0.013 0.001 TYR A2011 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/Z covalent geometry : bond 0.00291 / 0.13 ( 9019) covalent geometry : angle 0.47180 / 0.25 (12280) hydrogen bonds : bond 0.05858 / 3.73 ( 483) hydrogen bonds : angle 3.72947 / 2.61 ( 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 106 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 76 time to evaluate : 0.287 Fit side-chains revert: symmetry clash REVERT: A 1040 GLU cc_start: 0.7349 (pm20) cc_final: 0.6709 (pm20) REVERT: A 1243 PHE cc_start: 0.7909 (OUTLIER) cc_final: 0.7663 (m-80) REVERT: A 1680 ARG cc_start: 0.7927 (mmm160) cc_final: 0.7612 (mtp85) REVERT: A 1871 GLU cc_start: 0.8627 (OUTLIER) cc_final: 0.7595 (mm-30) REVERT: A 1898 ASP cc_start: 0.8306 (OUTLIER) cc_final: 0.7561 (t0) REVERT: A 1904 MET cc_start: 0.9010 (ttp) cc_final: 0.8785 (ttm) REVERT: A 1924 THR cc_start: 0.8820 (OUTLIER) cc_final: 0.8525 (p) REVERT: A 2013 GLN cc_start: 0.8135 (mm-40) cc_final: 0.7881 (mm110) REVERT: A 2091 GLU cc_start: 0.8332 (OUTLIER) cc_final: 0.7938 (tt0) outliers start: 30 outliers final: 21 residues processed: 103 average time/residue: 0.5971 time to fit residues: 65.2083 Evaluate side-chains 101 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 75 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1073 THR 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 1305 ASP Chi-restraints excluded: chain A residue 1319 VAL 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 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 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 1898 ASP Chi-restraints excluded: chain A residue 1924 THR Chi-restraints excluded: chain A residue 2012 ASP Chi-restraints excluded: chain A residue 2015 GLU Chi-restraints excluded: chain A residue 2047 LEU Chi-restraints excluded: chain A residue 2091 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 96 optimal weight: 0.6980 chunk 70 optimal weight: 0.2980 chunk 34 optimal weight: 0.0980 chunk 28 optimal weight: 0.9980 chunk 59 optimal weight: 2.9990 chunk 95 optimal weight: 0.5980 chunk 9 optimal weight: 0.8980 chunk 107 optimal weight: 0.6980 chunk 93 optimal weight: 0.9990 chunk 100 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3271 r_free = 0.3271 target = 0.096763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.071198 restraints weight = 14295.044| |-----------------------------------------------------------------------------| r_work (start): 0.2849 rms_B_bonded: 2.68 r_work: 0.2716 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.2716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.1992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 9019 Z= 0.115 Angle : 0.463 11.275 12280 Z= 0.246 Chirality : 0.038 0.150 1409 Planarity : 0.003 0.044 1539 Dihedral : 12.760 74.205 1385 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 2.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 3.28 % Allowed : 21.53 % Favored : 75.19 % 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: 1.90 (0.26), residues: 1093 helix: 2.56 (0.21), residues: 630 sheet: 0.39 (0.66), residues: 68 loop : -0.80 (0.29), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1831 TYR 0.008 0.001 TYR A1808 PHE 0.011 0.001 PHE A1392 TRP 0.005 0.001 TRP A1159 HIS 0.002 0.001 HIS A1092 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.12 ( 9019) covalent geometry : angle 0.46282 / 0.25 (12280) hydrogen bonds : bond 0.05296 / 3.37 ( 483) hydrogen bonds : angle 3.64149 / 2.55 ( 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 106 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 76 time to evaluate : 0.336 Fit side-chains revert: symmetry clash REVERT: A 1040 GLU cc_start: 0.7338 (pm20) cc_final: 0.6699 (pm20) REVERT: A 1243 PHE cc_start: 0.7965 (OUTLIER) cc_final: 0.7733 (m-80) REVERT: A 1680 ARG cc_start: 0.7892 (mmm160) cc_final: 0.7573 (mtp85) REVERT: A 1871 GLU cc_start: 0.8635 (OUTLIER) cc_final: 0.7606 (mm-30) REVERT: A 1898 ASP cc_start: 0.8290 (OUTLIER) cc_final: 0.7583 (t0) REVERT: A 1904 MET cc_start: 0.9040 (ttp) cc_final: 0.8831 (ttm) REVERT: A 1924 THR cc_start: 0.8814 (OUTLIER) cc_final: 0.8529 (p) REVERT: A 2013 GLN cc_start: 0.8127 (mm-40) cc_final: 0.7873 (mm110) outliers start: 30 outliers final: 19 residues processed: 103 average time/residue: 0.6157 time to fit residues: 67.2735 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 : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1073 THR Chi-restraints excluded: chain A residue 1243 PHE Chi-restraints excluded: chain A residue 1254 VAL Chi-restraints excluded: chain A residue 1305 ASP Chi-restraints excluded: chain A residue 1319 VAL Chi-restraints excluded: chain A residue 1353 ASP Chi-restraints excluded: chain A residue 1441 LEU Chi-restraints excluded: chain A residue 1474 THR Chi-restraints excluded: chain A residue 1481 SER 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 1715 MET Chi-restraints excluded: chain A residue 1753 VAL 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 1898 ASP Chi-restraints excluded: chain A residue 1924 THR Chi-restraints excluded: chain A residue 2012 ASP Chi-restraints excluded: chain A residue 2015 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 28 optimal weight: 0.9990 chunk 6 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 23 optimal weight: 0.6980 chunk 56 optimal weight: 0.9980 chunk 7 optimal weight: 0.6980 chunk 4 optimal weight: 0.9980 chunk 27 optimal weight: 2.9990 chunk 95 optimal weight: 0.9980 chunk 109 optimal weight: 10.0000 chunk 52 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.095877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.070380 restraints weight = 14340.852| |-----------------------------------------------------------------------------| r_work (start): 0.2828 rms_B_bonded: 2.68 r_work: 0.2693 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.2693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.1962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9019 Z= 0.147 Angle : 0.491 11.825 12280 Z= 0.258 Chirality : 0.039 0.149 1409 Planarity : 0.004 0.044 1539 Dihedral : 12.781 72.441 1385 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 2.73 % Allowed : 21.97 % Favored : 75.30 % 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: 2.44 (0.21), residues: 637 sheet: 0.23 (0.65), residues: 70 loop : -0.90 (0.29), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1831 TYR 0.012 0.001 TYR A2011 PHE 0.018 0.001 PHE A1278 TRP 0.006 0.001 TRP A1159 HIS 0.002 0.001 HIS A1092 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.15 ( 9019) covalent geometry : angle 0.49149 / 0.26 (12280) hydrogen bonds : bond 0.05880 / 3.74 ( 483) hydrogen bonds : angle 3.69097 / 2.58 ( 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 100 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 75 time to evaluate : 0.209 Fit side-chains revert: symmetry clash REVERT: A 1040 GLU cc_start: 0.7383 (pm20) cc_final: 0.6719 (pm20) REVERT: A 1243 PHE cc_start: 0.7890 (OUTLIER) cc_final: 0.7681 (m-80) REVERT: A 1345 GLN cc_start: 0.7760 (OUTLIER) cc_final: 0.7474 (mt0) REVERT: A 1871 GLU cc_start: 0.8627 (OUTLIER) cc_final: 0.7594 (mm-30) REVERT: A 1898 ASP cc_start: 0.8311 (OUTLIER) cc_final: 0.7556 (t0) REVERT: A 1924 THR cc_start: 0.8833 (OUTLIER) cc_final: 0.8534 (p) REVERT: A 2013 GLN cc_start: 0.8131 (mm-40) cc_final: 0.7858 (mm110) outliers start: 25 outliers final: 18 residues processed: 97 average time/residue: 0.5989 time to fit residues: 61.5825 Evaluate side-chains 95 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 72 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1073 THR Chi-restraints excluded: chain A residue 1243 PHE Chi-restraints excluded: chain A residue 1254 VAL Chi-restraints excluded: chain A residue 1305 ASP Chi-restraints excluded: chain A residue 1319 VAL Chi-restraints excluded: chain A residue 1345 GLN Chi-restraints excluded: chain A residue 1353 ASP Chi-restraints excluded: chain A residue 1474 THR Chi-restraints excluded: chain A residue 1481 SER 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 1715 MET Chi-restraints excluded: chain A residue 1753 VAL 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 1898 ASP Chi-restraints excluded: chain A residue 1924 THR Chi-restraints excluded: chain A residue 2012 ASP Chi-restraints excluded: chain A residue 2015 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 0.7980 chunk 51 optimal weight: 0.0870 chunk 78 optimal weight: 0.0970 chunk 87 optimal weight: 2.9990 chunk 40 optimal weight: 0.8980 chunk 3 optimal weight: 1.9990 chunk 4 optimal weight: 0.0370 chunk 24 optimal weight: 3.9990 chunk 32 optimal weight: 0.6980 chunk 2 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 overall best weight: 0.3434 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3275 r_free = 0.3275 target = 0.097152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.071553 restraints weight = 14241.439| |-----------------------------------------------------------------------------| r_work (start): 0.2859 rms_B_bonded: 2.68 r_work: 0.2726 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.2726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.2095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 9019 Z= 0.110 Angle : 0.491 11.638 12280 Z= 0.259 Chirality : 0.038 0.153 1409 Planarity : 0.003 0.044 1539 Dihedral : 12.768 72.585 1385 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 2.62 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: 1.99 (0.26), residues: 1093 helix: 2.65 (0.21), residues: 630 sheet: 0.34 (0.67), residues: 68 loop : -0.77 (0.29), residues: 395 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 0.004 0.001 TRP A1159 HIS 0.002 0.001 HIS A1092 Details of bonding type rmsd/Z covalent geometry : bond 0.00225 / 0.11 ( 9019) covalent geometry : angle 0.49122 / 0.26 (12280) hydrogen bonds : bond 0.05066 / 3.23 ( 483) hydrogen bonds : angle 3.60011 / 2.52 ( 1387) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2282.56 seconds wall clock time: 39 minutes 36.72 seconds (2376.72 seconds total)