Starting phenix.real_space_refine on Sat Sep 12 04:33:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9y68_72556/09_2026/9y68_72556.cif Found real_map, /net/cci-nas-00/data/ceres_data/9y68_72556/09_2026/9y68_72556.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9y68_72556/09_2026/9y68_72556.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9y68_72556/09_2026/9y68_72556.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9y68_72556/09_2026/9y68_72556.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9y68_72556/09_2026/9y68_72556.map" } resolution = 3.25 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= 0.001 sd= 0.025 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 2 5.49 5 S 74 5.16 5 C 8317 2.51 5 N 2255 2.21 5 O 2398 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-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13046 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 13018 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1700, 13008 Classifications: {'peptide': 1700} Incomplete info: {'truncation_to_alanine': 150} Link IDs: {'PTRANS': 72, 'TRANS': 1627} Chain breaks: 12 Unresolved non-hydrogen bonds: 536 Unresolved non-hydrogen angles: 667 Unresolved non-hydrogen dihedrals: 441 Unresolved non-hydrogen chiralities: 41 Planarities with less than four sites: {'HIS:plan': 5, 'TYR:plan': 4, 'ARG:plan': 8, 'PHE:plan': 7, 'ASP:plan': 15, 'GLU:plan': 13, 'GLN:plan1': 12, 'ASN:plan1': 6} Unresolved non-hydrogen planarities: 298 Conformer: "B" Number of residues, atoms: 1700, 13008 Classifications: {'peptide': 1700} Incomplete info: {'truncation_to_alanine': 150} Link IDs: {'PTRANS': 72, 'TRANS': 1627} Chain breaks: 12 Unresolved non-hydrogen bonds: 536 Unresolved non-hydrogen angles: 667 Unresolved non-hydrogen dihedrals: 441 Unresolved non-hydrogen chiralities: 41 Planarities with less than four sites: {'HIS:plan': 5, 'TYR:plan': 4, 'ARG:plan': 8, 'PHE:plan': 7, 'ASP:plan': 15, 'GLU:plan': 13, 'GLN:plan1': 12, 'ASN:plan1': 6} Unresolved non-hydrogen planarities: 298 bond proxies already assigned to first conformer: 13228 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AHIS A1039 " occ=0.83 ... (18 atoms not shown) pdb=" NE2BHIS A1039 " occ=0.17 Time building chain proxies: 5.63, per 1000 atoms: 0.43 Number of scatterers: 13046 At special positions: 0 Unit cell: (106.59, 113.135, 142.12, 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 74 16.00 P 2 15.00 O 2398 8.00 N 2255 7.00 C 8317 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.36 Conformation dependent library (CDL) restraints added in 1.1 seconds 3354 Ramachandran restraints generated. 1677 Oldfield, 0 Emsley, 1677 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3244 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 20 sheets defined 32.6% alpha, 12.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.55 Creating SS restraints... Processing helix chain 'A' and resid 624 through 639 Processing helix chain 'A' and resid 642 through 659 removed outlier: 4.064A pdb=" N THR A 646 " --> pdb=" O ALA A 642 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LYS A 647 " --> pdb=" O GLU A 643 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LEU A 658 " --> pdb=" O ALA A 654 " (cutoff:3.500A) Processing helix chain 'A' and resid 659 through 670 removed outlier: 3.688A pdb=" N SER A 663 " --> pdb=" O SER A 659 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LYS A 664 " --> pdb=" O ALA A 660 " (cutoff:3.500A) Processing helix chain 'A' and resid 670 through 680 removed outlier: 3.665A pdb=" N VAL A 674 " --> pdb=" O SER A 670 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 703 Processing helix chain 'A' and resid 706 through 717 removed outlier: 3.568A pdb=" N VAL A 711 " --> pdb=" O TYR A 707 " (cutoff:3.500A) Processing helix chain 'A' and resid 721 through 731 Processing helix chain 'A' and resid 743 through 751 Processing helix chain 'A' and resid 754 through 764 Processing helix chain 'A' and resid 767 through 781 Processing helix chain 'A' and resid 785 through 795 removed outlier: 3.728A pdb=" N LEU A 789 " --> pdb=" O GLN A 785 " (cutoff:3.500A) Processing helix chain 'A' and resid 833 through 854 Processing helix chain 'A' and resid 997 through 1001 Processing helix chain 'A' and resid 1027 through 1034 removed outlier: 3.548A pdb=" N CYS A1031 " --> pdb=" O PRO A1027 " (cutoff:3.500A) Processing helix chain 'A' and resid 1053 through 1057 removed outlier: 3.794A pdb=" N MET A1057 " --> pdb=" O LEU A1054 " (cutoff:3.500A) Processing helix chain 'A' and resid 1189 through 1194 removed outlier: 3.565A pdb=" N LEU A1193 " --> pdb=" O PRO A1189 " (cutoff:3.500A) Processing helix chain 'A' and resid 1213 through 1217 removed outlier: 3.763A pdb=" N TRP A1217 " --> pdb=" O PRO A1214 " (cutoff:3.500A) Processing helix chain 'A' and resid 1240 through 1245 Processing helix chain 'A' and resid 1261 through 1267 removed outlier: 3.535A pdb=" N GLY A1265 " --> pdb=" O PRO A1262 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU A1267 " --> pdb=" O ILE A1264 " (cutoff:3.500A) Processing helix chain 'A' and resid 1316 through 1328 Processing helix chain 'A' and resid 1348 through 1355 Processing helix chain 'A' and resid 1398 through 1402 Processing helix chain 'A' and resid 1404 through 1409 removed outlier: 3.549A pdb=" N MET A1409 " --> pdb=" O PRO A1406 " (cutoff:3.500A) Processing helix chain 'A' and resid 1420 through 1424 Processing helix chain 'A' and resid 1431 through 1442 Processing helix chain 'A' and resid 1466 through 1474 removed outlier: 3.501A pdb=" N LEU A1474 " --> pdb=" O THR A1470 " (cutoff:3.500A) Processing helix chain 'A' and resid 1494 through 1509 Processing helix chain 'A' and resid 1517 through 1520 Processing helix chain 'A' and resid 1525 through 1538 Processing helix chain 'A' and resid 1549 through 1560 removed outlier: 4.012A pdb=" N LEU A1553 " --> pdb=" O ASP A1549 " (cutoff:3.500A) Processing helix chain 'A' and resid 1568 through 1579 removed outlier: 6.148A pdb=" N HIS A1574 " --> pdb=" O PRO A1570 " (cutoff:3.500A) Processing helix chain 'A' and resid 1599 through 1608 removed outlier: 3.805A pdb=" N LEU A1603 " --> pdb=" O GLU A1599 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ALA A1608 " --> pdb=" O CYS A1604 " (cutoff:3.500A) Processing helix chain 'A' and resid 1646 through 1655 removed outlier: 3.571A pdb=" N LYS A1655 " --> pdb=" O LYS A1651 " (cutoff:3.500A) Processing helix chain 'A' and resid 1703 through 1716 removed outlier: 3.974A pdb=" N ASN A1710 " --> pdb=" O SER A1706 " (cutoff:3.500A) Processing helix chain 'A' and resid 1770 through 1792 removed outlier: 3.753A pdb=" N ILE A1784 " --> pdb=" O VAL A1780 " (cutoff:3.500A) Processing helix chain 'A' and resid 1828 through 1835 Processing helix chain 'A' and resid 1853 through 1855 No H-bonds generated for 'chain 'A' and resid 1853 through 1855' Processing helix chain 'A' and resid 1881 through 1885 removed outlier: 4.624A pdb=" N LEU A1884 " --> pdb=" O PRO A1881 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N LEU A1885 " --> pdb=" O GLU A1882 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1881 through 1885' Processing helix chain 'A' and resid 1913 through 1925 removed outlier: 4.029A pdb=" N VAL A1923 " --> pdb=" O GLN A1919 " (cutoff:3.500A) Processing helix chain 'A' and resid 1954 through 1962 Processing helix chain 'A' and resid 1969 through 1988 Processing helix chain 'A' and resid 1996 through 1998 No H-bonds generated for 'chain 'A' and resid 1996 through 1998' Processing helix chain 'A' and resid 2040 through 2046 removed outlier: 3.521A pdb=" N ARG A2045 " --> pdb=" O PRO A2041 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLY A2046 " --> pdb=" O GLU A2042 " (cutoff:3.500A) Processing helix chain 'A' and resid 2053 through 2069 removed outlier: 3.609A pdb=" N TYR A2057 " --> pdb=" O GLN A2053 " (cutoff:3.500A) Processing helix chain 'A' and resid 2072 through 2077 removed outlier: 4.123A pdb=" N LEU A2077 " --> pdb=" O ILE A2073 " (cutoff:3.500A) Processing helix chain 'A' and resid 2079 through 2089 removed outlier: 4.312A pdb=" N GLU A2087 " --> pdb=" O PHE A2083 " (cutoff:3.500A) Processing helix chain 'A' and resid 2094 through 2099 removed outlier: 3.972A pdb=" N GLU A2098 " --> pdb=" O ASP A2094 " (cutoff:3.500A) Processing helix chain 'A' and resid 2104 through 2115 removed outlier: 3.726A pdb=" N GLU A2108 " --> pdb=" O TRP A2104 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LEU A2110 " --> pdb=" O MET A2106 " (cutoff:3.500A) Processing helix chain 'A' and resid 2124 through 2134 removed outlier: 3.563A pdb=" N SER A2134 " --> pdb=" O ASP A2130 " (cutoff:3.500A) Processing helix chain 'A' and resid 2135 through 2139 Processing helix chain 'A' and resid 2277 through 2281 removed outlier: 4.195A pdb=" N VAL A2280 " --> pdb=" O ASP A2277 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N LYS A2281 " --> pdb=" O LYS A2278 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2277 through 2281' Processing helix chain 'A' and resid 2389 through 2397 removed outlier: 5.200A pdb=" N GLU A2395 " --> pdb=" O HIS A2391 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N VAL A2396 " --> pdb=" O PHE A2392 " (cutoff:3.500A) Processing helix chain 'A' and resid 2499 through 2524 removed outlier: 3.593A pdb=" N GLN A2505 " --> pdb=" O PRO A2501 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 802 through 804 removed outlier: 6.770A pdb=" N ILE A 803 " --> pdb=" O ASP A 988 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N LEU A 987 " --> pdb=" O GLU A1017 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 1063 through 1064 removed outlier: 6.976A pdb=" N LEU A1063 " --> pdb=" O ASN A1089 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ILE A1113 " --> pdb=" O PHE A1088 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1157 through 1159 removed outlier: 6.858A pdb=" N PHE A1158 " --> pdb=" O LYS A1179 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ASP A1202 " --> pdb=" O LEU A1178 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1249 through 1251 Processing sheet with id=AA5, first strand: chain 'A' and resid 1329 through 1331 Processing sheet with id=AA6, first strand: chain 'A' and resid 1373 through 1377 removed outlier: 3.622A pdb=" N VAL A1418 " --> pdb=" O VAL A1340 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N TYR A1415 " --> pdb=" O ILE A1448 " (cutoff:3.500A) removed outlier: 7.857A pdb=" N VAL A1450 " --> pdb=" O TYR A1415 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N ALA A1417 " --> pdb=" O VAL A1450 " (cutoff:3.500A) removed outlier: 7.981A pdb=" N VAL A1447 " --> pdb=" O ARG A1483 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N TYR A1485 " --> pdb=" O VAL A1447 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N LEU A1449 " --> pdb=" O TYR A1485 " (cutoff:3.500A) removed outlier: 5.340A pdb=" N PHE A1487 " --> pdb=" O LEU A1449 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N GLY A1451 " --> pdb=" O PHE A1487 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1547 through 1548 removed outlier: 3.645A pdb=" N ILE A1548 " --> pdb=" O TYR A1596 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1730 through 1734 removed outlier: 3.835A pdb=" N ASN A1730 " --> pdb=" O ASN A1741 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N TRP A1734 " --> pdb=" O GLY A1737 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLY A1737 " --> pdb=" O TRP A1734 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N CYS A1748 " --> pdb=" O LEU A1740 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N PHE A1762 " --> pdb=" O GLU A1753 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1840 through 1841 removed outlier: 3.629A pdb=" N VAL A1841 " --> pdb=" O ILE A1850 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 1875 through 1876 removed outlier: 3.619A pdb=" N GLU A1876 " --> pdb=" O ALA A1897 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N ALA A1897 " --> pdb=" O GLU A1876 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 1893 through 1895 removed outlier: 3.904A pdb=" N ALA A1937 " --> pdb=" O VAL A1946 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 2000 through 2002 Processing sheet with id=AB4, first strand: chain 'A' and resid 2140 through 2145 removed outlier: 6.428A pdb=" N LEU A2140 " --> pdb=" O ASP A2497 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N ASP A2497 " --> pdb=" O LEU A2140 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ARG A2142 " --> pdb=" O VAL A2495 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLY A2474 " --> pdb=" O CYS A2492 " (cutoff:3.500A) removed outlier: 7.729A pdb=" N LYS A2467 " --> pdb=" O GLN A2462 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N GLN A2462 " --> pdb=" O LYS A2467 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N VAL A2469 " --> pdb=" O THR A2460 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N THR A2460 " --> pdb=" O VAL A2469 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N LEU A2471 " --> pdb=" O MET A2458 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N MET A2458 " --> pdb=" O LEU A2471 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N LEU A2473 " --> pdb=" O ARG A2456 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 2155 through 2156 Processing sheet with id=AB6, first strand: chain 'A' and resid 2199 through 2205 removed outlier: 3.841A pdb=" N CYS A2201 " --> pdb=" O GLY A2218 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N THR A2219 " --> pdb=" O THR A2223 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N THR A2223 " --> pdb=" O THR A2219 " (cutoff:3.500A) removed outlier: 4.988A pdb=" N LEU A2224 " --> pdb=" O LEU A2238 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N VAL A2226 " --> pdb=" O HIS A2236 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N HIS A2236 " --> pdb=" O VAL A2226 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 2245 through 2249 removed outlier: 3.518A pdb=" N CYS A2247 " --> pdb=" O GLY A2266 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 2271 through 2273 Processing sheet with id=AB9, first strand: chain 'A' and resid 2300 through 2302 removed outlier: 4.044A pdb=" N CYS A2302 " --> pdb=" O GLY A2318 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N SER A2325 " --> pdb=" O LYS A2334 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N LYS A2334 " --> pdb=" O SER A2325 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 2354 through 2359 removed outlier: 6.890A pdb=" N ALA A2366 " --> pdb=" O ILE A2355 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N VAL A2357 " --> pdb=" O TYR A2364 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N TYR A2364 " --> pdb=" O VAL A2357 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N LYS A2367 " --> pdb=" O VAL A2372 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N VAL A2372 " --> pdb=" O LYS A2367 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLY A2385 " --> pdb=" O VAL A2375 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 2414 through 2419 removed outlier: 6.577A pdb=" N GLY A2428 " --> pdb=" O LYS A2415 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N LEU A2417 " --> pdb=" O TRP A2426 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N TRP A2426 " --> pdb=" O LEU A2417 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N ILE A2434 " --> pdb=" O VAL A2447 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N VAL A2447 " --> pdb=" O ILE A2434 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N LEU A2436 " --> pdb=" O ILE A2445 " (cutoff:3.500A) 426 hydrogen bonds defined for protein. 1179 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.16 Time building geometry restraints manager: 1.77 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: 4267 1.34 - 1.46: 2349 1.46 - 1.58: 6552 1.58 - 1.70: 6 1.70 - 1.82: 108 Bond restraints: 13282 Sorted by residual: bond pdb=" C5 GDP A2601 " pdb=" C4 GDP A2601 " ideal model delta sigma weight residual 1.490 1.373 0.117 2.00e-02 2.50e+03 3.41e+01 bond pdb=" C5 GDP A2601 " pdb=" C6 GDP A2601 " ideal model delta sigma weight residual 1.490 1.411 0.079 2.00e-02 2.50e+03 1.56e+01 bond pdb=" C ALA A1880 " pdb=" N PRO A1881 " ideal model delta sigma weight residual 1.332 1.370 -0.038 1.12e-02 7.97e+03 1.16e+01 bond pdb=" C6 GDP A2601 " pdb=" N1 GDP A2601 " ideal model delta sigma weight residual 1.337 1.390 -0.053 2.00e-02 2.50e+03 6.97e+00 bond pdb=" C ARG A1941 " pdb=" N PRO A1942 " ideal model delta sigma weight residual 1.333 1.353 -0.020 7.80e-03 1.64e+04 6.44e+00 ... (remaining 13277 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.67: 17652 2.67 - 5.34: 300 5.34 - 8.02: 46 8.02 - 10.69: 14 10.69 - 13.36: 3 Bond angle restraints: 18015 Sorted by residual: angle pdb=" CA PRO A1622 " pdb=" N PRO A1622 " pdb=" CD PRO A1622 " ideal model delta sigma weight residual 112.00 105.13 6.87 1.40e+00 5.10e-01 2.41e+01 angle pdb=" CA PRO A1546 " pdb=" N PRO A1546 " pdb=" CD PRO A1546 " ideal model delta sigma weight residual 112.00 105.23 6.77 1.40e+00 5.10e-01 2.34e+01 angle pdb=" C PRO A1570 " pdb=" N HIS A1571 " pdb=" CA HIS A1571 " ideal model delta sigma weight residual 121.54 129.71 -8.17 1.91e+00 2.74e-01 1.83e+01 angle pdb=" CA LEU A1042 " pdb=" CB LEU A1042 " pdb=" CG LEU A1042 " ideal model delta sigma weight residual 116.30 129.66 -13.36 3.50e+00 8.16e-02 1.46e+01 angle pdb=" C ASP A1756 " pdb=" N ASN A1757 " pdb=" CA ASN A1757 " ideal model delta sigma weight residual 121.54 128.74 -7.20 1.91e+00 2.74e-01 1.42e+01 ... (remaining 18010 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 7301 17.92 - 35.83: 652 35.83 - 53.75: 122 53.75 - 71.66: 15 71.66 - 89.58: 15 Dihedral angle restraints: 8105 sinusoidal: 3134 harmonic: 4971 Sorted by residual: dihedral pdb=" CA LEU A1569 " pdb=" C LEU A1569 " pdb=" N PRO A1570 " pdb=" CA PRO A1570 " ideal model delta harmonic sigma weight residual 180.00 153.39 26.61 0 5.00e+00 4.00e-02 2.83e+01 dihedral pdb=" CA TYR A1419 " pdb=" C TYR A1419 " pdb=" N ASP A1420 " pdb=" CA ASP A1420 " ideal model delta harmonic sigma weight residual 180.00 -155.96 -24.04 0 5.00e+00 4.00e-02 2.31e+01 dihedral pdb=" C4' GDP A2601 " pdb=" O5' GDP A2601 " pdb=" C5' GDP A2601 " pdb=" PA GDP A2601 " ideal model delta sinusoidal sigma weight residual 180.02 97.34 82.68 1 2.00e+01 2.50e-03 2.09e+01 ... (remaining 8102 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 1589 0.055 - 0.110: 456 0.110 - 0.165: 72 0.165 - 0.220: 5 0.220 - 0.275: 1 Chirality restraints: 2123 Sorted by residual: chirality pdb=" CB ILE A2011 " pdb=" CA ILE A2011 " pdb=" CG1 ILE A2011 " pdb=" CG2 ILE A2011 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.28 2.00e-01 2.50e+01 1.90e+00 chirality pdb=" CB VAL A 748 " pdb=" CA VAL A 748 " pdb=" CG1 VAL A 748 " pdb=" CG2 VAL A 748 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.20 2.00e-01 2.50e+01 1.03e+00 chirality pdb=" CB ILE A1765 " pdb=" CA ILE A1765 " pdb=" CG1 ILE A1765 " pdb=" CG2 ILE A1765 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.20 2.00e-01 2.50e+01 1.02e+00 ... (remaining 2120 not shown) Planarity restraints: 2286 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE A2079 " 0.084 5.00e-02 4.00e+02 1.25e-01 2.52e+01 pdb=" N PRO A2080 " -0.217 5.00e-02 4.00e+02 pdb=" CA PRO A2080 " 0.067 5.00e-02 4.00e+02 pdb=" CD PRO A2080 " 0.066 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA HIS A1571 " 0.019 2.00e-02 2.50e+03 3.71e-02 1.37e+01 pdb=" C HIS A1571 " -0.064 2.00e-02 2.50e+03 pdb=" O HIS A1571 " 0.024 2.00e-02 2.50e+03 pdb=" N ALA A1572 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA A2102 " -0.053 5.00e-02 4.00e+02 8.10e-02 1.05e+01 pdb=" N PRO A2103 " 0.140 5.00e-02 4.00e+02 pdb=" CA PRO A2103 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO A2103 " -0.044 5.00e-02 4.00e+02 ... (remaining 2283 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.74: 1076 2.74 - 3.28: 12791 3.28 - 3.82: 20832 3.82 - 4.36: 24275 4.36 - 4.90: 42102 Nonbonded interactions: 101076 Sorted by model distance: nonbonded pdb=" OG1 THR A2246 " pdb=" O LEU A2300 " model vdw 2.205 3.040 nonbonded pdb=" NH1 ARG A 767 " pdb=" OD2 ASP A 770 " model vdw 2.239 3.120 nonbonded pdb=" OD1 ASP A1420 " pdb=" ND1 HIS A1453 " model vdw 2.242 3.120 nonbonded pdb=" OG SER A1931 " pdb=" O HIS A1977 " model vdw 2.270 3.040 nonbonded pdb=" O THR A2321 " pdb=" OG1 THR A2338 " model vdw 2.285 3.040 ... (remaining 101071 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.17 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: 4.420 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: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 18.280 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 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 : 0.005 0.117 13282 Z= 0.198 Angle : 0.886 13.360 18015 Z= 0.439 Chirality : 0.051 0.275 2123 Planarity : 0.008 0.125 2286 Dihedral : 14.427 89.576 4861 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.44 % Favored : 90.50 % Rotamer: Outliers : 0.00 % Allowed : 0.07 % Favored : 99.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.40 (0.19), residues: 1677 helix: -0.81 (0.22), residues: 524 sheet: -0.85 (0.34), residues: 252 loop : -2.36 (0.19), residues: 901 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A1558 TYR 0.024 0.002 TYR A1419 PHE 0.021 0.002 PHE A2451 TRP 0.039 0.002 TRP A1742 HIS 0.014 0.001 HIS A1574 Details of bonding type rmsd/Z covalent geometry : bond 0.00467 / 0.20 (13282) covalent geometry : angle 0.88618 / 0.44 (18015) hydrogen bonds : bond 0.18416 / 14.21 ( 426) hydrogen bonds : angle 7.38562 / 5.14 ( 1179) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3354 Ramachandran restraints generated. 1677 Oldfield, 0 Emsley, 1677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3354 Ramachandran restraints generated. 1677 Oldfield, 0 Emsley, 1677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 183 time to evaluate : 0.545 Fit side-chains revert: symmetry clash REVERT: A 1207 ASP cc_start: 0.8268 (p0) cc_final: 0.7723 (m-30) REVERT: A 1715 ILE cc_start: 0.9122 (tp) cc_final: 0.8872 (tp) REVERT: A 1928 HIS cc_start: 0.7056 (m-70) cc_final: 0.6785 (m-70) outliers start: 0 outliers final: 0 residues processed: 183 average time/residue: 0.0985 time to fit residues: 28.1324 Evaluate side-chains 146 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 146 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 98 optimal weight: 0.9990 chunk 107 optimal weight: 9.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 0.2980 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 800 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 992 ASN A1021 ASN ** A1139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1687 ASN A1971 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.181666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.129064 restraints weight = 30509.559| |-----------------------------------------------------------------------------| r_work (start): 0.3594 rms_B_bonded: 4.49 r_work: 0.3441 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.3441 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3469 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3469 r_free = 0.3469 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3469 r_free = 0.3469 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3469 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.1037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 13282 Z= 0.144 Angle : 0.676 10.276 18015 Z= 0.341 Chirality : 0.046 0.182 2123 Planarity : 0.006 0.086 2286 Dihedral : 5.521 73.649 1811 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.78 % Favored : 91.16 % Rotamer: Outliers : 0.72 % Allowed : 7.73 % Favored : 91.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.99 (0.20), residues: 1677 helix: -0.17 (0.23), residues: 525 sheet: -0.91 (0.32), residues: 270 loop : -2.23 (0.20), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A1558 TYR 0.019 0.001 TYR A1419 PHE 0.014 0.001 PHE A1088 TRP 0.011 0.001 TRP A1434 HIS 0.006 0.001 HIS A1911 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.14 (13282) covalent geometry : angle 0.67628 / 0.34 (18015) hydrogen bonds : bond 0.03868 / 2.97 ( 426) hydrogen bonds : angle 5.42916 / 3.86 ( 1179) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3354 Ramachandran restraints generated. 1677 Oldfield, 0 Emsley, 1677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3354 Ramachandran restraints generated. 1677 Oldfield, 0 Emsley, 1677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 160 time to evaluate : 0.550 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 817 TRP cc_start: 0.8088 (m-10) cc_final: 0.7852 (m-10) REVERT: A 1207 ASP cc_start: 0.8671 (p0) cc_final: 0.8380 (p0) REVERT: A 1715 ILE cc_start: 0.9074 (tp) cc_final: 0.8852 (tp) REVERT: A 1831 MET cc_start: 0.7862 (mmt) cc_final: 0.7598 (mmt) outliers start: 10 outliers final: 10 residues processed: 165 average time/residue: 0.0919 time to fit residues: 23.9453 Evaluate side-chains 157 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 147 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1012 HIS Chi-restraints excluded: chain A residue 1234 ILE Chi-restraints excluded: chain A residue 1469 ILE Chi-restraints excluded: chain A residue 1509 LEU Chi-restraints excluded: chain A residue 1621 HIS Chi-restraints excluded: chain A residue 1720 LEU Chi-restraints excluded: chain A residue 1742 TRP Chi-restraints excluded: chain A residue 1940 ILE Chi-restraints excluded: chain A residue 1962 ASP Chi-restraints excluded: chain A residue 2356 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 10 optimal weight: 0.0040 chunk 136 optimal weight: 1.9990 chunk 157 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 chunk 113 optimal weight: 0.8980 chunk 80 optimal weight: 1.9990 chunk 34 optimal weight: 0.2980 chunk 159 optimal weight: 0.8980 chunk 111 optimal weight: 3.9990 overall best weight: 0.8194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 785 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 800 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1571 HIS ** A1574 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.180199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.128761 restraints weight = 25303.694| |-----------------------------------------------------------------------------| r_work (start): 0.3605 rms_B_bonded: 4.07 r_work: 0.3456 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.3456 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3466 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3466 r_free = 0.3466 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3466 r_free = 0.3466 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3466 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.1389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 13282 Z= 0.136 Angle : 0.641 10.305 18015 Z= 0.320 Chirality : 0.045 0.199 2123 Planarity : 0.005 0.071 2286 Dihedral : 5.257 66.613 1811 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.78 % Favored : 91.16 % Rotamer: Outliers : 1.16 % Allowed : 9.39 % Favored : 89.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.84 (0.20), residues: 1677 helix: 0.06 (0.23), residues: 527 sheet: -0.88 (0.33), residues: 265 loop : -2.20 (0.20), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 767 TYR 0.016 0.001 TYR A1419 PHE 0.015 0.001 PHE A1088 TRP 0.012 0.001 TRP A1742 HIS 0.004 0.001 HIS A1998 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.14 (13282) covalent geometry : angle 0.64122 / 0.32 (18015) hydrogen bonds : bond 0.03522 / 2.71 ( 426) hydrogen bonds : angle 4.97497 / 3.56 ( 1179) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3354 Ramachandran restraints generated. 1677 Oldfield, 0 Emsley, 1677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3354 Ramachandran restraints generated. 1677 Oldfield, 0 Emsley, 1677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 163 time to evaluate : 0.493 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1207 ASP cc_start: 0.8624 (p0) cc_final: 0.8346 (p0) REVERT: A 1715 ILE cc_start: 0.9116 (tp) cc_final: 0.8869 (tp) REVERT: A 1831 MET cc_start: 0.7792 (mmt) cc_final: 0.7567 (mmt) REVERT: A 1855 ILE cc_start: 0.7796 (mm) cc_final: 0.7518 (tp) REVERT: A 1869 MET cc_start: 0.7632 (mtt) cc_final: 0.7161 (mtt) REVERT: A 1928 HIS cc_start: 0.6868 (m-70) cc_final: 0.6564 (m-70) REVERT: A 2459 MET cc_start: 0.6997 (ptm) cc_final: 0.6010 (mtt) REVERT: A 2512 GLU cc_start: 0.7867 (mm-30) cc_final: 0.7659 (mm-30) outliers start: 16 outliers final: 14 residues processed: 172 average time/residue: 0.1057 time to fit residues: 27.9123 Evaluate side-chains 161 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 147 time to evaluate : 0.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1012 HIS Chi-restraints excluded: chain A residue 1234 ILE Chi-restraints excluded: chain A residue 1259 GLU Chi-restraints excluded: chain A residue 1509 LEU Chi-restraints excluded: chain A residue 1621 HIS Chi-restraints excluded: chain A residue 1685 CYS Chi-restraints excluded: chain A residue 1720 LEU Chi-restraints excluded: chain A residue 1742 TRP Chi-restraints excluded: chain A residue 1853 SER Chi-restraints excluded: chain A residue 1907 ILE Chi-restraints excluded: chain A residue 1940 ILE Chi-restraints excluded: chain A residue 1962 ASP Chi-restraints excluded: chain A residue 2074 VAL Chi-restraints excluded: chain A residue 2096 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 101 optimal weight: 0.9990 chunk 158 optimal weight: 0.7980 chunk 11 optimal weight: 10.0000 chunk 91 optimal weight: 1.9990 chunk 164 optimal weight: 4.9990 chunk 44 optimal weight: 1.9990 chunk 79 optimal weight: 5.9990 chunk 109 optimal weight: 0.8980 chunk 127 optimal weight: 5.9990 chunk 40 optimal weight: 0.5980 chunk 72 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 785 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 800 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1574 HIS ** 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 = 0.4169 r_free = 0.4169 target = 0.177818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.126705 restraints weight = 23051.384| |-----------------------------------------------------------------------------| r_work (start): 0.3586 rms_B_bonded: 3.35 r_work: 0.3448 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3448 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3457 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3457 r_free = 0.3457 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3457 r_free = 0.3457 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3457 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.1783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 13282 Z= 0.153 Angle : 0.653 10.677 18015 Z= 0.325 Chirality : 0.046 0.260 2123 Planarity : 0.005 0.064 2286 Dihedral : 5.247 60.222 1811 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.02 % Favored : 90.92 % Rotamer: Outliers : 1.73 % Allowed : 10.26 % Favored : 88.01 % 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: -1.79 (0.20), residues: 1677 helix: 0.11 (0.23), residues: 533 sheet: -0.97 (0.32), residues: 275 loop : -2.16 (0.20), residues: 869 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG A 767 TYR 0.017 0.001 TYR A1419 PHE 0.021 0.002 PHE A2324 TRP 0.017 0.002 TRP A1742 HIS 0.005 0.001 HIS A1998 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.15 (13282) covalent geometry : angle 0.65308 / 0.33 (18015) hydrogen bonds : bond 0.03361 / 2.59 ( 426) hydrogen bonds : angle 4.77917 / 3.43 ( 1179) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3354 Ramachandran restraints generated. 1677 Oldfield, 0 Emsley, 1677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3354 Ramachandran restraints generated. 1677 Oldfield, 0 Emsley, 1677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 157 time to evaluate : 0.487 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1207 ASP cc_start: 0.8553 (p0) cc_final: 0.8342 (p0) REVERT: A 1715 ILE cc_start: 0.9136 (tp) cc_final: 0.8879 (tp) REVERT: A 1796 LEU cc_start: 0.9098 (OUTLIER) cc_final: 0.8708 (pp) REVERT: A 1831 MET cc_start: 0.7736 (mmt) cc_final: 0.7524 (mmt) REVERT: A 1855 ILE cc_start: 0.7953 (mm) cc_final: 0.7670 (tp) REVERT: A 1869 MET cc_start: 0.7716 (mtt) cc_final: 0.7337 (mtt) REVERT: A 1901 GLU cc_start: 0.7364 (pm20) cc_final: 0.7060 (pm20) REVERT: A 2369 ASN cc_start: 0.7537 (t0) cc_final: 0.7193 (t0) REVERT: A 2512 GLU cc_start: 0.7992 (mm-30) cc_final: 0.7725 (mm-30) outliers start: 24 outliers final: 21 residues processed: 170 average time/residue: 0.1136 time to fit residues: 29.4278 Evaluate side-chains 170 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 148 time to evaluate : 0.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1012 HIS Chi-restraints excluded: chain A residue 1177 ILE Chi-restraints excluded: chain A residue 1234 ILE Chi-restraints excluded: chain A residue 1259 GLU Chi-restraints excluded: chain A residue 1335 MET Chi-restraints excluded: chain A residue 1509 LEU Chi-restraints excluded: chain A residue 1564 LEU Chi-restraints excluded: chain A residue 1621 HIS Chi-restraints excluded: chain A residue 1685 CYS Chi-restraints excluded: chain A residue 1714 GLU Chi-restraints excluded: chain A residue 1720 LEU Chi-restraints excluded: chain A residue 1742 TRP Chi-restraints excluded: chain A residue 1796 LEU Chi-restraints excluded: chain A residue 1842 ASN Chi-restraints excluded: chain A residue 1907 ILE Chi-restraints excluded: chain A residue 1940 ILE Chi-restraints excluded: chain A residue 1962 ASP Chi-restraints excluded: chain A residue 2074 VAL Chi-restraints excluded: chain A residue 2096 VAL Chi-restraints excluded: chain A residue 2356 THR Chi-restraints excluded: chain A residue 2425 LEU Chi-restraints excluded: chain A residue 2463 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 109 optimal weight: 0.0670 chunk 69 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 chunk 157 optimal weight: 4.9990 chunk 68 optimal weight: 0.8980 chunk 56 optimal weight: 1.9990 chunk 130 optimal weight: 9.9990 chunk 32 optimal weight: 0.0000 chunk 46 optimal weight: 0.6980 chunk 95 optimal weight: 3.9990 chunk 135 optimal weight: 0.1980 overall best weight: 0.3322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 800 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1574 HIS ** 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 = 0.4202 r_free = 0.4202 target = 0.180962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.130094 restraints weight = 27934.681| |-----------------------------------------------------------------------------| r_work (start): 0.3636 rms_B_bonded: 4.16 r_work: 0.3472 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.3472 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3477 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3477 r_free = 0.3477 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3477 r_free = 0.3477 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3477 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.1856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 13282 Z= 0.105 Angle : 0.609 10.364 18015 Z= 0.302 Chirality : 0.044 0.250 2123 Planarity : 0.005 0.059 2286 Dihedral : 5.009 57.353 1811 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.18 % Favored : 91.76 % Rotamer: Outliers : 1.45 % Allowed : 11.05 % Favored : 87.50 % 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: -1.64 (0.20), residues: 1677 helix: 0.33 (0.24), residues: 533 sheet: -1.00 (0.33), residues: 261 loop : -2.08 (0.20), residues: 883 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 767 TYR 0.010 0.001 TYR A1419 PHE 0.010 0.001 PHE A2083 TRP 0.021 0.002 TRP A 817 HIS 0.005 0.001 HIS A1571 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.11 (13282) covalent geometry : angle 0.60930 / 0.30 (18015) hydrogen bonds : bond 0.02981 / 2.30 ( 426) hydrogen bonds : angle 4.60048 / 3.30 ( 1179) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3354 Ramachandran restraints generated. 1677 Oldfield, 0 Emsley, 1677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3354 Ramachandran restraints generated. 1677 Oldfield, 0 Emsley, 1677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 158 time to evaluate : 0.599 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1207 ASP cc_start: 0.8584 (p0) cc_final: 0.8363 (p0) REVERT: A 1715 ILE cc_start: 0.9124 (tp) cc_final: 0.8849 (tp) REVERT: A 1796 LEU cc_start: 0.9043 (OUTLIER) cc_final: 0.8670 (pp) REVERT: A 1855 ILE cc_start: 0.7860 (mm) cc_final: 0.7559 (tp) REVERT: A 1869 MET cc_start: 0.7740 (mtt) cc_final: 0.7388 (mtt) REVERT: A 1901 GLU cc_start: 0.7411 (pm20) cc_final: 0.7110 (pm20) REVERT: A 1941 ARG cc_start: 0.7673 (tpp-160) cc_final: 0.7310 (mmt-90) REVERT: A 1942 PRO cc_start: 0.8186 (Cg_endo) cc_final: 0.7412 (Cg_exo) REVERT: A 1944 MET cc_start: 0.7813 (OUTLIER) cc_final: 0.6614 (pmm) REVERT: A 2324 PHE cc_start: 0.5353 (p90) cc_final: 0.5015 (p90) REVERT: A 2369 ASN cc_start: 0.7711 (t0) cc_final: 0.7413 (t0) REVERT: A 2459 MET cc_start: 0.7026 (ptm) cc_final: 0.6109 (mtt) REVERT: A 2512 GLU cc_start: 0.8005 (mm-30) cc_final: 0.7726 (mm-30) outliers start: 20 outliers final: 14 residues processed: 168 average time/residue: 0.1052 time to fit residues: 27.6318 Evaluate side-chains 165 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 149 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1012 HIS Chi-restraints excluded: chain A residue 1234 ILE Chi-restraints excluded: chain A residue 1335 MET Chi-restraints excluded: chain A residue 1509 LEU Chi-restraints excluded: chain A residue 1564 LEU Chi-restraints excluded: chain A residue 1621 HIS Chi-restraints excluded: chain A residue 1685 CYS Chi-restraints excluded: chain A residue 1720 LEU Chi-restraints excluded: chain A residue 1742 TRP Chi-restraints excluded: chain A residue 1796 LEU Chi-restraints excluded: chain A residue 1907 ILE Chi-restraints excluded: chain A residue 1940 ILE Chi-restraints excluded: chain A residue 1944 MET Chi-restraints excluded: chain A residue 2074 VAL Chi-restraints excluded: chain A residue 2096 VAL Chi-restraints excluded: chain A residue 2356 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 12 optimal weight: 1.9990 chunk 161 optimal weight: 7.9990 chunk 112 optimal weight: 6.9990 chunk 9 optimal weight: 5.9990 chunk 152 optimal weight: 4.9990 chunk 56 optimal weight: 0.0570 chunk 16 optimal weight: 0.8980 chunk 70 optimal weight: 4.9990 chunk 147 optimal weight: 8.9990 chunk 150 optimal weight: 6.9990 chunk 67 optimal weight: 0.9990 overall best weight: 1.7904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 800 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1574 HIS ** 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 = 0.4124 r_free = 0.4124 target = 0.173541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.120503 restraints weight = 30911.106| |-----------------------------------------------------------------------------| r_work (start): 0.3494 rms_B_bonded: 4.38 r_work: 0.3338 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3347 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3347 r_free = 0.3347 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3347 r_free = 0.3347 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (11 function evaluations) r_final: 0.3347 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.2256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 13282 Z= 0.220 Angle : 0.721 11.685 18015 Z= 0.359 Chirality : 0.048 0.294 2123 Planarity : 0.006 0.095 2286 Dihedral : 5.399 56.442 1811 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.86 % Favored : 90.08 % Rotamer: Outliers : 1.66 % Allowed : 12.14 % Favored : 86.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.77 (0.20), residues: 1677 helix: 0.16 (0.23), residues: 530 sheet: -0.98 (0.32), residues: 285 loop : -2.16 (0.20), residues: 862 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A1412 TYR 0.017 0.002 TYR A1419 PHE 0.031 0.002 PHE A1170 TRP 0.023 0.002 TRP A1742 HIS 0.005 0.001 HIS A1998 Details of bonding type rmsd/Z covalent geometry : bond 0.00545 / 0.22 (13282) covalent geometry : angle 0.72062 / 0.36 (18015) hydrogen bonds : bond 0.03700 / 2.85 ( 426) hydrogen bonds : angle 4.75322 / 3.41 ( 1179) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3354 Ramachandran restraints generated. 1677 Oldfield, 0 Emsley, 1677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3354 Ramachandran restraints generated. 1677 Oldfield, 0 Emsley, 1677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 155 time to evaluate : 0.539 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1621 HIS cc_start: 0.6490 (OUTLIER) cc_final: 0.5522 (t-90) REVERT: A 1715 ILE cc_start: 0.9214 (tp) cc_final: 0.8959 (tp) REVERT: A 1720 LEU cc_start: 0.8045 (OUTLIER) cc_final: 0.7790 (pp) REVERT: A 1796 LEU cc_start: 0.9147 (OUTLIER) cc_final: 0.8666 (pp) REVERT: A 1869 MET cc_start: 0.7866 (mtt) cc_final: 0.7608 (mtt) REVERT: A 1901 GLU cc_start: 0.7478 (pm20) cc_final: 0.7186 (pm20) REVERT: A 1944 MET cc_start: 0.7922 (OUTLIER) cc_final: 0.6529 (pmm) REVERT: A 2148 LYS cc_start: 0.7029 (tptt) cc_final: 0.6820 (tptt) REVERT: A 2369 ASN cc_start: 0.7592 (t0) cc_final: 0.7256 (t0) outliers start: 23 outliers final: 16 residues processed: 170 average time/residue: 0.1103 time to fit residues: 28.5431 Evaluate side-chains 168 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 148 time to evaluate : 0.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1012 HIS Chi-restraints excluded: chain A residue 1177 ILE Chi-restraints excluded: chain A residue 1234 ILE Chi-restraints excluded: chain A residue 1259 GLU Chi-restraints excluded: chain A residue 1474 LEU Chi-restraints excluded: chain A residue 1564 LEU Chi-restraints excluded: chain A residue 1621 HIS Chi-restraints excluded: chain A residue 1685 CYS Chi-restraints excluded: chain A residue 1720 LEU Chi-restraints excluded: chain A residue 1742 TRP Chi-restraints excluded: chain A residue 1796 LEU Chi-restraints excluded: chain A residue 1861 LEU Chi-restraints excluded: chain A residue 1940 ILE Chi-restraints excluded: chain A residue 1944 MET Chi-restraints excluded: chain A residue 1960 GLN Chi-restraints excluded: chain A residue 1962 ASP Chi-restraints excluded: chain A residue 2074 VAL Chi-restraints excluded: chain A residue 2096 VAL Chi-restraints excluded: chain A residue 2356 THR Chi-restraints excluded: chain A residue 2425 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 68 optimal weight: 0.7980 chunk 118 optimal weight: 1.9990 chunk 93 optimal weight: 0.6980 chunk 159 optimal weight: 6.9990 chunk 132 optimal weight: 3.9990 chunk 57 optimal weight: 0.6980 chunk 122 optimal weight: 1.9990 chunk 105 optimal weight: 0.9990 chunk 8 optimal weight: 0.6980 chunk 25 optimal weight: 0.8980 chunk 47 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 800 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1574 HIS ** 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 = 0.4156 r_free = 0.4156 target = 0.176575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.122500 restraints weight = 42265.940| |-----------------------------------------------------------------------------| r_work (start): 0.3521 rms_B_bonded: 5.06 r_work: 0.3356 rms_B_bonded: 4.70 restraints_weight: 0.5000 r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3365 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3365 r_free = 0.3365 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3365 r_free = 0.3365 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3365 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.2292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.118 13282 Z= 0.134 Angle : 0.642 11.317 18015 Z= 0.320 Chirality : 0.045 0.260 2123 Planarity : 0.005 0.082 2286 Dihedral : 5.210 56.011 1811 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.60 % Favored : 91.34 % Rotamer: Outliers : 1.59 % Allowed : 13.01 % Favored : 85.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.66 (0.21), residues: 1677 helix: 0.32 (0.23), residues: 535 sheet: -1.02 (0.33), residues: 266 loop : -2.10 (0.20), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A1968 TYR 0.014 0.001 TYR A1419 PHE 0.026 0.001 PHE A2324 TRP 0.024 0.002 TRP A1742 HIS 0.005 0.001 HIS A1998 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.13 (13282) covalent geometry : angle 0.64248 / 0.32 (18015) hydrogen bonds : bond 0.03124 / 2.41 ( 426) hydrogen bonds : angle 4.61074 / 3.31 ( 1179) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3354 Ramachandran restraints generated. 1677 Oldfield, 0 Emsley, 1677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3354 Ramachandran restraints generated. 1677 Oldfield, 0 Emsley, 1677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 152 time to evaluate : 0.539 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1418 VAL cc_start: 0.7141 (m) cc_final: 0.5915 (p) REVERT: A 1715 ILE cc_start: 0.9114 (tp) cc_final: 0.8834 (tp) REVERT: A 1720 LEU cc_start: 0.7934 (OUTLIER) cc_final: 0.7659 (pp) REVERT: A 1796 LEU cc_start: 0.9125 (OUTLIER) cc_final: 0.8678 (pp) REVERT: A 1855 ILE cc_start: 0.7879 (mm) cc_final: 0.7503 (tp) REVERT: A 1869 MET cc_start: 0.7882 (mtt) cc_final: 0.7632 (mtt) REVERT: A 1942 PRO cc_start: 0.8216 (Cg_endo) cc_final: 0.7494 (Cg_exo) REVERT: A 1943 ARG cc_start: 0.7313 (mtp85) cc_final: 0.6899 (mmm-85) REVERT: A 1944 MET cc_start: 0.7936 (OUTLIER) cc_final: 0.6783 (pmm) REVERT: A 2369 ASN cc_start: 0.7667 (t0) cc_final: 0.7299 (t0) outliers start: 22 outliers final: 17 residues processed: 166 average time/residue: 0.1049 time to fit residues: 27.0824 Evaluate side-chains 159 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 139 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1012 HIS Chi-restraints excluded: chain A residue 1130 GLU Chi-restraints excluded: chain A residue 1177 ILE Chi-restraints excluded: chain A residue 1234 ILE Chi-restraints excluded: chain A residue 1335 MET Chi-restraints excluded: chain A residue 1564 LEU Chi-restraints excluded: chain A residue 1621 HIS Chi-restraints excluded: chain A residue 1685 CYS Chi-restraints excluded: chain A residue 1714 GLU Chi-restraints excluded: chain A residue 1720 LEU Chi-restraints excluded: chain A residue 1742 TRP Chi-restraints excluded: chain A residue 1796 LEU Chi-restraints excluded: chain A residue 1853 SER Chi-restraints excluded: chain A residue 1940 ILE Chi-restraints excluded: chain A residue 1944 MET Chi-restraints excluded: chain A residue 1962 ASP Chi-restraints excluded: chain A residue 2074 VAL Chi-restraints excluded: chain A residue 2096 VAL Chi-restraints excluded: chain A residue 2104 TRP Chi-restraints excluded: chain A residue 2356 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 156 optimal weight: 9.9990 chunk 29 optimal weight: 0.8980 chunk 25 optimal weight: 0.0970 chunk 52 optimal weight: 4.9990 chunk 161 optimal weight: 0.0970 chunk 140 optimal weight: 5.9990 chunk 145 optimal weight: 5.9990 chunk 49 optimal weight: 0.6980 chunk 104 optimal weight: 3.9990 chunk 1 optimal weight: 20.0000 chunk 124 optimal weight: 5.9990 overall best weight: 1.1578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 800 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1574 HIS ** 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 = 0.4137 r_free = 0.4137 target = 0.174756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.122654 restraints weight = 29003.064| |-----------------------------------------------------------------------------| r_work (start): 0.3544 rms_B_bonded: 4.24 r_work: 0.3390 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3380 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3380 r_free = 0.3380 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3380 r_free = 0.3380 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3380 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.2450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.118 13282 Z= 0.165 Angle : 0.671 11.234 18015 Z= 0.333 Chirality : 0.047 0.287 2123 Planarity : 0.005 0.080 2286 Dihedral : 5.255 55.008 1811 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.26 % Favored : 90.68 % Rotamer: Outliers : 1.66 % Allowed : 13.44 % Favored : 84.90 % 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: -1.68 (0.21), residues: 1677 helix: 0.24 (0.23), residues: 541 sheet: -0.92 (0.33), residues: 269 loop : -2.13 (0.20), residues: 867 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A1968 TYR 0.015 0.001 TYR A1419 PHE 0.033 0.001 PHE A1170 TRP 0.025 0.002 TRP A1742 HIS 0.005 0.001 HIS A1998 Details of bonding type rmsd/Z covalent geometry : bond 0.00420 / 0.16 (13282) covalent geometry : angle 0.67076 / 0.33 (18015) hydrogen bonds : bond 0.03295 / 2.54 ( 426) hydrogen bonds : angle 4.61419 / 3.32 ( 1179) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3354 Ramachandran restraints generated. 1677 Oldfield, 0 Emsley, 1677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3354 Ramachandran restraints generated. 1677 Oldfield, 0 Emsley, 1677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 146 time to evaluate : 0.370 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1207 ASP cc_start: 0.8547 (p0) cc_final: 0.8096 (m-30) REVERT: A 1529 GLU cc_start: 0.7688 (OUTLIER) cc_final: 0.7451 (tp30) REVERT: A 1715 ILE cc_start: 0.9180 (tp) cc_final: 0.8910 (tp) REVERT: A 1720 LEU cc_start: 0.7997 (OUTLIER) cc_final: 0.7726 (pp) REVERT: A 1796 LEU cc_start: 0.9131 (OUTLIER) cc_final: 0.8657 (pp) REVERT: A 1855 ILE cc_start: 0.7952 (mm) cc_final: 0.7594 (tp) REVERT: A 1869 MET cc_start: 0.7855 (mtt) cc_final: 0.7629 (mtt) REVERT: A 1944 MET cc_start: 0.7922 (OUTLIER) cc_final: 0.6710 (pmm) REVERT: A 2148 LYS cc_start: 0.6884 (tptt) cc_final: 0.6543 (tptm) REVERT: A 2369 ASN cc_start: 0.7724 (t0) cc_final: 0.7302 (t0) outliers start: 23 outliers final: 18 residues processed: 161 average time/residue: 0.1067 time to fit residues: 25.9113 Evaluate side-chains 165 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 143 time to evaluate : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1012 HIS Chi-restraints excluded: chain A residue 1177 ILE Chi-restraints excluded: chain A residue 1234 ILE Chi-restraints excluded: chain A residue 1474 LEU Chi-restraints excluded: chain A residue 1529 GLU Chi-restraints excluded: chain A residue 1564 LEU Chi-restraints excluded: chain A residue 1621 HIS Chi-restraints excluded: chain A residue 1685 CYS Chi-restraints excluded: chain A residue 1714 GLU Chi-restraints excluded: chain A residue 1720 LEU Chi-restraints excluded: chain A residue 1742 TRP Chi-restraints excluded: chain A residue 1796 LEU Chi-restraints excluded: chain A residue 1940 ILE Chi-restraints excluded: chain A residue 1944 MET Chi-restraints excluded: chain A residue 1960 GLN Chi-restraints excluded: chain A residue 1962 ASP Chi-restraints excluded: chain A residue 2074 VAL Chi-restraints excluded: chain A residue 2096 VAL Chi-restraints excluded: chain A residue 2104 TRP Chi-restraints excluded: chain A residue 2248 LEU Chi-restraints excluded: chain A residue 2356 THR Chi-restraints excluded: chain A residue 2425 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 124 optimal weight: 5.9990 chunk 32 optimal weight: 0.0040 chunk 84 optimal weight: 0.6980 chunk 57 optimal weight: 0.6980 chunk 159 optimal weight: 0.9990 chunk 118 optimal weight: 0.9990 chunk 153 optimal weight: 6.9990 chunk 55 optimal weight: 0.9990 chunk 162 optimal weight: 0.3980 chunk 51 optimal weight: 0.3980 chunk 167 optimal weight: 0.6980 overall best weight: 0.4392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 800 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1574 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1854 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.178322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.126688 restraints weight = 30633.734| |-----------------------------------------------------------------------------| r_work (start): 0.3577 rms_B_bonded: 4.36 r_work: 0.3423 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.3423 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3443 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3443 r_free = 0.3443 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3443 r_free = 0.3443 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3443 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.2433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.129 13282 Z= 0.114 Angle : 0.626 11.066 18015 Z= 0.310 Chirality : 0.045 0.249 2123 Planarity : 0.005 0.053 2286 Dihedral : 5.059 53.041 1811 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.18 % Favored : 91.76 % Rotamer: Outliers : 1.52 % Allowed : 13.80 % Favored : 84.68 % 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: -1.57 (0.21), residues: 1677 helix: 0.38 (0.23), residues: 542 sheet: -1.01 (0.33), residues: 254 loop : -2.03 (0.20), residues: 881 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A1968 TYR 0.012 0.001 TYR A1419 PHE 0.033 0.001 PHE A1170 TRP 0.023 0.001 TRP A1742 HIS 0.005 0.001 HIS A1571 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.11 (13282) covalent geometry : angle 0.62597 / 0.31 (18015) hydrogen bonds : bond 0.02932 / 2.26 ( 426) hydrogen bonds : angle 4.52251 / 3.26 ( 1179) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3354 Ramachandran restraints generated. 1677 Oldfield, 0 Emsley, 1677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3354 Ramachandran restraints generated. 1677 Oldfield, 0 Emsley, 1677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 153 time to evaluate : 0.513 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1207 ASP cc_start: 0.8518 (p0) cc_final: 0.8092 (m-30) REVERT: A 1529 GLU cc_start: 0.7626 (OUTLIER) cc_final: 0.7382 (tp30) REVERT: A 1715 ILE cc_start: 0.9096 (tp) cc_final: 0.8817 (tp) REVERT: A 1720 LEU cc_start: 0.8038 (OUTLIER) cc_final: 0.7750 (pp) REVERT: A 1796 LEU cc_start: 0.9048 (OUTLIER) cc_final: 0.8589 (pp) REVERT: A 1869 MET cc_start: 0.7830 (mtt) cc_final: 0.7557 (mtt) REVERT: A 1941 ARG cc_start: 0.7628 (tpp-160) cc_final: 0.7067 (mmt-90) REVERT: A 1942 PRO cc_start: 0.8223 (Cg_endo) cc_final: 0.7473 (Cg_exo) REVERT: A 1943 ARG cc_start: 0.7268 (mtp85) cc_final: 0.6865 (mmm-85) REVERT: A 1944 MET cc_start: 0.7923 (OUTLIER) cc_final: 0.6697 (pmm) REVERT: A 2148 LYS cc_start: 0.6916 (tptt) cc_final: 0.6662 (tptm) REVERT: A 2324 PHE cc_start: 0.5499 (p90) cc_final: 0.5154 (p90) REVERT: A 2369 ASN cc_start: 0.7565 (t0) cc_final: 0.7188 (t0) outliers start: 21 outliers final: 14 residues processed: 168 average time/residue: 0.0992 time to fit residues: 26.2780 Evaluate side-chains 165 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 147 time to evaluate : 0.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 798 VAL Chi-restraints excluded: chain A residue 1012 HIS Chi-restraints excluded: chain A residue 1177 ILE Chi-restraints excluded: chain A residue 1234 ILE Chi-restraints excluded: chain A residue 1529 GLU Chi-restraints excluded: chain A residue 1621 HIS Chi-restraints excluded: chain A residue 1685 CYS Chi-restraints excluded: chain A residue 1714 GLU Chi-restraints excluded: chain A residue 1720 LEU Chi-restraints excluded: chain A residue 1742 TRP Chi-restraints excluded: chain A residue 1796 LEU Chi-restraints excluded: chain A residue 1944 MET Chi-restraints excluded: chain A residue 1962 ASP Chi-restraints excluded: chain A residue 2074 VAL Chi-restraints excluded: chain A residue 2104 TRP Chi-restraints excluded: chain A residue 2356 THR Chi-restraints excluded: chain A residue 2425 LEU Chi-restraints excluded: chain A residue 2512 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 9 optimal weight: 2.9990 chunk 146 optimal weight: 7.9990 chunk 34 optimal weight: 0.4980 chunk 80 optimal weight: 5.9990 chunk 90 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 chunk 136 optimal weight: 3.9990 chunk 6 optimal weight: 30.0000 chunk 96 optimal weight: 0.5980 chunk 109 optimal weight: 0.9980 chunk 121 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1574 HIS ** 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 = 0.4159 r_free = 0.4159 target = 0.176847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.126073 restraints weight = 25279.254| |-----------------------------------------------------------------------------| r_work (start): 0.3571 rms_B_bonded: 4.05 r_work: 0.3417 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3425 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3425 r_free = 0.3425 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3425 r_free = 0.3425 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3425 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.2494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.121 13282 Z= 0.131 Angle : 0.636 10.650 18015 Z= 0.315 Chirality : 0.045 0.278 2123 Planarity : 0.005 0.056 2286 Dihedral : 5.013 51.624 1811 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.36 % Favored : 91.58 % Rotamer: Outliers : 1.45 % Allowed : 14.31 % Favored : 84.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.54 (0.21), residues: 1677 helix: 0.39 (0.23), residues: 542 sheet: -1.09 (0.33), residues: 254 loop : -1.97 (0.21), residues: 881 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 767 TYR 0.012 0.001 TYR A1419 PHE 0.026 0.001 PHE A2324 TRP 0.023 0.002 TRP A1742 HIS 0.004 0.001 HIS A1998 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.13 (13282) covalent geometry : angle 0.63617 / 0.32 (18015) hydrogen bonds : bond 0.03016 / 2.33 ( 426) hydrogen bonds : angle 4.46675 / 3.22 ( 1179) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3354 Ramachandran restraints generated. 1677 Oldfield, 0 Emsley, 1677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3354 Ramachandran restraints generated. 1677 Oldfield, 0 Emsley, 1677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 145 time to evaluate : 0.408 Fit side-chains revert: symmetry clash REVERT: A 1418 VAL cc_start: 0.7089 (m) cc_final: 0.5912 (p) REVERT: A 1529 GLU cc_start: 0.7651 (OUTLIER) cc_final: 0.7422 (tp30) REVERT: A 1715 ILE cc_start: 0.9173 (tp) cc_final: 0.8905 (tp) REVERT: A 1720 LEU cc_start: 0.7984 (OUTLIER) cc_final: 0.7712 (pp) REVERT: A 1796 LEU cc_start: 0.9070 (OUTLIER) cc_final: 0.8631 (pp) REVERT: A 1869 MET cc_start: 0.7838 (mtt) cc_final: 0.7588 (mtt) REVERT: A 1941 ARG cc_start: 0.7580 (tpp-160) cc_final: 0.7070 (mmt-90) REVERT: A 1942 PRO cc_start: 0.8199 (Cg_endo) cc_final: 0.7439 (Cg_exo) REVERT: A 1944 MET cc_start: 0.7976 (OUTLIER) cc_final: 0.6759 (pmm) REVERT: A 2148 LYS cc_start: 0.6967 (tptt) cc_final: 0.6717 (tptm) REVERT: A 2324 PHE cc_start: 0.5553 (p90) cc_final: 0.5190 (p90) outliers start: 20 outliers final: 15 residues processed: 159 average time/residue: 0.1056 time to fit residues: 26.3562 Evaluate side-chains 160 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 141 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 798 VAL Chi-restraints excluded: chain A residue 1012 HIS Chi-restraints excluded: chain A residue 1177 ILE Chi-restraints excluded: chain A residue 1234 ILE Chi-restraints excluded: chain A residue 1474 LEU Chi-restraints excluded: chain A residue 1529 GLU Chi-restraints excluded: chain A residue 1621 HIS Chi-restraints excluded: chain A residue 1685 CYS Chi-restraints excluded: chain A residue 1720 LEU Chi-restraints excluded: chain A residue 1742 TRP Chi-restraints excluded: chain A residue 1796 LEU Chi-restraints excluded: chain A residue 1940 ILE Chi-restraints excluded: chain A residue 1944 MET Chi-restraints excluded: chain A residue 1962 ASP Chi-restraints excluded: chain A residue 2074 VAL Chi-restraints excluded: chain A residue 2104 TRP Chi-restraints excluded: chain A residue 2356 THR Chi-restraints excluded: chain A residue 2425 LEU Chi-restraints excluded: chain A residue 2512 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 59 optimal weight: 0.7980 chunk 119 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 71 optimal weight: 0.7980 chunk 44 optimal weight: 0.9980 chunk 106 optimal weight: 5.9990 chunk 87 optimal weight: 0.0870 chunk 98 optimal weight: 0.0570 chunk 65 optimal weight: 0.7980 chunk 82 optimal weight: 0.6980 chunk 35 optimal weight: 0.0030 overall best weight: 0.3286 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1574 HIS ** 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 = 0.4185 r_free = 0.4185 target = 0.179400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.127948 restraints weight = 30601.861| |-----------------------------------------------------------------------------| r_work (start): 0.3597 rms_B_bonded: 4.37 r_work: 0.3442 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.3442 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3453 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3453 r_free = 0.3453 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3453 r_free = 0.3453 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3453 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.2513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.121 13282 Z= 0.110 Angle : 0.621 10.691 18015 Z= 0.305 Chirality : 0.045 0.258 2123 Planarity : 0.005 0.053 2286 Dihedral : 4.890 49.137 1811 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.00 % Favored : 91.94 % Rotamer: Outliers : 1.30 % Allowed : 14.60 % Favored : 84.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.45 (0.21), residues: 1677 helix: 0.49 (0.23), residues: 543 sheet: -1.06 (0.33), residues: 259 loop : -1.93 (0.21), residues: 875 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 767 TYR 0.010 0.001 TYR A1419 PHE 0.028 0.001 PHE A2324 TRP 0.022 0.001 TRP A1742 HIS 0.005 0.001 HIS A1571 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.11 (13282) covalent geometry : angle 0.62147 / 0.31 (18015) hydrogen bonds : bond 0.02924 / 2.23 ( 426) hydrogen bonds : angle 4.41847 / 3.18 ( 1179) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3965.55 seconds wall clock time: 68 minutes 34.14 seconds (4114.14 seconds total)