Starting phenix.real_space_refine on Sat Sep 12 07:56:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9om2_70604/09_2026/9om2_70604.cif Found real_map, /net/cci-nas-00/data/ceres_data/9om2_70604/09_2026/9om2_70604.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.31 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9om2_70604/09_2026/9om2_70604.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9om2_70604/09_2026/9om2_70604.map" model { file = "/net/cci-nas-00/data/ceres_data/9om2_70604/09_2026/9om2_70604.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9om2_70604/09_2026/9om2_70604.cif" } resolution = 3.31 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.019 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 85 5.16 5 C 8944 2.51 5 N 2404 2.21 5 O 2545 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.02s 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: 13980 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 13952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1782, 13952 Classifications: {'peptide': 1782} Incomplete info: {'truncation_to_alanine': 55} Link IDs: {'PCIS': 1, 'PTRANS': 76, 'TRANS': 1704} Chain breaks: 10 Unresolved non-hydrogen bonds: 195 Unresolved non-hydrogen angles: 238 Unresolved non-hydrogen dihedrals: 156 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'HIS:plan': 2, 'ASP:plan': 17, 'GLU:plan': 12, 'GLN:plan1': 3, 'ASN:plan1': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 134 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.17, per 1000 atoms: 0.23 Number of scatterers: 13980 At special positions: 0 Unit cell: (106.59, 129.03, 161.755, 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 85 16.00 P 2 15.00 O 2545 8.00 N 2404 7.00 C 8944 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: 1.31 Conformation dependent library (CDL) restraints added in 782.4 milliseconds 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3392 Finding SS restraints... Secondary structure from input PDB file: 65 helices and 19 sheets defined 37.2% alpha, 11.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.79 Creating SS restraints... Processing helix chain 'A' and resid 544 through 555 removed outlier: 4.306A pdb=" N ARG A 552 " --> pdb=" O ALA A 548 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 571 Processing helix chain 'A' and resid 585 through 596 Processing helix chain 'A' and resid 599 through 612 removed outlier: 3.905A pdb=" N GLN A 603 " --> pdb=" O ASP A 599 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N LEU A 605 " --> pdb=" O GLU A 601 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLY A 606 " --> pdb=" O ILE A 602 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N SER A 608 " --> pdb=" O CYS A 604 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N TYR A 612 " --> pdb=" O SER A 608 " (cutoff:3.500A) Processing helix chain 'A' and resid 625 through 638 removed outlier: 4.076A pdb=" N LYS A 629 " --> pdb=" O HIS A 625 " (cutoff:3.500A) Processing helix chain 'A' and resid 643 through 657 removed outlier: 3.542A pdb=" N LYS A 647 " --> pdb=" O GLU A 643 " (cutoff:3.500A) Processing helix chain 'A' and resid 660 through 670 removed outlier: 3.931A pdb=" N LYS A 664 " --> pdb=" O ALA A 660 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N SER A 670 " --> pdb=" O LEU A 666 " (cutoff:3.500A) Processing helix chain 'A' and resid 670 through 681 removed outlier: 3.951A pdb=" N VAL A 674 " --> pdb=" O SER A 670 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N HIS A 677 " --> pdb=" O LEU A 673 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 703 removed outlier: 3.719A pdb=" N LYS A 701 " --> pdb=" O LYS A 697 " (cutoff:3.500A) Processing helix chain 'A' and resid 705 through 719 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 786 through 795 Processing helix chain 'A' and resid 814 through 819 removed outlier: 3.639A pdb=" N LEU A 818 " --> pdb=" O GLU A 814 " (cutoff:3.500A) Processing helix chain 'A' and resid 833 through 853 removed outlier: 3.607A pdb=" N SER A 837 " --> pdb=" O THR A 833 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N GLU A 853 " --> pdb=" O LYS A 849 " (cutoff:3.500A) Processing helix chain 'A' and resid 997 through 1001 Processing helix chain 'A' and resid 1004 through 1013 removed outlier: 3.580A pdb=" N VAL A1008 " --> pdb=" O CYS A1005 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N LEU A1010 " --> pdb=" O SER A1007 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N GLU A1011 " --> pdb=" O VAL A1008 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU A1013 " --> pdb=" O LEU A1010 " (cutoff:3.500A) Processing helix chain 'A' and resid 1027 through 1034 Processing helix chain 'A' and resid 1053 through 1057 removed outlier: 4.127A pdb=" N MET A1057 " --> pdb=" O LEU A1054 " (cutoff:3.500A) Processing helix chain 'A' and resid 1101 through 1106 removed outlier: 3.593A pdb=" N VAL A1106 " --> pdb=" O LEU A1102 " (cutoff:3.500A) Processing helix chain 'A' and resid 1189 through 1194 Processing helix chain 'A' and resid 1213 through 1218 removed outlier: 3.593A pdb=" N TRP A1217 " --> pdb=" O PRO A1214 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N LYS A1218 " --> pdb=" O ALA A1215 " (cutoff:3.500A) Processing helix chain 'A' and resid 1241 through 1245 removed outlier: 3.587A pdb=" N TRP A1244 " --> pdb=" O ALA A1241 " (cutoff:3.500A) Processing helix chain 'A' and resid 1261 through 1267 removed outlier: 3.539A pdb=" N LEU A1267 " --> pdb=" O ILE A1264 " (cutoff:3.500A) Processing helix chain 'A' and resid 1285 through 1291 Processing helix chain 'A' and resid 1316 through 1328 Processing helix chain 'A' and resid 1347 through 1356 Processing helix chain 'A' and resid 1398 through 1409 removed outlier: 3.991A pdb=" N SER A1403 " --> pdb=" O GLU A1400 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N HIS A1405 " --> pdb=" O TYR A1402 " (cutoff:3.500A) Proline residue: A1406 - end of helix Processing helix chain 'A' and resid 1420 through 1424 removed outlier: 3.544A pdb=" N GLY A1424 " --> pdb=" O LEU A1421 " (cutoff:3.500A) Processing helix chain 'A' and resid 1426 through 1431 Processing helix chain 'A' and resid 1431 through 1442 Processing helix chain 'A' and resid 1465 through 1473 removed outlier: 4.158A pdb=" N ILE A1469 " --> pdb=" O CYS A1465 " (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 1550 through 1560 Processing helix chain 'A' and resid 1568 through 1580 Processing helix chain 'A' and resid 1599 through 1608 removed outlier: 3.523A pdb=" N LEU A1603 " --> pdb=" O GLU A1599 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ALA A1608 " --> pdb=" O CYS A1604 " (cutoff:3.500A) Processing helix chain 'A' and resid 1609 through 1612 Processing helix chain 'A' and resid 1645 through 1656 removed outlier: 3.920A pdb=" N PHE A1650 " --> pdb=" O MET A1646 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N LYS A1651 " --> pdb=" O SER A1647 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU A1652 " --> pdb=" O GLN A1648 " (cutoff:3.500A) Processing helix chain 'A' and resid 1703 through 1714 removed outlier: 4.063A pdb=" N ASN A1710 " --> pdb=" O SER A1706 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLU A1714 " --> pdb=" O ASN A1710 " (cutoff:3.500A) Processing helix chain 'A' and resid 1770 through 1792 removed outlier: 3.598A pdb=" N HIS A1783 " --> pdb=" O GLN A1779 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LEU A1787 " --> pdb=" O HIS A1783 " (cutoff:3.500A) Processing helix chain 'A' and resid 1828 through 1835 Processing helix chain 'A' and resid 1852 through 1856 Processing helix chain 'A' and resid 1865 through 1869 removed outlier: 4.059A pdb=" N MET A1869 " --> pdb=" O ARG A1866 " (cutoff:3.500A) Processing helix chain 'A' and resid 1871 through 1875 Processing helix chain 'A' and resid 1881 through 1885 removed outlier: 4.214A pdb=" N LEU A1884 " --> pdb=" O PRO A1881 " (cutoff:3.500A) Processing helix chain 'A' and resid 1913 through 1924 removed outlier: 3.742A pdb=" N GLN A1919 " --> pdb=" O ARG A1915 " (cutoff:3.500A) Processing helix chain 'A' and resid 1954 through 1962 Processing helix chain 'A' and resid 1963 through 1966 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 Processing helix chain 'A' and resid 2051 through 2069 removed outlier: 4.172A pdb=" N ASP A2055 " --> pdb=" O ASN A2051 " (cutoff:3.500A) Processing helix chain 'A' and resid 2071 through 2077 Processing helix chain 'A' and resid 2079 through 2089 removed outlier: 4.034A pdb=" N GLU A2087 " --> pdb=" O PHE A2083 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N GLN A2089 " --> pdb=" O GLU A2085 " (cutoff:3.500A) Processing helix chain 'A' and resid 2094 through 2099 Processing helix chain 'A' and resid 2104 through 2115 removed outlier: 3.572A pdb=" N LYS A2109 " --> pdb=" O PRO A2105 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU A2110 " --> pdb=" O MET A2106 " (cutoff:3.500A) Processing helix chain 'A' and resid 2118 through 2122 Processing helix chain 'A' and resid 2124 through 2134 removed outlier: 3.774A pdb=" N SER A2134 " --> pdb=" O ASP A2130 " (cutoff:3.500A) Processing helix chain 'A' and resid 2278 through 2280 No H-bonds generated for 'chain 'A' and resid 2278 through 2280' Processing helix chain 'A' and resid 2389 through 2397 Processing helix chain 'A' and resid 2499 through 2527 removed outlier: 3.516A 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 Processing sheet with id=AA2, first strand: chain 'A' and resid 1063 through 1064 removed outlier: 7.074A pdb=" N LEU A1063 " --> pdb=" O ASN A1089 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1177 through 1179 removed outlier: 6.928A pdb=" N LEU A1201 " --> pdb=" O LEU A1226 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1329 through 1331 Processing sheet with id=AA5, first strand: chain 'A' and resid 1336 through 1337 Processing sheet with id=AA6, first strand: chain 'A' and resid 1415 through 1416 removed outlier: 7.365A pdb=" N TYR A1415 " --> pdb=" O ILE A1448 " (cutoff:3.500A) removed outlier: 8.054A pdb=" N VAL A1450 " --> pdb=" O TYR A1415 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N VAL A1447 " --> pdb=" O ARG A1483 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N TYR A1485 " --> pdb=" O VAL A1447 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N LEU A1449 " --> pdb=" O TYR A1485 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 1548 through 1549 Processing sheet with id=AA8, first strand: chain 'A' and resid 1690 through 1693 removed outlier: 3.933A pdb=" N PHE A1762 " --> pdb=" O GLU A1753 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLU A1753 " --> pdb=" O PHE A1762 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N TYR A1747 " --> pdb=" O PRO A1768 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N ALA A1746 " --> pdb=" O TRP A1742 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N TRP A1742 " --> pdb=" O ALA A1746 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1840 through 1841 Processing sheet with id=AB1, first strand: chain 'A' and resid 1896 through 1898 removed outlier: 3.662A pdb=" N ALA A1937 " --> pdb=" O VAL A1946 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 2000 through 2002 Processing sheet with id=AB3, first strand: chain 'A' and resid 2142 through 2145 removed outlier: 3.727A pdb=" N GLN A2490 " --> pdb=" O ASN A2476 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N LYS A2467 " --> pdb=" O LEU A2463 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N LEU A2463 " --> pdb=" O LYS A2467 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N VAL A2469 " --> pdb=" O ALA A2461 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N TYR A2475 " --> pdb=" O VAL A2455 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N VAL A2455 " --> pdb=" O TYR A2475 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 2155 through 2157 Processing sheet with id=AB5, first strand: chain 'A' and resid 2199 through 2207 removed outlier: 6.521A pdb=" N GLY A2218 " --> pdb=" O LEU A2200 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N LEU A2202 " --> pdb=" O VAL A2216 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N VAL A2216 " --> pdb=" O LEU A2202 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N LEU A2204 " --> pdb=" O TRP A2214 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N TRP A2214 " --> pdb=" O LEU A2204 " (cutoff:3.500A) removed outlier: 5.183A pdb=" N HIS A2206 " --> pdb=" O GLU A2212 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N GLU A2212 " --> pdb=" O HIS A2206 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU A2225 " --> pdb=" O SER A2217 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 2245 through 2252 removed outlier: 6.712A pdb=" N GLY A2266 " --> pdb=" O THR A2246 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N LEU A2248 " --> pdb=" O LEU A2264 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N LEU A2264 " --> pdb=" O LEU A2248 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N CYS A2250 " --> pdb=" O PHE A2262 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N PHE A2262 " --> pdb=" O CYS A2250 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 2271 through 2273 Processing sheet with id=AB8, first strand: chain 'A' and resid 2315 through 2319 Processing sheet with id=AB9, first strand: chain 'A' and resid 2354 through 2359 removed outlier: 6.812A pdb=" N ALA A2366 " --> pdb=" O ILE A2355 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N VAL A2357 " --> pdb=" O TYR A2364 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N TYR A2364 " --> pdb=" O VAL A2357 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N LYS A2367 " --> pdb=" O VAL A2372 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N VAL A2372 " --> pdb=" O LYS A2367 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ILE A2387 " --> pdb=" O VAL A2373 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N VAL A2375 " --> pdb=" O GLY A2385 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N GLY A2385 " --> pdb=" O VAL A2375 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 2414 through 2419 removed outlier: 3.914A pdb=" N ARG A2446 " --> pdb=" O LEU A2436 " (cutoff:3.500A) 476 hydrogen bonds defined for protein. 1296 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: 3.79 Time building geometry restraints manager: 1.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4535 1.34 - 1.46: 2466 1.46 - 1.58: 7111 1.58 - 1.69: 7 1.69 - 1.81: 125 Bond restraints: 14244 Sorted by residual: bond pdb=" C5 GDP A2601 " pdb=" C4 GDP A2601 " ideal model delta sigma weight residual 1.490 1.375 0.115 2.00e-02 2.50e+03 3.31e+01 bond pdb=" C5 GDP A2601 " pdb=" C6 GDP A2601 " ideal model delta sigma weight residual 1.490 1.410 0.080 2.00e-02 2.50e+03 1.58e+01 bond pdb=" CB PRO A1759 " pdb=" CG PRO A1759 " ideal model delta sigma weight residual 1.492 1.650 -0.158 5.00e-02 4.00e+02 1.00e+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 7.11e+00 bond pdb=" CB PRO A1083 " pdb=" CG PRO A1083 " ideal model delta sigma weight residual 1.492 1.615 -0.123 5.00e-02 4.00e+02 6.03e+00 ... (remaining 14239 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.17: 19143 3.17 - 6.35: 121 6.35 - 9.52: 17 9.52 - 12.69: 5 12.69 - 15.87: 1 Bond angle restraints: 19287 Sorted by residual: angle pdb=" CA PRO A1759 " pdb=" N PRO A1759 " pdb=" CD PRO A1759 " ideal model delta sigma weight residual 112.00 99.95 12.05 1.40e+00 5.10e-01 7.40e+01 angle pdb=" N ILE A1658 " pdb=" CA ILE A1658 " pdb=" C ILE A1658 " ideal model delta sigma weight residual 113.71 108.14 5.57 9.50e-01 1.11e+00 3.43e+01 angle pdb=" CA PRO A1083 " pdb=" N PRO A1083 " pdb=" CD PRO A1083 " ideal model delta sigma weight residual 112.00 105.19 6.81 1.40e+00 5.10e-01 2.37e+01 angle pdb=" CA LEU A1924 " pdb=" CB LEU A1924 " pdb=" CG LEU A1924 " ideal model delta sigma weight residual 116.30 132.17 -15.87 3.50e+00 8.16e-02 2.05e+01 angle pdb=" CA PRO A1570 " pdb=" N PRO A1570 " pdb=" CD PRO A1570 " ideal model delta sigma weight residual 112.00 105.66 6.34 1.40e+00 5.10e-01 2.05e+01 ... (remaining 19282 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.84: 7389 18.84 - 37.68: 1044 37.68 - 56.52: 219 56.52 - 75.36: 34 75.36 - 94.20: 15 Dihedral angle restraints: 8701 sinusoidal: 3495 harmonic: 5206 Sorted by residual: 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 85.82 94.20 1 2.00e+01 2.50e-03 2.58e+01 dihedral pdb=" CA HIS A 543 " pdb=" C HIS A 543 " pdb=" N LYS A 544 " pdb=" CA LYS A 544 " ideal model delta harmonic sigma weight residual 180.00 -158.73 -21.27 0 5.00e+00 4.00e-02 1.81e+01 dihedral pdb=" CA VAL A1065 " pdb=" C VAL A1065 " pdb=" N SER A1066 " pdb=" CA SER A1066 " ideal model delta harmonic sigma weight residual 180.00 -161.60 -18.40 0 5.00e+00 4.00e-02 1.35e+01 ... (remaining 8698 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 1440 0.034 - 0.068: 553 0.068 - 0.101: 185 0.101 - 0.135: 68 0.135 - 0.169: 9 Chirality restraints: 2255 Sorted by residual: chirality pdb=" C3' GDP A2601 " pdb=" C4' GDP A2601 " pdb=" O3' GDP A2601 " pdb=" C2' GDP A2601 " both_signs ideal model delta sigma weight residual False -2.51 -2.68 0.17 2.00e-01 2.50e+01 7.15e-01 chirality pdb=" CG LEU A1509 " pdb=" CB LEU A1509 " pdb=" CD1 LEU A1509 " pdb=" CD2 LEU A1509 " both_signs ideal model delta sigma weight residual False -2.59 -2.42 -0.17 2.00e-01 2.50e+01 7.02e-01 chirality pdb=" CA VAL A1065 " pdb=" N VAL A1065 " pdb=" C VAL A1065 " pdb=" CB VAL A1065 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.16 2.00e-01 2.50e+01 6.28e-01 ... (remaining 2252 not shown) Planarity restraints: 2431 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A1569 " 0.069 5.00e-02 4.00e+02 1.01e-01 1.63e+01 pdb=" N PRO A1570 " -0.175 5.00e-02 4.00e+02 pdb=" CA PRO A1570 " 0.050 5.00e-02 4.00e+02 pdb=" CD PRO A1570 " 0.055 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A1171 " 0.049 5.00e-02 4.00e+02 7.17e-02 8.23e+00 pdb=" N PRO A1172 " -0.124 5.00e-02 4.00e+02 pdb=" CA PRO A1172 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO A1172 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS A1758 " 0.050 5.00e-02 4.00e+02 7.03e-02 7.91e+00 pdb=" N PRO A1759 " -0.121 5.00e-02 4.00e+02 pdb=" CA PRO A1759 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO A1759 " 0.039 5.00e-02 4.00e+02 ... (remaining 2428 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.69: 364 2.69 - 3.24: 13653 3.24 - 3.79: 21441 3.79 - 4.35: 28412 4.35 - 4.90: 46338 Nonbonded interactions: 110208 Sorted by model distance: nonbonded pdb=" O LEU A1195 " pdb=" OG SER A1219 " model vdw 2.132 3.040 nonbonded pdb=" O SER A 990 " pdb=" ND2 ASN A1021 " model vdw 2.198 3.120 nonbonded pdb=" O PHE A 808 " pdb=" ND2 ASN A 992 " model vdw 2.200 3.120 nonbonded pdb=" O PRO A 597 " pdb=" NH2 ARG A 637 " model vdw 2.205 3.120 nonbonded pdb=" OG SER A2166 " pdb=" O LEU A2182 " model vdw 2.229 3.040 ... (remaining 110203 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 16.550 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 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:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.158 14244 Z= 0.153 Angle : 0.694 15.865 19287 Z= 0.343 Chirality : 0.043 0.169 2255 Planarity : 0.005 0.101 2431 Dihedral : 17.814 94.205 5309 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 12.67 Ramachandran Plot: Outliers : 0.17 % Allowed : 9.49 % Favored : 90.34 % Rotamer: Outliers : 0.58 % Allowed : 32.11 % Favored : 67.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % 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: 1760 helix: 0.38 (0.23), residues: 566 sheet: -1.65 (0.32), residues: 293 loop : -2.08 (0.20), residues: 901 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 552 TYR 0.016 0.001 TYR A1649 PHE 0.018 0.001 PHE A2324 TRP 0.031 0.002 TRP A 817 HIS 0.004 0.001 HIS A2510 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.15 (14244) covalent geometry : angle 0.69435 / 0.34 (19287) hydrogen bonds : bond 0.17339 / 11.54 ( 476) hydrogen bonds : angle 6.65810 / 4.88 ( 1296) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 170 time to evaluate : 0.559 Fit side-chains REVERT: A 1577 ASN cc_start: 0.8386 (t0) cc_final: 0.8182 (t0) outliers start: 9 outliers final: 4 residues processed: 176 average time/residue: 0.0969 time to fit residues: 27.4288 Evaluate side-chains 165 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 161 time to evaluate : 0.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1548 ILE Chi-restraints excluded: chain A residue 1796 LEU Chi-restraints excluded: chain A residue 2167 ILE Chi-restraints excluded: chain A residue 2423 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 0.5980 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 0.5980 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 0.6980 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 10.0000 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 594 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 693 ASN ** A 720 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1021 ASN A1324 GLN ** A1405 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1879 GLN A2236 HIS A2502 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4367 r_free = 0.4367 target = 0.186645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.156196 restraints weight = 19611.032| |-----------------------------------------------------------------------------| r_work (start): 0.4134 rms_B_bonded: 2.25 r_work: 0.3682 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.3682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.0852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 14244 Z= 0.188 Angle : 0.667 13.086 19287 Z= 0.332 Chirality : 0.045 0.155 2255 Planarity : 0.005 0.063 2431 Dihedral : 5.535 82.898 1909 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.17 % Allowed : 9.94 % Favored : 89.89 % Rotamer: Outliers : 4.59 % Allowed : 29.26 % Favored : 66.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.87 (0.20), residues: 1760 helix: 0.32 (0.23), residues: 563 sheet: -1.69 (0.31), residues: 296 loop : -2.15 (0.20), residues: 901 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 552 TYR 0.013 0.001 TYR A1402 PHE 0.019 0.002 PHE A1883 TRP 0.021 0.002 TRP A 817 HIS 0.005 0.001 HIS A1043 Details of bonding type rmsd/Z covalent geometry : bond 0.00465 / 0.19 (14244) covalent geometry : angle 0.66721 / 0.33 (19287) hydrogen bonds : bond 0.03952 / 2.66 ( 476) hydrogen bonds : angle 5.29101 / 3.89 ( 1296) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 170 time to evaluate : 0.551 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 605 LEU cc_start: 0.7894 (OUTLIER) cc_final: 0.7598 (pp) REVERT: A 1067 ARG cc_start: 0.8511 (OUTLIER) cc_final: 0.8153 (mmt-90) REVERT: A 1484 ASP cc_start: 0.8297 (OUTLIER) cc_final: 0.8049 (m-30) REVERT: A 1732 MET cc_start: 0.7826 (ppp) cc_final: 0.7557 (ppp) REVERT: A 1890 PHE cc_start: 0.4046 (OUTLIER) cc_final: 0.3743 (t80) REVERT: A 1998 HIS cc_start: 0.8140 (OUTLIER) cc_final: 0.7636 (m-70) REVERT: A 2104 TRP cc_start: 0.9237 (OUTLIER) cc_final: 0.8902 (t60) REVERT: A 2311 GLU cc_start: 0.3141 (OUTLIER) cc_final: 0.2345 (mm-30) outliers start: 71 outliers final: 33 residues processed: 224 average time/residue: 0.1015 time to fit residues: 35.9040 Evaluate side-chains 197 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 157 time to evaluate : 0.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 592 THR Chi-restraints excluded: chain A residue 593 LEU Chi-restraints excluded: chain A residue 605 LEU Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain A residue 684 MET Chi-restraints excluded: chain A residue 757 LEU Chi-restraints excluded: chain A residue 1023 LEU Chi-restraints excluded: chain A residue 1054 LEU Chi-restraints excluded: chain A residue 1067 ARG Chi-restraints excluded: chain A residue 1128 LEU Chi-restraints excluded: chain A residue 1159 SER Chi-restraints excluded: chain A residue 1220 LEU Chi-restraints excluded: chain A residue 1477 ARG Chi-restraints excluded: chain A residue 1484 ASP Chi-restraints excluded: chain A residue 1509 LEU Chi-restraints excluded: chain A residue 1513 ILE Chi-restraints excluded: chain A residue 1530 LEU Chi-restraints excluded: chain A residue 1548 ILE Chi-restraints excluded: chain A residue 1612 THR Chi-restraints excluded: chain A residue 1733 TYR Chi-restraints excluded: chain A residue 1754 VAL Chi-restraints excluded: chain A residue 1767 VAL Chi-restraints excluded: chain A residue 1796 LEU Chi-restraints excluded: chain A residue 1816 PHE Chi-restraints excluded: chain A residue 1890 PHE Chi-restraints excluded: chain A residue 1905 VAL Chi-restraints excluded: chain A residue 1946 VAL Chi-restraints excluded: chain A residue 1998 HIS Chi-restraints excluded: chain A residue 2031 THR Chi-restraints excluded: chain A residue 2086 LEU Chi-restraints excluded: chain A residue 2104 TRP Chi-restraints excluded: chain A residue 2107 VAL Chi-restraints excluded: chain A residue 2138 VAL Chi-restraints excluded: chain A residue 2199 ILE Chi-restraints excluded: chain A residue 2300 LEU Chi-restraints excluded: chain A residue 2311 GLU Chi-restraints excluded: chain A residue 2312 ARG Chi-restraints excluded: chain A residue 2370 SER Chi-restraints excluded: chain A residue 2419 LEU Chi-restraints excluded: chain A residue 2423 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 41 optimal weight: 1.9990 chunk 7 optimal weight: 0.7980 chunk 16 optimal weight: 0.8980 chunk 100 optimal weight: 3.9990 chunk 115 optimal weight: 4.9990 chunk 56 optimal weight: 0.9990 chunk 60 optimal weight: 0.8980 chunk 86 optimal weight: 2.9990 chunk 145 optimal weight: 9.9990 chunk 30 optimal weight: 0.4980 chunk 38 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 594 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 720 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1405 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1879 GLN A1998 HIS A2502 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4425 r_free = 0.4425 target = 0.193853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.162723 restraints weight = 19909.737| |-----------------------------------------------------------------------------| r_work (start): 0.4121 rms_B_bonded: 2.17 r_work: 0.3705 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.1083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 14244 Z= 0.146 Angle : 0.638 13.166 19287 Z= 0.313 Chirality : 0.044 0.161 2255 Planarity : 0.005 0.064 2431 Dihedral : 5.338 80.018 1907 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.69 % Favored : 91.14 % Rotamer: Outliers : 4.52 % Allowed : 29.59 % Favored : 65.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % 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: -1.88 (0.20), residues: 1760 helix: 0.22 (0.23), residues: 575 sheet: -1.67 (0.31), residues: 291 loop : -2.13 (0.20), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 637 TYR 0.015 0.001 TYR A1984 PHE 0.016 0.001 PHE A1883 TRP 0.014 0.002 TRP A 817 HIS 0.005 0.001 HIS A2510 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.15 (14244) covalent geometry : angle 0.63806 / 0.31 (19287) hydrogen bonds : bond 0.03487 / 2.33 ( 476) hydrogen bonds : angle 5.03348 / 3.71 ( 1296) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 172 time to evaluate : 0.583 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 605 LEU cc_start: 0.7901 (OUTLIER) cc_final: 0.7544 (pp) REVERT: A 996 ASP cc_start: 0.7759 (t0) cc_final: 0.6921 (t0) REVERT: A 998 ASP cc_start: 0.8632 (p0) cc_final: 0.8246 (p0) REVERT: A 1067 ARG cc_start: 0.8439 (OUTLIER) cc_final: 0.8091 (mmt-90) REVERT: A 1416 LEU cc_start: 0.8481 (OUTLIER) cc_final: 0.8243 (mp) REVERT: A 1477 ARG cc_start: 0.5726 (OUTLIER) cc_final: 0.5460 (ptp-110) REVERT: A 1484 ASP cc_start: 0.8198 (OUTLIER) cc_final: 0.7970 (m-30) REVERT: A 1710 ASN cc_start: 0.8605 (OUTLIER) cc_final: 0.8239 (m-40) REVERT: A 1732 MET cc_start: 0.7693 (ppp) cc_final: 0.7405 (ppp) REVERT: A 1890 PHE cc_start: 0.3972 (OUTLIER) cc_final: 0.3668 (t80) REVERT: A 2104 TRP cc_start: 0.9206 (OUTLIER) cc_final: 0.8806 (t60) REVERT: A 2311 GLU cc_start: 0.2961 (OUTLIER) cc_final: 0.2140 (mm-30) outliers start: 70 outliers final: 37 residues processed: 226 average time/residue: 0.1045 time to fit residues: 36.8966 Evaluate side-chains 210 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 164 time to evaluate : 0.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 542 ILE Chi-restraints excluded: chain A residue 592 THR Chi-restraints excluded: chain A residue 593 LEU Chi-restraints excluded: chain A residue 605 LEU Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain A residue 684 MET Chi-restraints excluded: chain A residue 692 LEU Chi-restraints excluded: chain A residue 757 LEU Chi-restraints excluded: chain A residue 983 TYR Chi-restraints excluded: chain A residue 1023 LEU Chi-restraints excluded: chain A residue 1054 LEU Chi-restraints excluded: chain A residue 1067 ARG Chi-restraints excluded: chain A residue 1098 VAL Chi-restraints excluded: chain A residue 1128 LEU Chi-restraints excluded: chain A residue 1159 SER Chi-restraints excluded: chain A residue 1220 LEU Chi-restraints excluded: chain A residue 1416 LEU Chi-restraints excluded: chain A residue 1477 ARG Chi-restraints excluded: chain A residue 1484 ASP Chi-restraints excluded: chain A residue 1513 ILE Chi-restraints excluded: chain A residue 1530 LEU Chi-restraints excluded: chain A residue 1548 ILE Chi-restraints excluded: chain A residue 1710 ASN Chi-restraints excluded: chain A residue 1733 TYR Chi-restraints excluded: chain A residue 1754 VAL Chi-restraints excluded: chain A residue 1767 VAL Chi-restraints excluded: chain A residue 1796 LEU Chi-restraints excluded: chain A residue 1816 PHE Chi-restraints excluded: chain A residue 1885 LEU Chi-restraints excluded: chain A residue 1890 PHE Chi-restraints excluded: chain A residue 1903 VAL Chi-restraints excluded: chain A residue 1905 VAL Chi-restraints excluded: chain A residue 1946 VAL Chi-restraints excluded: chain A residue 1987 SER Chi-restraints excluded: chain A residue 2031 THR Chi-restraints excluded: chain A residue 2104 TRP Chi-restraints excluded: chain A residue 2138 VAL Chi-restraints excluded: chain A residue 2199 ILE Chi-restraints excluded: chain A residue 2216 VAL Chi-restraints excluded: chain A residue 2253 PHE Chi-restraints excluded: chain A residue 2300 LEU Chi-restraints excluded: chain A residue 2311 GLU Chi-restraints excluded: chain A residue 2312 ARG Chi-restraints excluded: chain A residue 2370 SER Chi-restraints excluded: chain A residue 2423 THR Chi-restraints excluded: chain A residue 2441 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 21 optimal weight: 2.9990 chunk 93 optimal weight: 8.9990 chunk 56 optimal weight: 1.9990 chunk 134 optimal weight: 0.5980 chunk 155 optimal weight: 6.9990 chunk 15 optimal weight: 0.9980 chunk 97 optimal weight: 6.9990 chunk 100 optimal weight: 2.9990 chunk 102 optimal weight: 2.9990 chunk 146 optimal weight: 0.8980 chunk 135 optimal weight: 0.7980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 594 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 603 GLN A 720 ASN ** A1068 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1405 HIS ** A1879 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2502 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4417 r_free = 0.4417 target = 0.192575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.162740 restraints weight = 19820.262| |-----------------------------------------------------------------------------| r_work (start): 0.4150 rms_B_bonded: 2.14 r_work: 0.3685 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.3685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.1349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 14244 Z= 0.171 Angle : 0.654 13.424 19287 Z= 0.320 Chirality : 0.044 0.152 2255 Planarity : 0.005 0.070 2431 Dihedral : 5.363 77.005 1907 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.17 % Allowed : 9.55 % Favored : 90.28 % Rotamer: Outliers : 4.72 % Allowed : 29.84 % Favored : 65.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % 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: -1.92 (0.20), residues: 1760 helix: 0.20 (0.23), residues: 574 sheet: -1.70 (0.31), residues: 288 loop : -2.15 (0.20), residues: 898 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 637 TYR 0.011 0.001 TYR A1984 PHE 0.019 0.002 PHE A 676 TRP 0.011 0.002 TRP A2426 HIS 0.004 0.001 HIS A1977 Details of bonding type rmsd/Z covalent geometry : bond 0.00422 / 0.17 (14244) covalent geometry : angle 0.65418 / 0.32 (19287) hydrogen bonds : bond 0.03478 / 2.34 ( 476) hydrogen bonds : angle 4.98779 / 3.67 ( 1296) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 172 time to evaluate : 0.585 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 605 LEU cc_start: 0.8042 (OUTLIER) cc_final: 0.7589 (pp) REVERT: A 996 ASP cc_start: 0.7972 (t0) cc_final: 0.7082 (t0) REVERT: A 998 ASP cc_start: 0.8934 (p0) cc_final: 0.8467 (p0) REVERT: A 1067 ARG cc_start: 0.8524 (OUTLIER) cc_final: 0.8087 (mmt180) REVERT: A 1710 ASN cc_start: 0.8669 (OUTLIER) cc_final: 0.8237 (m-40) REVERT: A 1732 MET cc_start: 0.7840 (ppp) cc_final: 0.7597 (ppp) REVERT: A 1890 PHE cc_start: 0.4240 (OUTLIER) cc_final: 0.3912 (t80) REVERT: A 2104 TRP cc_start: 0.9236 (OUTLIER) cc_final: 0.8847 (t60) REVERT: A 2168 TRP cc_start: 0.6727 (t-100) cc_final: 0.6377 (t-100) REVERT: A 2311 GLU cc_start: 0.2975 (OUTLIER) cc_final: 0.2326 (mm-30) REVERT: A 2337 GLU cc_start: 0.7034 (OUTLIER) cc_final: 0.6212 (tm-30) REVERT: A 2456 ARG cc_start: 0.8247 (mmm160) cc_final: 0.7841 (tpt-90) outliers start: 73 outliers final: 44 residues processed: 233 average time/residue: 0.0982 time to fit residues: 36.2100 Evaluate side-chains 208 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 157 time to evaluate : 0.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 542 ILE Chi-restraints excluded: chain A residue 592 THR Chi-restraints excluded: chain A residue 593 LEU Chi-restraints excluded: chain A residue 605 LEU Chi-restraints excluded: chain A residue 627 LEU Chi-restraints excluded: chain A residue 684 MET Chi-restraints excluded: chain A residue 692 LEU Chi-restraints excluded: chain A residue 757 LEU Chi-restraints excluded: chain A residue 826 THR Chi-restraints excluded: chain A residue 983 TYR Chi-restraints excluded: chain A residue 1023 LEU Chi-restraints excluded: chain A residue 1031 CYS Chi-restraints excluded: chain A residue 1054 LEU Chi-restraints excluded: chain A residue 1067 ARG Chi-restraints excluded: chain A residue 1098 VAL Chi-restraints excluded: chain A residue 1128 LEU Chi-restraints excluded: chain A residue 1159 SER Chi-restraints excluded: chain A residue 1200 SER Chi-restraints excluded: chain A residue 1477 ARG Chi-restraints excluded: chain A residue 1484 ASP Chi-restraints excluded: chain A residue 1513 ILE Chi-restraints excluded: chain A residue 1530 LEU Chi-restraints excluded: chain A residue 1548 ILE Chi-restraints excluded: chain A residue 1569 LEU Chi-restraints excluded: chain A residue 1612 THR Chi-restraints excluded: chain A residue 1710 ASN Chi-restraints excluded: chain A residue 1733 TYR Chi-restraints excluded: chain A residue 1754 VAL Chi-restraints excluded: chain A residue 1765 ILE Chi-restraints excluded: chain A residue 1767 VAL Chi-restraints excluded: chain A residue 1816 PHE Chi-restraints excluded: chain A residue 1885 LEU Chi-restraints excluded: chain A residue 1890 PHE Chi-restraints excluded: chain A residue 1903 VAL Chi-restraints excluded: chain A residue 1905 VAL Chi-restraints excluded: chain A residue 1946 VAL Chi-restraints excluded: chain A residue 2031 THR Chi-restraints excluded: chain A residue 2086 LEU Chi-restraints excluded: chain A residue 2104 TRP Chi-restraints excluded: chain A residue 2107 VAL Chi-restraints excluded: chain A residue 2138 VAL Chi-restraints excluded: chain A residue 2199 ILE Chi-restraints excluded: chain A residue 2216 VAL Chi-restraints excluded: chain A residue 2253 PHE Chi-restraints excluded: chain A residue 2300 LEU Chi-restraints excluded: chain A residue 2311 GLU Chi-restraints excluded: chain A residue 2312 ARG Chi-restraints excluded: chain A residue 2337 GLU Chi-restraints excluded: chain A residue 2370 SER Chi-restraints excluded: chain A residue 2441 THR Chi-restraints excluded: chain A residue 2460 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 22 optimal weight: 2.9990 chunk 50 optimal weight: 0.7980 chunk 90 optimal weight: 3.9990 chunk 53 optimal weight: 0.0970 chunk 159 optimal weight: 10.0000 chunk 56 optimal weight: 0.9990 chunk 152 optimal weight: 0.7980 chunk 176 optimal weight: 0.7980 chunk 134 optimal weight: 0.9980 chunk 169 optimal weight: 5.9990 chunk 18 optimal weight: 0.7980 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 594 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1783 HIS A2502 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4434 r_free = 0.4434 target = 0.194607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.167441 restraints weight = 19927.852| |-----------------------------------------------------------------------------| r_work (start): 0.4166 rms_B_bonded: 1.99 r_work: 0.3753 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.1425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 14244 Z= 0.130 Angle : 0.623 13.837 19287 Z= 0.304 Chirality : 0.043 0.175 2255 Planarity : 0.005 0.074 2431 Dihedral : 5.124 74.890 1904 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.17 % Allowed : 9.03 % Favored : 90.80 % Rotamer: Outliers : 3.94 % Allowed : 30.43 % Favored : 65.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.81 (0.20), residues: 1760 helix: 0.32 (0.23), residues: 574 sheet: -1.66 (0.31), residues: 287 loop : -2.11 (0.20), residues: 899 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 637 TYR 0.010 0.001 TYR A1984 PHE 0.015 0.001 PHE A1883 TRP 0.011 0.002 TRP A2496 HIS 0.004 0.001 HIS A2510 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.13 (14244) covalent geometry : angle 0.62304 / 0.30 (19287) hydrogen bonds : bond 0.03201 / 2.14 ( 476) hydrogen bonds : angle 4.86811 / 3.59 ( 1296) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 180 time to evaluate : 0.529 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 605 LEU cc_start: 0.7919 (OUTLIER) cc_final: 0.7551 (pp) REVERT: A 996 ASP cc_start: 0.7651 (t0) cc_final: 0.6645 (t0) REVERT: A 998 ASP cc_start: 0.8683 (p0) cc_final: 0.8180 (p0) REVERT: A 1067 ARG cc_start: 0.8410 (OUTLIER) cc_final: 0.8062 (mmt-90) REVERT: A 1379 GLN cc_start: 0.5461 (mm-40) cc_final: 0.5106 (mm-40) REVERT: A 1555 GLN cc_start: 0.8384 (tm-30) cc_final: 0.8159 (tm-30) REVERT: A 1732 MET cc_start: 0.7651 (ppp) cc_final: 0.7417 (ppp) REVERT: A 1869 MET cc_start: 0.7442 (mmt) cc_final: 0.7096 (mmt) REVERT: A 1890 PHE cc_start: 0.4194 (OUTLIER) cc_final: 0.3863 (t80) REVERT: A 2104 TRP cc_start: 0.9163 (OUTLIER) cc_final: 0.8763 (t60) REVERT: A 2311 GLU cc_start: 0.3040 (OUTLIER) cc_final: 0.2212 (mm-30) REVERT: A 2337 GLU cc_start: 0.6953 (OUTLIER) cc_final: 0.6123 (tm-30) REVERT: A 2443 ARG cc_start: 0.6431 (mmm160) cc_final: 0.6057 (mmp-170) REVERT: A 2456 ARG cc_start: 0.8210 (mmm160) cc_final: 0.7765 (tpt-90) outliers start: 61 outliers final: 42 residues processed: 229 average time/residue: 0.1015 time to fit residues: 36.5854 Evaluate side-chains 217 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 169 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 542 ILE Chi-restraints excluded: chain A residue 592 THR Chi-restraints excluded: chain A residue 593 LEU Chi-restraints excluded: chain A residue 605 LEU Chi-restraints excluded: chain A residue 627 LEU Chi-restraints excluded: chain A residue 684 MET Chi-restraints excluded: chain A residue 692 LEU Chi-restraints excluded: chain A residue 757 LEU Chi-restraints excluded: chain A residue 816 SER Chi-restraints excluded: chain A residue 826 THR Chi-restraints excluded: chain A residue 983 TYR Chi-restraints excluded: chain A residue 1023 LEU Chi-restraints excluded: chain A residue 1031 CYS Chi-restraints excluded: chain A residue 1054 LEU Chi-restraints excluded: chain A residue 1067 ARG Chi-restraints excluded: chain A residue 1128 LEU Chi-restraints excluded: chain A residue 1159 SER Chi-restraints excluded: chain A residue 1200 SER Chi-restraints excluded: chain A residue 1220 LEU Chi-restraints excluded: chain A residue 1477 ARG Chi-restraints excluded: chain A residue 1484 ASP Chi-restraints excluded: chain A residue 1513 ILE Chi-restraints excluded: chain A residue 1548 ILE Chi-restraints excluded: chain A residue 1569 LEU Chi-restraints excluded: chain A residue 1733 TYR Chi-restraints excluded: chain A residue 1754 VAL Chi-restraints excluded: chain A residue 1765 ILE Chi-restraints excluded: chain A residue 1767 VAL Chi-restraints excluded: chain A residue 1796 LEU Chi-restraints excluded: chain A residue 1868 ILE Chi-restraints excluded: chain A residue 1885 LEU Chi-restraints excluded: chain A residue 1890 PHE Chi-restraints excluded: chain A residue 1903 VAL Chi-restraints excluded: chain A residue 1921 LEU Chi-restraints excluded: chain A residue 1946 VAL Chi-restraints excluded: chain A residue 2031 THR Chi-restraints excluded: chain A residue 2104 TRP Chi-restraints excluded: chain A residue 2124 THR Chi-restraints excluded: chain A residue 2138 VAL Chi-restraints excluded: chain A residue 2167 ILE Chi-restraints excluded: chain A residue 2253 PHE Chi-restraints excluded: chain A residue 2300 LEU Chi-restraints excluded: chain A residue 2311 GLU Chi-restraints excluded: chain A residue 2312 ARG Chi-restraints excluded: chain A residue 2337 GLU Chi-restraints excluded: chain A residue 2370 SER Chi-restraints excluded: chain A residue 2441 THR Chi-restraints excluded: chain A residue 2460 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 91 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 chunk 60 optimal weight: 0.8980 chunk 137 optimal weight: 0.6980 chunk 9 optimal weight: 0.8980 chunk 153 optimal weight: 5.9990 chunk 75 optimal weight: 0.9990 chunk 101 optimal weight: 8.9990 chunk 79 optimal weight: 0.7980 chunk 95 optimal weight: 2.9990 chunk 112 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 594 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1961 GLN A2502 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4427 r_free = 0.4427 target = 0.193664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.164127 restraints weight = 19731.190| |-----------------------------------------------------------------------------| r_work (start): 0.4165 rms_B_bonded: 2.23 r_work: 0.3705 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.3705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.1527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 14244 Z= 0.148 Angle : 0.646 15.270 19287 Z= 0.315 Chirality : 0.044 0.169 2255 Planarity : 0.005 0.073 2431 Dihedral : 5.129 73.009 1904 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.17 % Allowed : 9.60 % Favored : 90.23 % Rotamer: Outliers : 4.84 % Allowed : 29.72 % Favored : 65.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % 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: -1.82 (0.20), residues: 1760 helix: 0.33 (0.23), residues: 573 sheet: -1.67 (0.31), residues: 290 loop : -2.12 (0.20), residues: 897 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 637 TYR 0.016 0.001 TYR A2249 PHE 0.021 0.001 PHE A 676 TRP 0.022 0.002 TRP A1791 HIS 0.004 0.001 HIS A1043 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.15 (14244) covalent geometry : angle 0.64586 / 0.32 (19287) hydrogen bonds : bond 0.03267 / 2.19 ( 476) hydrogen bonds : angle 4.87631 / 3.59 ( 1296) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 174 time to evaluate : 0.617 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 605 LEU cc_start: 0.8068 (OUTLIER) cc_final: 0.7684 (pp) REVERT: A 728 LEU cc_start: 0.8997 (OUTLIER) cc_final: 0.8691 (mm) REVERT: A 996 ASP cc_start: 0.8017 (t0) cc_final: 0.6973 (t0) REVERT: A 998 ASP cc_start: 0.8885 (p0) cc_final: 0.8390 (p0) REVERT: A 1067 ARG cc_start: 0.8512 (OUTLIER) cc_final: 0.8176 (mmt180) REVERT: A 1379 GLN cc_start: 0.5633 (mm-40) cc_final: 0.5276 (mm-40) REVERT: A 1555 GLN cc_start: 0.8394 (tm-30) cc_final: 0.8174 (tm-30) REVERT: A 1710 ASN cc_start: 0.8664 (OUTLIER) cc_final: 0.8230 (m-40) REVERT: A 1732 MET cc_start: 0.7789 (ppp) cc_final: 0.7577 (ppp) REVERT: A 1890 PHE cc_start: 0.4376 (OUTLIER) cc_final: 0.3949 (t80) REVERT: A 2104 TRP cc_start: 0.9206 (OUTLIER) cc_final: 0.8809 (t60) REVERT: A 2311 GLU cc_start: 0.3033 (OUTLIER) cc_final: 0.2234 (mm-30) REVERT: A 2456 ARG cc_start: 0.8262 (mmm160) cc_final: 0.7874 (tpt-90) outliers start: 75 outliers final: 54 residues processed: 233 average time/residue: 0.1022 time to fit residues: 37.5198 Evaluate side-chains 232 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 171 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 542 ILE Chi-restraints excluded: chain A residue 592 THR Chi-restraints excluded: chain A residue 593 LEU Chi-restraints excluded: chain A residue 605 LEU Chi-restraints excluded: chain A residue 627 LEU Chi-restraints excluded: chain A residue 684 MET Chi-restraints excluded: chain A residue 692 LEU Chi-restraints excluded: chain A residue 728 LEU Chi-restraints excluded: chain A residue 757 LEU Chi-restraints excluded: chain A residue 816 SER Chi-restraints excluded: chain A residue 826 THR Chi-restraints excluded: chain A residue 983 TYR Chi-restraints excluded: chain A residue 1023 LEU Chi-restraints excluded: chain A residue 1031 CYS Chi-restraints excluded: chain A residue 1033 THR Chi-restraints excluded: chain A residue 1054 LEU Chi-restraints excluded: chain A residue 1067 ARG Chi-restraints excluded: chain A residue 1098 VAL Chi-restraints excluded: chain A residue 1128 LEU Chi-restraints excluded: chain A residue 1159 SER Chi-restraints excluded: chain A residue 1200 SER Chi-restraints excluded: chain A residue 1390 LEU Chi-restraints excluded: chain A residue 1477 ARG Chi-restraints excluded: chain A residue 1484 ASP Chi-restraints excluded: chain A residue 1509 LEU Chi-restraints excluded: chain A residue 1513 ILE Chi-restraints excluded: chain A residue 1530 LEU Chi-restraints excluded: chain A residue 1548 ILE Chi-restraints excluded: chain A residue 1569 LEU Chi-restraints excluded: chain A residue 1612 THR Chi-restraints excluded: chain A residue 1710 ASN Chi-restraints excluded: chain A residue 1733 TYR Chi-restraints excluded: chain A residue 1754 VAL Chi-restraints excluded: chain A residue 1765 ILE Chi-restraints excluded: chain A residue 1767 VAL Chi-restraints excluded: chain A residue 1796 LEU Chi-restraints excluded: chain A residue 1816 PHE Chi-restraints excluded: chain A residue 1868 ILE Chi-restraints excluded: chain A residue 1885 LEU Chi-restraints excluded: chain A residue 1890 PHE Chi-restraints excluded: chain A residue 1903 VAL Chi-restraints excluded: chain A residue 1905 VAL Chi-restraints excluded: chain A residue 1921 LEU Chi-restraints excluded: chain A residue 1946 VAL Chi-restraints excluded: chain A residue 1961 GLN Chi-restraints excluded: chain A residue 2031 THR Chi-restraints excluded: chain A residue 2086 LEU Chi-restraints excluded: chain A residue 2104 TRP Chi-restraints excluded: chain A residue 2107 VAL Chi-restraints excluded: chain A residue 2124 THR Chi-restraints excluded: chain A residue 2138 VAL Chi-restraints excluded: chain A residue 2167 ILE Chi-restraints excluded: chain A residue 2216 VAL Chi-restraints excluded: chain A residue 2253 PHE Chi-restraints excluded: chain A residue 2300 LEU Chi-restraints excluded: chain A residue 2311 GLU Chi-restraints excluded: chain A residue 2312 ARG Chi-restraints excluded: chain A residue 2370 SER Chi-restraints excluded: chain A residue 2423 THR Chi-restraints excluded: chain A residue 2441 THR Chi-restraints excluded: chain A residue 2460 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 157 optimal weight: 9.9990 chunk 63 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 172 optimal weight: 4.9990 chunk 139 optimal weight: 0.7980 chunk 21 optimal weight: 1.9990 chunk 94 optimal weight: 0.0370 chunk 5 optimal weight: 0.9990 chunk 173 optimal weight: 0.8980 chunk 144 optimal weight: 0.6980 overall best weight: 0.6860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 594 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2502 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4386 r_free = 0.4386 target = 0.188824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.158651 restraints weight = 19531.516| |-----------------------------------------------------------------------------| r_work (start): 0.4166 rms_B_bonded: 2.17 r_work: 0.3731 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.3731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.1586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 14244 Z= 0.134 Angle : 0.639 13.979 19287 Z= 0.312 Chirality : 0.043 0.160 2255 Planarity : 0.005 0.077 2431 Dihedral : 5.075 71.702 1904 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.17 % Allowed : 9.38 % Favored : 90.45 % Rotamer: Outliers : 4.59 % Allowed : 30.30 % Favored : 65.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % 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: 1760 helix: 0.34 (0.23), residues: 573 sheet: -1.72 (0.32), residues: 282 loop : -2.07 (0.20), residues: 905 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 637 TYR 0.010 0.001 TYR A1739 PHE 0.017 0.001 PHE A 676 TRP 0.024 0.002 TRP A 817 HIS 0.004 0.001 HIS A2510 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.13 (14244) covalent geometry : angle 0.63885 / 0.31 (19287) hydrogen bonds : bond 0.03212 / 2.15 ( 476) hydrogen bonds : angle 4.84994 / 3.58 ( 1296) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 170 time to evaluate : 0.447 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 605 LEU cc_start: 0.8071 (OUTLIER) cc_final: 0.7690 (pp) REVERT: A 728 LEU cc_start: 0.8987 (OUTLIER) cc_final: 0.8674 (mm) REVERT: A 996 ASP cc_start: 0.7934 (t0) cc_final: 0.6862 (t0) REVERT: A 998 ASP cc_start: 0.8829 (p0) cc_final: 0.8314 (p0) REVERT: A 1067 ARG cc_start: 0.8507 (OUTLIER) cc_final: 0.8197 (mmt-90) REVERT: A 1379 GLN cc_start: 0.5620 (mm-40) cc_final: 0.5273 (mm-40) REVERT: A 1555 GLN cc_start: 0.8364 (tm-30) cc_final: 0.7796 (tm-30) REVERT: A 1710 ASN cc_start: 0.8668 (OUTLIER) cc_final: 0.8266 (m-40) REVERT: A 1732 MET cc_start: 0.7857 (ppp) cc_final: 0.7647 (ppp) REVERT: A 1890 PHE cc_start: 0.4423 (OUTLIER) cc_final: 0.4016 (t80) REVERT: A 2104 TRP cc_start: 0.9186 (OUTLIER) cc_final: 0.8843 (t60) REVERT: A 2311 GLU cc_start: 0.2957 (OUTLIER) cc_final: 0.2219 (mm-30) REVERT: A 2456 ARG cc_start: 0.8222 (mmm160) cc_final: 0.7847 (tpt-90) outliers start: 71 outliers final: 55 residues processed: 227 average time/residue: 0.1011 time to fit residues: 36.1446 Evaluate side-chains 230 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 168 time to evaluate : 0.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 542 ILE Chi-restraints excluded: chain A residue 592 THR Chi-restraints excluded: chain A residue 593 LEU Chi-restraints excluded: chain A residue 605 LEU Chi-restraints excluded: chain A residue 627 LEU Chi-restraints excluded: chain A residue 684 MET Chi-restraints excluded: chain A residue 692 LEU Chi-restraints excluded: chain A residue 728 LEU Chi-restraints excluded: chain A residue 757 LEU Chi-restraints excluded: chain A residue 816 SER Chi-restraints excluded: chain A residue 826 THR Chi-restraints excluded: chain A residue 983 TYR Chi-restraints excluded: chain A residue 1023 LEU Chi-restraints excluded: chain A residue 1031 CYS Chi-restraints excluded: chain A residue 1042 LEU Chi-restraints excluded: chain A residue 1054 LEU Chi-restraints excluded: chain A residue 1067 ARG Chi-restraints excluded: chain A residue 1098 VAL Chi-restraints excluded: chain A residue 1128 LEU Chi-restraints excluded: chain A residue 1159 SER Chi-restraints excluded: chain A residue 1200 SER Chi-restraints excluded: chain A residue 1380 ILE Chi-restraints excluded: chain A residue 1477 ARG Chi-restraints excluded: chain A residue 1484 ASP Chi-restraints excluded: chain A residue 1509 LEU Chi-restraints excluded: chain A residue 1513 ILE Chi-restraints excluded: chain A residue 1530 LEU Chi-restraints excluded: chain A residue 1548 ILE Chi-restraints excluded: chain A residue 1569 LEU Chi-restraints excluded: chain A residue 1612 THR Chi-restraints excluded: chain A residue 1710 ASN Chi-restraints excluded: chain A residue 1733 TYR Chi-restraints excluded: chain A residue 1754 VAL Chi-restraints excluded: chain A residue 1765 ILE Chi-restraints excluded: chain A residue 1767 VAL Chi-restraints excluded: chain A residue 1796 LEU Chi-restraints excluded: chain A residue 1868 ILE Chi-restraints excluded: chain A residue 1885 LEU Chi-restraints excluded: chain A residue 1890 PHE Chi-restraints excluded: chain A residue 1903 VAL Chi-restraints excluded: chain A residue 1905 VAL Chi-restraints excluded: chain A residue 1921 LEU Chi-restraints excluded: chain A residue 1946 VAL Chi-restraints excluded: chain A residue 1990 ILE Chi-restraints excluded: chain A residue 2031 THR Chi-restraints excluded: chain A residue 2086 LEU Chi-restraints excluded: chain A residue 2104 TRP Chi-restraints excluded: chain A residue 2107 VAL Chi-restraints excluded: chain A residue 2124 THR Chi-restraints excluded: chain A residue 2138 VAL Chi-restraints excluded: chain A residue 2167 ILE Chi-restraints excluded: chain A residue 2216 VAL Chi-restraints excluded: chain A residue 2253 PHE Chi-restraints excluded: chain A residue 2300 LEU Chi-restraints excluded: chain A residue 2311 GLU Chi-restraints excluded: chain A residue 2312 ARG Chi-restraints excluded: chain A residue 2370 SER Chi-restraints excluded: chain A residue 2423 THR Chi-restraints excluded: chain A residue 2435 LEU Chi-restraints excluded: chain A residue 2441 THR Chi-restraints excluded: chain A residue 2460 THR Chi-restraints excluded: chain A residue 2517 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 9 optimal weight: 0.9990 chunk 109 optimal weight: 0.0970 chunk 78 optimal weight: 0.1980 chunk 106 optimal weight: 0.5980 chunk 121 optimal weight: 0.4980 chunk 160 optimal weight: 1.9990 chunk 140 optimal weight: 0.9990 chunk 71 optimal weight: 0.9990 chunk 88 optimal weight: 0.9980 chunk 146 optimal weight: 0.9990 chunk 114 optimal weight: 0.9980 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 594 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1879 GLN A2502 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4403 r_free = 0.4403 target = 0.190464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.160429 restraints weight = 19529.214| |-----------------------------------------------------------------------------| r_work (start): 0.4155 rms_B_bonded: 2.08 r_work: 0.3756 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.1623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14244 Z= 0.116 Angle : 0.626 15.844 19287 Z= 0.304 Chirality : 0.043 0.153 2255 Planarity : 0.005 0.079 2431 Dihedral : 4.929 68.929 1904 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.17 % Allowed : 9.15 % Favored : 90.68 % Rotamer: Outliers : 4.13 % Allowed : 30.94 % Favored : 64.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.71 (0.20), residues: 1760 helix: 0.44 (0.23), residues: 569 sheet: -1.73 (0.32), residues: 285 loop : -2.00 (0.20), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 552 TYR 0.013 0.001 TYR A1649 PHE 0.021 0.001 PHE A 676 TRP 0.026 0.002 TRP A 817 HIS 0.004 0.001 HIS A2510 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 (14244) covalent geometry : angle 0.62601 / 0.30 (19287) hydrogen bonds : bond 0.03113 / 2.08 ( 476) hydrogen bonds : angle 4.82443 / 3.57 ( 1296) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 178 time to evaluate : 0.659 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 605 LEU cc_start: 0.7966 (OUTLIER) cc_final: 0.7554 (pp) REVERT: A 728 LEU cc_start: 0.8903 (OUTLIER) cc_final: 0.8577 (mm) REVERT: A 996 ASP cc_start: 0.7652 (t0) cc_final: 0.7411 (t0) REVERT: A 1128 LEU cc_start: 0.8010 (OUTLIER) cc_final: 0.7711 (mp) REVERT: A 1379 GLN cc_start: 0.5535 (mm-40) cc_final: 0.5202 (mm-40) REVERT: A 1555 GLN cc_start: 0.8414 (tm-30) cc_final: 0.7866 (tm-30) REVERT: A 1710 ASN cc_start: 0.8576 (OUTLIER) cc_final: 0.8180 (m-40) REVERT: A 1732 MET cc_start: 0.7723 (ppp) cc_final: 0.7522 (ppp) REVERT: A 1890 PHE cc_start: 0.4445 (OUTLIER) cc_final: 0.4101 (t80) REVERT: A 2104 TRP cc_start: 0.9138 (OUTLIER) cc_final: 0.8812 (t60) REVERT: A 2168 TRP cc_start: 0.6718 (t-100) cc_final: 0.6429 (t-100) REVERT: A 2311 GLU cc_start: 0.3052 (OUTLIER) cc_final: 0.2267 (mm-30) REVERT: A 2456 ARG cc_start: 0.8212 (mmm160) cc_final: 0.7783 (tpt-90) outliers start: 64 outliers final: 47 residues processed: 231 average time/residue: 0.0965 time to fit residues: 35.5563 Evaluate side-chains 226 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 172 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 542 ILE Chi-restraints excluded: chain A residue 592 THR Chi-restraints excluded: chain A residue 593 LEU Chi-restraints excluded: chain A residue 605 LEU Chi-restraints excluded: chain A residue 684 MET Chi-restraints excluded: chain A residue 692 LEU Chi-restraints excluded: chain A residue 728 LEU Chi-restraints excluded: chain A residue 816 SER Chi-restraints excluded: chain A residue 826 THR Chi-restraints excluded: chain A residue 983 TYR Chi-restraints excluded: chain A residue 1023 LEU Chi-restraints excluded: chain A residue 1098 VAL Chi-restraints excluded: chain A residue 1128 LEU Chi-restraints excluded: chain A residue 1159 SER Chi-restraints excluded: chain A residue 1220 LEU Chi-restraints excluded: chain A residue 1335 MET Chi-restraints excluded: chain A residue 1380 ILE Chi-restraints excluded: chain A residue 1477 ARG Chi-restraints excluded: chain A residue 1509 LEU Chi-restraints excluded: chain A residue 1513 ILE Chi-restraints excluded: chain A residue 1530 LEU Chi-restraints excluded: chain A residue 1548 ILE Chi-restraints excluded: chain A residue 1569 LEU Chi-restraints excluded: chain A residue 1710 ASN Chi-restraints excluded: chain A residue 1733 TYR Chi-restraints excluded: chain A residue 1754 VAL Chi-restraints excluded: chain A residue 1765 ILE Chi-restraints excluded: chain A residue 1767 VAL Chi-restraints excluded: chain A residue 1796 LEU Chi-restraints excluded: chain A residue 1853 SER Chi-restraints excluded: chain A residue 1868 ILE Chi-restraints excluded: chain A residue 1885 LEU Chi-restraints excluded: chain A residue 1890 PHE Chi-restraints excluded: chain A residue 1903 VAL Chi-restraints excluded: chain A residue 1905 VAL Chi-restraints excluded: chain A residue 1946 VAL Chi-restraints excluded: chain A residue 1987 SER Chi-restraints excluded: chain A residue 1990 ILE Chi-restraints excluded: chain A residue 2031 THR Chi-restraints excluded: chain A residue 2086 LEU Chi-restraints excluded: chain A residue 2104 TRP Chi-restraints excluded: chain A residue 2128 VAL Chi-restraints excluded: chain A residue 2167 ILE Chi-restraints excluded: chain A residue 2197 SER Chi-restraints excluded: chain A residue 2216 VAL Chi-restraints excluded: chain A residue 2253 PHE Chi-restraints excluded: chain A residue 2300 LEU Chi-restraints excluded: chain A residue 2311 GLU Chi-restraints excluded: chain A residue 2312 ARG Chi-restraints excluded: chain A residue 2370 SER Chi-restraints excluded: chain A residue 2423 THR Chi-restraints excluded: chain A residue 2435 LEU Chi-restraints excluded: chain A residue 2441 THR Chi-restraints excluded: chain A residue 2460 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 22 optimal weight: 0.9990 chunk 149 optimal weight: 9.9990 chunk 4 optimal weight: 0.7980 chunk 174 optimal weight: 4.9990 chunk 53 optimal weight: 0.9980 chunk 101 optimal weight: 0.0370 chunk 75 optimal weight: 0.7980 chunk 148 optimal weight: 2.9990 chunk 102 optimal weight: 0.7980 chunk 44 optimal weight: 0.9990 chunk 95 optimal weight: 0.5980 overall best weight: 0.6058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 594 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2502 HIS ** A2510 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 = 0.4445 r_free = 0.4445 target = 0.195600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.164643 restraints weight = 19930.590| |-----------------------------------------------------------------------------| r_work (start): 0.4138 rms_B_bonded: 2.36 r_work: 0.3714 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.1698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14244 Z= 0.128 Angle : 0.647 15.277 19287 Z= 0.314 Chirality : 0.043 0.153 2255 Planarity : 0.005 0.080 2431 Dihedral : 4.920 66.598 1904 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.17 % Allowed : 9.26 % Favored : 90.57 % Rotamer: Outliers : 4.07 % Allowed : 31.40 % Favored : 64.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % 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: -1.70 (0.20), residues: 1760 helix: 0.50 (0.23), residues: 562 sheet: -1.76 (0.32), residues: 283 loop : -2.01 (0.20), residues: 915 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 637 TYR 0.011 0.001 TYR A1984 PHE 0.022 0.001 PHE A 676 TRP 0.023 0.002 TRP A 817 HIS 0.004 0.001 HIS A2510 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.13 (14244) covalent geometry : angle 0.64747 / 0.31 (19287) hydrogen bonds : bond 0.03182 / 2.13 ( 476) hydrogen bonds : angle 4.81720 / 3.56 ( 1296) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 176 time to evaluate : 0.577 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 728 LEU cc_start: 0.8896 (OUTLIER) cc_final: 0.8593 (mm) REVERT: A 996 ASP cc_start: 0.7727 (t0) cc_final: 0.7482 (t0) REVERT: A 1379 GLN cc_start: 0.5588 (mm-40) cc_final: 0.5237 (mm-40) REVERT: A 1555 GLN cc_start: 0.8435 (tm-30) cc_final: 0.7887 (tm-30) REVERT: A 1710 ASN cc_start: 0.8601 (OUTLIER) cc_final: 0.8244 (m-40) REVERT: A 1732 MET cc_start: 0.7813 (ppp) cc_final: 0.7602 (ppp) REVERT: A 1824 LYS cc_start: 0.6553 (OUTLIER) cc_final: 0.6157 (mtpt) REVERT: A 1836 GLU cc_start: 0.7047 (OUTLIER) cc_final: 0.5830 (tp30) REVERT: A 1871 ASN cc_start: 0.8488 (t0) cc_final: 0.8241 (t0) REVERT: A 1890 PHE cc_start: 0.4490 (OUTLIER) cc_final: 0.4100 (t80) REVERT: A 2104 TRP cc_start: 0.9161 (OUTLIER) cc_final: 0.8830 (t60) REVERT: A 2168 TRP cc_start: 0.6590 (t-100) cc_final: 0.6240 (t-100) REVERT: A 2311 GLU cc_start: 0.3232 (OUTLIER) cc_final: 0.2378 (mm-30) REVERT: A 2377 ASP cc_start: 0.6105 (t0) cc_final: 0.5880 (t0) REVERT: A 2456 ARG cc_start: 0.8260 (mmm160) cc_final: 0.7789 (tpt-90) outliers start: 63 outliers final: 52 residues processed: 228 average time/residue: 0.1006 time to fit residues: 36.3762 Evaluate side-chains 229 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 170 time to evaluate : 0.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 542 ILE Chi-restraints excluded: chain A residue 592 THR Chi-restraints excluded: chain A residue 593 LEU Chi-restraints excluded: chain A residue 627 LEU Chi-restraints excluded: chain A residue 692 LEU Chi-restraints excluded: chain A residue 728 LEU Chi-restraints excluded: chain A residue 816 SER Chi-restraints excluded: chain A residue 826 THR Chi-restraints excluded: chain A residue 983 TYR Chi-restraints excluded: chain A residue 1023 LEU Chi-restraints excluded: chain A residue 1098 VAL Chi-restraints excluded: chain A residue 1128 LEU Chi-restraints excluded: chain A residue 1159 SER Chi-restraints excluded: chain A residue 1203 MET Chi-restraints excluded: chain A residue 1220 LEU Chi-restraints excluded: chain A residue 1335 MET Chi-restraints excluded: chain A residue 1380 ILE Chi-restraints excluded: chain A residue 1477 ARG Chi-restraints excluded: chain A residue 1509 LEU Chi-restraints excluded: chain A residue 1513 ILE Chi-restraints excluded: chain A residue 1530 LEU Chi-restraints excluded: chain A residue 1548 ILE Chi-restraints excluded: chain A residue 1569 LEU Chi-restraints excluded: chain A residue 1710 ASN Chi-restraints excluded: chain A residue 1733 TYR Chi-restraints excluded: chain A residue 1754 VAL Chi-restraints excluded: chain A residue 1765 ILE Chi-restraints excluded: chain A residue 1767 VAL Chi-restraints excluded: chain A residue 1796 LEU Chi-restraints excluded: chain A residue 1824 LYS Chi-restraints excluded: chain A residue 1836 GLU Chi-restraints excluded: chain A residue 1853 SER Chi-restraints excluded: chain A residue 1868 ILE Chi-restraints excluded: chain A residue 1885 LEU Chi-restraints excluded: chain A residue 1890 PHE Chi-restraints excluded: chain A residue 1903 VAL Chi-restraints excluded: chain A residue 1905 VAL Chi-restraints excluded: chain A residue 1921 LEU Chi-restraints excluded: chain A residue 1946 VAL Chi-restraints excluded: chain A residue 1987 SER Chi-restraints excluded: chain A residue 1990 ILE Chi-restraints excluded: chain A residue 2031 THR Chi-restraints excluded: chain A residue 2086 LEU Chi-restraints excluded: chain A residue 2104 TRP Chi-restraints excluded: chain A residue 2128 VAL Chi-restraints excluded: chain A residue 2138 VAL Chi-restraints excluded: chain A residue 2167 ILE Chi-restraints excluded: chain A residue 2197 SER Chi-restraints excluded: chain A residue 2216 VAL Chi-restraints excluded: chain A residue 2253 PHE Chi-restraints excluded: chain A residue 2300 LEU Chi-restraints excluded: chain A residue 2311 GLU Chi-restraints excluded: chain A residue 2312 ARG Chi-restraints excluded: chain A residue 2370 SER Chi-restraints excluded: chain A residue 2423 THR Chi-restraints excluded: chain A residue 2435 LEU Chi-restraints excluded: chain A residue 2441 THR Chi-restraints excluded: chain A residue 2460 THR Chi-restraints excluded: chain A residue 2517 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 108 optimal weight: 2.9990 chunk 25 optimal weight: 0.0070 chunk 88 optimal weight: 0.8980 chunk 76 optimal weight: 0.0980 chunk 133 optimal weight: 0.9980 chunk 164 optimal weight: 5.9990 chunk 130 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 chunk 93 optimal weight: 10.0000 chunk 11 optimal weight: 0.7980 chunk 31 optimal weight: 0.0870 overall best weight: 0.3776 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 594 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2502 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4462 r_free = 0.4462 target = 0.197248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.168860 restraints weight = 19867.642| |-----------------------------------------------------------------------------| r_work (start): 0.4186 rms_B_bonded: 2.14 r_work: 0.3770 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.1779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 14244 Z= 0.112 Angle : 0.641 15.657 19287 Z= 0.309 Chirality : 0.042 0.150 2255 Planarity : 0.005 0.087 2431 Dihedral : 4.795 63.638 1904 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.98 % Favored : 90.85 % Rotamer: Outliers : 3.88 % Allowed : 31.65 % Favored : 64.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % 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 (0.20), residues: 1760 helix: 0.52 (0.23), residues: 563 sheet: -1.74 (0.32), residues: 283 loop : -1.97 (0.20), residues: 914 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 637 TYR 0.011 0.001 TYR A1649 PHE 0.014 0.001 PHE A 676 TRP 0.019 0.002 TRP A 817 HIS 0.004 0.001 HIS A2510 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.11 (14244) covalent geometry : angle 0.64089 / 0.31 (19287) hydrogen bonds : bond 0.03114 / 2.09 ( 476) hydrogen bonds : angle 4.80807 / 3.56 ( 1296) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 185 time to evaluate : 0.591 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 728 LEU cc_start: 0.8884 (OUTLIER) cc_final: 0.8559 (mm) REVERT: A 996 ASP cc_start: 0.7611 (t0) cc_final: 0.7366 (t0) REVERT: A 1128 LEU cc_start: 0.7933 (OUTLIER) cc_final: 0.7626 (mp) REVERT: A 1379 GLN cc_start: 0.5508 (mm-40) cc_final: 0.5199 (mm-40) REVERT: A 1555 GLN cc_start: 0.8415 (tm-30) cc_final: 0.7895 (tm-30) REVERT: A 1824 LYS cc_start: 0.6410 (OUTLIER) cc_final: 0.6026 (mtpt) REVERT: A 1836 GLU cc_start: 0.7028 (OUTLIER) cc_final: 0.5786 (tp30) REVERT: A 1853 SER cc_start: 0.7890 (OUTLIER) cc_final: 0.7605 (m) REVERT: A 1871 ASN cc_start: 0.8441 (t0) cc_final: 0.8209 (t0) REVERT: A 1890 PHE cc_start: 0.4302 (OUTLIER) cc_final: 0.4061 (t80) REVERT: A 2168 TRP cc_start: 0.6534 (t-100) cc_final: 0.6168 (t-100) REVERT: A 2311 GLU cc_start: 0.3180 (OUTLIER) cc_final: 0.2365 (mm-30) REVERT: A 2377 ASP cc_start: 0.6111 (t0) cc_final: 0.5866 (t0) REVERT: A 2456 ARG cc_start: 0.8224 (mmm160) cc_final: 0.7759 (tpt-90) outliers start: 60 outliers final: 49 residues processed: 233 average time/residue: 0.1019 time to fit residues: 37.8078 Evaluate side-chains 234 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 178 time to evaluate : 0.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 542 ILE Chi-restraints excluded: chain A residue 592 THR Chi-restraints excluded: chain A residue 593 LEU Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain A residue 627 LEU Chi-restraints excluded: chain A residue 692 LEU Chi-restraints excluded: chain A residue 728 LEU Chi-restraints excluded: chain A residue 816 SER Chi-restraints excluded: chain A residue 826 THR Chi-restraints excluded: chain A residue 983 TYR Chi-restraints excluded: chain A residue 1023 LEU Chi-restraints excluded: chain A residue 1098 VAL Chi-restraints excluded: chain A residue 1128 LEU Chi-restraints excluded: chain A residue 1159 SER Chi-restraints excluded: chain A residue 1203 MET Chi-restraints excluded: chain A residue 1220 LEU Chi-restraints excluded: chain A residue 1335 MET Chi-restraints excluded: chain A residue 1380 ILE Chi-restraints excluded: chain A residue 1477 ARG Chi-restraints excluded: chain A residue 1513 ILE Chi-restraints excluded: chain A residue 1530 LEU Chi-restraints excluded: chain A residue 1548 ILE Chi-restraints excluded: chain A residue 1569 LEU Chi-restraints excluded: chain A residue 1733 TYR Chi-restraints excluded: chain A residue 1754 VAL Chi-restraints excluded: chain A residue 1765 ILE Chi-restraints excluded: chain A residue 1767 VAL Chi-restraints excluded: chain A residue 1796 LEU Chi-restraints excluded: chain A residue 1824 LYS Chi-restraints excluded: chain A residue 1836 GLU Chi-restraints excluded: chain A residue 1853 SER Chi-restraints excluded: chain A residue 1868 ILE Chi-restraints excluded: chain A residue 1885 LEU Chi-restraints excluded: chain A residue 1890 PHE Chi-restraints excluded: chain A residue 1903 VAL Chi-restraints excluded: chain A residue 1905 VAL Chi-restraints excluded: chain A residue 1921 LEU Chi-restraints excluded: chain A residue 1946 VAL Chi-restraints excluded: chain A residue 1987 SER Chi-restraints excluded: chain A residue 1990 ILE Chi-restraints excluded: chain A residue 2031 THR Chi-restraints excluded: chain A residue 2086 LEU Chi-restraints excluded: chain A residue 2128 VAL Chi-restraints excluded: chain A residue 2138 VAL Chi-restraints excluded: chain A residue 2197 SER Chi-restraints excluded: chain A residue 2216 VAL Chi-restraints excluded: chain A residue 2253 PHE Chi-restraints excluded: chain A residue 2300 LEU Chi-restraints excluded: chain A residue 2311 GLU Chi-restraints excluded: chain A residue 2312 ARG Chi-restraints excluded: chain A residue 2370 SER Chi-restraints excluded: chain A residue 2423 THR Chi-restraints excluded: chain A residue 2435 LEU Chi-restraints excluded: chain A residue 2441 THR Chi-restraints excluded: chain A residue 2460 THR Chi-restraints excluded: chain A residue 2517 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 111 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 130 optimal weight: 2.9990 chunk 169 optimal weight: 5.9990 chunk 128 optimal weight: 0.8980 chunk 142 optimal weight: 2.9990 chunk 1 optimal weight: 10.0000 chunk 97 optimal weight: 0.4980 chunk 5 optimal weight: 0.0070 chunk 125 optimal weight: 1.9990 chunk 117 optimal weight: 0.3980 overall best weight: 0.7600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 594 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1407 HIS A2502 HIS ** A2510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4439 r_free = 0.4439 target = 0.195012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.164760 restraints weight = 19797.227| |-----------------------------------------------------------------------------| r_work (start): 0.4141 rms_B_bonded: 2.23 r_work: 0.3706 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.1848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 14244 Z= 0.144 Angle : 0.670 14.710 19287 Z= 0.326 Chirality : 0.044 0.153 2255 Planarity : 0.005 0.082 2431 Dihedral : 4.891 62.353 1904 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.17 % Allowed : 9.72 % Favored : 90.11 % Rotamer: Outliers : 3.62 % Allowed : 32.17 % Favored : 64.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % 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 (0.20), residues: 1760 helix: 0.56 (0.23), residues: 555 sheet: -1.73 (0.32), residues: 283 loop : -2.01 (0.20), residues: 922 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A2522 TYR 0.010 0.001 TYR A1649 PHE 0.016 0.001 PHE A 676 TRP 0.023 0.002 TRP A 817 HIS 0.006 0.001 HIS A1407 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.14 (14244) covalent geometry : angle 0.67031 / 0.33 (19287) hydrogen bonds : bond 0.03295 / 2.21 ( 476) hydrogen bonds : angle 4.83899 / 3.57 ( 1296) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3395.37 seconds wall clock time: 59 minutes 8.49 seconds (3548.49 seconds total)