Starting phenix.real_space_refine on Thu Sep 18 04:31:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9qle_53225/09_2025/9qle_53225.cif Found real_map, /net/cci-nas-00/data/ceres_data/9qle_53225/09_2025/9qle_53225.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9qle_53225/09_2025/9qle_53225.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9qle_53225/09_2025/9qle_53225.map" model { file = "/net/cci-nas-00/data/ceres_data/9qle_53225/09_2025/9qle_53225.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9qle_53225/09_2025/9qle_53225.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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: 6 Type Number sf(0) Gaussians Ca 10 9.91 5 P 2 5.49 5 S 59 5.16 5 C 8815 2.51 5 N 2363 2.21 5 O 2571 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 52 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13820 Number of models: 1 Model: "" Number of chains: 2 Chain: "D" Number of atoms: 13750 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1695, 13750 Classifications: {'peptide': 1695} Link IDs: {'PCIS': 3, 'PTRANS': 103, 'TRANS': 1588} Chain breaks: 5 Chain: "D" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 70 Unusual residues: {' CA': 10, 'PSF': 2} Classifications: {'undetermined': 12} Link IDs: {None: 11} Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N PSF D2001 " occ=0.76 ... (28 atoms not shown) pdb=" P PSF D2001 " occ=0.76 residue: pdb=" N PSF D2010 " occ=0.88 ... (28 atoms not shown) pdb=" P PSF D2010 " occ=0.88 Time building chain proxies: 3.08, per 1000 atoms: 0.22 Number of scatterers: 13820 At special positions: 0 Unit cell: (100.08, 126.72, 154.08, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 10 19.99 S 59 16.00 P 2 15.00 O 2571 8.00 N 2363 7.00 C 8815 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: 1.05 Conformation dependent library (CDL) restraints added in 625.2 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 3366 Ramachandran restraints generated. 1683 Oldfield, 0 Emsley, 1683 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3192 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 19 sheets defined 17.9% alpha, 27.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.73 Creating SS restraints... Processing helix chain 'D' and resid 172 through 187 Processing helix chain 'D' and resid 252 through 257 removed outlier: 3.557A pdb=" N MET D 257 " --> pdb=" O PRO D 253 " (cutoff:3.500A) Processing helix chain 'D' and resid 285 through 290 Processing helix chain 'D' and resid 307 through 311 removed outlier: 3.708A pdb=" N GLY D 311 " --> pdb=" O THR D 308 " (cutoff:3.500A) Processing helix chain 'D' and resid 342 through 346 Processing helix chain 'D' and resid 522 through 526 removed outlier: 3.549A pdb=" N THR D 525 " --> pdb=" O GLU D 522 " (cutoff:3.500A) Processing helix chain 'D' and resid 558 through 565 Processing helix chain 'D' and resid 566 through 569 Processing helix chain 'D' and resid 650 through 680 removed outlier: 4.295A pdb=" N ALA D 656 " --> pdb=" O HIS D 652 " (cutoff:3.500A) Processing helix chain 'D' and resid 683 through 702 Processing helix chain 'D' and resid 716 through 744 removed outlier: 4.069A pdb=" N SER D 742 " --> pdb=" O VAL D 738 " (cutoff:3.500A) Processing helix chain 'D' and resid 746 through 765 removed outlier: 3.835A pdb=" N THR D 750 " --> pdb=" O ASP D 746 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N ALA D 752 " --> pdb=" O LYS D 748 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N GLU D 753 " --> pdb=" O SER D 749 " (cutoff:3.500A) Processing helix chain 'D' and resid 792 through 796 Processing helix chain 'D' and resid 845 through 852 Processing helix chain 'D' and resid 895 through 899 removed outlier: 3.982A pdb=" N PHE D 899 " --> pdb=" O ARG D 896 " (cutoff:3.500A) Processing helix chain 'D' and resid 921 through 925 removed outlier: 4.299A pdb=" N ASP D 924 " --> pdb=" O THR D 921 " (cutoff:3.500A) Processing helix chain 'D' and resid 963 through 967 removed outlier: 3.530A pdb=" N LEU D 967 " --> pdb=" O PRO D 964 " (cutoff:3.500A) Processing helix chain 'D' and resid 1086 through 1094 removed outlier: 3.595A pdb=" N ALA D1089 " --> pdb=" O HIS D1086 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA D1090 " --> pdb=" O GLY D1087 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ILE D1091 " --> pdb=" O ALA D1088 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N LEU D1094 " --> pdb=" O ILE D1091 " (cutoff:3.500A) Processing helix chain 'D' and resid 1200 through 1207 Processing helix chain 'D' and resid 1239 through 1243 removed outlier: 3.916A pdb=" N MET D1242 " --> pdb=" O ASN D1239 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ASP D1243 " --> pdb=" O SER D1240 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1239 through 1243' Processing helix chain 'D' and resid 1381 through 1385 removed outlier: 3.928A pdb=" N GLY D1384 " --> pdb=" O ARG D1381 " (cutoff:3.500A) Processing helix chain 'D' and resid 1396 through 1400 removed outlier: 4.164A pdb=" N ARG D1399 " --> pdb=" O ARG D1396 " (cutoff:3.500A) Processing helix chain 'D' and resid 1452 through 1462 removed outlier: 3.694A pdb=" N LYS D1456 " --> pdb=" O ASP D1452 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLY D1462 " --> pdb=" O TYR D1458 " (cutoff:3.500A) Processing helix chain 'D' and resid 1470 through 1474 Processing helix chain 'D' and resid 1484 through 1495 removed outlier: 3.514A pdb=" N VAL D1488 " --> pdb=" O LEU D1485 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N ALA D1489 " --> pdb=" O GLU D1486 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N GLU D1490 " --> pdb=" O ASN D1487 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLU D1492 " --> pdb=" O ALA D1489 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N GLY D1493 " --> pdb=" O GLU D1490 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N THR D1495 " --> pdb=" O GLU D1492 " (cutoff:3.500A) Processing helix chain 'D' and resid 1508 through 1512 removed outlier: 3.885A pdb=" N ASN D1511 " --> pdb=" O SER D1508 " (cutoff:3.500A) Processing helix chain 'D' and resid 1590 through 1593 removed outlier: 3.750A pdb=" N TYR D1593 " --> pdb=" O ARG D1590 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1590 through 1593' Processing helix chain 'D' and resid 1641 through 1647 Processing helix chain 'D' and resid 1672 through 1684 Processing helix chain 'D' and resid 1708 through 1710 No H-bonds generated for 'chain 'D' and resid 1708 through 1710' Processing helix chain 'D' and resid 1722 through 1734 removed outlier: 4.046A pdb=" N THR D1734 " --> pdb=" O HIS D1730 " (cutoff:3.500A) Processing helix chain 'D' and resid 1770 through 1772 No H-bonds generated for 'chain 'D' and resid 1770 through 1772' Processing helix chain 'D' and resid 1824 through 1828 removed outlier: 3.645A pdb=" N LYS D1828 " --> pdb=" O GLU D1825 " (cutoff:3.500A) Processing helix chain 'D' and resid 1975 through 1981 Processing sheet with id=AA1, first strand: chain 'D' and resid 240 through 250 removed outlier: 6.921A pdb=" N PHE D 241 " --> pdb=" O GLU D 207 " (cutoff:3.500A) removed outlier: 7.361A pdb=" N GLU D 207 " --> pdb=" O PHE D 241 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLU D 243 " --> pdb=" O VAL D 205 " (cutoff:3.500A) removed outlier: 5.537A pdb=" N VAL D 205 " --> pdb=" O SER D 319 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N SER D 319 " --> pdb=" O VAL D 205 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLU D 207 " --> pdb=" O LYS D 317 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLY D 314 " --> pdb=" O LEU D 302 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 227 through 230 removed outlier: 6.621A pdb=" N ILE D 261 " --> pdb=" O LYS D 281 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N LYS D 281 " --> pdb=" O ILE D 261 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N ILE D 263 " --> pdb=" O GLU D 279 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N GLU D 279 " --> pdb=" O ILE D 263 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N VAL D 265 " --> pdb=" O MET D 277 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 357 through 368 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 423 through 430 current: chain 'D' and resid 532 through 541 Processing sheet with id=AA4, first strand: chain 'D' and resid 406 through 409 removed outlier: 6.724A pdb=" N ILE D 438 " --> pdb=" O TYR D 458 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N TYR D 458 " --> pdb=" O ILE D 438 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N LEU D 440 " --> pdb=" O THR D 456 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N THR D 456 " --> pdb=" O LEU D 440 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ILE D 442 " --> pdb=" O VAL D 454 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 572 through 584 removed outlier: 8.546A pdb=" N SER D 582 " --> pdb=" O THR D 637 " (cutoff:3.500A) removed outlier: 12.151A pdb=" N THR D 637 " --> pdb=" O SER D 582 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 637 through 647 current: chain 'D' and resid 833 through 842 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 833 through 842 current: chain 'D' and resid 873 through 875 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 873 through 875 current: chain 'D' and resid 1071 through 1082 Processing sheet with id=AA6, first strand: chain 'D' and resid 593 through 599 removed outlier: 3.624A pdb=" N ALA D 787 " --> pdb=" O MET D 779 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N ARG D 781 " --> pdb=" O ARG D 785 " (cutoff:3.500A) removed outlier: 5.638A pdb=" N ARG D 785 " --> pdb=" O ARG D 781 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 623 through 624 Processing sheet with id=AA8, first strand: chain 'D' and resid 930 through 939 removed outlier: 11.841A pdb=" N GLU D 933 " --> pdb=" O TYR D 953 " (cutoff:3.500A) removed outlier: 10.375A pdb=" N TYR D 953 " --> pdb=" O GLU D 933 " (cutoff:3.500A) removed outlier: 8.774A pdb=" N TYR D 935 " --> pdb=" O ASP D 951 " (cutoff:3.500A) removed outlier: 9.390A pdb=" N ASP D 951 " --> pdb=" O TYR D 935 " (cutoff:3.500A) removed outlier: 7.503A pdb=" N ASN D 937 " --> pdb=" O ALA D 949 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ALA D 949 " --> pdb=" O ASN D 937 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 947 through 954 current: chain 'D' and resid 1018 through 1028 Processing sheet with id=AA9, first strand: chain 'D' and resid 1137 through 1149 removed outlier: 6.813A pdb=" N TYR D1137 " --> pdb=" O GLU D1196 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N GLU D1196 " --> pdb=" O TYR D1137 " (cutoff:3.500A) removed outlier: 5.814A pdb=" N TYR D1139 " --> pdb=" O GLU D1194 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 1188 through 1197 current: chain 'D' and resid 1258 through 1271 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 1258 through 1271 current: chain 'D' and resid 1290 through 1292 Processing sheet with id=AB1, first strand: chain 'D' and resid 1171 through 1174 removed outlier: 3.535A pdb=" N GLY D1228 " --> pdb=" O LEU D1215 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N ASP D1217 " --> pdb=" O PHE D1226 " (cutoff:3.500A) removed outlier: 5.928A pdb=" N PHE D1226 " --> pdb=" O ASP D1217 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 1356 through 1364 Processing sheet with id=AB3, first strand: chain 'D' and resid 1312 through 1314 removed outlier: 3.618A pdb=" N GLY D1312 " --> pdb=" O LYS D1521 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N VAL D1516 " --> pdb=" O ARG D1505 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N ARG D1505 " --> pdb=" O VAL D1516 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLY D1518 " --> pdb=" O LEU D1503 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLY D1522 " --> pdb=" O ASP D1499 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 1336 through 1339 removed outlier: 3.576A pdb=" N GLY D1390 " --> pdb=" O VAL D1377 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ASP D1379 " --> pdb=" O VAL D1388 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N VAL D1388 " --> pdb=" O ASP D1379 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 1479 through 1481 removed outlier: 6.984A pdb=" N LYS D1479 " --> pdb=" O VAL D1742 " (cutoff:3.500A) removed outlier: 7.503A pdb=" N THR D1744 " --> pdb=" O LYS D1479 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N TYR D1481 " --> pdb=" O THR D1744 " (cutoff:3.500A) removed outlier: 8.628A pdb=" N THR D1746 " --> pdb=" O TYR D1481 " (cutoff:3.500A) removed outlier: 8.308A pdb=" N HIS D1741 " --> pdb=" O VAL D1764 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N VAL D1764 " --> pdb=" O HIS D1741 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N LYS D1759 " --> pdb=" O GLY D1562 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N GLY D1562 " --> pdb=" O LYS D1759 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N GLN D1761 " --> pdb=" O VAL D1560 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 1585 through 1588 removed outlier: 6.679A pdb=" N LEU D1618 " --> pdb=" O ILE D1638 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N ILE D1638 " --> pdb=" O LEU D1618 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ILE D1620 " --> pdb=" O GLU D1636 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N GLU D1636 " --> pdb=" O ILE D1620 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N VAL D1622 " --> pdb=" O VAL D1634 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLU D1632 " --> pdb=" O ASP D1624 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 1690 through 1691 removed outlier: 3.639A pdb=" N ILE D1690 " --> pdb=" O ARG D1699 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ILE D1698 " --> pdb=" O TYR D1705 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N TYR D1705 " --> pdb=" O ILE D1698 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 1875 through 1879 removed outlier: 3.578A pdb=" N THR D1875 " --> pdb=" O LYS D1865 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LYS D1865 " --> pdb=" O THR D1875 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LEU D1860 " --> pdb=" O LEU D1855 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ASP D1853 " --> pdb=" O ILE D1862 " (cutoff:3.500A) removed outlier: 8.927A pdb=" N ALA D1864 " --> pdb=" O PRO D1851 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N GLY D1842 " --> pdb=" O LYS D1798 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N LYS D1798 " --> pdb=" O GLY D1842 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N PHE D1844 " --> pdb=" O ASN D1796 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N ASN D1796 " --> pdb=" O PHE D1844 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N TRP D1846 " --> pdb=" O ILE D1794 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ILE D1793 " --> pdb=" O THR D1969 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N THR D1969 " --> pdb=" O ILE D1793 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N GLU D1967 " --> pdb=" O TRP D1795 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N THR D1797 " --> pdb=" O LYS D1965 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N LYS D1965 " --> pdb=" O THR D1797 " (cutoff:3.500A) removed outlier: 5.010A pdb=" N ARG D1960 " --> pdb=" O LYS D1956 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N LYS D1956 " --> pdb=" O ARG D1960 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N MET D1962 " --> pdb=" O ALA D1954 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N ALA D1954 " --> pdb=" O MET D1962 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N MET D1946 " --> pdb=" O LEU D1970 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 1829 through 1830 removed outlier: 5.746A pdb=" N ASP D1889 " --> pdb=" O TYR D1898 " (cutoff:3.500A) removed outlier: 5.672A pdb=" N TYR D1898 " --> pdb=" O ASP D1889 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 1909 through 1910 364 hydrogen bonds defined for protein. 945 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: 2.92 Time building geometry restraints manager: 1.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 2678 1.33 - 1.45: 3539 1.45 - 1.58: 7842 1.58 - 1.70: 5 1.70 - 1.83: 93 Bond restraints: 14157 Sorted by residual: bond pdb=" C ALA D1287 " pdb=" N PRO D1288 " ideal model delta sigma weight residual 1.333 1.363 -0.031 1.17e-02 7.31e+03 6.86e+00 bond pdb=" CB PHE D 286 " pdb=" CG PHE D 286 " ideal model delta sigma weight residual 1.502 1.560 -0.058 2.30e-02 1.89e+03 6.36e+00 bond pdb=" C TYR D 820 " pdb=" N PRO D 821 " ideal model delta sigma weight residual 1.337 1.364 -0.027 1.11e-02 8.12e+03 5.99e+00 bond pdb=" C3 PSF D2010 " pdb=" O11 PSF D2010 " ideal model delta sigma weight residual 1.429 1.475 -0.046 2.00e-02 2.50e+03 5.29e+00 bond pdb=" CB GLU D1463 " pdb=" CG GLU D1463 " ideal model delta sigma weight residual 1.520 1.582 -0.062 3.00e-02 1.11e+03 4.34e+00 ... (remaining 14152 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.56: 18965 3.56 - 7.12: 165 7.12 - 10.67: 38 10.67 - 14.23: 10 14.23 - 17.79: 3 Bond angle restraints: 19181 Sorted by residual: angle pdb=" CB MET D 316 " pdb=" CG MET D 316 " pdb=" SD MET D 316 " ideal model delta sigma weight residual 112.70 130.49 -17.79 3.00e+00 1.11e-01 3.52e+01 angle pdb=" CA GLU D1510 " pdb=" CB GLU D1510 " pdb=" CG GLU D1510 " ideal model delta sigma weight residual 114.10 125.68 -11.58 2.00e+00 2.50e-01 3.35e+01 angle pdb=" CB MET D 191 " pdb=" CG MET D 191 " pdb=" SD MET D 191 " ideal model delta sigma weight residual 112.70 129.03 -16.33 3.00e+00 1.11e-01 2.96e+01 angle pdb=" CA GLU D1825 " pdb=" CB GLU D1825 " pdb=" CG GLU D1825 " ideal model delta sigma weight residual 114.10 124.10 -10.00 2.00e+00 2.50e-01 2.50e+01 angle pdb=" C GLU D 546 " pdb=" N LYS D 547 " pdb=" CA LYS D 547 " ideal model delta sigma weight residual 121.54 130.91 -9.37 1.91e+00 2.74e-01 2.41e+01 ... (remaining 19176 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.23: 8289 33.23 - 66.47: 266 66.47 - 99.70: 23 99.70 - 132.93: 1 132.93 - 166.17: 1 Dihedral angle restraints: 8580 sinusoidal: 3633 harmonic: 4947 Sorted by residual: dihedral pdb=" CA ASP D1922 " pdb=" C ASP D1922 " pdb=" N MET D1923 " pdb=" CA MET D1923 " ideal model delta harmonic sigma weight residual 180.00 153.53 26.47 0 5.00e+00 4.00e-02 2.80e+01 dihedral pdb=" CB PSF D2010 " pdb=" O1 PSF D2010 " pdb=" P PSF D2010 " pdb=" O3 PSF D2010 " ideal model delta sinusoidal sigma weight residual -29.12 137.05 -166.17 1 3.00e+01 1.11e-03 2.10e+01 dihedral pdb=" CA LYS D 195 " pdb=" C LYS D 195 " pdb=" N PRO D 196 " pdb=" CA PRO D 196 " ideal model delta harmonic sigma weight residual 180.00 157.56 22.44 0 5.00e+00 4.00e-02 2.01e+01 ... (remaining 8577 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 1739 0.075 - 0.150: 283 0.150 - 0.225: 18 0.225 - 0.299: 4 0.299 - 0.374: 2 Chirality restraints: 2046 Sorted by residual: chirality pdb=" C3 PSF D2010 " pdb=" C2 PSF D2010 " pdb=" C4 PSF D2010 " pdb=" O11 PSF D2010 " both_signs ideal model delta sigma weight residual False -2.53 -2.15 -0.37 2.00e-01 2.50e+01 3.50e+00 chirality pdb=" CB ILE D1128 " pdb=" CA ILE D1128 " pdb=" CG1 ILE D1128 " pdb=" CG2 ILE D1128 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.30 2.00e-01 2.50e+01 2.26e+00 chirality pdb=" CA ASP D 335 " pdb=" N ASP D 335 " pdb=" C ASP D 335 " pdb=" CB ASP D 335 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.91e+00 ... (remaining 2043 not shown) Planarity restraints: 2483 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE D1901 " -0.018 2.00e-02 2.50e+03 2.60e-02 1.19e+01 pdb=" CG PHE D1901 " 0.059 2.00e-02 2.50e+03 pdb=" CD1 PHE D1901 " -0.022 2.00e-02 2.50e+03 pdb=" CD2 PHE D1901 " -0.022 2.00e-02 2.50e+03 pdb=" CE1 PHE D1901 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE D1901 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE D1901 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU D1917 " -0.016 2.00e-02 2.50e+03 3.16e-02 1.00e+01 pdb=" CD GLU D1917 " 0.055 2.00e-02 2.50e+03 pdb=" OE1 GLU D1917 " -0.020 2.00e-02 2.50e+03 pdb=" OE2 GLU D1917 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP D1708 " 0.012 2.00e-02 2.50e+03 2.52e-02 6.36e+00 pdb=" CG ASP D1708 " -0.044 2.00e-02 2.50e+03 pdb=" OD1 ASP D1708 " 0.016 2.00e-02 2.50e+03 pdb=" OD2 ASP D1708 " 0.015 2.00e-02 2.50e+03 ... (remaining 2480 not shown) Histogram of nonbonded interaction distances: 2.37 - 2.88: 4543 2.88 - 3.38: 12136 3.38 - 3.89: 23450 3.89 - 4.39: 25809 4.39 - 4.90: 44757 Nonbonded interactions: 110695 Sorted by model distance: nonbonded pdb=" OD1 ASP D 452 " pdb="CA CA D2008 " model vdw 2.373 2.510 nonbonded pdb=" O ASN D1218 " pdb="CA CA D2004 " model vdw 2.377 2.510 nonbonded pdb=" O MET D 373 " pdb="CA CA D2003 " model vdw 2.378 2.510 nonbonded pdb=" OG1 THR D 449 " pdb="CA CA D2008 " model vdw 2.379 2.510 nonbonded pdb=" OD1 ASP D 446 " pdb="CA CA D2003 " model vdw 2.379 2.510 ... (remaining 110690 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.76 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: 3.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.320 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 13.920 Find NCS groups from input model: 0.060 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: 0.000 Load rotamer database and sin/cos tables:6.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 14157 Z= 0.220 Angle : 0.969 17.791 19181 Z= 0.510 Chirality : 0.054 0.374 2046 Planarity : 0.007 0.079 2483 Dihedral : 15.675 166.168 5388 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 1.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 1.52 % Allowed : 16.94 % Favored : 81.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % 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 aren not related in a simple way. whole: -1.38 (0.19), residues: 1683 helix: -1.92 (0.28), residues: 223 sheet: -0.33 (0.22), residues: 508 loop : -0.94 (0.19), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG D 264 TYR 0.034 0.002 TYR D 458 PHE 0.059 0.002 PHE D1901 TRP 0.032 0.001 TRP D1888 HIS 0.003 0.001 HIS D1165 Details of bonding type rmsd covalent geometry : bond 0.00452 (14157) covalent geometry : angle 0.96869 (19181) hydrogen bonds : bond 0.21481 ( 364) hydrogen bonds : angle 8.90520 ( 945) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3366 Ramachandran restraints generated. 1683 Oldfield, 0 Emsley, 1683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3366 Ramachandran restraints generated. 1683 Oldfield, 0 Emsley, 1683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 121 time to evaluate : 0.372 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 204 ARG cc_start: 0.8303 (ttm110) cc_final: 0.8034 (ttt-90) REVERT: D 377 PHE cc_start: 0.7584 (p90) cc_final: 0.7296 (p90) REVERT: D 437 LYS cc_start: 0.8418 (tttt) cc_final: 0.8215 (ttmt) REVERT: D 518 ASP cc_start: 0.8236 (t0) cc_final: 0.7745 (t0) REVERT: D 521 ASP cc_start: 0.8748 (m-30) cc_final: 0.8482 (m-30) REVERT: D 522 GLU cc_start: 0.8818 (mm-30) cc_final: 0.8378 (tm-30) REVERT: D 751 LEU cc_start: 0.8229 (tt) cc_final: 0.7860 (pp) REVERT: D 762 MET cc_start: 0.8003 (mmm) cc_final: 0.7326 (mmm) REVERT: D 1086 HIS cc_start: 0.8497 (m90) cc_final: 0.8170 (m90) REVERT: D 1367 GLU cc_start: 0.8505 (mp0) cc_final: 0.8177 (mm-30) REVERT: D 1630 ARG cc_start: 0.7380 (ptt90) cc_final: 0.7178 (pmt-80) REVERT: D 1636 GLU cc_start: 0.8466 (tt0) cc_final: 0.8106 (tp30) REVERT: D 1754 ASN cc_start: 0.8671 (t0) cc_final: 0.8148 (t0) REVERT: D 1868 HIS cc_start: 0.6733 (OUTLIER) cc_final: 0.4525 (t-170) REVERT: D 1869 PHE cc_start: 0.8208 (p90) cc_final: 0.7876 (p90) REVERT: D 1903 GLU cc_start: 0.8609 (tt0) cc_final: 0.8361 (tt0) REVERT: D 1962 MET cc_start: 0.7919 (tpt) cc_final: 0.7228 (tpt) outliers start: 23 outliers final: 14 residues processed: 137 average time/residue: 0.5878 time to fit residues: 88.9023 Evaluate side-chains 125 residues out of total 1511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 110 time to evaluate : 0.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 210 GLN Chi-restraints excluded: chain D residue 263 ILE Chi-restraints excluded: chain D residue 296 MET Chi-restraints excluded: chain D residue 301 LEU Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 565 VAL Chi-restraints excluded: chain D residue 738 VAL Chi-restraints excluded: chain D residue 754 ILE Chi-restraints excluded: chain D residue 1304 THR Chi-restraints excluded: chain D residue 1655 ILE Chi-restraints excluded: chain D residue 1792 VAL Chi-restraints excluded: chain D residue 1868 HIS Chi-restraints excluded: chain D residue 1875 THR Chi-restraints excluded: chain D residue 1921 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 30.0000 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 0.0010 chunk 77 optimal weight: 30.0000 chunk 122 optimal weight: 7.9990 chunk 91 optimal weight: 0.9990 chunk 149 optimal weight: 5.9990 overall best weight: 2.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 200 GLN D 293 HIS D 601 ASN D 618 GLN D1568 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.132946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.092056 restraints weight = 29086.750| |-----------------------------------------------------------------------------| r_work (start): 0.3349 rms_B_bonded: 3.86 r_work: 0.3197 rms_B_bonded: 4.48 restraints_weight: 0.5000 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3206 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3206 r_free = 0.3206 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.76 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3206 r_free = 0.3206 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.76 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3206 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.1637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 14157 Z= 0.266 Angle : 0.622 9.015 19181 Z= 0.316 Chirality : 0.046 0.178 2046 Planarity : 0.004 0.039 2483 Dihedral : 8.377 143.792 1943 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 3.64 % Allowed : 15.49 % Favored : 80.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % 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 aren not related in a simple way. whole: -0.58 (0.20), residues: 1683 helix: -0.48 (0.32), residues: 227 sheet: -0.09 (0.22), residues: 523 loop : -0.45 (0.21), residues: 933 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 264 TYR 0.023 0.002 TYR D1558 PHE 0.023 0.002 PHE D 245 TRP 0.018 0.001 TRP D1763 HIS 0.005 0.001 HIS D1464 Details of bonding type rmsd covalent geometry : bond 0.00614 (14157) covalent geometry : angle 0.62236 (19181) hydrogen bonds : bond 0.03555 ( 364) hydrogen bonds : angle 6.31876 ( 945) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3366 Ramachandran restraints generated. 1683 Oldfield, 0 Emsley, 1683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3366 Ramachandran restraints generated. 1683 Oldfield, 0 Emsley, 1683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 106 time to evaluate : 0.587 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 204 ARG cc_start: 0.8048 (ttm110) cc_final: 0.7609 (mtp85) REVERT: D 232 ARG cc_start: 0.8907 (pmm-80) cc_final: 0.8402 (pmm-80) REVERT: D 373 MET cc_start: 0.8316 (mtp) cc_final: 0.7852 (mtp) REVERT: D 437 LYS cc_start: 0.8446 (tttt) cc_final: 0.8228 (ttmt) REVERT: D 518 ASP cc_start: 0.8309 (t0) cc_final: 0.7708 (t0) REVERT: D 522 GLU cc_start: 0.8901 (mm-30) cc_final: 0.8017 (tm-30) REVERT: D 527 LYS cc_start: 0.9134 (OUTLIER) cc_final: 0.8408 (mmmm) REVERT: D 751 LEU cc_start: 0.7851 (tt) cc_final: 0.7530 (pp) REVERT: D 766 GLU cc_start: 0.8590 (mm-30) cc_final: 0.8356 (mm-30) REVERT: D 1086 HIS cc_start: 0.8739 (m90) cc_final: 0.8208 (m90) REVERT: D 1290 LEU cc_start: 0.8663 (OUTLIER) cc_final: 0.8405 (tp) REVERT: D 1367 GLU cc_start: 0.8919 (mp0) cc_final: 0.8198 (mm-30) REVERT: D 1599 ASN cc_start: 0.8270 (m110) cc_final: 0.7977 (m-40) REVERT: D 1605 MET cc_start: 0.8270 (OUTLIER) cc_final: 0.7962 (tmm) REVERT: D 1630 ARG cc_start: 0.7480 (OUTLIER) cc_final: 0.7153 (pmt-80) REVERT: D 1636 GLU cc_start: 0.8803 (tt0) cc_final: 0.8272 (tt0) REVERT: D 1698 ILE cc_start: 0.8390 (OUTLIER) cc_final: 0.8094 (mm) REVERT: D 1754 ASN cc_start: 0.8698 (t0) cc_final: 0.8183 (t0) REVERT: D 1815 ILE cc_start: 0.8500 (mt) cc_final: 0.7972 (pt) REVERT: D 1903 GLU cc_start: 0.8933 (tt0) cc_final: 0.8593 (tt0) REVERT: D 1923 MET cc_start: 0.8261 (OUTLIER) cc_final: 0.6735 (pmt) REVERT: D 1962 MET cc_start: 0.7927 (tpt) cc_final: 0.7581 (tpt) outliers start: 55 outliers final: 22 residues processed: 144 average time/residue: 0.4855 time to fit residues: 78.1326 Evaluate side-chains 127 residues out of total 1511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 99 time to evaluate : 0.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 263 ILE Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 396 ASP Chi-restraints excluded: chain D residue 424 VAL Chi-restraints excluded: chain D residue 527 LYS Chi-restraints excluded: chain D residue 563 LEU Chi-restraints excluded: chain D residue 676 SER Chi-restraints excluded: chain D residue 687 LEU Chi-restraints excluded: chain D residue 756 ASP Chi-restraints excluded: chain D residue 1235 VAL Chi-restraints excluded: chain D residue 1290 LEU Chi-restraints excluded: chain D residue 1304 THR Chi-restraints excluded: chain D residue 1581 THR Chi-restraints excluded: chain D residue 1605 MET Chi-restraints excluded: chain D residue 1630 ARG Chi-restraints excluded: chain D residue 1655 ILE Chi-restraints excluded: chain D residue 1698 ILE Chi-restraints excluded: chain D residue 1727 LEU Chi-restraints excluded: chain D residue 1750 THR Chi-restraints excluded: chain D residue 1792 VAL Chi-restraints excluded: chain D residue 1855 LEU Chi-restraints excluded: chain D residue 1868 HIS Chi-restraints excluded: chain D residue 1875 THR Chi-restraints excluded: chain D residue 1902 LEU Chi-restraints excluded: chain D residue 1922 ASP Chi-restraints excluded: chain D residue 1923 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 55 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 chunk 96 optimal weight: 0.8980 chunk 41 optimal weight: 0.7980 chunk 54 optimal weight: 0.0870 chunk 28 optimal weight: 0.8980 chunk 125 optimal weight: 0.9980 chunk 61 optimal weight: 0.7980 chunk 48 optimal weight: 2.9990 chunk 100 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 overall best weight: 0.6958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 210 GLN D 293 HIS D 601 ASN D 618 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.135194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.094824 restraints weight = 29149.191| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 3.83 r_work: 0.3253 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3244 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3244 r_free = 0.3244 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.76 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3244 r_free = 0.3244 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3244 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.1585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 14157 Z= 0.108 Angle : 0.526 6.705 19181 Z= 0.262 Chirality : 0.044 0.171 2046 Planarity : 0.003 0.034 2483 Dihedral : 7.486 139.028 1929 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 3.51 % Allowed : 16.41 % Favored : 80.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % 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 aren not related in a simple way. whole: -0.18 (0.21), residues: 1683 helix: 0.30 (0.34), residues: 229 sheet: 0.06 (0.22), residues: 524 loop : -0.24 (0.21), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 264 TYR 0.015 0.001 TYR D1558 PHE 0.026 0.001 PHE D1751 TRP 0.022 0.001 TRP D1888 HIS 0.003 0.000 HIS D1464 Details of bonding type rmsd covalent geometry : bond 0.00244 (14157) covalent geometry : angle 0.52644 (19181) hydrogen bonds : bond 0.02974 ( 364) hydrogen bonds : angle 5.78761 ( 945) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3366 Ramachandran restraints generated. 1683 Oldfield, 0 Emsley, 1683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3366 Ramachandran restraints generated. 1683 Oldfield, 0 Emsley, 1683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 105 time to evaluate : 0.472 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 191 MET cc_start: 0.5913 (ppp) cc_final: 0.5474 (ppp) REVERT: D 204 ARG cc_start: 0.8020 (ttm110) cc_final: 0.7456 (mtp85) REVERT: D 243 GLU cc_start: 0.7608 (mt-10) cc_final: 0.7014 (pt0) REVERT: D 377 PHE cc_start: 0.8746 (t80) cc_final: 0.8477 (p90) REVERT: D 437 LYS cc_start: 0.8311 (tttt) cc_final: 0.8058 (tttp) REVERT: D 518 ASP cc_start: 0.8311 (t0) cc_final: 0.7742 (t0) REVERT: D 522 GLU cc_start: 0.8904 (mm-30) cc_final: 0.7971 (tm-30) REVERT: D 751 LEU cc_start: 0.7850 (tt) cc_final: 0.7526 (pp) REVERT: D 1014 MET cc_start: 0.2311 (pmm) cc_final: 0.1745 (tpt) REVERT: D 1086 HIS cc_start: 0.8689 (m90) cc_final: 0.8201 (m90) REVERT: D 1367 GLU cc_start: 0.8896 (mp0) cc_final: 0.8235 (mm-30) REVERT: D 1599 ASN cc_start: 0.8083 (m110) cc_final: 0.7790 (m-40) REVERT: D 1630 ARG cc_start: 0.7424 (OUTLIER) cc_final: 0.7056 (pmt-80) REVERT: D 1636 GLU cc_start: 0.8666 (tt0) cc_final: 0.8166 (tt0) REVERT: D 1698 ILE cc_start: 0.8446 (OUTLIER) cc_final: 0.8132 (mm) REVERT: D 1754 ASN cc_start: 0.8613 (t0) cc_final: 0.7935 (t0) REVERT: D 1815 ILE cc_start: 0.8466 (mt) cc_final: 0.8064 (tt) REVERT: D 1903 GLU cc_start: 0.8899 (tt0) cc_final: 0.8543 (tt0) REVERT: D 1923 MET cc_start: 0.8459 (OUTLIER) cc_final: 0.6756 (pmt) outliers start: 53 outliers final: 16 residues processed: 143 average time/residue: 0.5080 time to fit residues: 81.2346 Evaluate side-chains 121 residues out of total 1511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 102 time to evaluate : 0.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 252 THR Chi-restraints excluded: chain D residue 263 ILE Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 563 LEU Chi-restraints excluded: chain D residue 676 SER Chi-restraints excluded: chain D residue 738 VAL Chi-restraints excluded: chain D residue 756 ASP Chi-restraints excluded: chain D residue 1158 SER Chi-restraints excluded: chain D residue 1304 THR Chi-restraints excluded: chain D residue 1630 ARG Chi-restraints excluded: chain D residue 1698 ILE Chi-restraints excluded: chain D residue 1750 THR Chi-restraints excluded: chain D residue 1792 VAL Chi-restraints excluded: chain D residue 1855 LEU Chi-restraints excluded: chain D residue 1868 HIS Chi-restraints excluded: chain D residue 1902 LEU Chi-restraints excluded: chain D residue 1919 CYS Chi-restraints excluded: chain D residue 1923 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 151 optimal weight: 6.9990 chunk 87 optimal weight: 0.0020 chunk 116 optimal weight: 0.9980 chunk 121 optimal weight: 4.9990 chunk 67 optimal weight: 40.0000 chunk 31 optimal weight: 6.9990 chunk 112 optimal weight: 0.9990 chunk 90 optimal weight: 1.9990 chunk 140 optimal weight: 6.9990 chunk 131 optimal weight: 1.9990 chunk 136 optimal weight: 4.9990 overall best weight: 1.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 200 GLN D 210 GLN D 293 HIS D 601 ASN D 618 GLN ** D1834 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.134097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.094052 restraints weight = 28974.352| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 3.78 r_work: 0.3236 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3227 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3227 r_free = 0.3227 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3227 r_free = 0.3227 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3227 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.1815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14157 Z= 0.142 Angle : 0.519 6.641 19181 Z= 0.261 Chirality : 0.044 0.193 2046 Planarity : 0.003 0.033 2483 Dihedral : 7.328 147.680 1926 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 3.51 % Allowed : 16.81 % Favored : 79.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % 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 aren not related in a simple way. whole: -0.03 (0.21), residues: 1683 helix: 0.48 (0.34), residues: 235 sheet: 0.16 (0.22), residues: 523 loop : -0.16 (0.21), residues: 925 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 264 TYR 0.012 0.001 TYR D1470 PHE 0.007 0.001 PHE D1852 TRP 0.023 0.001 TRP D1888 HIS 0.007 0.001 HIS D1464 Details of bonding type rmsd covalent geometry : bond 0.00325 (14157) covalent geometry : angle 0.51868 (19181) hydrogen bonds : bond 0.02823 ( 364) hydrogen bonds : angle 5.56103 ( 945) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3366 Ramachandran restraints generated. 1683 Oldfield, 0 Emsley, 1683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3366 Ramachandran restraints generated. 1683 Oldfield, 0 Emsley, 1683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 105 time to evaluate : 0.611 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 191 MET cc_start: 0.6012 (ppp) cc_final: 0.5462 (ppp) REVERT: D 377 PHE cc_start: 0.8711 (t80) cc_final: 0.8401 (p90) REVERT: D 437 LYS cc_start: 0.8335 (tttt) cc_final: 0.8079 (ttmt) REVERT: D 518 ASP cc_start: 0.8274 (t0) cc_final: 0.7637 (t0) REVERT: D 522 GLU cc_start: 0.8895 (mm-30) cc_final: 0.7940 (tm-30) REVERT: D 751 LEU cc_start: 0.7865 (OUTLIER) cc_final: 0.7523 (pp) REVERT: D 766 GLU cc_start: 0.8568 (mm-30) cc_final: 0.8335 (mm-30) REVERT: D 1014 MET cc_start: 0.2305 (pmm) cc_final: 0.1774 (tpt) REVERT: D 1086 HIS cc_start: 0.8676 (m90) cc_final: 0.8235 (m90) REVERT: D 1158 SER cc_start: 0.9294 (OUTLIER) cc_final: 0.9068 (p) REVERT: D 1367 GLU cc_start: 0.8930 (mp0) cc_final: 0.8215 (mm-30) REVERT: D 1398 ASP cc_start: 0.9181 (m-30) cc_final: 0.8914 (m-30) REVERT: D 1630 ARG cc_start: 0.7423 (OUTLIER) cc_final: 0.7063 (pmt-80) REVERT: D 1636 GLU cc_start: 0.8692 (tt0) cc_final: 0.8221 (tt0) REVERT: D 1698 ILE cc_start: 0.8531 (OUTLIER) cc_final: 0.8216 (mm) REVERT: D 1754 ASN cc_start: 0.8615 (t0) cc_final: 0.7942 (t0) REVERT: D 1815 ILE cc_start: 0.8518 (mt) cc_final: 0.8110 (tt) REVERT: D 1903 GLU cc_start: 0.8920 (tt0) cc_final: 0.8591 (tt0) outliers start: 53 outliers final: 24 residues processed: 144 average time/residue: 0.5246 time to fit residues: 84.6601 Evaluate side-chains 130 residues out of total 1511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 102 time to evaluate : 0.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 210 GLN Chi-restraints excluded: chain D residue 252 THR Chi-restraints excluded: chain D residue 263 ILE Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 396 ASP Chi-restraints excluded: chain D residue 563 LEU Chi-restraints excluded: chain D residue 565 VAL Chi-restraints excluded: chain D residue 676 SER Chi-restraints excluded: chain D residue 708 LEU Chi-restraints excluded: chain D residue 738 VAL Chi-restraints excluded: chain D residue 751 LEU Chi-restraints excluded: chain D residue 754 ILE Chi-restraints excluded: chain D residue 756 ASP Chi-restraints excluded: chain D residue 816 ILE Chi-restraints excluded: chain D residue 1158 SER Chi-restraints excluded: chain D residue 1292 MET Chi-restraints excluded: chain D residue 1304 THR Chi-restraints excluded: chain D residue 1581 THR Chi-restraints excluded: chain D residue 1630 ARG Chi-restraints excluded: chain D residue 1698 ILE Chi-restraints excluded: chain D residue 1727 LEU Chi-restraints excluded: chain D residue 1750 THR Chi-restraints excluded: chain D residue 1792 VAL Chi-restraints excluded: chain D residue 1855 LEU Chi-restraints excluded: chain D residue 1868 HIS Chi-restraints excluded: chain D residue 1902 LEU Chi-restraints excluded: chain D residue 1919 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 21 optimal weight: 7.9990 chunk 73 optimal weight: 20.0000 chunk 69 optimal weight: 1.9990 chunk 6 optimal weight: 0.7980 chunk 30 optimal weight: 0.8980 chunk 133 optimal weight: 4.9990 chunk 4 optimal weight: 0.6980 chunk 97 optimal weight: 4.9990 chunk 47 optimal weight: 0.9980 chunk 54 optimal weight: 5.9990 chunk 151 optimal weight: 6.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 293 HIS D 601 ASN D 618 GLN ** D1834 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.134181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.093504 restraints weight = 29307.666| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 3.84 r_work: 0.3233 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3225 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3225 r_free = 0.3225 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3225 r_free = 0.3225 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3225 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.1932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14157 Z= 0.133 Angle : 0.517 7.168 19181 Z= 0.259 Chirality : 0.044 0.289 2046 Planarity : 0.003 0.032 2483 Dihedral : 7.240 153.366 1926 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 3.38 % Allowed : 17.01 % Favored : 79.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % 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 aren not related in a simple way. whole: 0.02 (0.21), residues: 1683 helix: 0.59 (0.34), residues: 237 sheet: 0.16 (0.22), residues: 530 loop : -0.13 (0.22), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 264 TYR 0.017 0.001 TYR D1558 PHE 0.026 0.001 PHE D1751 TRP 0.025 0.001 TRP D1888 HIS 0.005 0.001 HIS D1464 Details of bonding type rmsd covalent geometry : bond 0.00305 (14157) covalent geometry : angle 0.51740 (19181) hydrogen bonds : bond 0.02743 ( 364) hydrogen bonds : angle 5.43457 ( 945) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3366 Ramachandran restraints generated. 1683 Oldfield, 0 Emsley, 1683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3366 Ramachandran restraints generated. 1683 Oldfield, 0 Emsley, 1683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 104 time to evaluate : 0.687 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 191 MET cc_start: 0.6030 (ppp) cc_final: 0.5450 (ppp) REVERT: D 243 GLU cc_start: 0.7329 (mt-10) cc_final: 0.6839 (pt0) REVERT: D 296 MET cc_start: 0.8331 (mmp) cc_final: 0.8035 (tpp) REVERT: D 373 MET cc_start: 0.8309 (mtp) cc_final: 0.7958 (mtp) REVERT: D 377 PHE cc_start: 0.8739 (t80) cc_final: 0.8396 (p90) REVERT: D 407 LYS cc_start: 0.9160 (mttm) cc_final: 0.8581 (tttm) REVERT: D 437 LYS cc_start: 0.8324 (tttt) cc_final: 0.8111 (ttmt) REVERT: D 518 ASP cc_start: 0.8286 (t0) cc_final: 0.7629 (t0) REVERT: D 522 GLU cc_start: 0.8889 (mm-30) cc_final: 0.7962 (tm-30) REVERT: D 751 LEU cc_start: 0.7866 (OUTLIER) cc_final: 0.7526 (pp) REVERT: D 1014 MET cc_start: 0.2320 (pmm) cc_final: 0.1831 (tpt) REVERT: D 1086 HIS cc_start: 0.8694 (m90) cc_final: 0.8256 (m90) REVERT: D 1158 SER cc_start: 0.9298 (OUTLIER) cc_final: 0.9057 (p) REVERT: D 1367 GLU cc_start: 0.8945 (mp0) cc_final: 0.8236 (mm-30) REVERT: D 1398 ASP cc_start: 0.9182 (m-30) cc_final: 0.8910 (m-30) REVERT: D 1630 ARG cc_start: 0.7389 (OUTLIER) cc_final: 0.7043 (pmt-80) REVERT: D 1636 GLU cc_start: 0.8681 (tt0) cc_final: 0.8211 (tt0) REVERT: D 1698 ILE cc_start: 0.8555 (OUTLIER) cc_final: 0.8231 (mm) REVERT: D 1754 ASN cc_start: 0.8613 (t0) cc_final: 0.7939 (t0) REVERT: D 1815 ILE cc_start: 0.8495 (mt) cc_final: 0.8072 (tt) REVERT: D 1903 GLU cc_start: 0.8926 (tt0) cc_final: 0.8620 (tt0) REVERT: D 1962 MET cc_start: 0.7900 (tpt) cc_final: 0.7664 (tpt) outliers start: 51 outliers final: 23 residues processed: 144 average time/residue: 0.5122 time to fit residues: 83.1397 Evaluate side-chains 127 residues out of total 1511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 100 time to evaluate : 0.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 252 THR Chi-restraints excluded: chain D residue 263 ILE Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 396 ASP Chi-restraints excluded: chain D residue 563 LEU Chi-restraints excluded: chain D residue 676 SER Chi-restraints excluded: chain D residue 696 ASP Chi-restraints excluded: chain D residue 708 LEU Chi-restraints excluded: chain D residue 738 VAL Chi-restraints excluded: chain D residue 751 LEU Chi-restraints excluded: chain D residue 756 ASP Chi-restraints excluded: chain D residue 1158 SER Chi-restraints excluded: chain D residue 1292 MET Chi-restraints excluded: chain D residue 1304 THR Chi-restraints excluded: chain D residue 1581 THR Chi-restraints excluded: chain D residue 1630 ARG Chi-restraints excluded: chain D residue 1655 ILE Chi-restraints excluded: chain D residue 1698 ILE Chi-restraints excluded: chain D residue 1727 LEU Chi-restraints excluded: chain D residue 1750 THR Chi-restraints excluded: chain D residue 1792 VAL Chi-restraints excluded: chain D residue 1855 LEU Chi-restraints excluded: chain D residue 1868 HIS Chi-restraints excluded: chain D residue 1875 THR Chi-restraints excluded: chain D residue 1902 LEU Chi-restraints excluded: chain D residue 1919 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 77 optimal weight: 0.7980 chunk 73 optimal weight: 10.0000 chunk 159 optimal weight: 1.9990 chunk 29 optimal weight: 0.1980 chunk 104 optimal weight: 0.9980 chunk 27 optimal weight: 5.9990 chunk 98 optimal weight: 3.9990 chunk 68 optimal weight: 4.9990 chunk 1 optimal weight: 6.9990 chunk 129 optimal weight: 0.4980 chunk 99 optimal weight: 0.4980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 210 GLN D 293 HIS D 601 ASN D 618 GLN ** D1834 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.135245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.095088 restraints weight = 28996.186| |-----------------------------------------------------------------------------| r_work (start): 0.3404 rms_B_bonded: 3.83 r_work: 0.3257 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3268 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3268 r_free = 0.3268 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3268 r_free = 0.3268 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3268 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.1956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 14157 Z= 0.101 Angle : 0.507 8.132 19181 Z= 0.254 Chirality : 0.044 0.224 2046 Planarity : 0.003 0.031 2483 Dihedral : 7.139 161.956 1926 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 3.18 % Allowed : 17.41 % Favored : 79.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % 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 aren not related in a simple way. whole: 0.13 (0.21), residues: 1683 helix: 0.94 (0.35), residues: 231 sheet: 0.17 (0.22), residues: 530 loop : -0.08 (0.22), residues: 922 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 264 TYR 0.015 0.001 TYR D1558 PHE 0.023 0.001 PHE D1901 TRP 0.026 0.001 TRP D1888 HIS 0.004 0.000 HIS D1464 Details of bonding type rmsd covalent geometry : bond 0.00231 (14157) covalent geometry : angle 0.50749 (19181) hydrogen bonds : bond 0.02593 ( 364) hydrogen bonds : angle 5.28754 ( 945) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3366 Ramachandran restraints generated. 1683 Oldfield, 0 Emsley, 1683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3366 Ramachandran restraints generated. 1683 Oldfield, 0 Emsley, 1683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 109 time to evaluate : 0.574 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 191 MET cc_start: 0.5978 (ppp) cc_final: 0.5345 (ppp) REVERT: D 243 GLU cc_start: 0.7331 (mt-10) cc_final: 0.6927 (pt0) REVERT: D 296 MET cc_start: 0.8218 (OUTLIER) cc_final: 0.7910 (tpp) REVERT: D 377 PHE cc_start: 0.8771 (t80) cc_final: 0.8381 (p90) REVERT: D 407 LYS cc_start: 0.9147 (mttm) cc_final: 0.8595 (tttm) REVERT: D 437 LYS cc_start: 0.8271 (tttt) cc_final: 0.8053 (ttmt) REVERT: D 498 THR cc_start: 0.7831 (OUTLIER) cc_final: 0.7220 (p) REVERT: D 518 ASP cc_start: 0.8297 (t0) cc_final: 0.7640 (t0) REVERT: D 522 GLU cc_start: 0.8883 (mm-30) cc_final: 0.8340 (tp30) REVERT: D 751 LEU cc_start: 0.7874 (OUTLIER) cc_final: 0.7530 (pp) REVERT: D 1014 MET cc_start: 0.2254 (pmm) cc_final: 0.1773 (tpt) REVERT: D 1086 HIS cc_start: 0.8664 (m90) cc_final: 0.8237 (m90) REVERT: D 1158 SER cc_start: 0.9294 (OUTLIER) cc_final: 0.9044 (p) REVERT: D 1367 GLU cc_start: 0.8924 (mp0) cc_final: 0.8206 (mm-30) REVERT: D 1398 ASP cc_start: 0.9154 (m-30) cc_final: 0.8880 (m-30) REVERT: D 1630 ARG cc_start: 0.7357 (OUTLIER) cc_final: 0.7018 (pmt-80) REVERT: D 1636 GLU cc_start: 0.8598 (tt0) cc_final: 0.8130 (tt0) REVERT: D 1698 ILE cc_start: 0.8512 (OUTLIER) cc_final: 0.8199 (mm) REVERT: D 1754 ASN cc_start: 0.8590 (t0) cc_final: 0.7903 (t0) REVERT: D 1815 ILE cc_start: 0.8494 (mt) cc_final: 0.8061 (tt) REVERT: D 1903 GLU cc_start: 0.8910 (tt0) cc_final: 0.8619 (tt0) REVERT: D 1962 MET cc_start: 0.7874 (tpt) cc_final: 0.7589 (tpt) outliers start: 48 outliers final: 21 residues processed: 143 average time/residue: 0.5408 time to fit residues: 86.5634 Evaluate side-chains 129 residues out of total 1511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 102 time to evaluate : 0.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 263 ILE Chi-restraints excluded: chain D residue 296 MET Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 396 ASP Chi-restraints excluded: chain D residue 498 THR Chi-restraints excluded: chain D residue 563 LEU Chi-restraints excluded: chain D residue 565 VAL Chi-restraints excluded: chain D residue 676 SER Chi-restraints excluded: chain D residue 696 ASP Chi-restraints excluded: chain D residue 708 LEU Chi-restraints excluded: chain D residue 738 VAL Chi-restraints excluded: chain D residue 751 LEU Chi-restraints excluded: chain D residue 754 ILE Chi-restraints excluded: chain D residue 756 ASP Chi-restraints excluded: chain D residue 1158 SER Chi-restraints excluded: chain D residue 1292 MET Chi-restraints excluded: chain D residue 1581 THR Chi-restraints excluded: chain D residue 1630 ARG Chi-restraints excluded: chain D residue 1698 ILE Chi-restraints excluded: chain D residue 1727 LEU Chi-restraints excluded: chain D residue 1750 THR Chi-restraints excluded: chain D residue 1792 VAL Chi-restraints excluded: chain D residue 1855 LEU Chi-restraints excluded: chain D residue 1868 HIS Chi-restraints excluded: chain D residue 1919 CYS Chi-restraints excluded: chain D residue 1955 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 161 optimal weight: 4.9990 chunk 123 optimal weight: 0.7980 chunk 31 optimal weight: 6.9990 chunk 119 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 chunk 88 optimal weight: 0.7980 chunk 137 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 96 optimal weight: 0.7980 chunk 48 optimal weight: 5.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 210 GLN D 293 HIS D 618 GLN ** D1834 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.134732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.094227 restraints weight = 28979.431| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 3.86 r_work: 0.3247 rms_B_bonded: 4.46 restraints_weight: 0.5000 r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3254 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3254 r_free = 0.3254 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3254 r_free = 0.3254 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3254 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.2075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 14157 Z= 0.118 Angle : 0.525 8.558 19181 Z= 0.262 Chirality : 0.044 0.202 2046 Planarity : 0.003 0.031 2483 Dihedral : 7.127 167.119 1925 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 3.51 % Allowed : 17.14 % Favored : 79.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % 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 aren not related in a simple way. whole: 0.19 (0.21), residues: 1683 helix: 1.07 (0.35), residues: 229 sheet: 0.18 (0.22), residues: 536 loop : -0.04 (0.22), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 264 TYR 0.011 0.001 TYR D 315 PHE 0.030 0.001 PHE D1751 TRP 0.030 0.001 TRP D1888 HIS 0.003 0.000 HIS D1464 Details of bonding type rmsd covalent geometry : bond 0.00273 (14157) covalent geometry : angle 0.52482 (19181) hydrogen bonds : bond 0.02599 ( 364) hydrogen bonds : angle 5.19389 ( 945) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3366 Ramachandran restraints generated. 1683 Oldfield, 0 Emsley, 1683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3366 Ramachandran restraints generated. 1683 Oldfield, 0 Emsley, 1683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 107 time to evaluate : 0.510 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 191 MET cc_start: 0.6194 (ppp) cc_final: 0.5557 (ppp) REVERT: D 243 GLU cc_start: 0.7513 (mt-10) cc_final: 0.7092 (pt0) REVERT: D 296 MET cc_start: 0.8191 (OUTLIER) cc_final: 0.7882 (tpp) REVERT: D 306 GLU cc_start: 0.8597 (OUTLIER) cc_final: 0.8327 (pp20) REVERT: D 377 PHE cc_start: 0.8788 (t80) cc_final: 0.8351 (p90) REVERT: D 407 LYS cc_start: 0.9145 (mttm) cc_final: 0.8582 (tttm) REVERT: D 437 LYS cc_start: 0.8291 (tttt) cc_final: 0.8058 (ttmt) REVERT: D 498 THR cc_start: 0.7844 (OUTLIER) cc_final: 0.7234 (p) REVERT: D 518 ASP cc_start: 0.8303 (t0) cc_final: 0.7626 (t0) REVERT: D 522 GLU cc_start: 0.8882 (mm-30) cc_final: 0.7942 (tp30) REVERT: D 601 ASN cc_start: 0.8943 (t0) cc_final: 0.8724 (t0) REVERT: D 751 LEU cc_start: 0.7876 (OUTLIER) cc_final: 0.7516 (pp) REVERT: D 1014 MET cc_start: 0.2260 (pmm) cc_final: 0.1775 (tpt) REVERT: D 1086 HIS cc_start: 0.8664 (m90) cc_final: 0.8217 (m90) REVERT: D 1158 SER cc_start: 0.9297 (OUTLIER) cc_final: 0.9041 (p) REVERT: D 1367 GLU cc_start: 0.8945 (mp0) cc_final: 0.8227 (mm-30) REVERT: D 1398 ASP cc_start: 0.9148 (m-30) cc_final: 0.8871 (m-30) REVERT: D 1630 ARG cc_start: 0.7382 (OUTLIER) cc_final: 0.7056 (pmt-80) REVERT: D 1636 GLU cc_start: 0.8618 (tt0) cc_final: 0.8130 (tt0) REVERT: D 1698 ILE cc_start: 0.8550 (OUTLIER) cc_final: 0.8230 (mm) REVERT: D 1754 ASN cc_start: 0.8582 (t0) cc_final: 0.7896 (t0) REVERT: D 1815 ILE cc_start: 0.8509 (mt) cc_final: 0.8063 (tt) REVERT: D 1903 GLU cc_start: 0.8917 (tt0) cc_final: 0.8619 (tt0) REVERT: D 1962 MET cc_start: 0.7842 (tpt) cc_final: 0.7561 (tpt) outliers start: 53 outliers final: 23 residues processed: 146 average time/residue: 0.5505 time to fit residues: 89.4670 Evaluate side-chains 133 residues out of total 1511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 103 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 210 GLN Chi-restraints excluded: chain D residue 252 THR Chi-restraints excluded: chain D residue 263 ILE Chi-restraints excluded: chain D residue 296 MET Chi-restraints excluded: chain D residue 306 GLU Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 396 ASP Chi-restraints excluded: chain D residue 498 THR Chi-restraints excluded: chain D residue 529 GLU Chi-restraints excluded: chain D residue 563 LEU Chi-restraints excluded: chain D residue 696 ASP Chi-restraints excluded: chain D residue 708 LEU Chi-restraints excluded: chain D residue 738 VAL Chi-restraints excluded: chain D residue 751 LEU Chi-restraints excluded: chain D residue 754 ILE Chi-restraints excluded: chain D residue 756 ASP Chi-restraints excluded: chain D residue 1158 SER Chi-restraints excluded: chain D residue 1292 MET Chi-restraints excluded: chain D residue 1581 THR Chi-restraints excluded: chain D residue 1630 ARG Chi-restraints excluded: chain D residue 1698 ILE Chi-restraints excluded: chain D residue 1727 LEU Chi-restraints excluded: chain D residue 1750 THR Chi-restraints excluded: chain D residue 1792 VAL Chi-restraints excluded: chain D residue 1855 LEU Chi-restraints excluded: chain D residue 1868 HIS Chi-restraints excluded: chain D residue 1875 THR Chi-restraints excluded: chain D residue 1902 LEU Chi-restraints excluded: chain D residue 1955 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 53 optimal weight: 0.8980 chunk 69 optimal weight: 6.9990 chunk 28 optimal weight: 3.9990 chunk 93 optimal weight: 0.4980 chunk 83 optimal weight: 0.0670 chunk 13 optimal weight: 3.9990 chunk 114 optimal weight: 3.9990 chunk 54 optimal weight: 0.9980 chunk 2 optimal weight: 4.9990 chunk 92 optimal weight: 0.8980 chunk 163 optimal weight: 0.0770 overall best weight: 0.4876 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 210 GLN D 293 HIS D 618 GLN ** D1834 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.135569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.095123 restraints weight = 28869.964| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 3.87 r_work: 0.3265 rms_B_bonded: 4.49 restraints_weight: 0.5000 r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3274 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3274 r_free = 0.3274 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3274 r_free = 0.3274 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3274 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.2082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 14157 Z= 0.099 Angle : 0.540 10.239 19181 Z= 0.267 Chirality : 0.044 0.212 2046 Planarity : 0.003 0.031 2483 Dihedral : 7.115 173.233 1925 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.51 % Allowed : 18.46 % Favored : 79.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % 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 aren not related in a simple way. whole: 0.24 (0.21), residues: 1683 helix: 1.28 (0.35), residues: 223 sheet: 0.22 (0.22), residues: 526 loop : -0.06 (0.21), residues: 934 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 264 TYR 0.019 0.001 TYR D1625 PHE 0.029 0.001 PHE D1751 TRP 0.033 0.001 TRP D1888 HIS 0.002 0.000 HIS D1464 Details of bonding type rmsd covalent geometry : bond 0.00227 (14157) covalent geometry : angle 0.53962 (19181) hydrogen bonds : bond 0.02520 ( 364) hydrogen bonds : angle 5.11772 ( 945) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3366 Ramachandran restraints generated. 1683 Oldfield, 0 Emsley, 1683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3366 Ramachandran restraints generated. 1683 Oldfield, 0 Emsley, 1683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 106 time to evaluate : 0.568 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 191 MET cc_start: 0.6213 (ppp) cc_final: 0.5543 (ppp) REVERT: D 243 GLU cc_start: 0.7471 (mt-10) cc_final: 0.7069 (pt0) REVERT: D 296 MET cc_start: 0.8082 (OUTLIER) cc_final: 0.7781 (tpp) REVERT: D 377 PHE cc_start: 0.8775 (t80) cc_final: 0.8329 (p90) REVERT: D 407 LYS cc_start: 0.9127 (mttm) cc_final: 0.8584 (tttm) REVERT: D 437 LYS cc_start: 0.8213 (tttt) cc_final: 0.7978 (ttmt) REVERT: D 498 THR cc_start: 0.7815 (OUTLIER) cc_final: 0.7188 (p) REVERT: D 518 ASP cc_start: 0.8305 (t0) cc_final: 0.7662 (t0) REVERT: D 522 GLU cc_start: 0.8892 (mm-30) cc_final: 0.7982 (tp30) REVERT: D 601 ASN cc_start: 0.8927 (t0) cc_final: 0.8716 (t0) REVERT: D 751 LEU cc_start: 0.7871 (OUTLIER) cc_final: 0.7522 (pp) REVERT: D 1014 MET cc_start: 0.2271 (pmm) cc_final: 0.1789 (tpt) REVERT: D 1086 HIS cc_start: 0.8645 (m90) cc_final: 0.8211 (m90) REVERT: D 1158 SER cc_start: 0.9289 (OUTLIER) cc_final: 0.9027 (p) REVERT: D 1367 GLU cc_start: 0.8934 (mp0) cc_final: 0.8201 (mm-30) REVERT: D 1398 ASP cc_start: 0.9151 (m-30) cc_final: 0.8879 (m-30) REVERT: D 1630 ARG cc_start: 0.7376 (OUTLIER) cc_final: 0.7036 (pmt-80) REVERT: D 1636 GLU cc_start: 0.8540 (tt0) cc_final: 0.8076 (tt0) REVERT: D 1698 ILE cc_start: 0.8526 (OUTLIER) cc_final: 0.8208 (mm) REVERT: D 1708 ASP cc_start: 0.8898 (p0) cc_final: 0.8598 (m-30) REVERT: D 1754 ASN cc_start: 0.8574 (t0) cc_final: 0.7979 (t0) REVERT: D 1815 ILE cc_start: 0.8496 (mt) cc_final: 0.8046 (tt) REVERT: D 1903 GLU cc_start: 0.8843 (tt0) cc_final: 0.8569 (tt0) outliers start: 38 outliers final: 21 residues processed: 132 average time/residue: 0.5475 time to fit residues: 80.6231 Evaluate side-chains 131 residues out of total 1511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 104 time to evaluate : 0.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 210 GLN Chi-restraints excluded: chain D residue 252 THR Chi-restraints excluded: chain D residue 263 ILE Chi-restraints excluded: chain D residue 296 MET Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 396 ASP Chi-restraints excluded: chain D residue 498 THR Chi-restraints excluded: chain D residue 529 GLU Chi-restraints excluded: chain D residue 696 ASP Chi-restraints excluded: chain D residue 708 LEU Chi-restraints excluded: chain D residue 738 VAL Chi-restraints excluded: chain D residue 751 LEU Chi-restraints excluded: chain D residue 754 ILE Chi-restraints excluded: chain D residue 756 ASP Chi-restraints excluded: chain D residue 1158 SER Chi-restraints excluded: chain D residue 1292 MET Chi-restraints excluded: chain D residue 1581 THR Chi-restraints excluded: chain D residue 1630 ARG Chi-restraints excluded: chain D residue 1698 ILE Chi-restraints excluded: chain D residue 1727 LEU Chi-restraints excluded: chain D residue 1750 THR Chi-restraints excluded: chain D residue 1792 VAL Chi-restraints excluded: chain D residue 1855 LEU Chi-restraints excluded: chain D residue 1868 HIS Chi-restraints excluded: chain D residue 1875 THR Chi-restraints excluded: chain D residue 1955 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 40 optimal weight: 2.9990 chunk 119 optimal weight: 0.4980 chunk 162 optimal weight: 0.8980 chunk 105 optimal weight: 3.9990 chunk 74 optimal weight: 20.0000 chunk 95 optimal weight: 1.9990 chunk 87 optimal weight: 0.0040 chunk 63 optimal weight: 0.6980 chunk 7 optimal weight: 2.9990 chunk 128 optimal weight: 3.9990 chunk 88 optimal weight: 1.9990 overall best weight: 0.8194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 210 GLN D 293 HIS D 618 GLN ** D1834 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.135119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.095562 restraints weight = 28931.529| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 3.78 r_work: 0.3267 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3254 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3254 r_free = 0.3254 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3254 r_free = 0.3254 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3254 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.2126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14157 Z= 0.116 Angle : 0.548 9.970 19181 Z= 0.269 Chirality : 0.044 0.196 2046 Planarity : 0.003 0.031 2483 Dihedral : 7.127 175.864 1925 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.58 % Allowed : 18.27 % Favored : 79.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % 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 aren not related in a simple way. whole: 0.26 (0.21), residues: 1683 helix: 1.31 (0.35), residues: 223 sheet: 0.24 (0.22), residues: 526 loop : -0.05 (0.22), residues: 934 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 209 TYR 0.012 0.001 TYR D1470 PHE 0.030 0.001 PHE D1751 TRP 0.040 0.001 TRP D1888 HIS 0.002 0.000 HIS D1165 Details of bonding type rmsd covalent geometry : bond 0.00269 (14157) covalent geometry : angle 0.54782 (19181) hydrogen bonds : bond 0.02538 ( 364) hydrogen bonds : angle 5.07847 ( 945) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3366 Ramachandran restraints generated. 1683 Oldfield, 0 Emsley, 1683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3366 Ramachandran restraints generated. 1683 Oldfield, 0 Emsley, 1683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 105 time to evaluate : 0.640 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 191 MET cc_start: 0.6188 (ppp) cc_final: 0.5512 (ppp) REVERT: D 243 GLU cc_start: 0.7508 (mt-10) cc_final: 0.7106 (pt0) REVERT: D 264 ARG cc_start: 0.8058 (ptp-110) cc_final: 0.7731 (mtt-85) REVERT: D 296 MET cc_start: 0.8095 (OUTLIER) cc_final: 0.7539 (tpp) REVERT: D 306 GLU cc_start: 0.8606 (OUTLIER) cc_final: 0.8337 (pp20) REVERT: D 407 LYS cc_start: 0.9124 (mttm) cc_final: 0.8584 (tttm) REVERT: D 437 LYS cc_start: 0.8218 (tttt) cc_final: 0.7969 (ttmt) REVERT: D 498 THR cc_start: 0.7840 (OUTLIER) cc_final: 0.7232 (p) REVERT: D 518 ASP cc_start: 0.8301 (t0) cc_final: 0.7627 (t0) REVERT: D 522 GLU cc_start: 0.8886 (mm-30) cc_final: 0.7977 (tp30) REVERT: D 751 LEU cc_start: 0.7897 (OUTLIER) cc_final: 0.7538 (pp) REVERT: D 1014 MET cc_start: 0.2321 (pmm) cc_final: 0.1819 (tpt) REVERT: D 1086 HIS cc_start: 0.8652 (m90) cc_final: 0.8219 (m90) REVERT: D 1158 SER cc_start: 0.9289 (OUTLIER) cc_final: 0.9035 (p) REVERT: D 1367 GLU cc_start: 0.8919 (mp0) cc_final: 0.8189 (mm-30) REVERT: D 1398 ASP cc_start: 0.9153 (m-30) cc_final: 0.8884 (m-30) REVERT: D 1630 ARG cc_start: 0.7380 (OUTLIER) cc_final: 0.7028 (pmt-80) REVERT: D 1636 GLU cc_start: 0.8565 (tt0) cc_final: 0.8086 (tt0) REVERT: D 1698 ILE cc_start: 0.8549 (OUTLIER) cc_final: 0.8230 (mm) REVERT: D 1708 ASP cc_start: 0.8899 (p0) cc_final: 0.8593 (m-30) REVERT: D 1754 ASN cc_start: 0.8545 (t0) cc_final: 0.7940 (t0) REVERT: D 1815 ILE cc_start: 0.8520 (mt) cc_final: 0.8035 (pt) REVERT: D 1903 GLU cc_start: 0.8847 (tt0) cc_final: 0.8563 (tt0) REVERT: D 1962 MET cc_start: 0.7859 (tpt) cc_final: 0.7636 (tpt) outliers start: 39 outliers final: 22 residues processed: 134 average time/residue: 0.5688 time to fit residues: 84.3656 Evaluate side-chains 132 residues out of total 1511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 103 time to evaluate : 0.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 252 THR Chi-restraints excluded: chain D residue 263 ILE Chi-restraints excluded: chain D residue 296 MET Chi-restraints excluded: chain D residue 306 GLU Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 396 ASP Chi-restraints excluded: chain D residue 498 THR Chi-restraints excluded: chain D residue 509 SER Chi-restraints excluded: chain D residue 529 GLU Chi-restraints excluded: chain D residue 696 ASP Chi-restraints excluded: chain D residue 738 VAL Chi-restraints excluded: chain D residue 751 LEU Chi-restraints excluded: chain D residue 754 ILE Chi-restraints excluded: chain D residue 756 ASP Chi-restraints excluded: chain D residue 1158 SER Chi-restraints excluded: chain D residue 1213 MET Chi-restraints excluded: chain D residue 1292 MET Chi-restraints excluded: chain D residue 1581 THR Chi-restraints excluded: chain D residue 1630 ARG Chi-restraints excluded: chain D residue 1655 ILE Chi-restraints excluded: chain D residue 1698 ILE Chi-restraints excluded: chain D residue 1727 LEU Chi-restraints excluded: chain D residue 1750 THR Chi-restraints excluded: chain D residue 1792 VAL Chi-restraints excluded: chain D residue 1855 LEU Chi-restraints excluded: chain D residue 1868 HIS Chi-restraints excluded: chain D residue 1875 THR Chi-restraints excluded: chain D residue 1955 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 45 optimal weight: 0.8980 chunk 137 optimal weight: 6.9990 chunk 6 optimal weight: 0.8980 chunk 2 optimal weight: 1.9990 chunk 85 optimal weight: 8.9990 chunk 155 optimal weight: 9.9990 chunk 148 optimal weight: 0.0970 chunk 104 optimal weight: 0.9980 chunk 90 optimal weight: 2.9990 chunk 143 optimal weight: 0.9990 chunk 59 optimal weight: 0.9980 overall best weight: 0.7778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 293 HIS D 601 ASN D 618 GLN ** D1834 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.135279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.094673 restraints weight = 29062.281| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 3.92 r_work: 0.3261 rms_B_bonded: 4.51 restraints_weight: 0.5000 r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3249 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3249 r_free = 0.3249 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3249 r_free = 0.3249 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.74 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3249 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.2200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14157 Z= 0.114 Angle : 0.555 11.455 19181 Z= 0.273 Chirality : 0.044 0.201 2046 Planarity : 0.003 0.030 2483 Dihedral : 7.115 177.854 1925 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.32 % Allowed : 18.66 % Favored : 79.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % 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 aren not related in a simple way. whole: 0.26 (0.21), residues: 1683 helix: 1.35 (0.36), residues: 223 sheet: 0.24 (0.22), residues: 526 loop : -0.06 (0.22), residues: 934 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 264 TYR 0.011 0.001 TYR D1558 PHE 0.031 0.001 PHE D1901 TRP 0.041 0.001 TRP D1888 HIS 0.002 0.000 HIS D1165 Details of bonding type rmsd covalent geometry : bond 0.00266 (14157) covalent geometry : angle 0.55482 (19181) hydrogen bonds : bond 0.02514 ( 364) hydrogen bonds : angle 5.04216 ( 945) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3366 Ramachandran restraints generated. 1683 Oldfield, 0 Emsley, 1683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3366 Ramachandran restraints generated. 1683 Oldfield, 0 Emsley, 1683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 109 time to evaluate : 0.633 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 191 MET cc_start: 0.6125 (ppp) cc_final: 0.5500 (ppp) REVERT: D 243 GLU cc_start: 0.7594 (mt-10) cc_final: 0.7219 (pt0) REVERT: D 296 MET cc_start: 0.8093 (mmp) cc_final: 0.7547 (tpp) REVERT: D 306 GLU cc_start: 0.8620 (OUTLIER) cc_final: 0.8353 (pp20) REVERT: D 407 LYS cc_start: 0.9136 (mttm) cc_final: 0.8583 (tttm) REVERT: D 437 LYS cc_start: 0.8223 (tttt) cc_final: 0.8015 (ttmt) REVERT: D 498 THR cc_start: 0.7873 (OUTLIER) cc_final: 0.7270 (p) REVERT: D 518 ASP cc_start: 0.8306 (t0) cc_final: 0.7651 (t0) REVERT: D 522 GLU cc_start: 0.8886 (mm-30) cc_final: 0.7969 (tp30) REVERT: D 585 MET cc_start: 0.9481 (mtm) cc_final: 0.9256 (mtt) REVERT: D 751 LEU cc_start: 0.7898 (OUTLIER) cc_final: 0.7545 (pp) REVERT: D 1014 MET cc_start: 0.2334 (pmm) cc_final: 0.1849 (tpt) REVERT: D 1086 HIS cc_start: 0.8642 (m90) cc_final: 0.8202 (m90) REVERT: D 1158 SER cc_start: 0.9284 (OUTLIER) cc_final: 0.9028 (p) REVERT: D 1367 GLU cc_start: 0.8924 (mp0) cc_final: 0.8185 (mm-30) REVERT: D 1398 ASP cc_start: 0.9162 (m-30) cc_final: 0.8884 (m-30) REVERT: D 1630 ARG cc_start: 0.7361 (OUTLIER) cc_final: 0.7009 (pmt-80) REVERT: D 1636 GLU cc_start: 0.8559 (tt0) cc_final: 0.8075 (tt0) REVERT: D 1698 ILE cc_start: 0.8564 (OUTLIER) cc_final: 0.8246 (mm) REVERT: D 1708 ASP cc_start: 0.8894 (p0) cc_final: 0.8583 (m-30) REVERT: D 1754 ASN cc_start: 0.8538 (t0) cc_final: 0.7843 (t0) REVERT: D 1815 ILE cc_start: 0.8517 (mt) cc_final: 0.8055 (pt) REVERT: D 1899 LEU cc_start: 0.8751 (mt) cc_final: 0.8533 (mt) REVERT: D 1903 GLU cc_start: 0.8839 (tt0) cc_final: 0.8571 (tt0) REVERT: D 1962 MET cc_start: 0.7855 (tpt) cc_final: 0.7651 (tpt) outliers start: 35 outliers final: 23 residues processed: 133 average time/residue: 0.5453 time to fit residues: 80.9214 Evaluate side-chains 134 residues out of total 1511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 105 time to evaluate : 0.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 198 ASP Chi-restraints excluded: chain D residue 252 THR Chi-restraints excluded: chain D residue 263 ILE Chi-restraints excluded: chain D residue 306 GLU Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 396 ASP Chi-restraints excluded: chain D residue 498 THR Chi-restraints excluded: chain D residue 509 SER Chi-restraints excluded: chain D residue 529 GLU Chi-restraints excluded: chain D residue 563 LEU Chi-restraints excluded: chain D residue 738 VAL Chi-restraints excluded: chain D residue 751 LEU Chi-restraints excluded: chain D residue 754 ILE Chi-restraints excluded: chain D residue 756 ASP Chi-restraints excluded: chain D residue 1158 SER Chi-restraints excluded: chain D residue 1213 MET Chi-restraints excluded: chain D residue 1292 MET Chi-restraints excluded: chain D residue 1581 THR Chi-restraints excluded: chain D residue 1630 ARG Chi-restraints excluded: chain D residue 1655 ILE Chi-restraints excluded: chain D residue 1698 ILE Chi-restraints excluded: chain D residue 1727 LEU Chi-restraints excluded: chain D residue 1750 THR Chi-restraints excluded: chain D residue 1792 VAL Chi-restraints excluded: chain D residue 1855 LEU Chi-restraints excluded: chain D residue 1868 HIS Chi-restraints excluded: chain D residue 1875 THR Chi-restraints excluded: chain D residue 1955 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 41 optimal weight: 0.9990 chunk 133 optimal weight: 4.9990 chunk 42 optimal weight: 3.9990 chunk 76 optimal weight: 8.9990 chunk 155 optimal weight: 9.9990 chunk 91 optimal weight: 0.8980 chunk 98 optimal weight: 3.9990 chunk 166 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 chunk 137 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 293 HIS D 618 GLN ** D1834 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 = 0.4027 r_free = 0.4027 target = 0.132224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.092006 restraints weight = 29055.763| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 3.75 r_work: 0.3189 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3195 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3195 r_free = 0.3195 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.74 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3195 r_free = 0.3195 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.74 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3195 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.2511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 14157 Z= 0.233 Angle : 0.619 12.907 19181 Z= 0.305 Chirality : 0.046 0.189 2046 Planarity : 0.003 0.030 2483 Dihedral : 7.455 179.513 1925 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 2.32 % Allowed : 18.86 % Favored : 78.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % 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 aren not related in a simple way. whole: 0.12 (0.21), residues: 1683 helix: 0.91 (0.35), residues: 231 sheet: 0.15 (0.22), residues: 532 loop : -0.07 (0.22), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 785 TYR 0.023 0.001 TYR D1625 PHE 0.033 0.001 PHE D1901 TRP 0.049 0.001 TRP D1888 HIS 0.003 0.001 HIS D1165 Details of bonding type rmsd covalent geometry : bond 0.00546 (14157) covalent geometry : angle 0.61926 (19181) hydrogen bonds : bond 0.02967 ( 364) hydrogen bonds : angle 5.39277 ( 945) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5701.30 seconds wall clock time: 97 minutes 50.28 seconds (5870.28 seconds total)