Starting phenix.real_space_refine on Sat Aug 23 18:34:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9qkv_53222/08_2025/9qkv_53222.cif Found real_map, /net/cci-nas-00/data/ceres_data/9qkv_53222/08_2025/9qkv_53222.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.74 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9qkv_53222/08_2025/9qkv_53222.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9qkv_53222/08_2025/9qkv_53222.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9qkv_53222/08_2025/9qkv_53222.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9qkv_53222/08_2025/9qkv_53222.map" } resolution = 2.74 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 58 5.16 5 C 8782 2.51 5 N 2352 2.21 5 O 2560 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 63 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13764 Number of models: 1 Model: "" Number of chains: 2 Chain: "D" Number of atoms: 13694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1688, 13694 Classifications: {'peptide': 1688} Link IDs: {'PCIS': 3, 'PTRANS': 103, 'TRANS': 1581} Chain breaks: 6 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=0.91 ... (28 atoms not shown) pdb=" P PSF D2001 " occ=0.91 residue: pdb=" N PSF D2010 " occ=0.81 ... (28 atoms not shown) pdb=" P PSF D2010 " occ=0.81 Time building chain proxies: 2.74, per 1000 atoms: 0.20 Number of scatterers: 13764 At special positions: 0 Unit cell: (101.52, 123.12, 155.52, 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 58 16.00 P 2 15.00 O 2560 8.00 N 2352 7.00 C 8782 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.77 Conformation dependent library (CDL) restraints added in 473.7 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3180 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 18 sheets defined 17.1% alpha, 28.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.69 Creating SS restraints... Processing helix chain 'D' and resid 172 through 189 Processing helix chain 'D' and resid 252 through 257 Processing helix chain 'D' and resid 284 through 290 Processing helix chain 'D' and resid 307 through 310 Processing helix chain 'D' and resid 343 through 347 removed outlier: 3.975A pdb=" N LEU D 347 " --> pdb=" O GLU D 344 " (cutoff:3.500A) Processing helix chain 'D' and resid 377 through 382 Processing helix chain 'D' and resid 390 through 394 removed outlier: 3.677A pdb=" N ASN D 393 " --> pdb=" O ASP D 390 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N LEU D 394 " --> pdb=" O LYS D 391 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 390 through 394' Processing helix chain 'D' and resid 520 through 525 removed outlier: 3.901A pdb=" N ASN D 524 " --> pdb=" O TYR D 520 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N THR D 525 " --> pdb=" O ASP D 521 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 520 through 525' Processing helix chain 'D' and resid 560 through 565 Processing helix chain 'D' and resid 566 through 569 Processing helix chain 'D' and resid 650 through 680 removed outlier: 4.458A 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: 4.004A pdb=" N SER D 742 " --> pdb=" O VAL D 738 " (cutoff:3.500A) Processing helix chain 'D' and resid 746 through 765 removed outlier: 3.903A pdb=" N THR D 750 " --> pdb=" O ASP D 746 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N ALA D 752 " --> pdb=" O LYS D 748 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N GLU D 753 " --> pdb=" O SER D 749 " (cutoff:3.500A) Processing helix chain 'D' and resid 792 through 796 removed outlier: 3.511A pdb=" N VAL D 796 " --> pdb=" O ALA D 793 " (cutoff:3.500A) Processing helix chain 'D' and resid 844 through 852 removed outlier: 5.296A pdb=" N LYS D 847 " --> pdb=" O ALA D 844 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N SER D 851 " --> pdb=" O LYS D 848 " (cutoff:3.500A) Processing helix chain 'D' and resid 1086 through 1094 removed outlier: 3.606A pdb=" N ALA D1089 " --> pdb=" O HIS D1086 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ALA D1090 " --> pdb=" O GLY D1087 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ILE D1091 " --> pdb=" O ALA D1088 " (cutoff:3.500A) removed outlier: 3.971A 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 1275 through 1279 removed outlier: 4.387A pdb=" N ASN D1278 " --> pdb=" O ASP D1275 " (cutoff:3.500A) Processing helix chain 'D' and resid 1381 through 1385 removed outlier: 3.766A pdb=" N GLY D1384 " --> pdb=" O ARG D1381 " (cutoff:3.500A) Processing helix chain 'D' and resid 1452 through 1462 removed outlier: 3.702A pdb=" N LYS D1456 " --> pdb=" O ASP D1452 " (cutoff:3.500A) Processing helix chain 'D' and resid 1470 through 1474 Processing helix chain 'D' and resid 1488 through 1495 removed outlier: 3.517A pdb=" N PHE D1491 " --> pdb=" O VAL D1488 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLU D1492 " --> pdb=" O ALA D1489 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N GLY D1493 " --> pdb=" O GLU D1490 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N THR D1495 " --> pdb=" O GLU D1492 " (cutoff:3.500A) Processing helix chain 'D' and resid 1590 through 1593 removed outlier: 3.915A 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 1662 through 1666 removed outlier: 4.198A pdb=" N ASN D1665 " --> pdb=" O SER D1662 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N THR D1666 " --> pdb=" O GLY D1663 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1662 through 1666' Processing helix chain 'D' and resid 1672 through 1685 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: 3.903A 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 1975 through 1981 removed outlier: 3.534A pdb=" N ASP D1979 " --> pdb=" O GLU D1975 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 240 through 250 removed outlier: 6.766A pdb=" N PHE D 241 " --> pdb=" O GLU D 207 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N GLU D 207 " --> pdb=" O PHE D 241 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N LYS D 317 " --> pdb=" O ILE D 206 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N GLY D 208 " --> pdb=" O TYR D 315 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N TYR D 315 " --> pdb=" O GLY D 208 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N GLY D 314 " --> pdb=" O LEU D 302 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N MET D 316 " --> pdb=" O LEU D 300 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 227 through 230 removed outlier: 6.864A pdb=" N ILE D 261 " --> pdb=" O LYS D 281 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N LYS D 281 " --> pdb=" O ILE D 261 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N ILE D 263 " --> pdb=" O GLU D 279 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N GLU D 279 " --> pdb=" O ILE D 263 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N VAL D 265 " --> pdb=" O MET D 277 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 499 through 508 removed outlier: 5.281A pdb=" N GLY D 500 " --> pdb=" O LEU D 541 " (cutoff:3.500A) removed outlier: 5.606A pdb=" N LEU D 541 " --> pdb=" O GLY D 500 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N GLY D 535 " --> pdb=" O LEU D 506 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N GLY D 508 " --> pdb=" O TYR D 533 " (cutoff:3.500A) removed outlier: 5.822A pdb=" N TYR D 533 " --> pdb=" O GLY D 508 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ARG D 536 " --> pdb=" O ALA D 367 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N ALA D 367 " --> pdb=" O ARG D 536 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N LEU D 538 " --> pdb=" O TYR D 365 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N ARG D 366 " --> pdb=" O TRP D 421 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N TRP D 421 " --> pdb=" O ARG D 366 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 406 through 409 removed outlier: 6.746A pdb=" N ILE D 438 " --> pdb=" O TYR D 458 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N TYR D 458 " --> pdb=" O ILE D 438 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N LEU D 440 " --> pdb=" O THR D 456 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N THR D 456 " --> pdb=" O LEU D 440 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N ILE D 442 " --> pdb=" O VAL D 454 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 571 through 584 removed outlier: 8.647A pdb=" N SER D 582 " --> pdb=" O THR D 637 " (cutoff:3.500A) removed outlier: 12.298A 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 648 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: 3.529A pdb=" N ALA D 787 " --> pdb=" O MET D 779 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N ARG D 781 " --> pdb=" O ARG D 785 " (cutoff:3.500A) removed outlier: 5.381A 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: 12.777A pdb=" N GLU D 933 " --> pdb=" O TYR D 953 " (cutoff:3.500A) removed outlier: 11.006A pdb=" N TYR D 953 " --> pdb=" O GLU D 933 " (cutoff:3.500A) removed outlier: 8.977A pdb=" N TYR D 935 " --> pdb=" O ASP D 951 " (cutoff:3.500A) removed outlier: 9.503A pdb=" N ASP D 951 " --> pdb=" O TYR D 935 " (cutoff:3.500A) removed outlier: 7.596A pdb=" N ASN D 937 " --> pdb=" O ALA D 949 " (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: 6.938A pdb=" N TYR D1137 " --> pdb=" O GLU D1196 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N GLU D1196 " --> pdb=" O TYR D1137 " (cutoff:3.500A) removed outlier: 5.895A 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: 3.605A pdb=" N GLY D1228 " --> pdb=" O LEU D1215 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N ASP D1217 " --> pdb=" O PHE D1226 " (cutoff:3.500A) removed outlier: 5.940A 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 removed outlier: 5.323A pdb=" N ILE D1306 " --> pdb=" O TYR D1527 " (cutoff:3.500A) removed outlier: 7.659A pdb=" N TYR D1527 " --> pdb=" O ILE D1306 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N ILE D1308 " --> pdb=" O ARG D1525 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N ARG D1525 " --> pdb=" O ILE D1308 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N ALA D1310 " --> pdb=" O SER D1523 " (cutoff:3.500A) removed outlier: 7.963A pdb=" N SER D1523 " --> pdb=" O ALA D1310 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLY D1312 " --> pdb=" O LYS D1521 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N VAL D1516 " --> pdb=" O ARG D1505 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N ARG D1505 " --> pdb=" O VAL D1516 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLY D1518 " --> pdb=" O LEU D1503 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 1336 through 1339 removed outlier: 3.854A pdb=" N GLY D1390 " --> pdb=" O VAL D1377 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 1479 through 1480 removed outlier: 6.846A pdb=" N LYS D1479 " --> pdb=" O VAL D1742 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N THR D1744 " --> pdb=" O LYS D1479 " (cutoff:3.500A) removed outlier: 8.291A pdb=" N HIS D1741 " --> pdb=" O VAL D1764 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N VAL D1764 " --> pdb=" O HIS D1741 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N LYS D1759 " --> pdb=" O GLY D1562 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N GLY D1562 " --> pdb=" O LYS D1759 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N GLN D1761 " --> pdb=" O VAL D1560 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 1585 through 1588 removed outlier: 6.538A pdb=" N LEU D1618 " --> pdb=" O ILE D1638 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N ILE D1638 " --> pdb=" O LEU D1618 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N ILE D1620 " --> pdb=" O GLU D1636 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N GLU D1636 " --> pdb=" O ILE D1620 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N VAL D1622 " --> pdb=" O VAL D1634 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLU D1632 " --> pdb=" O ASP D1624 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 1690 through 1691 removed outlier: 3.710A pdb=" N TYR D1705 " --> pdb=" O ILE D1698 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N TYR D1700 " --> pdb=" O ARG D1703 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 1875 through 1879 removed outlier: 3.882A pdb=" N ASP D1853 " --> pdb=" O ILE D1862 " (cutoff:3.500A) removed outlier: 9.099A pdb=" N ALA D1864 " --> pdb=" O PRO D1851 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N GLY D1842 " --> pdb=" O LYS D1798 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N LYS D1798 " --> pdb=" O GLY D1842 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N PHE D1844 " --> pdb=" O ASN D1796 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N ASN D1796 " --> pdb=" O PHE D1844 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N TRP D1846 " --> pdb=" O ILE D1794 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILE D1793 " --> pdb=" O THR D1969 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N THR D1969 " --> pdb=" O ILE D1793 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N GLU D1967 " --> pdb=" O TRP D1795 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N THR D1797 " --> pdb=" O LYS D1965 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N LYS D1965 " --> pdb=" O THR D1797 " (cutoff:3.500A) removed outlier: 5.172A pdb=" N ARG D1960 " --> pdb=" O LYS D1956 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N LYS D1956 " --> pdb=" O ARG D1960 " (cutoff:3.500A) removed outlier: 5.205A pdb=" N MET D1962 " --> pdb=" O ALA D1954 " (cutoff:3.500A) removed outlier: 5.745A pdb=" N ALA D1954 " --> pdb=" O MET D1962 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 1813 through 1820 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 1829 through 1830 current: chain 'D' and resid 1897 through 1905 Processing sheet with id=AB9, first strand: chain 'D' and resid 1909 through 1910 365 hydrogen bonds defined for protein. 978 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: 2.69 Time building geometry restraints manager: 1.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 2781 1.33 - 1.45: 3474 1.45 - 1.58: 7744 1.58 - 1.70: 8 1.70 - 1.83: 92 Bond restraints: 14099 Sorted by residual: bond pdb=" C PHE D 431 " pdb=" N PRO D 432 " ideal model delta sigma weight residual 1.335 1.375 -0.040 1.28e-02 6.10e+03 9.95e+00 bond pdb=" C LYS D 947 " pdb=" N PRO D 948 " ideal model delta sigma weight residual 1.332 1.363 -0.031 1.30e-02 5.92e+03 5.75e+00 bond pdb=" C ALA D1287 " pdb=" N PRO D1288 " ideal model delta sigma weight residual 1.331 1.358 -0.027 1.20e-02 6.94e+03 5.16e+00 bond pdb=" CB GLU D1826 " pdb=" CG GLU D1826 " ideal model delta sigma weight residual 1.520 1.585 -0.065 3.00e-02 1.11e+03 4.66e+00 bond pdb=" O2 PSF D2001 " pdb=" P PSF D2001 " ideal model delta sigma weight residual 1.637 1.594 0.043 2.00e-02 2.50e+03 4.52e+00 ... (remaining 14094 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.66: 18941 3.66 - 7.32: 122 7.32 - 10.98: 30 10.98 - 14.64: 6 14.64 - 18.29: 5 Bond angle restraints: 19104 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 112.70 130.99 -18.29 3.00e+00 1.11e-01 3.72e+01 angle pdb=" CA GLU D 344 " pdb=" CB GLU D 344 " pdb=" CG GLU D 344 " ideal model delta sigma weight residual 114.10 126.28 -12.18 2.00e+00 2.50e-01 3.71e+01 angle pdb=" CB MET D 191 " pdb=" CG MET D 191 " pdb=" SD MET D 191 " ideal model delta sigma weight residual 112.70 128.95 -16.25 3.00e+00 1.11e-01 2.93e+01 angle pdb=" CB GLU D1826 " pdb=" CG GLU D1826 " pdb=" CD GLU D1826 " ideal model delta sigma weight residual 112.60 121.33 -8.73 1.70e+00 3.46e-01 2.64e+01 angle pdb=" C PRO D1595 " pdb=" N ASN D1596 " pdb=" CA ASN D1596 " ideal model delta sigma weight residual 121.54 131.24 -9.70 1.91e+00 2.74e-01 2.58e+01 ... (remaining 19099 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.74: 8083 26.74 - 53.48: 394 53.48 - 80.22: 55 80.22 - 106.96: 10 106.96 - 133.70: 1 Dihedral angle restraints: 8543 sinusoidal: 3616 harmonic: 4927 Sorted by residual: dihedral pdb=" CA GLU D1811 " pdb=" C GLU D1811 " pdb=" N MET D1812 " pdb=" CA MET D1812 " ideal model delta harmonic sigma weight residual 180.00 -155.42 -24.58 0 5.00e+00 4.00e-02 2.42e+01 dihedral pdb=" CA LYS D 547 " pdb=" C LYS D 547 " pdb=" N THR D 548 " pdb=" CA THR D 548 " ideal model delta harmonic sigma weight residual 180.00 157.33 22.67 0 5.00e+00 4.00e-02 2.06e+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 180.00 157.62 22.38 0 5.00e+00 4.00e-02 2.00e+01 ... (remaining 8540 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 1471 0.051 - 0.102: 411 0.102 - 0.153: 141 0.153 - 0.204: 12 0.204 - 0.255: 5 Chirality restraints: 2040 Sorted by residual: chirality pdb=" CA ASN D1596 " pdb=" N ASN D1596 " pdb=" C ASN D1596 " pdb=" CB ASN D1596 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.26 2.00e-01 2.50e+01 1.63e+00 chirality pdb=" CB VAL D 343 " pdb=" CA VAL D 343 " pdb=" CG1 VAL D 343 " pdb=" CG2 VAL D 343 " both_signs ideal model delta sigma weight residual False -2.63 -2.38 -0.24 2.00e-01 2.50e+01 1.49e+00 chirality pdb=" CB THR D 548 " pdb=" CA THR D 548 " pdb=" OG1 THR D 548 " pdb=" CG2 THR D 548 " both_signs ideal model delta sigma weight residual False 2.55 2.31 0.24 2.00e-01 2.50e+01 1.46e+00 ... (remaining 2037 not shown) Planarity restraints: 2472 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE D1645 " 0.018 2.00e-02 2.50e+03 2.77e-02 1.35e+01 pdb=" CG PHE D1645 " -0.063 2.00e-02 2.50e+03 pdb=" CD1 PHE D1645 " 0.025 2.00e-02 2.50e+03 pdb=" CD2 PHE D1645 " 0.022 2.00e-02 2.50e+03 pdb=" CE1 PHE D1645 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE D1645 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE D1645 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 286 " -0.021 2.00e-02 2.50e+03 2.74e-02 1.31e+01 pdb=" CG PHE D 286 " 0.063 2.00e-02 2.50e+03 pdb=" CD1 PHE D 286 " -0.024 2.00e-02 2.50e+03 pdb=" CD2 PHE D 286 " -0.017 2.00e-02 2.50e+03 pdb=" CE1 PHE D 286 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE D 286 " -0.004 2.00e-02 2.50e+03 pdb=" CZ PHE D 286 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE D1751 " 0.020 2.00e-02 2.50e+03 2.73e-02 1.30e+01 pdb=" CG PHE D1751 " -0.063 2.00e-02 2.50e+03 pdb=" CD1 PHE D1751 " 0.022 2.00e-02 2.50e+03 pdb=" CD2 PHE D1751 " 0.020 2.00e-02 2.50e+03 pdb=" CE1 PHE D1751 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE D1751 " 0.000 2.00e-02 2.50e+03 pdb=" CZ PHE D1751 " -0.000 2.00e-02 2.50e+03 ... (remaining 2469 not shown) Histogram of nonbonded interaction distances: 2.35 - 2.86: 4260 2.86 - 3.37: 12054 3.37 - 3.88: 23568 3.88 - 4.39: 26282 4.39 - 4.90: 45535 Nonbonded interactions: 111699 Sorted by model distance: nonbonded pdb="CA CA D2007 " pdb=" O3 PSF D2010 " model vdw 2.345 2.510 nonbonded pdb=" OD1 ASP D1569 " pdb="CA CA D2006 " model vdw 2.350 2.510 nonbonded pdb=" OD2 ASP D1624 " pdb="CA CA D2007 " model vdw 2.351 2.510 nonbonded pdb=" OD1 ASP D1569 " pdb="CA CA D2007 " model vdw 2.354 2.510 nonbonded pdb=" O4 PSF D2001 " pdb="CA CA D2003 " model vdw 2.367 2.510 ... (remaining 111694 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=0.81 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.320 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: 0.280 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 11.950 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 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 0.065 14099 Z= 0.232 Angle : 0.974 18.294 19104 Z= 0.515 Chirality : 0.053 0.255 2040 Planarity : 0.007 0.086 2472 Dihedral : 15.624 133.701 5363 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 2.01 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.88 % Favored : 96.06 % Rotamer: Outliers : 0.73 % Allowed : 14.95 % Favored : 84.32 % 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: -1.33 (0.19), residues: 1674 helix: -1.69 (0.29), residues: 215 sheet: -0.39 (0.23), residues: 493 loop : -0.90 (0.18), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.001 ARG D 781 TYR 0.019 0.002 TYR D 533 PHE 0.063 0.003 PHE D 286 TRP 0.054 0.002 TRP D1076 HIS 0.004 0.001 HIS D1018 Details of bonding type rmsd covalent geometry : bond 0.00487 (14099) covalent geometry : angle 0.97352 (19104) hydrogen bonds : bond 0.18801 ( 365) hydrogen bonds : angle 8.69747 ( 978) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 118 time to evaluate : 0.521 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 210 GLN cc_start: 0.8163 (tt0) cc_final: 0.7886 (tt0) REVERT: D 227 GLN cc_start: 0.8216 (tp-100) cc_final: 0.7941 (tt0) REVERT: D 255 GLU cc_start: 0.8663 (OUTLIER) cc_final: 0.8454 (tm-30) REVERT: D 277 MET cc_start: 0.7872 (mmt) cc_final: 0.7433 (mmm) REVERT: D 280 PHE cc_start: 0.8718 (t80) cc_final: 0.8432 (t80) REVERT: D 348 LEU cc_start: 0.8440 (tp) cc_final: 0.8143 (pt) REVERT: D 450 LYS cc_start: 0.8976 (ttmm) cc_final: 0.8690 (pmtt) REVERT: D 518 ASP cc_start: 0.7561 (t70) cc_final: 0.7242 (t70) REVERT: D 756 ASP cc_start: 0.6740 (t70) cc_final: 0.6458 (t70) REVERT: D 762 MET cc_start: 0.8512 (mmm) cc_final: 0.8238 (ptt) REVERT: D 784 LYS cc_start: 0.8908 (OUTLIER) cc_final: 0.8669 (mtpp) REVERT: D 870 MET cc_start: 0.1160 (mpt) cc_final: -0.0166 (ptp) REVERT: D 1014 MET cc_start: 0.5051 (mtp) cc_final: 0.4533 (mtm) REVERT: D 1321 MET cc_start: 0.8535 (mmm) cc_final: 0.8158 (mpt) REVERT: D 1519 GLU cc_start: 0.8468 (mt-10) cc_final: 0.8202 (mt-10) REVERT: D 1564 GLU cc_start: 0.8394 (mt-10) cc_final: 0.8189 (pt0) REVERT: D 1640 ASP cc_start: 0.8281 (t0) cc_final: 0.7975 (t0) REVERT: D 1812 MET cc_start: 0.5316 (tpt) cc_final: 0.5021 (tmt) REVERT: D 1870 TRP cc_start: 0.8368 (p-90) cc_final: 0.7977 (p90) REVERT: D 1962 MET cc_start: 0.8082 (tpp) cc_final: 0.7756 (tpp) outliers start: 11 outliers final: 5 residues processed: 128 average time/residue: 0.5065 time to fit residues: 71.7048 Evaluate side-chains 117 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 110 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 255 GLU Chi-restraints excluded: chain D residue 496 VAL Chi-restraints excluded: chain D residue 589 VAL Chi-restraints excluded: chain D residue 738 VAL Chi-restraints excluded: chain D residue 784 LYS Chi-restraints excluded: chain D residue 1290 LEU Chi-restraints excluded: chain D residue 1792 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 8.9990 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 0.0980 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 2.9990 overall best weight: 1.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 177 GLN D 215 ASN D 269 HIS D 618 GLN D1206 GLN D1568 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.146514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.096033 restraints weight = 26128.080| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 3.56 r_work: 0.3212 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3235 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3235 r_free = 0.3235 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.81 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3235 r_free = 0.3235 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.81 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3235 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.1067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 14099 Z= 0.196 Angle : 0.574 9.223 19104 Z= 0.295 Chirality : 0.045 0.163 2040 Planarity : 0.005 0.042 2472 Dihedral : 8.388 132.101 1923 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.93 % Favored : 97.01 % Rotamer: Outliers : 2.06 % Allowed : 13.89 % Favored : 84.05 % 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: -0.65 (0.20), residues: 1674 helix: -0.33 (0.33), residues: 221 sheet: -0.21 (0.22), residues: 514 loop : -0.50 (0.20), residues: 939 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 781 TYR 0.013 0.001 TYR D1558 PHE 0.022 0.001 PHE D1751 TRP 0.019 0.001 TRP D1888 HIS 0.003 0.001 HIS D 734 Details of bonding type rmsd covalent geometry : bond 0.00449 (14099) covalent geometry : angle 0.57437 (19104) hydrogen bonds : bond 0.03574 ( 365) hydrogen bonds : angle 6.25893 ( 978) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 109 time to evaluate : 0.512 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 210 GLN cc_start: 0.7684 (tt0) cc_final: 0.7365 (tt0) REVERT: D 227 GLN cc_start: 0.7683 (tp-100) cc_final: 0.7291 (tt0) REVERT: D 230 ARG cc_start: 0.8234 (OUTLIER) cc_final: 0.7861 (tmm160) REVERT: D 277 MET cc_start: 0.7654 (mmt) cc_final: 0.7230 (mmm) REVERT: D 450 LYS cc_start: 0.8764 (ttmm) cc_final: 0.8176 (pmtt) REVERT: D 522 GLU cc_start: 0.8085 (tm-30) cc_final: 0.7702 (tm-30) REVERT: D 527 LYS cc_start: 0.8663 (mppt) cc_final: 0.8305 (mttt) REVERT: D 588 ASP cc_start: 0.8663 (OUTLIER) cc_final: 0.8312 (p0) REVERT: D 655 ASP cc_start: 0.8214 (m-30) cc_final: 0.8012 (m-30) REVERT: D 756 ASP cc_start: 0.7560 (t70) cc_final: 0.7129 (t0) REVERT: D 762 MET cc_start: 0.8619 (mmm) cc_final: 0.7795 (ptm) REVERT: D 870 MET cc_start: 0.1436 (mpt) cc_final: 0.0199 (ptp) REVERT: D 1014 MET cc_start: 0.4580 (mtp) cc_final: 0.4306 (mtm) REVERT: D 1321 MET cc_start: 0.9017 (mmm) cc_final: 0.8298 (mpt) REVERT: D 1519 GLU cc_start: 0.8885 (mt-10) cc_final: 0.8458 (mt-10) REVERT: D 1547 ASP cc_start: 0.9204 (t0) cc_final: 0.8985 (t0) REVERT: D 1640 ASP cc_start: 0.8580 (t0) cc_final: 0.7923 (t0) REVERT: D 1812 MET cc_start: 0.5492 (tpt) cc_final: 0.5193 (tmt) REVERT: D 1870 TRP cc_start: 0.8407 (p-90) cc_final: 0.7964 (p90) REVERT: D 1943 GLN cc_start: 0.8109 (OUTLIER) cc_final: 0.7786 (tm-30) outliers start: 31 outliers final: 9 residues processed: 135 average time/residue: 0.5472 time to fit residues: 80.8959 Evaluate side-chains 112 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 100 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 177 GLN Chi-restraints excluded: chain D residue 230 ARG Chi-restraints excluded: chain D residue 260 ILE Chi-restraints excluded: chain D residue 320 MET Chi-restraints excluded: chain D residue 509 SER Chi-restraints excluded: chain D residue 588 ASP Chi-restraints excluded: chain D residue 589 VAL Chi-restraints excluded: chain D residue 747 VAL Chi-restraints excluded: chain D residue 1203 THR Chi-restraints excluded: chain D residue 1290 LEU Chi-restraints excluded: chain D residue 1792 VAL Chi-restraints excluded: chain D residue 1943 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 73 optimal weight: 20.0000 chunk 83 optimal weight: 6.9990 chunk 152 optimal weight: 10.0000 chunk 120 optimal weight: 0.8980 chunk 47 optimal weight: 0.9980 chunk 158 optimal weight: 0.9990 chunk 63 optimal weight: 0.8980 chunk 129 optimal weight: 5.9990 chunk 5 optimal weight: 0.9990 chunk 20 optimal weight: 0.0980 chunk 161 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 618 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.147512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.097513 restraints weight = 26248.689| |-----------------------------------------------------------------------------| r_work (start): 0.3391 rms_B_bonded: 3.52 r_work: 0.3244 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3262 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3262 r_free = 0.3262 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.81 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3262 r_free = 0.3262 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.82 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3262 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.1160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 14099 Z= 0.111 Angle : 0.515 8.506 19104 Z= 0.263 Chirality : 0.043 0.163 2040 Planarity : 0.004 0.036 2472 Dihedral : 7.637 135.003 1914 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.87 % Favored : 97.07 % Rotamer: Outliers : 2.46 % Allowed : 13.89 % Favored : 83.65 % 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: -0.37 (0.20), residues: 1674 helix: 0.20 (0.34), residues: 221 sheet: -0.15 (0.22), residues: 519 loop : -0.31 (0.20), residues: 934 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 781 TYR 0.011 0.001 TYR D 443 PHE 0.024 0.001 PHE D1751 TRP 0.017 0.001 TRP D1888 HIS 0.002 0.000 HIS D 223 Details of bonding type rmsd covalent geometry : bond 0.00245 (14099) covalent geometry : angle 0.51501 (19104) hydrogen bonds : bond 0.03031 ( 365) hydrogen bonds : angle 5.76249 ( 978) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 112 time to evaluate : 0.361 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 210 GLN cc_start: 0.7731 (tt0) cc_final: 0.7361 (tt0) REVERT: D 227 GLN cc_start: 0.7606 (tp-100) cc_final: 0.7226 (tt0) REVERT: D 242 ASP cc_start: 0.8266 (t0) cc_final: 0.7900 (t0) REVERT: D 277 MET cc_start: 0.7622 (mmt) cc_final: 0.7172 (mmm) REVERT: D 450 LYS cc_start: 0.8744 (ttmm) cc_final: 0.8164 (pmtt) REVERT: D 522 GLU cc_start: 0.8044 (tm-30) cc_final: 0.7696 (tm-30) REVERT: D 756 ASP cc_start: 0.7464 (t70) cc_final: 0.7040 (t0) REVERT: D 762 MET cc_start: 0.8559 (mmm) cc_final: 0.7763 (ptm) REVERT: D 803 GLU cc_start: 0.7667 (OUTLIER) cc_final: 0.7423 (tm-30) REVERT: D 870 MET cc_start: 0.1291 (mpt) cc_final: 0.0177 (ptp) REVERT: D 1014 MET cc_start: 0.4642 (mtp) cc_final: 0.4266 (mtm) REVERT: D 1321 MET cc_start: 0.9012 (mmm) cc_final: 0.8324 (mpt) REVERT: D 1519 GLU cc_start: 0.8880 (mt-10) cc_final: 0.8452 (mt-10) REVERT: D 1547 ASP cc_start: 0.9201 (t0) cc_final: 0.8972 (t0) REVERT: D 1564 GLU cc_start: 0.8482 (mt-10) cc_final: 0.8030 (pt0) REVERT: D 1640 ASP cc_start: 0.8529 (t0) cc_final: 0.7858 (t0) REVERT: D 1697 ARG cc_start: 0.8890 (ptm160) cc_final: 0.8556 (ptm160) REVERT: D 1812 MET cc_start: 0.5584 (tpt) cc_final: 0.5200 (tmt) REVERT: D 1820 TRP cc_start: 0.8417 (p-90) cc_final: 0.8206 (p-90) REVERT: D 1870 TRP cc_start: 0.8444 (p-90) cc_final: 0.8006 (p90) outliers start: 37 outliers final: 12 residues processed: 143 average time/residue: 0.4961 time to fit residues: 78.1807 Evaluate side-chains 116 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 103 time to evaluate : 0.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 260 ILE Chi-restraints excluded: chain D residue 509 SER Chi-restraints excluded: chain D residue 564 VAL Chi-restraints excluded: chain D residue 589 VAL Chi-restraints excluded: chain D residue 708 LEU Chi-restraints excluded: chain D residue 738 VAL Chi-restraints excluded: chain D residue 747 VAL Chi-restraints excluded: chain D residue 803 GLU Chi-restraints excluded: chain D residue 913 VAL Chi-restraints excluded: chain D residue 1290 LEU Chi-restraints excluded: chain D residue 1512 GLU Chi-restraints excluded: chain D residue 1792 VAL Chi-restraints excluded: chain D residue 1887 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 54 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 103 optimal weight: 10.0000 chunk 157 optimal weight: 0.0570 chunk 97 optimal weight: 3.9990 chunk 44 optimal weight: 0.9980 chunk 87 optimal weight: 0.0980 chunk 55 optimal weight: 0.7980 chunk 81 optimal weight: 50.0000 chunk 79 optimal weight: 0.3980 overall best weight: 0.4698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 293 HIS D 618 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.148472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.098946 restraints weight = 26209.547| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 3.57 r_work: 0.3260 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3285 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3285 r_free = 0.3285 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.82 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3285 r_free = 0.3285 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.83 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3285 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.1386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 14099 Z= 0.091 Angle : 0.496 7.562 19104 Z= 0.253 Chirality : 0.043 0.157 2040 Planarity : 0.004 0.035 2472 Dihedral : 7.345 136.736 1914 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.69 % Favored : 97.25 % Rotamer: Outliers : 2.79 % Allowed : 14.42 % Favored : 82.79 % 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 (0.20), residues: 1674 helix: 0.58 (0.35), residues: 221 sheet: -0.05 (0.22), residues: 519 loop : -0.16 (0.21), residues: 934 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 781 TYR 0.017 0.001 TYR D 288 PHE 0.026 0.001 PHE D1751 TRP 0.018 0.001 TRP D1888 HIS 0.002 0.000 HIS D 652 Details of bonding type rmsd covalent geometry : bond 0.00202 (14099) covalent geometry : angle 0.49641 (19104) hydrogen bonds : bond 0.02686 ( 365) hydrogen bonds : angle 5.36454 ( 978) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 112 time to evaluate : 0.514 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 210 GLN cc_start: 0.7766 (tt0) cc_final: 0.7390 (tt0) REVERT: D 227 GLN cc_start: 0.7522 (tp-100) cc_final: 0.7149 (tt0) REVERT: D 242 ASP cc_start: 0.8243 (t0) cc_final: 0.7872 (t0) REVERT: D 277 MET cc_start: 0.7597 (mmt) cc_final: 0.7117 (mmm) REVERT: D 450 LYS cc_start: 0.8709 (ttmm) cc_final: 0.8139 (pmtt) REVERT: D 522 GLU cc_start: 0.8084 (tm-30) cc_final: 0.7782 (tm-30) REVERT: D 756 ASP cc_start: 0.7463 (t70) cc_final: 0.7038 (t0) REVERT: D 762 MET cc_start: 0.8521 (mmm) cc_final: 0.7721 (ptm) REVERT: D 870 MET cc_start: 0.1287 (mpt) cc_final: 0.0256 (ptp) REVERT: D 1014 MET cc_start: 0.4502 (mtp) cc_final: 0.4177 (mtm) REVERT: D 1321 MET cc_start: 0.9011 (mmm) cc_final: 0.8354 (mpt) REVERT: D 1519 GLU cc_start: 0.8869 (mt-10) cc_final: 0.8502 (mt-10) REVERT: D 1547 ASP cc_start: 0.9216 (t0) cc_final: 0.9011 (t0) REVERT: D 1564 GLU cc_start: 0.8506 (mt-10) cc_final: 0.8050 (pt0) REVERT: D 1636 GLU cc_start: 0.8101 (tm-30) cc_final: 0.7678 (tm-30) REVERT: D 1640 ASP cc_start: 0.8504 (t0) cc_final: 0.7809 (t0) REVERT: D 1870 TRP cc_start: 0.8436 (p-90) cc_final: 0.8004 (p90) outliers start: 42 outliers final: 16 residues processed: 145 average time/residue: 0.6211 time to fit residues: 99.4338 Evaluate side-chains 120 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 104 time to evaluate : 0.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 260 ILE Chi-restraints excluded: chain D residue 295 VAL Chi-restraints excluded: chain D residue 509 SER Chi-restraints excluded: chain D residue 589 VAL Chi-restraints excluded: chain D residue 708 LEU Chi-restraints excluded: chain D residue 738 VAL Chi-restraints excluded: chain D residue 747 VAL Chi-restraints excluded: chain D residue 913 VAL Chi-restraints excluded: chain D residue 1290 LEU Chi-restraints excluded: chain D residue 1512 GLU Chi-restraints excluded: chain D residue 1581 THR Chi-restraints excluded: chain D residue 1792 VAL Chi-restraints excluded: chain D residue 1861 CYS Chi-restraints excluded: chain D residue 1876 GLU Chi-restraints excluded: chain D residue 1887 ILE Chi-restraints excluded: chain D residue 1946 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 108 optimal weight: 0.3980 chunk 110 optimal weight: 0.7980 chunk 105 optimal weight: 0.8980 chunk 63 optimal weight: 3.9990 chunk 15 optimal weight: 7.9990 chunk 117 optimal weight: 0.0980 chunk 84 optimal weight: 7.9990 chunk 102 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 82 optimal weight: 10.0000 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 618 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.147855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.097851 restraints weight = 26197.058| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 3.60 r_work: 0.3240 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3263 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3263 r_free = 0.3263 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.83 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3263 r_free = 0.3263 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.82 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3263 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.1519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14099 Z= 0.114 Angle : 0.511 11.705 19104 Z= 0.256 Chirality : 0.043 0.155 2040 Planarity : 0.003 0.034 2472 Dihedral : 7.230 137.764 1914 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.93 % Favored : 97.01 % Rotamer: Outliers : 2.39 % Allowed : 15.28 % Favored : 82.33 % 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: -0.00 (0.20), residues: 1674 helix: 0.80 (0.35), residues: 222 sheet: -0.03 (0.21), residues: 536 loop : -0.07 (0.21), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D1697 TYR 0.011 0.001 TYR D1558 PHE 0.029 0.001 PHE D 286 TRP 0.017 0.001 TRP D1888 HIS 0.002 0.000 HIS D 734 Details of bonding type rmsd covalent geometry : bond 0.00261 (14099) covalent geometry : angle 0.51144 (19104) hydrogen bonds : bond 0.02680 ( 365) hydrogen bonds : angle 5.21683 ( 978) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 112 time to evaluate : 0.593 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 204 ARG cc_start: 0.7698 (ttm110) cc_final: 0.6861 (ttm-80) REVERT: D 210 GLN cc_start: 0.7851 (tt0) cc_final: 0.7481 (tt0) REVERT: D 227 GLN cc_start: 0.7530 (tp-100) cc_final: 0.7145 (tt0) REVERT: D 230 ARG cc_start: 0.8231 (OUTLIER) cc_final: 0.7712 (tmm160) REVERT: D 277 MET cc_start: 0.7605 (mmt) cc_final: 0.7136 (mmm) REVERT: D 450 LYS cc_start: 0.8755 (ttmm) cc_final: 0.8193 (pmtt) REVERT: D 522 GLU cc_start: 0.8139 (tm-30) cc_final: 0.7727 (tm-30) REVERT: D 527 LYS cc_start: 0.8660 (mppt) cc_final: 0.8312 (mttt) REVERT: D 571 ARG cc_start: 0.8386 (OUTLIER) cc_final: 0.8011 (mtt90) REVERT: D 762 MET cc_start: 0.8561 (mmm) cc_final: 0.7759 (ptm) REVERT: D 870 MET cc_start: 0.1197 (mpt) cc_final: 0.0017 (pmm) REVERT: D 1014 MET cc_start: 0.4588 (mtp) cc_final: 0.4181 (mtm) REVERT: D 1455 SER cc_start: 0.8941 (OUTLIER) cc_final: 0.8621 (p) REVERT: D 1519 GLU cc_start: 0.8894 (mt-10) cc_final: 0.8460 (mt-10) REVERT: D 1547 ASP cc_start: 0.9217 (t0) cc_final: 0.8974 (t0) REVERT: D 1564 GLU cc_start: 0.8535 (mt-10) cc_final: 0.7998 (pt0) REVERT: D 1636 GLU cc_start: 0.8157 (tm-30) cc_final: 0.7928 (tm-30) REVERT: D 1640 ASP cc_start: 0.8509 (t0) cc_final: 0.7844 (t0) REVERT: D 1688 GLN cc_start: 0.7861 (mm-40) cc_final: 0.7630 (tp-100) REVERT: D 1930 MET cc_start: 0.4676 (ppp) cc_final: 0.3202 (tpt) outliers start: 36 outliers final: 14 residues processed: 144 average time/residue: 0.6448 time to fit residues: 102.2343 Evaluate side-chains 120 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 103 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 230 ARG Chi-restraints excluded: chain D residue 260 ILE Chi-restraints excluded: chain D residue 295 VAL Chi-restraints excluded: chain D residue 509 SER Chi-restraints excluded: chain D residue 571 ARG Chi-restraints excluded: chain D residue 589 VAL Chi-restraints excluded: chain D residue 708 LEU Chi-restraints excluded: chain D residue 738 VAL Chi-restraints excluded: chain D residue 747 VAL Chi-restraints excluded: chain D residue 913 VAL Chi-restraints excluded: chain D residue 1238 LEU Chi-restraints excluded: chain D residue 1290 LEU Chi-restraints excluded: chain D residue 1455 SER Chi-restraints excluded: chain D residue 1512 GLU Chi-restraints excluded: chain D residue 1581 THR Chi-restraints excluded: chain D residue 1792 VAL Chi-restraints excluded: chain D residue 1863 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 35 optimal weight: 0.9980 chunk 138 optimal weight: 1.9990 chunk 39 optimal weight: 0.8980 chunk 32 optimal weight: 0.7980 chunk 112 optimal weight: 3.9990 chunk 26 optimal weight: 3.9990 chunk 91 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 31 optimal weight: 0.7980 chunk 65 optimal weight: 5.9990 chunk 51 optimal weight: 3.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 618 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.147293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.097001 restraints weight = 26053.487| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 3.56 r_work: 0.3231 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3254 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3254 r_free = 0.3254 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.82 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3254 r_free = 0.3254 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.81 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3254 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.1698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 14099 Z= 0.134 Angle : 0.531 15.472 19104 Z= 0.263 Chirality : 0.043 0.156 2040 Planarity : 0.004 0.033 2472 Dihedral : 7.208 138.823 1914 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.35 % Favored : 96.59 % Rotamer: Outliers : 2.72 % Allowed : 15.42 % Favored : 81.86 % 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: 0.07 (0.21), residues: 1674 helix: 0.83 (0.35), residues: 222 sheet: -0.00 (0.22), residues: 538 loop : -0.00 (0.22), residues: 914 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D1697 TYR 0.012 0.001 TYR D1558 PHE 0.027 0.001 PHE D1751 TRP 0.021 0.001 TRP D1888 HIS 0.009 0.001 HIS D 293 Details of bonding type rmsd covalent geometry : bond 0.00307 (14099) covalent geometry : angle 0.53051 (19104) hydrogen bonds : bond 0.02727 ( 365) hydrogen bonds : angle 5.18669 ( 978) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 111 time to evaluate : 0.660 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 175 GLU cc_start: 0.8140 (OUTLIER) cc_final: 0.7844 (pt0) REVERT: D 210 GLN cc_start: 0.7861 (tt0) cc_final: 0.7607 (tt0) REVERT: D 227 GLN cc_start: 0.7539 (tp-100) cc_final: 0.7162 (tt0) REVERT: D 230 ARG cc_start: 0.8281 (OUTLIER) cc_final: 0.7836 (tmm160) REVERT: D 242 ASP cc_start: 0.8264 (t0) cc_final: 0.7908 (t0) REVERT: D 277 MET cc_start: 0.7622 (mmt) cc_final: 0.7133 (mmm) REVERT: D 450 LYS cc_start: 0.8750 (ttmm) cc_final: 0.8180 (pmtt) REVERT: D 571 ARG cc_start: 0.8404 (OUTLIER) cc_final: 0.8033 (mtt90) REVERT: D 762 MET cc_start: 0.8539 (mmm) cc_final: 0.7751 (ptm) REVERT: D 824 LYS cc_start: 0.7332 (pmtt) cc_final: 0.6419 (ttpp) REVERT: D 870 MET cc_start: 0.1294 (mpt) cc_final: 0.0098 (pmm) REVERT: D 1014 MET cc_start: 0.4505 (mtp) cc_final: 0.4098 (mtm) REVERT: D 1257 ASP cc_start: 0.8633 (p0) cc_final: 0.8354 (p0) REVERT: D 1321 MET cc_start: 0.8917 (mmm) cc_final: 0.8186 (mpt) REVERT: D 1455 SER cc_start: 0.8956 (OUTLIER) cc_final: 0.8638 (p) REVERT: D 1519 GLU cc_start: 0.8899 (mt-10) cc_final: 0.8470 (mt-10) REVERT: D 1547 ASP cc_start: 0.9220 (t0) cc_final: 0.8981 (t0) REVERT: D 1564 GLU cc_start: 0.8533 (mt-10) cc_final: 0.8027 (pt0) REVERT: D 1640 ASP cc_start: 0.8510 (t0) cc_final: 0.7825 (t0) REVERT: D 1870 TRP cc_start: 0.8333 (p-90) cc_final: 0.7849 (p90) REVERT: D 1930 MET cc_start: 0.4617 (ppp) cc_final: 0.3235 (tpt) REVERT: D 1962 MET cc_start: 0.7362 (tpp) cc_final: 0.7148 (tpp) outliers start: 41 outliers final: 19 residues processed: 145 average time/residue: 0.6267 time to fit residues: 100.4750 Evaluate side-chains 126 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 103 time to evaluate : 0.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 175 GLU Chi-restraints excluded: chain D residue 230 ARG Chi-restraints excluded: chain D residue 260 ILE Chi-restraints excluded: chain D residue 287 VAL Chi-restraints excluded: chain D residue 295 VAL Chi-restraints excluded: chain D residue 459 LEU Chi-restraints excluded: chain D residue 509 SER Chi-restraints excluded: chain D residue 571 ARG Chi-restraints excluded: chain D residue 589 VAL Chi-restraints excluded: chain D residue 738 VAL Chi-restraints excluded: chain D residue 747 VAL Chi-restraints excluded: chain D residue 913 VAL Chi-restraints excluded: chain D residue 1238 LEU Chi-restraints excluded: chain D residue 1290 LEU Chi-restraints excluded: chain D residue 1455 SER Chi-restraints excluded: chain D residue 1512 GLU Chi-restraints excluded: chain D residue 1581 THR Chi-restraints excluded: chain D residue 1792 VAL Chi-restraints excluded: chain D residue 1861 CYS Chi-restraints excluded: chain D residue 1863 VAL Chi-restraints excluded: chain D residue 1887 ILE Chi-restraints excluded: chain D residue 1902 LEU Chi-restraints excluded: chain D residue 1946 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 146 optimal weight: 3.9990 chunk 128 optimal weight: 5.9990 chunk 114 optimal weight: 0.7980 chunk 92 optimal weight: 0.8980 chunk 99 optimal weight: 0.8980 chunk 12 optimal weight: 6.9990 chunk 131 optimal weight: 2.9990 chunk 87 optimal weight: 0.9980 chunk 106 optimal weight: 4.9990 chunk 21 optimal weight: 0.0270 chunk 125 optimal weight: 0.8980 overall best weight: 0.7038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 293 HIS D 618 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.147849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.097784 restraints weight = 26042.388| |-----------------------------------------------------------------------------| r_work (start): 0.3396 rms_B_bonded: 3.62 r_work: 0.3248 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3279 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3279 r_free = 0.3279 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.81 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3279 r_free = 0.3279 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.81 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3279 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.1743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 14099 Z= 0.106 Angle : 0.524 11.389 19104 Z= 0.259 Chirality : 0.043 0.154 2040 Planarity : 0.003 0.033 2472 Dihedral : 7.116 139.028 1914 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.87 % Favored : 97.07 % Rotamer: Outliers : 2.66 % Allowed : 15.75 % Favored : 81.59 % 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: 0.10 (0.21), residues: 1674 helix: 0.93 (0.35), residues: 223 sheet: 0.02 (0.22), residues: 528 loop : -0.00 (0.21), residues: 923 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D1697 TYR 0.011 0.001 TYR D1558 PHE 0.028 0.001 PHE D1751 TRP 0.026 0.001 TRP D1076 HIS 0.001 0.000 HIS D1018 Details of bonding type rmsd covalent geometry : bond 0.00242 (14099) covalent geometry : angle 0.52423 (19104) hydrogen bonds : bond 0.02590 ( 365) hydrogen bonds : angle 5.04568 ( 978) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 114 time to evaluate : 0.585 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 175 GLU cc_start: 0.8148 (OUTLIER) cc_final: 0.7854 (pt0) REVERT: D 210 GLN cc_start: 0.7825 (tt0) cc_final: 0.7484 (tt0) REVERT: D 227 GLN cc_start: 0.7534 (tp-100) cc_final: 0.7160 (tt0) REVERT: D 230 ARG cc_start: 0.8264 (OUTLIER) cc_final: 0.7833 (tmm160) REVERT: D 242 ASP cc_start: 0.8257 (t0) cc_final: 0.7896 (t0) REVERT: D 277 MET cc_start: 0.7566 (mmt) cc_final: 0.7145 (mmm) REVERT: D 407 LYS cc_start: 0.8804 (OUTLIER) cc_final: 0.7812 (pptt) REVERT: D 450 LYS cc_start: 0.8710 (ttmm) cc_final: 0.8143 (pmtt) REVERT: D 522 GLU cc_start: 0.8055 (tm-30) cc_final: 0.7628 (tm-30) REVERT: D 571 ARG cc_start: 0.8356 (OUTLIER) cc_final: 0.7999 (mtt90) REVERT: D 588 ASP cc_start: 0.8619 (OUTLIER) cc_final: 0.8261 (p0) REVERT: D 762 MET cc_start: 0.8484 (mmm) cc_final: 0.7693 (ptm) REVERT: D 824 LYS cc_start: 0.7488 (pmtt) cc_final: 0.6610 (ttpp) REVERT: D 870 MET cc_start: 0.1480 (mpt) cc_final: 0.0258 (pmm) REVERT: D 1014 MET cc_start: 0.4355 (mtp) cc_final: 0.3964 (mtm) REVERT: D 1076 TRP cc_start: 0.8090 (t-100) cc_final: 0.7865 (t-100) REVERT: D 1257 ASP cc_start: 0.8648 (p0) cc_final: 0.8373 (p0) REVERT: D 1321 MET cc_start: 0.8977 (mmm) cc_final: 0.8280 (mpt) REVERT: D 1455 SER cc_start: 0.8933 (OUTLIER) cc_final: 0.8612 (p) REVERT: D 1519 GLU cc_start: 0.8875 (mt-10) cc_final: 0.8441 (mt-10) REVERT: D 1547 ASP cc_start: 0.9229 (t0) cc_final: 0.8991 (t0) REVERT: D 1564 GLU cc_start: 0.8521 (mt-10) cc_final: 0.7969 (pt0) REVERT: D 1605 MET cc_start: 0.8745 (OUTLIER) cc_final: 0.8499 (ttp) REVERT: D 1640 ASP cc_start: 0.8479 (t0) cc_final: 0.7791 (t0) REVERT: D 1688 GLN cc_start: 0.7910 (mm-40) cc_final: 0.7640 (tp-100) REVERT: D 1704 ASP cc_start: 0.8924 (OUTLIER) cc_final: 0.8325 (p0) REVERT: D 1870 TRP cc_start: 0.8348 (p-90) cc_final: 0.7875 (p90) REVERT: D 1930 MET cc_start: 0.4625 (ppp) cc_final: 0.3308 (tpt) outliers start: 40 outliers final: 18 residues processed: 147 average time/residue: 0.6242 time to fit residues: 101.2841 Evaluate side-chains 130 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 104 time to evaluate : 0.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 175 GLU Chi-restraints excluded: chain D residue 230 ARG Chi-restraints excluded: chain D residue 260 ILE Chi-restraints excluded: chain D residue 295 VAL Chi-restraints excluded: chain D residue 396 ASP Chi-restraints excluded: chain D residue 407 LYS Chi-restraints excluded: chain D residue 509 SER Chi-restraints excluded: chain D residue 571 ARG Chi-restraints excluded: chain D residue 588 ASP Chi-restraints excluded: chain D residue 589 VAL Chi-restraints excluded: chain D residue 738 VAL Chi-restraints excluded: chain D residue 747 VAL Chi-restraints excluded: chain D residue 913 VAL Chi-restraints excluded: chain D residue 1238 LEU Chi-restraints excluded: chain D residue 1290 LEU Chi-restraints excluded: chain D residue 1455 SER Chi-restraints excluded: chain D residue 1512 GLU Chi-restraints excluded: chain D residue 1581 THR Chi-restraints excluded: chain D residue 1605 MET Chi-restraints excluded: chain D residue 1704 ASP Chi-restraints excluded: chain D residue 1792 VAL Chi-restraints excluded: chain D residue 1855 LEU Chi-restraints excluded: chain D residue 1861 CYS Chi-restraints excluded: chain D residue 1862 ILE Chi-restraints excluded: chain D residue 1863 VAL Chi-restraints excluded: chain D residue 1946 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 23 optimal weight: 1.9990 chunk 89 optimal weight: 3.9990 chunk 3 optimal weight: 3.9990 chunk 131 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 chunk 83 optimal weight: 30.0000 chunk 19 optimal weight: 3.9990 chunk 50 optimal weight: 0.9980 chunk 120 optimal weight: 3.9990 chunk 21 optimal weight: 0.7980 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.146135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.095546 restraints weight = 25870.927| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 3.57 r_work: 0.3202 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3227 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3227 r_free = 0.3227 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.81 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3227 r_free = 0.3227 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.80 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3227 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.1921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 14099 Z= 0.175 Angle : 0.555 11.380 19104 Z= 0.276 Chirality : 0.044 0.182 2040 Planarity : 0.004 0.031 2472 Dihedral : 7.220 139.959 1914 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.46 % Favored : 96.48 % Rotamer: Outliers : 2.06 % Allowed : 16.68 % Favored : 81.26 % 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: 0.09 (0.21), residues: 1674 helix: 0.89 (0.35), residues: 222 sheet: -0.03 (0.22), residues: 534 loop : 0.03 (0.22), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 232 TYR 0.013 0.001 TYR D1558 PHE 0.030 0.002 PHE D1751 TRP 0.028 0.001 TRP D1888 HIS 0.002 0.001 HIS D 734 Details of bonding type rmsd covalent geometry : bond 0.00404 (14099) covalent geometry : angle 0.55515 (19104) hydrogen bonds : bond 0.02883 ( 365) hydrogen bonds : angle 5.22203 ( 978) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 111 time to evaluate : 0.629 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 175 GLU cc_start: 0.8175 (OUTLIER) cc_final: 0.7880 (pt0) REVERT: D 227 GLN cc_start: 0.7620 (tp-100) cc_final: 0.7246 (tt0) REVERT: D 242 ASP cc_start: 0.8263 (t0) cc_final: 0.7891 (t0) REVERT: D 277 MET cc_start: 0.7597 (mmt) cc_final: 0.7181 (mmm) REVERT: D 450 LYS cc_start: 0.8769 (ttmm) cc_final: 0.8198 (pmtt) REVERT: D 498 THR cc_start: 0.7833 (OUTLIER) cc_final: 0.7461 (t) REVERT: D 522 GLU cc_start: 0.8089 (tm-30) cc_final: 0.7733 (tm-30) REVERT: D 571 ARG cc_start: 0.8429 (OUTLIER) cc_final: 0.8133 (mtt90) REVERT: D 588 ASP cc_start: 0.8630 (OUTLIER) cc_final: 0.8273 (p0) REVERT: D 762 MET cc_start: 0.8577 (mmm) cc_final: 0.7752 (ptm) REVERT: D 824 LYS cc_start: 0.7314 (pmtt) cc_final: 0.6362 (ttpp) REVERT: D 870 MET cc_start: 0.1407 (mpt) cc_final: 0.0163 (pmm) REVERT: D 1014 MET cc_start: 0.4326 (mtp) cc_final: 0.3873 (mtm) REVERT: D 1257 ASP cc_start: 0.8717 (p0) cc_final: 0.8470 (p0) REVERT: D 1321 MET cc_start: 0.9011 (mmm) cc_final: 0.8336 (mpt) REVERT: D 1519 GLU cc_start: 0.8920 (mt-10) cc_final: 0.8615 (mt-10) REVERT: D 1547 ASP cc_start: 0.9255 (t0) cc_final: 0.9032 (t0) REVERT: D 1564 GLU cc_start: 0.8529 (mt-10) cc_final: 0.7974 (pt0) REVERT: D 1640 ASP cc_start: 0.8534 (t0) cc_final: 0.7871 (t0) REVERT: D 1688 GLN cc_start: 0.7867 (mm-40) cc_final: 0.7623 (tp-100) REVERT: D 1827 ASN cc_start: 0.7989 (m-40) cc_final: 0.7673 (m110) REVERT: D 1870 TRP cc_start: 0.8376 (p-90) cc_final: 0.7882 (p90) REVERT: D 1930 MET cc_start: 0.4690 (ppp) cc_final: 0.3453 (tpt) outliers start: 31 outliers final: 16 residues processed: 136 average time/residue: 0.6390 time to fit residues: 96.4181 Evaluate side-chains 128 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 108 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 175 GLU Chi-restraints excluded: chain D residue 260 ILE Chi-restraints excluded: chain D residue 295 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 571 ARG Chi-restraints excluded: chain D residue 588 ASP Chi-restraints excluded: chain D residue 589 VAL Chi-restraints excluded: chain D residue 738 VAL Chi-restraints excluded: chain D residue 747 VAL Chi-restraints excluded: chain D residue 913 VAL Chi-restraints excluded: chain D residue 1290 LEU Chi-restraints excluded: chain D residue 1512 GLU Chi-restraints excluded: chain D residue 1581 THR Chi-restraints excluded: chain D residue 1792 VAL Chi-restraints excluded: chain D residue 1855 LEU Chi-restraints excluded: chain D residue 1861 CYS Chi-restraints excluded: chain D residue 1863 VAL Chi-restraints excluded: chain D residue 1946 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 65 optimal weight: 4.9990 chunk 115 optimal weight: 5.9990 chunk 23 optimal weight: 2.9990 chunk 107 optimal weight: 4.9990 chunk 159 optimal weight: 9.9990 chunk 37 optimal weight: 0.8980 chunk 135 optimal weight: 4.9990 chunk 3 optimal weight: 5.9990 chunk 54 optimal weight: 6.9990 chunk 30 optimal weight: 0.9990 chunk 48 optimal weight: 7.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 618 GLN D1652 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.143682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.092628 restraints weight = 26284.751| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 3.57 r_work: 0.3147 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3158 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3158 r_free = 0.3158 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.80 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3158 r_free = 0.3158 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.80 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3158 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.2206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.052 14099 Z= 0.298 Angle : 0.635 11.644 19104 Z= 0.318 Chirality : 0.046 0.189 2040 Planarity : 0.004 0.033 2472 Dihedral : 7.513 140.479 1914 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.64 % Favored : 96.30 % Rotamer: Outliers : 2.19 % Allowed : 16.54 % Favored : 81.26 % 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: -0.21 (0.21), residues: 1674 helix: 0.44 (0.34), residues: 229 sheet: -0.21 (0.22), residues: 522 loop : -0.13 (0.21), residues: 923 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D1697 TYR 0.014 0.001 TYR D1558 PHE 0.032 0.002 PHE D1751 TRP 0.039 0.001 TRP D1888 HIS 0.004 0.001 HIS D 734 Details of bonding type rmsd covalent geometry : bond 0.00692 (14099) covalent geometry : angle 0.63497 (19104) hydrogen bonds : bond 0.03380 ( 365) hydrogen bonds : angle 5.63899 ( 978) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 105 time to evaluate : 0.600 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 175 GLU cc_start: 0.8310 (OUTLIER) cc_final: 0.8053 (pt0) REVERT: D 210 GLN cc_start: 0.7873 (tt0) cc_final: 0.7653 (tt0) REVERT: D 227 GLN cc_start: 0.7718 (tp-100) cc_final: 0.7357 (tt0) REVERT: D 277 MET cc_start: 0.7671 (mmt) cc_final: 0.7247 (mmm) REVERT: D 346 ASN cc_start: 0.7705 (m-40) cc_final: 0.7467 (m-40) REVERT: D 450 LYS cc_start: 0.8787 (ttmm) cc_final: 0.8451 (mtmm) REVERT: D 571 ARG cc_start: 0.8501 (OUTLIER) cc_final: 0.8292 (mtt90) REVERT: D 588 ASP cc_start: 0.8651 (OUTLIER) cc_final: 0.8285 (p0) REVERT: D 824 LYS cc_start: 0.7390 (pmtt) cc_final: 0.7035 (pmtt) REVERT: D 870 MET cc_start: 0.1290 (mpt) cc_final: 0.0059 (pmm) REVERT: D 1014 MET cc_start: 0.4295 (mtp) cc_final: 0.3890 (mtm) REVERT: D 1321 MET cc_start: 0.9007 (mmm) cc_final: 0.8329 (mpt) REVERT: D 1359 MET cc_start: 0.8191 (ptp) cc_final: 0.7989 (ptp) REVERT: D 1547 ASP cc_start: 0.9303 (t0) cc_final: 0.9093 (t0) REVERT: D 1640 ASP cc_start: 0.8618 (t0) cc_final: 0.7960 (t0) REVERT: D 1704 ASP cc_start: 0.9063 (t0) cc_final: 0.8297 (p0) REVERT: D 1882 ARG cc_start: 0.8465 (ptp-170) cc_final: 0.8093 (ptp-170) REVERT: D 1930 MET cc_start: 0.4816 (ppp) cc_final: 0.3552 (tpt) outliers start: 33 outliers final: 17 residues processed: 131 average time/residue: 0.6330 time to fit residues: 91.7347 Evaluate side-chains 122 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 102 time to evaluate : 0.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 175 GLU Chi-restraints excluded: chain D residue 260 ILE Chi-restraints excluded: chain D residue 295 VAL Chi-restraints excluded: chain D residue 396 ASP Chi-restraints excluded: chain D residue 459 LEU Chi-restraints excluded: chain D residue 498 THR Chi-restraints excluded: chain D residue 509 SER Chi-restraints excluded: chain D residue 571 ARG Chi-restraints excluded: chain D residue 588 ASP Chi-restraints excluded: chain D residue 589 VAL Chi-restraints excluded: chain D residue 738 VAL Chi-restraints excluded: chain D residue 747 VAL Chi-restraints excluded: chain D residue 913 VAL Chi-restraints excluded: chain D residue 1290 LEU Chi-restraints excluded: chain D residue 1512 GLU Chi-restraints excluded: chain D residue 1581 THR Chi-restraints excluded: chain D residue 1792 VAL Chi-restraints excluded: chain D residue 1861 CYS Chi-restraints excluded: chain D residue 1863 VAL Chi-restraints excluded: chain D residue 1946 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 113 optimal weight: 1.9990 chunk 53 optimal weight: 0.8980 chunk 1 optimal weight: 2.9990 chunk 86 optimal weight: 3.9990 chunk 83 optimal weight: 8.9990 chunk 10 optimal weight: 7.9990 chunk 5 optimal weight: 0.6980 chunk 55 optimal weight: 0.8980 chunk 131 optimal weight: 0.9990 chunk 22 optimal weight: 0.5980 chunk 163 optimal weight: 4.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D1827 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.146417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.096274 restraints weight = 25949.650| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 3.52 r_work: 0.3217 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3241 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3241 r_free = 0.3241 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.80 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3241 r_free = 0.3241 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.80 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3241 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.2102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14099 Z= 0.121 Angle : 0.560 10.792 19104 Z= 0.279 Chirality : 0.044 0.172 2040 Planarity : 0.004 0.031 2472 Dihedral : 7.232 138.943 1914 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.99 % Favored : 96.95 % Rotamer: Outliers : 1.59 % Allowed : 17.54 % Favored : 80.86 % 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: -0.06 (0.21), residues: 1674 helix: 0.68 (0.35), residues: 228 sheet: -0.16 (0.22), residues: 526 loop : -0.03 (0.22), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D1907 TYR 0.015 0.001 TYR D1558 PHE 0.030 0.001 PHE D1751 TRP 0.042 0.001 TRP D1888 HIS 0.002 0.001 HIS D1086 Details of bonding type rmsd covalent geometry : bond 0.00272 (14099) covalent geometry : angle 0.55999 (19104) hydrogen bonds : bond 0.02776 ( 365) hydrogen bonds : angle 5.28358 ( 978) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 111 time to evaluate : 0.590 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 175 GLU cc_start: 0.8292 (OUTLIER) cc_final: 0.8033 (pt0) REVERT: D 210 GLN cc_start: 0.7783 (tt0) cc_final: 0.7511 (tt0) REVERT: D 227 GLN cc_start: 0.7598 (tp-100) cc_final: 0.7250 (tt0) REVERT: D 277 MET cc_start: 0.7615 (mmt) cc_final: 0.7168 (mmm) REVERT: D 450 LYS cc_start: 0.8741 (ttmm) cc_final: 0.8194 (pmtt) REVERT: D 498 THR cc_start: 0.7790 (OUTLIER) cc_final: 0.7445 (t) REVERT: D 522 GLU cc_start: 0.7994 (tm-30) cc_final: 0.7533 (tm-30) REVERT: D 588 ASP cc_start: 0.8609 (OUTLIER) cc_final: 0.8242 (p0) REVERT: D 700 GLU cc_start: 0.8896 (tp30) cc_final: 0.8662 (tp30) REVERT: D 762 MET cc_start: 0.8310 (mmt) cc_final: 0.7488 (ptm) REVERT: D 824 LYS cc_start: 0.7541 (pmtt) cc_final: 0.6767 (ttpp) REVERT: D 870 MET cc_start: 0.1103 (mpt) cc_final: -0.0066 (pmm) REVERT: D 1014 MET cc_start: 0.4472 (mtp) cc_final: 0.3968 (mtm) REVERT: D 1076 TRP cc_start: 0.8020 (t-100) cc_final: 0.7816 (t-100) REVERT: D 1321 MET cc_start: 0.8999 (mmm) cc_final: 0.8358 (mpt) REVERT: D 1547 ASP cc_start: 0.9247 (t0) cc_final: 0.9003 (t0) REVERT: D 1564 GLU cc_start: 0.8406 (mt-10) cc_final: 0.8022 (pt0) REVERT: D 1640 ASP cc_start: 0.8523 (t0) cc_final: 0.7863 (t0) REVERT: D 1704 ASP cc_start: 0.9046 (t0) cc_final: 0.8249 (p0) REVERT: D 1882 ARG cc_start: 0.8417 (ptp-170) cc_final: 0.8088 (ptp-170) REVERT: D 1930 MET cc_start: 0.4744 (ppp) cc_final: 0.3514 (tpt) outliers start: 24 outliers final: 14 residues processed: 129 average time/residue: 0.6210 time to fit residues: 88.5141 Evaluate side-chains 125 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 108 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 175 GLU Chi-restraints excluded: chain D residue 260 ILE Chi-restraints excluded: chain D residue 295 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 588 ASP Chi-restraints excluded: chain D residue 589 VAL Chi-restraints excluded: chain D residue 738 VAL Chi-restraints excluded: chain D residue 747 VAL Chi-restraints excluded: chain D residue 913 VAL Chi-restraints excluded: chain D residue 1290 LEU Chi-restraints excluded: chain D residue 1512 GLU Chi-restraints excluded: chain D residue 1581 THR Chi-restraints excluded: chain D residue 1792 VAL Chi-restraints excluded: chain D residue 1863 VAL Chi-restraints excluded: chain D residue 1946 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 137 optimal weight: 2.9990 chunk 136 optimal weight: 0.0870 chunk 162 optimal weight: 0.0870 chunk 51 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 167 optimal weight: 10.0000 chunk 19 optimal weight: 3.9990 chunk 74 optimal weight: 9.9990 chunk 48 optimal weight: 2.9990 chunk 150 optimal weight: 8.9990 chunk 14 optimal weight: 8.9990 overall best weight: 1.8342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D1827 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.145087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.094555 restraints weight = 26154.827| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 3.53 r_work: 0.3187 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3196 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3196 r_free = 0.3196 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.80 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3196 r_free = 0.3196 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.81 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3196 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.2198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 14099 Z= 0.199 Angle : 0.591 10.955 19104 Z= 0.294 Chirality : 0.045 0.178 2040 Planarity : 0.004 0.033 2472 Dihedral : 7.258 139.933 1914 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.06 % Favored : 95.88 % Rotamer: Outliers : 1.73 % Allowed : 17.54 % Favored : 80.73 % 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: -0.10 (0.21), residues: 1674 helix: 0.57 (0.35), residues: 228 sheet: -0.20 (0.22), residues: 523 loop : -0.02 (0.22), residues: 923 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D1907 TYR 0.018 0.001 TYR D1558 PHE 0.031 0.002 PHE D1751 TRP 0.046 0.001 TRP D1888 HIS 0.002 0.001 HIS D 734 Details of bonding type rmsd covalent geometry : bond 0.00462 (14099) covalent geometry : angle 0.59143 (19104) hydrogen bonds : bond 0.02960 ( 365) hydrogen bonds : angle 5.37268 ( 978) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5805.25 seconds wall clock time: 99 minutes 41.06 seconds (5981.06 seconds total)