Starting phenix.real_space_refine on Thu Sep 18 04:23:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9qlf_53226/09_2025/9qlf_53226.cif Found real_map, /net/cci-nas-00/data/ceres_data/9qlf_53226/09_2025/9qlf_53226.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.65 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9qlf_53226/09_2025/9qlf_53226.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9qlf_53226/09_2025/9qlf_53226.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9qlf_53226/09_2025/9qlf_53226.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9qlf_53226/09_2025/9qlf_53226.map" } resolution = 2.65 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Ca 10 9.91 5 P 2 5.49 5 S 59 5.16 5 C 8780 2.51 5 N 2352 2.21 5 O 2559 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13762 Number of models: 1 Model: "" Number of chains: 2 Chain: "D" Number of atoms: 13692 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1687, 13692 Classifications: {'peptide': 1687} Link IDs: {'PCIS': 3, 'PTRANS': 103, 'TRANS': 1580} 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=0.78 ... (28 atoms not shown) pdb=" P PSF D2001 " occ=0.78 residue: pdb=" N PSF D2010 " occ=0.89 ... (28 atoms not shown) pdb=" P PSF D2010 " occ=0.89 Time building chain proxies: 3.40, per 1000 atoms: 0.25 Number of scatterers: 13762 At special positions: 0 Unit cell: (102.24, 123.12, 153.36, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 10 19.99 S 59 16.00 P 2 15.00 O 2559 8.00 N 2352 7.00 C 8780 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.15 Conformation dependent library (CDL) restraints added in 689.7 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 3346 Ramachandran restraints generated. 1673 Oldfield, 0 Emsley, 1673 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3176 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 19 sheets defined 16.7% alpha, 28.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.71 Creating SS restraints... Processing helix chain 'D' and resid 172 through 189 Processing helix chain 'D' and resid 255 through 258 Processing helix chain 'D' and resid 284 through 290 Processing helix chain 'D' and resid 307 through 311 Processing helix chain 'D' and resid 335 through 340 Processing helix chain 'D' and resid 342 through 346 removed outlier: 3.687A pdb=" N SER D 345 " --> pdb=" O ASP D 342 " (cutoff:3.500A) Processing helix chain 'D' and resid 376 through 382 Processing helix chain 'D' and resid 520 through 524 Processing helix chain 'D' and resid 558 through 565 Processing helix chain 'D' and resid 566 through 569 Processing helix chain 'D' and resid 650 through 680 removed outlier: 4.015A 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 Processing helix chain 'D' and resid 750 through 765 Processing helix chain 'D' and resid 792 through 796 Processing helix chain 'D' and resid 844 through 847 removed outlier: 4.881A pdb=" N LYS D 847 " --> pdb=" O ALA D 844 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 844 through 847' Processing helix chain 'D' and resid 848 through 853 removed outlier: 4.112A pdb=" N PHE D 852 " --> pdb=" O LYS D 848 " (cutoff:3.500A) Processing helix chain 'D' and resid 895 through 899 removed outlier: 3.695A pdb=" N PHE D 898 " --> pdb=" O LYS D 895 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N PHE D 899 " --> pdb=" O ARG D 896 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 895 through 899' Processing helix chain 'D' and resid 1086 through 1093 removed outlier: 3.705A pdb=" N ALA D1089 " --> pdb=" O HIS D1086 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ALA D1090 " --> pdb=" O GLY D1087 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ILE D1091 " --> pdb=" O ALA D1088 " (cutoff:3.500A) Processing helix chain 'D' and resid 1200 through 1207 Processing helix chain 'D' and resid 1381 through 1385 removed outlier: 3.821A pdb=" N GLY D1384 " --> pdb=" O ARG D1381 " (cutoff:3.500A) Processing helix chain 'D' and resid 1452 through 1462 removed outlier: 3.748A pdb=" N LYS D1456 " --> pdb=" O ASP D1452 " (cutoff:3.500A) Processing helix chain 'D' and resid 1468 through 1473 removed outlier: 3.954A pdb=" N GLN D1472 " --> pdb=" O GLY D1468 " (cutoff:3.500A) Processing helix chain 'D' and resid 1484 through 1495 removed outlier: 3.602A pdb=" N VAL D1488 " --> pdb=" O LEU D1485 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N ALA D1489 " --> pdb=" O GLU D1486 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N GLU D1490 " --> pdb=" O ASN D1487 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLU D1492 " --> pdb=" O ALA D1489 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N GLY D1493 " --> pdb=" O GLU D1490 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N THR D1495 " --> pdb=" O GLU D1492 " (cutoff:3.500A) Processing helix chain 'D' and resid 1590 through 1593 removed outlier: 3.694A pdb=" N TYR D1593 " --> pdb=" O ARG D1590 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1590 through 1593' Processing helix chain 'D' and resid 1641 through 1647 Processing helix chain 'D' and resid 1672 through 1684 Processing helix chain 'D' and resid 1708 through 1710 No H-bonds generated for 'chain 'D' and resid 1708 through 1710' Processing helix chain 'D' and resid 1722 through 1731 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 Processing sheet with id=AA1, first strand: chain 'D' and resid 240 through 249 removed outlier: 6.876A pdb=" N PHE D 241 " --> pdb=" O GLU D 207 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N GLU D 207 " --> pdb=" O PHE D 241 " (cutoff:3.500A) removed outlier: 5.724A pdb=" N ILE D 201 " --> pdb=" O LEU D 323 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N LEU D 323 " --> pdb=" O ILE D 201 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N VAL D 203 " --> pdb=" O PHE D 321 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N PHE D 321 " --> pdb=" O VAL D 203 " (cutoff:3.500A) removed outlier: 5.400A pdb=" N VAL D 205 " --> pdb=" O SER D 319 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N SER D 319 " --> pdb=" O VAL D 205 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLU D 207 " --> pdb=" O LYS D 317 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLY D 314 " --> pdb=" O LEU D 302 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N MET D 316 " --> pdb=" O LEU D 300 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N MET D 320 " --> pdb=" O MET D 296 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N MET D 296 " --> pdb=" O MET D 320 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N VAL D 322 " --> pdb=" O ALA D 294 " (cutoff:3.500A) removed outlier: 5.159A pdb=" N ALA D 294 " --> pdb=" O VAL D 322 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 227 through 230 removed outlier: 5.882A pdb=" N ASN D 267 " --> pdb=" O LEU D 276 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N LEU D 276 " --> pdb=" O ASN D 267 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 499 through 508 removed outlier: 5.330A pdb=" N GLY D 500 " --> pdb=" O LEU D 541 " (cutoff:3.500A) removed outlier: 5.630A pdb=" N LEU D 541 " --> pdb=" O GLY D 500 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N GLY D 535 " --> pdb=" O LEU D 506 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N GLY D 508 " --> pdb=" O TYR D 533 " (cutoff:3.500A) removed outlier: 5.767A pdb=" N TYR D 533 " --> pdb=" O GLY D 508 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N ARG D 536 " --> pdb=" O ALA D 367 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N ALA D 367 " --> pdb=" O ARG D 536 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N LEU D 538 " --> pdb=" O TYR D 365 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N ARG D 366 " --> pdb=" O TRP D 421 " (cutoff:3.500A) removed outlier: 6.374A 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: 6.604A pdb=" N ILE D 438 " --> pdb=" O TYR D 458 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N TYR D 458 " --> pdb=" O ILE D 438 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N LEU D 440 " --> pdb=" O THR D 456 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N THR D 456 " --> pdb=" O LEU D 440 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N ILE D 442 " --> pdb=" O VAL D 454 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 572 through 584 removed outlier: 8.741A pdb=" N SER D 582 " --> pdb=" O THR D 637 " (cutoff:3.500A) removed outlier: 12.209A pdb=" N THR D 637 " --> pdb=" O SER D 582 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 637 through 647 current: chain 'D' and resid 833 through 842 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 833 through 842 current: chain 'D' and resid 873 through 875 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 873 through 875 current: chain 'D' and resid 1071 through 1082 Processing sheet with id=AA6, first strand: chain 'D' and resid 593 through 599 removed outlier: 3.557A pdb=" N ALA D 787 " --> pdb=" O MET D 779 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N ARG D 781 " --> pdb=" O ARG D 785 " (cutoff:3.500A) removed outlier: 5.533A 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 929 through 939 removed outlier: 11.684A pdb=" N GLU D 933 " --> pdb=" O TYR D 953 " (cutoff:3.500A) removed outlier: 10.283A pdb=" N TYR D 953 " --> pdb=" O GLU D 933 " (cutoff:3.500A) removed outlier: 8.296A pdb=" N TYR D 935 " --> pdb=" O ASP D 951 " (cutoff:3.500A) removed outlier: 8.782A pdb=" N ASP D 951 " --> pdb=" O TYR D 935 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N ASN D 937 " --> pdb=" O ALA D 949 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ALA D 949 " --> pdb=" O ASN D 937 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 947 through 954 current: chain 'D' and resid 1018 through 1028 Processing sheet with id=AA9, first strand: chain 'D' and resid 1137 through 1149 removed outlier: 6.622A pdb=" N TYR D1137 " --> pdb=" O GLU D1196 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N GLU D1196 " --> pdb=" O TYR D1137 " (cutoff:3.500A) removed outlier: 6.018A 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: 3.694A pdb=" N GLY D1228 " --> pdb=" O LEU D1215 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N ASP D1217 " --> pdb=" O PHE D1226 " (cutoff:3.500A) removed outlier: 5.749A pdb=" N PHE D1226 " --> pdb=" O ASP D1217 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 1356 through 1364 Processing sheet with id=AB3, first strand: chain 'D' and resid 1312 through 1314 removed outlier: 6.328A pdb=" N VAL D1516 " --> pdb=" O ARG D1505 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N ARG D1505 " --> pdb=" O VAL D1516 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N GLY D1518 " --> pdb=" O LEU D1503 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 1336 through 1339 removed outlier: 3.804A pdb=" N GLY D1390 " --> pdb=" O VAL D1377 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 1479 through 1480 removed outlier: 6.977A pdb=" N LYS D1479 " --> pdb=" O VAL D1742 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N THR D1744 " --> pdb=" O LYS D1479 " (cutoff:3.500A) removed outlier: 8.175A pdb=" N HIS D1741 " --> pdb=" O VAL D1764 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N VAL D1764 " --> pdb=" O HIS D1741 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N LYS D1759 " --> pdb=" O GLY D1562 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N GLY D1562 " --> pdb=" O LYS D1759 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N GLN D1761 " --> pdb=" O VAL D1560 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 1585 through 1588 removed outlier: 3.641A pdb=" N GLY D1635 " --> pdb=" O VAL D1622 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N ASP D1624 " --> pdb=" O LYS D1633 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N LYS D1633 " --> pdb=" O ASP D1624 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 1697 through 1700 Processing sheet with id=AB8, first strand: chain 'D' and resid 1876 through 1879 removed outlier: 3.973A pdb=" N ASP D1853 " --> pdb=" O ILE D1862 " (cutoff:3.500A) removed outlier: 9.327A pdb=" N ALA D1864 " --> pdb=" O PRO D1851 " (cutoff:3.500A) removed outlier: 7.504A pdb=" N GLY D1842 " --> pdb=" O LYS D1798 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N LYS D1798 " --> pdb=" O GLY D1842 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N PHE D1844 " --> pdb=" O ASN D1796 " (cutoff:3.500A) removed outlier: 7.890A pdb=" N ASN D1796 " --> pdb=" O PHE D1844 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N TRP D1846 " --> pdb=" O ILE D1794 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ILE D1794 " --> pdb=" O TRP D1846 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N GLU D1967 " --> pdb=" O TRP D1795 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N THR D1797 " --> pdb=" O LYS D1965 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N LYS D1965 " --> pdb=" O THR D1797 " (cutoff:3.500A) removed outlier: 5.247A pdb=" N ARG D1960 " --> pdb=" O LYS D1956 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N LYS D1956 " --> pdb=" O ARG D1960 " (cutoff:3.500A) removed outlier: 5.379A pdb=" N MET D1962 " --> pdb=" O ALA D1954 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N ALA D1954 " --> pdb=" O MET D1962 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLY D1964 " --> pdb=" O CYS D1952 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 1824 through 1830 removed outlier: 4.385A pdb=" N VAL D1821 " --> pdb=" O ASN D1824 " (cutoff:3.500A) removed outlier: 8.707A pdb=" N GLU D1826 " --> pdb=" O GLY D1819 " (cutoff:3.500A) removed outlier: 10.741A pdb=" N GLY D1819 " --> pdb=" O GLU D1826 " (cutoff:3.500A) removed outlier: 10.250A pdb=" N LYS D1828 " --> pdb=" O VAL D1817 " (cutoff:3.500A) removed outlier: 11.345A pdb=" N VAL D1817 " --> pdb=" O LYS D1828 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N GLY D1900 " --> pdb=" O ILE D1887 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N ASP D1889 " --> pdb=" O TYR D1898 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N TYR D1898 " --> pdb=" O ASP D1889 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 1909 through 1910 382 hydrogen bonds defined for protein. 1029 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: 2.93 Time building geometry restraints manager: 1.56 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: 2827 1.33 - 1.45: 3380 1.45 - 1.58: 7793 1.58 - 1.70: 5 1.70 - 1.83: 93 Bond restraints: 14098 Sorted by residual: bond pdb=" C THR D 252 " pdb=" N PRO D 253 " ideal model delta sigma weight residual 1.334 1.355 -0.022 8.40e-03 1.42e+04 6.73e+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 4.68e+00 bond pdb=" O2 PSF D2010 " pdb=" P PSF D2010 " ideal model delta sigma weight residual 1.637 1.594 0.043 2.00e-02 2.50e+03 4.57e+00 bond pdb=" CB GLU D 546 " pdb=" CG GLU D 546 " ideal model delta sigma weight residual 1.520 1.583 -0.063 3.00e-02 1.11e+03 4.47e+00 bond pdb=" O1 PSF D2001 " pdb=" P PSF D2001 " ideal model delta sigma weight residual 1.636 1.594 0.042 2.00e-02 2.50e+03 4.36e+00 ... (remaining 14093 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.37: 18988 4.37 - 8.75: 88 8.75 - 13.12: 17 13.12 - 17.50: 5 17.50 - 21.87: 1 Bond angle restraints: 19099 Sorted by residual: angle pdb=" CB MET D1242 " pdb=" CG MET D1242 " pdb=" SD MET D1242 " ideal model delta sigma weight residual 112.70 134.57 -21.87 3.00e+00 1.11e-01 5.32e+01 angle pdb=" C ASP D1509 " pdb=" N GLU D1510 " pdb=" CA GLU D1510 " ideal model delta sigma weight residual 121.54 133.02 -11.48 1.91e+00 2.74e-01 3.61e+01 angle pdb=" CB MET D1812 " pdb=" CG MET D1812 " pdb=" SD MET D1812 " ideal model delta sigma weight residual 112.70 128.30 -15.60 3.00e+00 1.11e-01 2.70e+01 angle pdb=" CB MET D 863 " pdb=" CG MET D 863 " pdb=" SD MET D 863 " ideal model delta sigma weight residual 112.70 128.13 -15.43 3.00e+00 1.11e-01 2.65e+01 angle pdb=" CB MET D 191 " pdb=" CG MET D 191 " pdb=" SD MET D 191 " ideal model delta sigma weight residual 112.70 128.10 -15.40 3.00e+00 1.11e-01 2.63e+01 ... (remaining 19094 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 7611 17.96 - 35.91: 694 35.91 - 53.87: 168 53.87 - 71.83: 47 71.83 - 89.79: 22 Dihedral angle restraints: 8542 sinusoidal: 3620 harmonic: 4922 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 -158.68 -21.32 0 5.00e+00 4.00e-02 1.82e+01 dihedral pdb=" CA GLU D1867 " pdb=" C GLU D1867 " pdb=" N HIS D1868 " pdb=" CA HIS D1868 " ideal model delta harmonic sigma weight residual 180.00 158.81 21.19 0 5.00e+00 4.00e-02 1.80e+01 dihedral pdb=" CA ASP D1922 " pdb=" C ASP D1922 " pdb=" N MET D1923 " pdb=" CA MET D1923 " ideal model delta harmonic sigma weight residual 180.00 159.58 20.42 0 5.00e+00 4.00e-02 1.67e+01 ... (remaining 8539 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.102: 1883 0.102 - 0.203: 147 0.203 - 0.305: 2 0.305 - 0.407: 2 0.407 - 0.508: 1 Chirality restraints: 2035 Sorted by residual: chirality pdb=" CB ILE D1793 " pdb=" CA ILE D1793 " pdb=" CG1 ILE D1793 " pdb=" CG2 ILE D1793 " both_signs ideal model delta sigma weight residual False 2.64 2.14 0.51 2.00e-01 2.50e+01 6.46e+00 chirality pdb=" CG LEU D 563 " pdb=" CB LEU D 563 " pdb=" CD1 LEU D 563 " pdb=" CD2 LEU D 563 " both_signs ideal model delta sigma weight residual False -2.59 -2.21 -0.38 2.00e-01 2.50e+01 3.66e+00 chirality pdb=" CB ILE D1862 " pdb=" CA ILE D1862 " pdb=" CG1 ILE D1862 " pdb=" CG2 ILE D1862 " both_signs ideal model delta sigma weight residual False 2.64 2.31 0.34 2.00e-01 2.50e+01 2.82e+00 ... (remaining 2032 not shown) Planarity restraints: 2472 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP D1076 " 0.023 2.00e-02 2.50e+03 2.02e-02 1.02e+01 pdb=" CG TRP D1076 " -0.055 2.00e-02 2.50e+03 pdb=" CD1 TRP D1076 " 0.022 2.00e-02 2.50e+03 pdb=" CD2 TRP D1076 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP D1076 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP D1076 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP D1076 " 0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP D1076 " 0.005 2.00e-02 2.50e+03 pdb=" CZ3 TRP D1076 " 0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP D1076 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE D 431 " -0.044 5.00e-02 4.00e+02 6.62e-02 7.00e+00 pdb=" N PRO D 432 " 0.114 5.00e-02 4.00e+02 pdb=" CA PRO D 432 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO D 432 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASP D 759 " 0.013 2.00e-02 2.50e+03 2.63e-02 6.93e+00 pdb=" CG ASP D 759 " -0.046 2.00e-02 2.50e+03 pdb=" OD1 ASP D 759 " 0.017 2.00e-02 2.50e+03 pdb=" OD2 ASP D 759 " 0.016 2.00e-02 2.50e+03 ... (remaining 2469 not shown) Histogram of nonbonded interaction distances: 2.35 - 2.86: 4329 2.86 - 3.37: 11952 3.37 - 3.88: 23461 3.88 - 4.39: 26444 4.39 - 4.90: 45415 Nonbonded interactions: 111601 Sorted by model distance: nonbonded pdb=" OD2 ASP D1155 " pdb="CA CA D2004 " model vdw 2.351 2.510 nonbonded pdb=" OG1 THR D 449 " pdb="CA CA D2008 " model vdw 2.361 2.510 nonbonded pdb=" O ASN D1218 " pdb="CA CA D2004 " model vdw 2.363 2.510 nonbonded pdb=" O4 PSF D2001 " pdb="CA CA D2003 " model vdw 2.365 2.510 nonbonded pdb=" O TYR D1625 " pdb="CA CA D2006 " model vdw 2.367 2.510 ... (remaining 111596 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=0.78 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.100 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: 0.310 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 14.470 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 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 0.063 14098 Z= 0.220 Angle : 0.902 21.872 19099 Z= 0.444 Chirality : 0.054 0.508 2035 Planarity : 0.007 0.066 2472 Dihedral : 15.714 89.787 5366 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 1.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 1.33 % Allowed : 16.94 % Favored : 81.73 % 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: -1.56 (0.19), residues: 1673 helix: -1.92 (0.27), residues: 234 sheet: -0.57 (0.22), residues: 528 loop : -1.00 (0.19), residues: 911 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D1630 TYR 0.018 0.002 TYR D1558 PHE 0.017 0.002 PHE D1192 TRP 0.055 0.002 TRP D1076 HIS 0.005 0.001 HIS D1868 Details of bonding type rmsd covalent geometry : bond 0.00502 (14098) covalent geometry : angle 0.90180 (19099) hydrogen bonds : bond 0.19054 ( 382) hydrogen bonds : angle 8.63502 ( 1029) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3346 Ramachandran restraints generated. 1673 Oldfield, 0 Emsley, 1673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3346 Ramachandran restraints generated. 1673 Oldfield, 0 Emsley, 1673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 96 time to evaluate : 0.726 Fit side-chains revert: symmetry clash REVERT: D 187 ASN cc_start: 0.8892 (p0) cc_final: 0.8460 (m110) REVERT: D 227 GLN cc_start: 0.7855 (mp10) cc_final: 0.7611 (mp10) REVERT: D 230 ARG cc_start: 0.8680 (tmt90) cc_final: 0.8451 (tmt90) REVERT: D 243 GLU cc_start: 0.8589 (mm-30) cc_final: 0.8306 (mm-30) REVERT: D 289 ASP cc_start: 0.8647 (m-30) cc_final: 0.8382 (m-30) REVERT: D 296 MET cc_start: 0.8508 (mmm) cc_final: 0.8223 (mmm) REVERT: D 824 LYS cc_start: 0.9156 (tttt) cc_final: 0.8509 (pmtt) REVERT: D 911 TRP cc_start: 0.7501 (m100) cc_final: 0.7039 (m100) REVERT: D 934 VAL cc_start: 0.6691 (OUTLIER) cc_final: 0.6391 (m) REVERT: D 1242 MET cc_start: 0.6805 (ppp) cc_final: 0.6578 (pp-130) REVERT: D 1289 ASN cc_start: 0.8785 (t0) cc_final: 0.8534 (t0) REVERT: D 1475 TYR cc_start: 0.7555 (m-80) cc_final: 0.7283 (m-80) REVERT: D 1795 TRP cc_start: 0.8010 (m100) cc_final: 0.6820 (m100) REVERT: D 1859 GLN cc_start: 0.7034 (OUTLIER) cc_final: 0.6290 (mp10) REVERT: D 1888 TRP cc_start: 0.8066 (m-90) cc_final: 0.7831 (m-90) REVERT: D 1901 PHE cc_start: 0.6964 (p90) cc_final: 0.6759 (p90) REVERT: D 1922 ASP cc_start: 0.8589 (m-30) cc_final: 0.7816 (t70) REVERT: D 1943 GLN cc_start: 0.8331 (tm-30) cc_final: 0.8129 (tp-100) REVERT: D 1946 MET cc_start: 0.6071 (ptm) cc_final: 0.5863 (ptt) outliers start: 20 outliers final: 8 residues processed: 116 average time/residue: 0.5710 time to fit residues: 73.6504 Evaluate side-chains 105 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 95 time to evaluate : 0.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 424 VAL Chi-restraints excluded: chain D residue 496 VAL Chi-restraints excluded: chain D residue 498 THR Chi-restraints excluded: chain D residue 934 VAL Chi-restraints excluded: chain D residue 1555 VAL Chi-restraints excluded: chain D residue 1581 THR Chi-restraints excluded: chain D residue 1597 THR Chi-restraints excluded: chain D residue 1671 LEU Chi-restraints excluded: chain D residue 1859 GLN Chi-restraints excluded: chain D residue 1915 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 20.0000 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 9.9990 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 6.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D1754 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.137482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.087466 restraints weight = 28002.023| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 3.40 r_work: 0.3116 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3153 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3153 r_free = 0.3153 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.78 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3153 r_free = 0.3153 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.78 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3153 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.0946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 14098 Z= 0.172 Angle : 0.548 9.492 19099 Z= 0.277 Chirality : 0.044 0.245 2035 Planarity : 0.004 0.052 2472 Dihedral : 6.130 52.863 1921 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.33 % Allowed : 15.48 % Favored : 82.19 % 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: -0.82 (0.20), residues: 1673 helix: -0.45 (0.32), residues: 236 sheet: -0.26 (0.22), residues: 533 loop : -0.66 (0.20), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 209 TYR 0.017 0.001 TYR D1816 PHE 0.022 0.001 PHE D 280 TRP 0.027 0.001 TRP D1076 HIS 0.003 0.001 HIS D1717 Details of bonding type rmsd covalent geometry : bond 0.00395 (14098) covalent geometry : angle 0.54847 (19099) hydrogen bonds : bond 0.03416 ( 382) hydrogen bonds : angle 6.10271 ( 1029) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3346 Ramachandran restraints generated. 1673 Oldfield, 0 Emsley, 1673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3346 Ramachandran restraints generated. 1673 Oldfield, 0 Emsley, 1673 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: 35 poor density : 94 time to evaluate : 0.581 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 187 ASN cc_start: 0.8848 (p0) cc_final: 0.8559 (p0) REVERT: D 230 ARG cc_start: 0.8460 (tmt90) cc_final: 0.8071 (tmt90) REVERT: D 281 LYS cc_start: 0.8625 (mttt) cc_final: 0.7983 (mttm) REVERT: D 296 MET cc_start: 0.8679 (mmm) cc_final: 0.8403 (mmm) REVERT: D 377 PHE cc_start: 0.7855 (m-80) cc_final: 0.7342 (m-10) REVERT: D 391 LYS cc_start: 0.8956 (mmtt) cc_final: 0.8736 (mmpt) REVERT: D 783 GLU cc_start: 0.8691 (OUTLIER) cc_final: 0.8453 (tp30) REVERT: D 829 LYS cc_start: 0.8920 (OUTLIER) cc_final: 0.8402 (mptm) REVERT: D 863 MET cc_start: 0.2455 (tpp) cc_final: 0.1860 (tpp) REVERT: D 1014 MET cc_start: 0.3869 (ptm) cc_final: 0.3247 (pmt) REVERT: D 1076 TRP cc_start: 0.7063 (t60) cc_final: 0.6781 (t60) REVERT: D 1289 ASN cc_start: 0.8999 (t0) cc_final: 0.8778 (t0) REVERT: D 1475 TYR cc_start: 0.7797 (m-80) cc_final: 0.7411 (m-80) REVERT: D 1547 ASP cc_start: 0.8927 (t0) cc_final: 0.8725 (t0) REVERT: D 1751 PHE cc_start: 0.8402 (t80) cc_final: 0.7817 (t80) REVERT: D 1795 TRP cc_start: 0.8015 (m100) cc_final: 0.7215 (m100) REVERT: D 1888 TRP cc_start: 0.8264 (m-90) cc_final: 0.7896 (m-90) REVERT: D 1922 ASP cc_start: 0.8684 (m-30) cc_final: 0.7871 (t70) REVERT: D 1943 GLN cc_start: 0.8148 (tm-30) cc_final: 0.7894 (tp-100) outliers start: 35 outliers final: 14 residues processed: 126 average time/residue: 0.5183 time to fit residues: 73.2821 Evaluate side-chains 107 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 91 time to evaluate : 0.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 286 PHE Chi-restraints excluded: chain D residue 394 LEU Chi-restraints excluded: chain D residue 424 VAL Chi-restraints excluded: chain D residue 448 LEU Chi-restraints excluded: chain D residue 457 THR Chi-restraints excluded: chain D residue 498 THR Chi-restraints excluded: chain D residue 772 MET Chi-restraints excluded: chain D residue 783 GLU Chi-restraints excluded: chain D residue 829 LYS Chi-restraints excluded: chain D residue 859 VAL Chi-restraints excluded: chain D residue 938 GLU Chi-restraints excluded: chain D residue 1290 LEU Chi-restraints excluded: chain D residue 1555 VAL Chi-restraints excluded: chain D residue 1655 ILE Chi-restraints excluded: chain D residue 1901 PHE Chi-restraints excluded: chain D residue 1902 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 105 optimal weight: 4.9990 chunk 53 optimal weight: 3.9990 chunk 73 optimal weight: 8.9990 chunk 83 optimal weight: 20.0000 chunk 152 optimal weight: 0.9990 chunk 120 optimal weight: 4.9990 chunk 47 optimal weight: 3.9990 chunk 158 optimal weight: 4.9990 chunk 63 optimal weight: 0.6980 chunk 129 optimal weight: 8.9990 chunk 5 optimal weight: 5.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 177 GLN D 428 GLN D1754 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.135203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.084974 restraints weight = 28372.417| |-----------------------------------------------------------------------------| r_work (start): 0.3206 rms_B_bonded: 3.33 r_work: 0.3066 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3101 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3101 r_free = 0.3101 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.78 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3101 r_free = 0.3101 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.79 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3101 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.1555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.060 14098 Z= 0.286 Angle : 0.605 8.366 19099 Z= 0.305 Chirality : 0.047 0.229 2035 Planarity : 0.004 0.045 2472 Dihedral : 5.800 51.268 1911 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 3.79 % Allowed : 14.62 % 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: -0.60 (0.20), residues: 1673 helix: 0.11 (0.33), residues: 235 sheet: -0.23 (0.21), residues: 541 loop : -0.55 (0.21), residues: 897 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D1561 TYR 0.017 0.002 TYR D 704 PHE 0.016 0.001 PHE D1192 TRP 0.018 0.001 TRP D1076 HIS 0.004 0.001 HIS D 581 Details of bonding type rmsd covalent geometry : bond 0.00665 (14098) covalent geometry : angle 0.60545 (19099) hydrogen bonds : bond 0.03575 ( 382) hydrogen bonds : angle 5.74705 ( 1029) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3346 Ramachandran restraints generated. 1673 Oldfield, 0 Emsley, 1673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3346 Ramachandran restraints generated. 1673 Oldfield, 0 Emsley, 1673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 90 time to evaluate : 0.591 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 187 ASN cc_start: 0.8844 (p0) cc_final: 0.8527 (p0) REVERT: D 230 ARG cc_start: 0.8457 (tmt90) cc_final: 0.8195 (tmt90) REVERT: D 281 LYS cc_start: 0.8621 (mttt) cc_final: 0.8095 (mttm) REVERT: D 296 MET cc_start: 0.8745 (mmm) cc_final: 0.8445 (mmm) REVERT: D 377 PHE cc_start: 0.7933 (m-80) cc_final: 0.7401 (m-10) REVERT: D 829 LYS cc_start: 0.8960 (OUTLIER) cc_final: 0.8075 (mptm) REVERT: D 863 MET cc_start: 0.3036 (tpp) cc_final: 0.2379 (tpp) REVERT: D 1014 MET cc_start: 0.3847 (ptm) cc_final: 0.3165 (pmt) REVERT: D 1076 TRP cc_start: 0.7185 (t60) cc_final: 0.6233 (t60) REVERT: D 1223 LYS cc_start: 0.8717 (mmtm) cc_final: 0.8499 (mmmt) REVERT: D 1242 MET cc_start: 0.7133 (ppp) cc_final: 0.6888 (ppp) REVERT: D 1289 ASN cc_start: 0.9062 (t0) cc_final: 0.8836 (t0) REVERT: D 1475 TYR cc_start: 0.7910 (m-80) cc_final: 0.7542 (m-80) REVERT: D 1859 GLN cc_start: 0.6950 (OUTLIER) cc_final: 0.6594 (tp40) REVERT: D 1888 TRP cc_start: 0.8253 (m-90) cc_final: 0.7904 (m-90) REVERT: D 1906 LEU cc_start: 0.6638 (OUTLIER) cc_final: 0.6438 (mm) outliers start: 57 outliers final: 24 residues processed: 136 average time/residue: 0.5699 time to fit residues: 86.3480 Evaluate side-chains 113 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 86 time to evaluate : 0.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 286 PHE Chi-restraints excluded: chain D residue 295 VAL Chi-restraints excluded: chain D residue 307 ASP Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain D residue 394 LEU Chi-restraints excluded: chain D residue 424 VAL Chi-restraints excluded: chain D residue 448 LEU Chi-restraints excluded: chain D residue 457 THR Chi-restraints excluded: chain D residue 496 VAL Chi-restraints excluded: chain D residue 498 THR Chi-restraints excluded: chain D residue 585 MET Chi-restraints excluded: chain D residue 772 MET Chi-restraints excluded: chain D residue 825 ASN Chi-restraints excluded: chain D residue 829 LYS Chi-restraints excluded: chain D residue 834 LEU Chi-restraints excluded: chain D residue 859 VAL Chi-restraints excluded: chain D residue 938 GLU Chi-restraints excluded: chain D residue 1290 LEU Chi-restraints excluded: chain D residue 1555 VAL Chi-restraints excluded: chain D residue 1561 ARG Chi-restraints excluded: chain D residue 1581 THR Chi-restraints excluded: chain D residue 1671 LEU Chi-restraints excluded: chain D residue 1746 THR Chi-restraints excluded: chain D residue 1797 THR Chi-restraints excluded: chain D residue 1859 GLN Chi-restraints excluded: chain D residue 1906 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 98 optimal weight: 0.9980 chunk 72 optimal weight: 7.9990 chunk 131 optimal weight: 2.9990 chunk 54 optimal weight: 0.9990 chunk 39 optimal weight: 0.7980 chunk 103 optimal weight: 0.8980 chunk 157 optimal weight: 0.0970 chunk 97 optimal weight: 0.8980 chunk 44 optimal weight: 0.5980 chunk 87 optimal weight: 0.0040 chunk 55 optimal weight: 0.7980 overall best weight: 0.4590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D1754 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.137746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.088516 restraints weight = 27904.148| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 3.36 r_work: 0.3138 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3173 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3173 r_free = 0.3173 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.79 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3173 r_free = 0.3173 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.80 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3173 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.1486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 14098 Z= 0.093 Angle : 0.509 8.507 19099 Z= 0.254 Chirality : 0.044 0.260 2035 Planarity : 0.004 0.056 2472 Dihedral : 5.227 41.852 1911 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.92 % Allowed : 16.35 % 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: -0.30 (0.20), residues: 1673 helix: 0.68 (0.35), residues: 234 sheet: -0.09 (0.21), residues: 543 loop : -0.41 (0.21), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D1298 TYR 0.017 0.001 TYR D1898 PHE 0.010 0.001 PHE D1192 TRP 0.017 0.001 TRP D1076 HIS 0.002 0.000 HIS D1717 Details of bonding type rmsd covalent geometry : bond 0.00209 (14098) covalent geometry : angle 0.50945 (19099) hydrogen bonds : bond 0.02815 ( 382) hydrogen bonds : angle 5.30136 ( 1029) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3346 Ramachandran restraints generated. 1673 Oldfield, 0 Emsley, 1673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3346 Ramachandran restraints generated. 1673 Oldfield, 0 Emsley, 1673 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: 44 poor density : 94 time to evaluate : 0.552 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 230 ARG cc_start: 0.8451 (tmt90) cc_final: 0.8189 (tmt90) REVERT: D 281 LYS cc_start: 0.8617 (mttt) cc_final: 0.7925 (mttm) REVERT: D 296 MET cc_start: 0.8684 (mmm) cc_final: 0.8400 (mmm) REVERT: D 377 PHE cc_start: 0.7909 (m-80) cc_final: 0.7362 (m-10) REVERT: D 763 GLN cc_start: 0.8946 (mm110) cc_final: 0.8692 (mm110) REVERT: D 863 MET cc_start: 0.2968 (tpp) cc_final: 0.2399 (tpp) REVERT: D 870 MET cc_start: 0.0523 (mmt) cc_final: 0.0004 (mpt) REVERT: D 1014 MET cc_start: 0.3816 (ptm) cc_final: 0.3141 (pmt) REVERT: D 1076 TRP cc_start: 0.7222 (t60) cc_final: 0.6811 (t60) REVERT: D 1242 MET cc_start: 0.7137 (ppp) cc_final: 0.6822 (ppp) REVERT: D 1289 ASN cc_start: 0.8983 (t0) cc_final: 0.8765 (t0) REVERT: D 1475 TYR cc_start: 0.7848 (m-80) cc_final: 0.7430 (m-80) REVERT: D 1751 PHE cc_start: 0.8365 (t80) cc_final: 0.7747 (t80) REVERT: D 1859 GLN cc_start: 0.6883 (OUTLIER) cc_final: 0.6546 (tp40) REVERT: D 1888 TRP cc_start: 0.8231 (m-90) cc_final: 0.7827 (m-90) REVERT: D 1898 TYR cc_start: 0.6202 (t80) cc_final: 0.5987 (t80) REVERT: D 1922 ASP cc_start: 0.8738 (m-30) cc_final: 0.8013 (t70) REVERT: D 1962 MET cc_start: 0.8392 (tpt) cc_final: 0.7997 (tpp) outliers start: 44 outliers final: 16 residues processed: 132 average time/residue: 0.5353 time to fit residues: 78.5197 Evaluate side-chains 104 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 87 time to evaluate : 0.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 260 ILE Chi-restraints excluded: chain D residue 286 PHE Chi-restraints excluded: chain D residue 295 VAL Chi-restraints excluded: chain D residue 394 LEU Chi-restraints excluded: chain D residue 396 ASP Chi-restraints excluded: chain D residue 448 LEU Chi-restraints excluded: chain D residue 457 THR Chi-restraints excluded: chain D residue 825 ASN Chi-restraints excluded: chain D residue 842 LEU Chi-restraints excluded: chain D residue 859 VAL Chi-restraints excluded: chain D residue 938 GLU Chi-restraints excluded: chain D residue 1290 LEU Chi-restraints excluded: chain D residue 1555 VAL Chi-restraints excluded: chain D residue 1746 THR Chi-restraints excluded: chain D residue 1792 VAL Chi-restraints excluded: chain D residue 1797 THR Chi-restraints excluded: chain D residue 1859 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 108 optimal weight: 0.0770 chunk 137 optimal weight: 0.9980 chunk 93 optimal weight: 0.8980 chunk 83 optimal weight: 4.9990 chunk 110 optimal weight: 0.7980 chunk 105 optimal weight: 2.9990 chunk 63 optimal weight: 0.9990 chunk 15 optimal weight: 4.9990 chunk 117 optimal weight: 10.0000 chunk 84 optimal weight: 8.9990 chunk 102 optimal weight: 5.9990 overall best weight: 0.7540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 936 GLN D1754 ASN ** D1868 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.137647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.088069 restraints weight = 28280.961| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 3.45 r_work: 0.3132 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3166 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3166 r_free = 0.3166 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.80 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3166 r_free = 0.3166 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.78 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3166 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.1587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 14098 Z= 0.108 Angle : 0.510 9.199 19099 Z= 0.253 Chirality : 0.044 0.271 2035 Planarity : 0.003 0.054 2472 Dihedral : 5.002 38.403 1909 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.72 % Allowed : 16.61 % Favored : 80.66 % 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: -0.15 (0.20), residues: 1673 helix: 0.94 (0.35), residues: 234 sheet: 0.01 (0.21), residues: 541 loop : -0.37 (0.21), residues: 898 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 232 TYR 0.012 0.001 TYR D1816 PHE 0.013 0.001 PHE D1192 TRP 0.014 0.001 TRP D1076 HIS 0.005 0.000 HIS D1868 Details of bonding type rmsd covalent geometry : bond 0.00247 (14098) covalent geometry : angle 0.51019 (19099) hydrogen bonds : bond 0.02759 ( 382) hydrogen bonds : angle 5.13386 ( 1029) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3346 Ramachandran restraints generated. 1673 Oldfield, 0 Emsley, 1673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3346 Ramachandran restraints generated. 1673 Oldfield, 0 Emsley, 1673 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: 41 poor density : 88 time to evaluate : 0.369 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 204 ARG cc_start: 0.8378 (OUTLIER) cc_final: 0.8039 (ptm160) REVERT: D 230 ARG cc_start: 0.8466 (tmt90) cc_final: 0.8207 (tmt90) REVERT: D 281 LYS cc_start: 0.8588 (mttt) cc_final: 0.7911 (mttm) REVERT: D 296 MET cc_start: 0.8641 (mmm) cc_final: 0.8354 (mmm) REVERT: D 377 PHE cc_start: 0.7924 (m-80) cc_final: 0.7351 (m-10) REVERT: D 763 GLN cc_start: 0.8857 (mm110) cc_final: 0.8644 (mm110) REVERT: D 786 LEU cc_start: 0.9345 (OUTLIER) cc_final: 0.9087 (tt) REVERT: D 863 MET cc_start: 0.3111 (tpp) cc_final: 0.2486 (tpp) REVERT: D 870 MET cc_start: 0.0593 (mmt) cc_final: 0.0143 (mpt) REVERT: D 1014 MET cc_start: 0.3812 (ptm) cc_final: 0.3186 (pmt) REVERT: D 1076 TRP cc_start: 0.7265 (t60) cc_final: 0.6816 (t60) REVERT: D 1242 MET cc_start: 0.7130 (ppp) cc_final: 0.6847 (ppp) REVERT: D 1289 ASN cc_start: 0.9029 (t0) cc_final: 0.8820 (t0) REVERT: D 1475 TYR cc_start: 0.7754 (m-80) cc_final: 0.7410 (m-80) REVERT: D 1751 PHE cc_start: 0.8342 (t80) cc_final: 0.7759 (t80) REVERT: D 1859 GLN cc_start: 0.6886 (OUTLIER) cc_final: 0.6579 (tp40) REVERT: D 1888 TRP cc_start: 0.8201 (m-90) cc_final: 0.7803 (m-90) REVERT: D 1962 MET cc_start: 0.8440 (tpt) cc_final: 0.8165 (tpp) outliers start: 41 outliers final: 21 residues processed: 124 average time/residue: 0.5351 time to fit residues: 74.2459 Evaluate side-chains 108 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 84 time to evaluate : 0.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 204 ARG Chi-restraints excluded: chain D residue 260 ILE Chi-restraints excluded: chain D residue 394 LEU Chi-restraints excluded: chain D residue 448 LEU Chi-restraints excluded: chain D residue 457 THR Chi-restraints excluded: chain D residue 496 VAL Chi-restraints excluded: chain D residue 754 ILE Chi-restraints excluded: chain D residue 786 LEU Chi-restraints excluded: chain D residue 825 ASN Chi-restraints excluded: chain D residue 842 LEU Chi-restraints excluded: chain D residue 938 GLU Chi-restraints excluded: chain D residue 1223 LYS Chi-restraints excluded: chain D residue 1290 LEU Chi-restraints excluded: chain D residue 1323 SER Chi-restraints excluded: chain D residue 1478 LEU Chi-restraints excluded: chain D residue 1555 VAL Chi-restraints excluded: chain D residue 1581 THR Chi-restraints excluded: chain D residue 1655 ILE Chi-restraints excluded: chain D residue 1746 THR Chi-restraints excluded: chain D residue 1792 VAL Chi-restraints excluded: chain D residue 1797 THR Chi-restraints excluded: chain D residue 1859 GLN Chi-restraints excluded: chain D residue 1868 HIS Chi-restraints excluded: chain D residue 1902 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 85 optimal weight: 8.9990 chunk 80 optimal weight: 40.0000 chunk 112 optimal weight: 0.0670 chunk 118 optimal weight: 0.8980 chunk 11 optimal weight: 6.9990 chunk 35 optimal weight: 1.9990 chunk 138 optimal weight: 9.9990 chunk 39 optimal weight: 3.9990 chunk 32 optimal weight: 0.9980 chunk 26 optimal weight: 2.9990 chunk 91 optimal weight: 0.6980 overall best weight: 0.9320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D1754 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 = 0.137646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.088038 restraints weight = 28075.223| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 3.37 r_work: 0.3132 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3166 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3166 r_free = 0.3166 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.78 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3166 r_free = 0.3166 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.79 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3166 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.1686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14098 Z= 0.118 Angle : 0.515 9.075 19099 Z= 0.254 Chirality : 0.044 0.287 2035 Planarity : 0.003 0.054 2472 Dihedral : 4.928 36.912 1909 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.59 % Allowed : 17.01 % Favored : 80.40 % 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: -0.05 (0.21), residues: 1673 helix: 1.08 (0.35), residues: 234 sheet: 0.09 (0.21), residues: 541 loop : -0.34 (0.21), residues: 898 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 209 TYR 0.013 0.001 TYR D1788 PHE 0.012 0.001 PHE D1192 TRP 0.014 0.001 TRP D1076 HIS 0.004 0.000 HIS D1868 Details of bonding type rmsd covalent geometry : bond 0.00272 (14098) covalent geometry : angle 0.51463 (19099) hydrogen bonds : bond 0.02720 ( 382) hydrogen bonds : angle 5.05808 ( 1029) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3346 Ramachandran restraints generated. 1673 Oldfield, 0 Emsley, 1673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3346 Ramachandran restraints generated. 1673 Oldfield, 0 Emsley, 1673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 87 time to evaluate : 0.586 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 204 ARG cc_start: 0.8397 (OUTLIER) cc_final: 0.7810 (ptm-80) REVERT: D 230 ARG cc_start: 0.8469 (tmt90) cc_final: 0.8210 (tmt90) REVERT: D 281 LYS cc_start: 0.8556 (mttt) cc_final: 0.7976 (mttp) REVERT: D 296 MET cc_start: 0.8644 (mmm) cc_final: 0.8354 (mmm) REVERT: D 377 PHE cc_start: 0.7924 (m-80) cc_final: 0.7335 (m-10) REVERT: D 763 GLN cc_start: 0.8862 (mm110) cc_final: 0.8648 (mm110) REVERT: D 786 LEU cc_start: 0.9328 (OUTLIER) cc_final: 0.9069 (tt) REVERT: D 863 MET cc_start: 0.3277 (tpp) cc_final: 0.2792 (tpp) REVERT: D 870 MET cc_start: 0.0407 (mmt) cc_final: 0.0130 (mpt) REVERT: D 1014 MET cc_start: 0.3894 (ptm) cc_final: 0.3198 (pmt) REVERT: D 1076 TRP cc_start: 0.7299 (t60) cc_final: 0.6837 (t60) REVERT: D 1242 MET cc_start: 0.7141 (ppp) cc_final: 0.6825 (ppp) REVERT: D 1475 TYR cc_start: 0.7774 (m-80) cc_final: 0.7434 (m-80) REVERT: D 1751 PHE cc_start: 0.8337 (t80) cc_final: 0.7734 (t80) REVERT: D 1859 GLN cc_start: 0.6875 (OUTLIER) cc_final: 0.6600 (tp40) REVERT: D 1888 TRP cc_start: 0.8158 (m-90) cc_final: 0.7751 (m-90) REVERT: D 1962 MET cc_start: 0.8450 (tpt) cc_final: 0.8202 (tpp) outliers start: 39 outliers final: 25 residues processed: 122 average time/residue: 0.5080 time to fit residues: 69.8551 Evaluate side-chains 112 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 84 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 204 ARG Chi-restraints excluded: chain D residue 260 ILE Chi-restraints excluded: chain D residue 286 PHE Chi-restraints excluded: chain D residue 295 VAL Chi-restraints excluded: chain D residue 394 LEU Chi-restraints excluded: chain D residue 396 ASP Chi-restraints excluded: chain D residue 408 VAL Chi-restraints excluded: chain D residue 424 VAL Chi-restraints excluded: chain D residue 448 LEU Chi-restraints excluded: chain D residue 457 THR Chi-restraints excluded: chain D residue 754 ILE Chi-restraints excluded: chain D residue 786 LEU Chi-restraints excluded: chain D residue 825 ASN Chi-restraints excluded: chain D residue 859 VAL Chi-restraints excluded: chain D residue 938 GLU Chi-restraints excluded: chain D residue 1223 LYS Chi-restraints excluded: chain D residue 1290 LEU Chi-restraints excluded: chain D residue 1323 SER Chi-restraints excluded: chain D residue 1478 LEU Chi-restraints excluded: chain D residue 1555 VAL Chi-restraints excluded: chain D residue 1581 THR Chi-restraints excluded: chain D residue 1746 THR Chi-restraints excluded: chain D residue 1792 VAL Chi-restraints excluded: chain D residue 1797 THR Chi-restraints excluded: chain D residue 1859 GLN Chi-restraints excluded: chain D residue 1868 HIS Chi-restraints excluded: chain D residue 1902 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 36 optimal weight: 0.7980 chunk 133 optimal weight: 0.9990 chunk 102 optimal weight: 0.5980 chunk 2 optimal weight: 8.9990 chunk 35 optimal weight: 0.6980 chunk 125 optimal weight: 4.9990 chunk 137 optimal weight: 0.6980 chunk 51 optimal weight: 0.7980 chunk 146 optimal weight: 0.7980 chunk 128 optimal weight: 2.9990 chunk 114 optimal weight: 0.0970 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D1754 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.138355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.089171 restraints weight = 28100.875| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 3.39 r_work: 0.3152 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3185 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3185 r_free = 0.3185 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.79 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3185 r_free = 0.3185 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.79 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3185 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.1726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 14098 Z= 0.095 Angle : 0.518 10.743 19099 Z= 0.252 Chirality : 0.044 0.284 2035 Planarity : 0.003 0.054 2472 Dihedral : 4.769 36.605 1909 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.59 % Allowed : 17.14 % Favored : 80.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.03 (0.21), residues: 1673 helix: 1.21 (0.36), residues: 234 sheet: 0.15 (0.21), residues: 541 loop : -0.30 (0.21), residues: 898 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 209 TYR 0.013 0.001 TYR D1558 PHE 0.011 0.001 PHE D1192 TRP 0.014 0.001 TRP D1076 HIS 0.003 0.000 HIS D1868 Details of bonding type rmsd covalent geometry : bond 0.00219 (14098) covalent geometry : angle 0.51800 (19099) hydrogen bonds : bond 0.02594 ( 382) hydrogen bonds : angle 4.95316 ( 1029) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3346 Ramachandran restraints generated. 1673 Oldfield, 0 Emsley, 1673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3346 Ramachandran restraints generated. 1673 Oldfield, 0 Emsley, 1673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 88 time to evaluate : 0.513 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 230 ARG cc_start: 0.8495 (tmt90) cc_final: 0.8242 (tmt90) REVERT: D 281 LYS cc_start: 0.8539 (mttt) cc_final: 0.7883 (mttm) REVERT: D 296 MET cc_start: 0.8600 (mmm) cc_final: 0.8293 (mmm) REVERT: D 377 PHE cc_start: 0.7919 (m-80) cc_final: 0.7323 (m-10) REVERT: D 763 GLN cc_start: 0.8829 (mm110) cc_final: 0.8627 (mm110) REVERT: D 786 LEU cc_start: 0.9336 (OUTLIER) cc_final: 0.9078 (tt) REVERT: D 863 MET cc_start: 0.3350 (tpp) cc_final: 0.2898 (tpp) REVERT: D 870 MET cc_start: 0.0273 (mmt) cc_final: -0.0028 (mpt) REVERT: D 1014 MET cc_start: 0.3935 (ptm) cc_final: 0.3235 (pmt) REVERT: D 1076 TRP cc_start: 0.7255 (t60) cc_final: 0.6790 (t60) REVERT: D 1242 MET cc_start: 0.7102 (ppp) cc_final: 0.6743 (ppp) REVERT: D 1475 TYR cc_start: 0.7740 (m-80) cc_final: 0.7414 (m-80) REVERT: D 1561 ARG cc_start: 0.8696 (OUTLIER) cc_final: 0.8423 (ptt180) REVERT: D 1619 LYS cc_start: 0.8658 (OUTLIER) cc_final: 0.8330 (ttmm) REVERT: D 1751 PHE cc_start: 0.8325 (t80) cc_final: 0.7725 (t80) REVERT: D 1859 GLN cc_start: 0.6841 (OUTLIER) cc_final: 0.6570 (tp40) REVERT: D 1888 TRP cc_start: 0.8143 (m-90) cc_final: 0.7803 (m-90) outliers start: 39 outliers final: 24 residues processed: 123 average time/residue: 0.5418 time to fit residues: 74.7089 Evaluate side-chains 115 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 87 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 260 ILE Chi-restraints excluded: chain D residue 286 PHE Chi-restraints excluded: chain D residue 295 VAL Chi-restraints excluded: chain D residue 424 VAL Chi-restraints excluded: chain D residue 448 LEU Chi-restraints excluded: chain D residue 457 THR Chi-restraints excluded: chain D residue 496 VAL Chi-restraints excluded: chain D residue 498 THR Chi-restraints excluded: chain D residue 514 THR Chi-restraints excluded: chain D residue 754 ILE Chi-restraints excluded: chain D residue 786 LEU Chi-restraints excluded: chain D residue 825 ASN Chi-restraints excluded: chain D residue 859 VAL Chi-restraints excluded: chain D residue 938 GLU Chi-restraints excluded: chain D residue 1223 LYS Chi-restraints excluded: chain D residue 1290 LEU Chi-restraints excluded: chain D residue 1323 SER Chi-restraints excluded: chain D residue 1392 CYS Chi-restraints excluded: chain D residue 1478 LEU Chi-restraints excluded: chain D residue 1555 VAL Chi-restraints excluded: chain D residue 1561 ARG Chi-restraints excluded: chain D residue 1581 THR Chi-restraints excluded: chain D residue 1619 LYS Chi-restraints excluded: chain D residue 1746 THR Chi-restraints excluded: chain D residue 1792 VAL Chi-restraints excluded: chain D residue 1797 THR Chi-restraints excluded: chain D residue 1859 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 155 optimal weight: 0.2980 chunk 149 optimal weight: 5.9990 chunk 146 optimal weight: 0.7980 chunk 166 optimal weight: 8.9990 chunk 77 optimal weight: 9.9990 chunk 15 optimal weight: 6.9990 chunk 76 optimal weight: 6.9990 chunk 58 optimal weight: 0.5980 chunk 59 optimal weight: 1.9990 chunk 109 optimal weight: 1.9990 chunk 23 optimal weight: 6.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 428 GLN D1754 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.137657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.087985 restraints weight = 27903.802| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 3.42 r_work: 0.3124 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3166 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3166 r_free = 0.3166 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.79 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3165 r_free = 0.3165 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.79 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3165 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.1805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 14098 Z= 0.133 Angle : 0.529 9.989 19099 Z= 0.259 Chirality : 0.044 0.284 2035 Planarity : 0.003 0.052 2472 Dihedral : 4.806 36.816 1909 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 2.66 % Allowed : 17.08 % Favored : 80.27 % 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: 1673 helix: 1.24 (0.36), residues: 234 sheet: 0.16 (0.21), residues: 547 loop : -0.27 (0.22), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 209 TYR 0.014 0.001 TYR D1558 PHE 0.013 0.001 PHE D1192 TRP 0.013 0.001 TRP D1076 HIS 0.004 0.000 HIS D1868 Details of bonding type rmsd covalent geometry : bond 0.00307 (14098) covalent geometry : angle 0.52896 (19099) hydrogen bonds : bond 0.02701 ( 382) hydrogen bonds : angle 4.97360 ( 1029) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3346 Ramachandran restraints generated. 1673 Oldfield, 0 Emsley, 1673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3346 Ramachandran restraints generated. 1673 Oldfield, 0 Emsley, 1673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 86 time to evaluate : 0.580 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 204 ARG cc_start: 0.8388 (OUTLIER) cc_final: 0.7823 (ptm-80) REVERT: D 230 ARG cc_start: 0.8513 (tmt90) cc_final: 0.8254 (tmt90) REVERT: D 281 LYS cc_start: 0.8546 (mttt) cc_final: 0.7896 (mttm) REVERT: D 296 MET cc_start: 0.8624 (mmm) cc_final: 0.8313 (mmm) REVERT: D 377 PHE cc_start: 0.7932 (m-80) cc_final: 0.7335 (m-10) REVERT: D 786 LEU cc_start: 0.9322 (OUTLIER) cc_final: 0.9062 (tt) REVERT: D 863 MET cc_start: 0.3466 (tpp) cc_final: 0.2945 (tpp) REVERT: D 870 MET cc_start: 0.0426 (mmt) cc_final: 0.0104 (mpt) REVERT: D 1014 MET cc_start: 0.3848 (ptm) cc_final: 0.3222 (pmt) REVERT: D 1076 TRP cc_start: 0.7335 (t60) cc_final: 0.6541 (t60) REVERT: D 1242 MET cc_start: 0.7129 (ppp) cc_final: 0.6754 (ppp) REVERT: D 1475 TYR cc_start: 0.7761 (m-80) cc_final: 0.7402 (m-80) REVERT: D 1561 ARG cc_start: 0.8673 (OUTLIER) cc_final: 0.7940 (ptp-170) REVERT: D 1619 LYS cc_start: 0.8667 (OUTLIER) cc_final: 0.8343 (ttmm) REVERT: D 1751 PHE cc_start: 0.8322 (t80) cc_final: 0.7697 (t80) REVERT: D 1859 GLN cc_start: 0.6861 (OUTLIER) cc_final: 0.6608 (tp40) REVERT: D 1888 TRP cc_start: 0.8103 (m-90) cc_final: 0.7830 (OUTLIER) outliers start: 40 outliers final: 26 residues processed: 123 average time/residue: 0.5595 time to fit residues: 76.6416 Evaluate side-chains 113 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 83 time to evaluate : 0.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 204 ARG Chi-restraints excluded: chain D residue 260 ILE Chi-restraints excluded: chain D residue 286 PHE Chi-restraints excluded: chain D residue 295 VAL Chi-restraints excluded: chain D residue 396 ASP Chi-restraints excluded: chain D residue 408 VAL Chi-restraints excluded: chain D residue 424 VAL Chi-restraints excluded: chain D residue 448 LEU Chi-restraints excluded: chain D residue 457 THR Chi-restraints excluded: chain D residue 496 VAL Chi-restraints excluded: chain D residue 498 THR Chi-restraints excluded: chain D residue 754 ILE Chi-restraints excluded: chain D residue 786 LEU Chi-restraints excluded: chain D residue 825 ASN Chi-restraints excluded: chain D residue 859 VAL Chi-restraints excluded: chain D residue 938 GLU Chi-restraints excluded: chain D residue 1223 LYS Chi-restraints excluded: chain D residue 1290 LEU Chi-restraints excluded: chain D residue 1323 SER Chi-restraints excluded: chain D residue 1555 VAL Chi-restraints excluded: chain D residue 1561 ARG Chi-restraints excluded: chain D residue 1581 THR Chi-restraints excluded: chain D residue 1597 THR Chi-restraints excluded: chain D residue 1619 LYS Chi-restraints excluded: chain D residue 1746 THR Chi-restraints excluded: chain D residue 1792 VAL Chi-restraints excluded: chain D residue 1797 THR Chi-restraints excluded: chain D residue 1859 GLN Chi-restraints excluded: chain D residue 1868 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 26 optimal weight: 2.9990 chunk 122 optimal weight: 0.7980 chunk 130 optimal weight: 0.7980 chunk 2 optimal weight: 6.9990 chunk 118 optimal weight: 0.9980 chunk 57 optimal weight: 1.9990 chunk 9 optimal weight: 5.9990 chunk 102 optimal weight: 0.5980 chunk 54 optimal weight: 6.9990 chunk 140 optimal weight: 0.8980 chunk 65 optimal weight: 4.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D1754 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.137859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.088516 restraints weight = 28054.331| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 3.39 r_work: 0.3141 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3174 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3174 r_free = 0.3174 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.79 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3174 r_free = 0.3174 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.79 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3174 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.1822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 14098 Z= 0.112 Angle : 0.524 10.301 19099 Z= 0.257 Chirality : 0.044 0.299 2035 Planarity : 0.003 0.052 2472 Dihedral : 4.758 36.987 1909 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.06 % Allowed : 17.67 % Favored : 80.27 % 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: 1673 helix: 1.19 (0.35), residues: 234 sheet: 0.14 (0.21), residues: 549 loop : -0.24 (0.22), residues: 890 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 209 TYR 0.016 0.001 TYR D1558 PHE 0.012 0.001 PHE D1192 TRP 0.013 0.001 TRP D1076 HIS 0.004 0.000 HIS D1868 Details of bonding type rmsd covalent geometry : bond 0.00258 (14098) covalent geometry : angle 0.52366 (19099) hydrogen bonds : bond 0.02634 ( 382) hydrogen bonds : angle 4.90234 ( 1029) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3346 Ramachandran restraints generated. 1673 Oldfield, 0 Emsley, 1673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3346 Ramachandran restraints generated. 1673 Oldfield, 0 Emsley, 1673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 85 time to evaluate : 0.599 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 187 ASN cc_start: 0.8879 (p0) cc_final: 0.8559 (p0) REVERT: D 230 ARG cc_start: 0.8526 (tmt90) cc_final: 0.8269 (tmt90) REVERT: D 281 LYS cc_start: 0.8525 (mttt) cc_final: 0.7876 (mttm) REVERT: D 296 MET cc_start: 0.8608 (mmm) cc_final: 0.8296 (mmm) REVERT: D 377 PHE cc_start: 0.7919 (m-80) cc_final: 0.7320 (m-10) REVERT: D 863 MET cc_start: 0.3438 (tpp) cc_final: 0.3014 (tpp) REVERT: D 1014 MET cc_start: 0.3895 (ptm) cc_final: 0.3221 (pmt) REVERT: D 1076 TRP cc_start: 0.7370 (t60) cc_final: 0.6902 (t60) REVERT: D 1242 MET cc_start: 0.7124 (ppp) cc_final: 0.6756 (ppp) REVERT: D 1475 TYR cc_start: 0.7757 (m-80) cc_final: 0.7389 (m-80) REVERT: D 1561 ARG cc_start: 0.8662 (OUTLIER) cc_final: 0.8374 (ptt180) REVERT: D 1619 LYS cc_start: 0.8657 (OUTLIER) cc_final: 0.8324 (ttmm) REVERT: D 1751 PHE cc_start: 0.8313 (t80) cc_final: 0.7683 (t80) REVERT: D 1859 GLN cc_start: 0.6848 (OUTLIER) cc_final: 0.6595 (tp40) REVERT: D 1888 TRP cc_start: 0.8043 (m-90) cc_final: 0.7772 (OUTLIER) outliers start: 31 outliers final: 26 residues processed: 114 average time/residue: 0.5300 time to fit residues: 67.7862 Evaluate side-chains 114 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 86 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 173 VAL 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 408 VAL Chi-restraints excluded: chain D residue 424 VAL Chi-restraints excluded: chain D residue 448 LEU Chi-restraints excluded: chain D residue 457 THR Chi-restraints excluded: chain D residue 496 VAL Chi-restraints excluded: chain D residue 498 THR Chi-restraints excluded: chain D residue 754 ILE Chi-restraints excluded: chain D residue 825 ASN Chi-restraints excluded: chain D residue 859 VAL Chi-restraints excluded: chain D residue 938 GLU Chi-restraints excluded: chain D residue 1223 LYS Chi-restraints excluded: chain D residue 1290 LEU Chi-restraints excluded: chain D residue 1323 SER Chi-restraints excluded: chain D residue 1392 CYS Chi-restraints excluded: chain D residue 1478 LEU Chi-restraints excluded: chain D residue 1555 VAL Chi-restraints excluded: chain D residue 1561 ARG Chi-restraints excluded: chain D residue 1581 THR Chi-restraints excluded: chain D residue 1597 THR Chi-restraints excluded: chain D residue 1619 LYS Chi-restraints excluded: chain D residue 1746 THR Chi-restraints excluded: chain D residue 1792 VAL Chi-restraints excluded: chain D residue 1797 THR Chi-restraints excluded: chain D residue 1859 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 52 optimal weight: 5.9990 chunk 73 optimal weight: 6.9990 chunk 25 optimal weight: 0.8980 chunk 89 optimal weight: 5.9990 chunk 45 optimal weight: 2.9990 chunk 95 optimal weight: 0.9990 chunk 93 optimal weight: 2.9990 chunk 143 optimal weight: 0.0870 chunk 113 optimal weight: 5.9990 chunk 53 optimal weight: 0.9980 chunk 1 optimal weight: 8.9990 overall best weight: 1.1962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D1754 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.137305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.087624 restraints weight = 28014.442| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 3.40 r_work: 0.3122 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3158 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3158 r_free = 0.3158 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.79 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3158 r_free = 0.3158 target_work(ls_wunit_k1) = 0.078 | | 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: 0.8055 moved from start: 0.1903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14098 Z= 0.141 Angle : 0.542 11.490 19099 Z= 0.266 Chirality : 0.044 0.292 2035 Planarity : 0.004 0.051 2472 Dihedral : 4.787 37.100 1909 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.19 % Allowed : 17.67 % Favored : 80.13 % 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: 1673 helix: 1.17 (0.36), residues: 233 sheet: 0.14 (0.21), residues: 549 loop : -0.25 (0.22), residues: 891 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 209 TYR 0.018 0.001 TYR D1558 PHE 0.042 0.001 PHE D 286 TRP 0.012 0.001 TRP D1076 HIS 0.004 0.001 HIS D1868 Details of bonding type rmsd covalent geometry : bond 0.00327 (14098) covalent geometry : angle 0.54213 (19099) hydrogen bonds : bond 0.02720 ( 382) hydrogen bonds : angle 4.94270 ( 1029) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3346 Ramachandran restraints generated. 1673 Oldfield, 0 Emsley, 1673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3346 Ramachandran restraints generated. 1673 Oldfield, 0 Emsley, 1673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 87 time to evaluate : 0.572 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 187 ASN cc_start: 0.8908 (p0) cc_final: 0.8596 (p0) REVERT: D 230 ARG cc_start: 0.8514 (tmt90) cc_final: 0.8258 (tmt90) REVERT: D 281 LYS cc_start: 0.8528 (mttt) cc_final: 0.7879 (mttm) REVERT: D 296 MET cc_start: 0.8620 (mmm) cc_final: 0.8305 (mmm) REVERT: D 377 PHE cc_start: 0.7910 (m-80) cc_final: 0.7311 (m-10) REVERT: D 863 MET cc_start: 0.3474 (tpp) cc_final: 0.2939 (tpp) REVERT: D 1014 MET cc_start: 0.3855 (ptm) cc_final: 0.3223 (pmt) REVERT: D 1076 TRP cc_start: 0.7399 (t60) cc_final: 0.6624 (t60) REVERT: D 1242 MET cc_start: 0.7140 (ppp) cc_final: 0.6772 (ppp) REVERT: D 1475 TYR cc_start: 0.7816 (m-80) cc_final: 0.7477 (m-80) REVERT: D 1561 ARG cc_start: 0.8690 (OUTLIER) cc_final: 0.7961 (ptp-170) REVERT: D 1619 LYS cc_start: 0.8663 (OUTLIER) cc_final: 0.8340 (ttmm) REVERT: D 1751 PHE cc_start: 0.8288 (t80) cc_final: 0.7666 (t80) REVERT: D 1859 GLN cc_start: 0.6845 (OUTLIER) cc_final: 0.6616 (tp40) REVERT: D 1888 TRP cc_start: 0.8040 (m-90) cc_final: 0.7740 (m-90) outliers start: 33 outliers final: 26 residues processed: 118 average time/residue: 0.5565 time to fit residues: 73.1018 Evaluate side-chains 115 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 86 time to evaluate : 0.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 260 ILE Chi-restraints excluded: chain D residue 286 PHE Chi-restraints excluded: chain D residue 295 VAL Chi-restraints excluded: chain D residue 408 VAL Chi-restraints excluded: chain D residue 424 VAL Chi-restraints excluded: chain D residue 448 LEU Chi-restraints excluded: chain D residue 457 THR Chi-restraints excluded: chain D residue 496 VAL Chi-restraints excluded: chain D residue 498 THR Chi-restraints excluded: chain D residue 754 ILE Chi-restraints excluded: chain D residue 825 ASN Chi-restraints excluded: chain D residue 859 VAL Chi-restraints excluded: chain D residue 938 GLU Chi-restraints excluded: chain D residue 1223 LYS Chi-restraints excluded: chain D residue 1290 LEU Chi-restraints excluded: chain D residue 1323 SER Chi-restraints excluded: chain D residue 1392 CYS Chi-restraints excluded: chain D residue 1478 LEU Chi-restraints excluded: chain D residue 1555 VAL Chi-restraints excluded: chain D residue 1561 ARG Chi-restraints excluded: chain D residue 1581 THR Chi-restraints excluded: chain D residue 1597 THR Chi-restraints excluded: chain D residue 1619 LYS Chi-restraints excluded: chain D residue 1746 THR Chi-restraints excluded: chain D residue 1792 VAL Chi-restraints excluded: chain D residue 1797 THR Chi-restraints excluded: chain D residue 1859 GLN Chi-restraints excluded: chain D residue 1868 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 99 optimal weight: 0.9980 chunk 84 optimal weight: 4.9990 chunk 56 optimal weight: 0.5980 chunk 20 optimal weight: 1.9990 chunk 55 optimal weight: 0.9990 chunk 52 optimal weight: 3.9990 chunk 12 optimal weight: 0.6980 chunk 150 optimal weight: 0.0020 chunk 151 optimal weight: 10.0000 chunk 123 optimal weight: 10.0000 chunk 137 optimal weight: 0.6980 overall best weight: 0.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 763 GLN D1754 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.138114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.088730 restraints weight = 28104.174| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 3.37 r_work: 0.3143 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3176 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3176 r_free = 0.3176 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.80 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3176 r_free = 0.3176 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.80 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3176 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.1897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 14098 Z= 0.102 Angle : 0.524 10.796 19099 Z= 0.259 Chirality : 0.044 0.302 2035 Planarity : 0.004 0.069 2472 Dihedral : 4.727 37.219 1909 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.73 % Allowed : 18.21 % Favored : 80.07 % 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: 1673 helix: 1.24 (0.36), residues: 233 sheet: 0.14 (0.21), residues: 544 loop : -0.23 (0.22), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 190 TYR 0.016 0.001 TYR D1558 PHE 0.040 0.001 PHE D 286 TRP 0.013 0.001 TRP D1076 HIS 0.004 0.000 HIS D1868 Details of bonding type rmsd covalent geometry : bond 0.00234 (14098) covalent geometry : angle 0.52431 (19099) hydrogen bonds : bond 0.02627 ( 382) hydrogen bonds : angle 4.89148 ( 1029) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6309.07 seconds wall clock time: 108 minutes 1.22 seconds (6481.22 seconds total)