Starting phenix.real_space_refine on Fri Jul 3 12:02:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9h6x_51902/07_2026/9h6x_51902.cif Found real_map, /net/cci-nas-00/data/ceres_data/9h6x_51902/07_2026/9h6x_51902.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.56 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9h6x_51902/07_2026/9h6x_51902.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9h6x_51902/07_2026/9h6x_51902.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9h6x_51902/07_2026/9h6x_51902.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9h6x_51902/07_2026/9h6x_51902.map" } resolution = 2.56 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= 0.005 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 8808 2.51 5 N 2360 2.21 5 O 2572 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 41 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13811 Number of models: 1 Model: "" Number of chains: 2 Chain: "D" Number of atoms: 13741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1693, 13741 Classifications: {'peptide': 1693} Link IDs: {'PCIS': 3, 'PTRANS': 103, 'TRANS': 1586} Chain breaks: 5 Chain: "D" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 60 Ad-hoc single atom residues: {' CA': 10} Unusual residues: {'PSF': 2} Classifications: {'undetermined': 2} Chain breaks: 10 Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N PSF D2001 " occ=0.66 ... (28 atoms not shown) pdb=" P PSF D2001 " occ=0.66 residue: pdb=" N PSF D2012 " occ=0.55 ... (28 atoms not shown) pdb=" P PSF D2012 " occ=0.55 Time building chain proxies: 2.74, per 1000 atoms: 0.20 Number of scatterers: 13811 At special positions: 0 Unit cell: (100.8, 124.56, 154.08, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 10 19.99 S 59 16.00 P 2 15.00 O 2572 8.00 N 2360 7.00 C 8808 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.65 Conformation dependent library (CDL) restraints added in 518.5 milliseconds 3362 Ramachandran restraints generated. 1681 Oldfield, 0 Emsley, 1681 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3190 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 19 sheets defined 17.8% alpha, 27.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.47 Creating SS restraints... Processing helix chain 'D' and resid 174 through 190 Processing helix chain 'D' and resid 252 through 259 removed outlier: 3.609A pdb=" N ASP D 258 " --> pdb=" O SER D 254 " (cutoff:3.500A) Processing helix chain 'D' and resid 284 through 290 removed outlier: 3.623A pdb=" N GLU D 290 " --> pdb=" O PHE D 286 " (cutoff:3.500A) Processing helix chain 'D' and resid 307 through 311 removed outlier: 3.610A pdb=" N GLY D 311 " --> pdb=" O THR D 308 " (cutoff:3.500A) Processing helix chain 'D' and resid 376 through 381 removed outlier: 3.926A pdb=" N VAL D 381 " --> pdb=" O PHE D 377 " (cutoff:3.500A) Processing helix chain 'D' and resid 390 through 394 removed outlier: 3.673A pdb=" N ASN D 393 " --> pdb=" O ASP D 390 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N LEU D 394 " --> pdb=" O LYS D 391 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 390 through 394' Processing helix chain 'D' and resid 462 through 465 removed outlier: 3.679A pdb=" N ALA D 465 " --> pdb=" O SER D 462 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 462 through 465' Processing helix chain 'D' and resid 520 through 526 Processing helix chain 'D' and resid 549 through 552 Processing helix chain 'D' and resid 558 through 565 removed outlier: 3.599A pdb=" N LEU D 562 " --> pdb=" O SER D 558 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LEU D 563 " --> pdb=" O ASN D 559 " (cutoff:3.500A) Processing helix chain 'D' and resid 566 through 569 removed outlier: 3.585A pdb=" N GLN D 569 " --> pdb=" O GLU D 566 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 566 through 569' Processing helix chain 'D' and resid 650 through 680 removed outlier: 4.278A pdb=" N ALA D 656 " --> pdb=" O HIS D 652 " (cutoff:3.500A) Processing helix chain 'D' and resid 683 through 702 Processing helix chain 'D' and resid 716 through 744 removed outlier: 3.688A pdb=" N SER D 742 " --> pdb=" O VAL D 738 " (cutoff:3.500A) Processing helix chain 'D' and resid 746 through 765 removed outlier: 3.610A pdb=" N THR D 750 " --> pdb=" O ASP D 746 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N ALA D 752 " --> pdb=" O LYS D 748 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N GLU D 753 " --> pdb=" O SER D 749 " (cutoff:3.500A) Processing helix chain 'D' and resid 792 through 796 Processing helix chain 'D' and resid 845 through 847 No H-bonds generated for 'chain 'D' and resid 845 through 847' Processing helix chain 'D' and resid 848 through 853 removed outlier: 4.231A pdb=" N PHE D 852 " --> pdb=" O LYS D 848 " (cutoff:3.500A) Processing helix chain 'D' and resid 1086 through 1094 removed outlier: 3.684A pdb=" N ILE D1091 " --> pdb=" O ALA D1088 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LEU D1094 " --> pdb=" O ILE D1091 " (cutoff:3.500A) Processing helix chain 'D' and resid 1200 through 1207 Processing helix chain 'D' and resid 1273 through 1277 removed outlier: 3.747A pdb=" N GLY D1276 " --> pdb=" O GLY D1273 " (cutoff:3.500A) Processing helix chain 'D' and resid 1381 through 1385 removed outlier: 3.582A pdb=" N GLY D1384 " --> pdb=" O ARG D1381 " (cutoff:3.500A) Processing helix chain 'D' and resid 1452 through 1462 removed outlier: 3.538A pdb=" N LYS D1456 " --> pdb=" O ASP D1452 " (cutoff:3.500A) Processing helix chain 'D' and resid 1468 through 1474 Processing helix chain 'D' and resid 1484 through 1488 Processing helix chain 'D' and resid 1491 through 1495 removed outlier: 3.754A pdb=" N THR D1495 " --> pdb=" O GLU D1492 " (cutoff:3.500A) Processing helix chain 'D' and resid 1590 through 1593 removed outlier: 3.667A 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 1646 Processing helix chain 'D' and resid 1672 through 1684 Processing helix chain 'D' and resid 1707 through 1711 Processing helix chain 'D' and resid 1722 through 1733 Processing helix chain 'D' and resid 1734 through 1736 No H-bonds generated for 'chain 'D' and resid 1734 through 1736' Processing helix chain 'D' and resid 1770 through 1772 No H-bonds generated for 'chain 'D' and resid 1770 through 1772' Processing helix chain 'D' and resid 1824 through 1828 removed outlier: 3.749A pdb=" N LYS D1828 " --> pdb=" O GLU D1825 " (cutoff:3.500A) Processing helix chain 'D' and resid 1975 through 1981 Processing sheet with id=AA1, first strand: chain 'D' and resid 240 through 250 removed outlier: 6.944A pdb=" N PHE D 241 " --> pdb=" O GLU D 207 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N GLU D 207 " --> pdb=" O PHE D 241 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N LYS D 317 " --> pdb=" O ILE D 206 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N GLY D 208 " --> pdb=" O TYR D 315 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N TYR D 315 " --> pdb=" O GLY D 208 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N MET D 320 " --> pdb=" O MET D 296 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N MET D 296 " --> pdb=" O MET D 320 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N VAL D 322 " --> pdb=" O ALA D 294 " (cutoff:3.500A) removed outlier: 5.277A 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: 4.080A pdb=" N GLY D 278 " --> pdb=" O VAL D 265 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N ASN D 267 " --> pdb=" O LEU D 276 " (cutoff:3.500A) removed outlier: 5.874A pdb=" N LEU D 276 " --> pdb=" O ASN D 267 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 498 through 508 removed outlier: 7.394A pdb=" N THR D 498 " --> pdb=" O THR D 543 " (cutoff:3.500A) removed outlier: 7.658A pdb=" N THR D 543 " --> pdb=" O THR D 498 " (cutoff:3.500A) removed outlier: 5.312A pdb=" N GLY D 500 " --> pdb=" O LEU D 541 " (cutoff:3.500A) removed outlier: 5.769A pdb=" N LEU D 541 " --> pdb=" O GLY D 500 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N GLY D 535 " --> pdb=" O LEU D 506 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N GLY D 508 " --> pdb=" O TYR D 533 " (cutoff:3.500A) removed outlier: 5.684A pdb=" N TYR D 533 " --> pdb=" O GLY D 508 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ARG D 536 " --> pdb=" O ALA D 367 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N ALA D 367 " --> pdb=" O ARG D 536 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N LEU D 538 " --> pdb=" O TYR D 365 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 406 through 409 removed outlier: 6.586A pdb=" N ILE D 438 " --> pdb=" O TYR D 458 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N TYR D 458 " --> pdb=" O ILE D 438 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N LEU D 440 " --> pdb=" O THR D 456 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N THR D 456 " --> pdb=" O LEU D 440 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N ILE D 442 " --> pdb=" O VAL D 454 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 571 through 586 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 571 through 586 current: chain 'D' and resid 630 through 632 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 630 through 632 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 No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'D' and resid 593 through 599 removed outlier: 6.254A pdb=" N ARG D 781 " --> pdb=" O ARG D 785 " (cutoff:3.500A) removed outlier: 5.505A pdb=" N ARG D 785 " --> pdb=" O ARG D 781 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 929 through 939 removed outlier: 5.176A pdb=" N THR D 952 " --> pdb=" O ASN D 937 " (cutoff:3.500A) removed outlier: 9.699A pdb=" N SER D 939 " --> pdb=" O GLU D 950 " (cutoff:3.500A) removed outlier: 7.699A pdb=" N GLU D 950 " --> pdb=" O SER D 939 " (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=AA8, first strand: chain 'D' and resid 1137 through 1149 removed outlier: 6.916A pdb=" N TYR D1137 " --> pdb=" O GLU D1196 " (cutoff:3.500A) removed outlier: 4.941A pdb=" N GLU D1196 " --> pdb=" O TYR D1137 " (cutoff:3.500A) removed outlier: 5.968A 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 Processing sheet with id=AA9, first strand: chain 'D' and resid 1171 through 1174 removed outlier: 3.678A pdb=" N GLY D1228 " --> pdb=" O LEU D1215 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N ASP D1217 " --> pdb=" O PHE D1226 " (cutoff:3.500A) removed outlier: 5.771A pdb=" N PHE D1226 " --> pdb=" O ASP D1217 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 1285 through 1287 removed outlier: 3.910A pdb=" N ALA D1287 " --> pdb=" O LEU D1290 " (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: 5.916A pdb=" N VAL D1516 " --> pdb=" O ARG D1505 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N ARG D1505 " --> pdb=" O VAL D1516 " (cutoff:3.500A) removed outlier: 4.111A 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: 6.372A pdb=" N LEU D1373 " --> pdb=" O THR D1393 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N THR D1393 " --> pdb=" O LEU D1373 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N ILE D1375 " --> pdb=" O GLN D1391 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N GLN D1391 " --> pdb=" O ILE D1375 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N VAL D1377 " --> pdb=" O VAL D1389 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 1479 through 1480 removed outlier: 6.866A pdb=" N LYS D1479 " --> pdb=" O VAL D1742 " (cutoff:3.500A) removed outlier: 7.933A pdb=" N THR D1744 " --> pdb=" O LYS D1479 " (cutoff:3.500A) removed outlier: 8.239A pdb=" N HIS D1741 " --> pdb=" O VAL D1764 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N VAL D1764 " --> pdb=" O HIS D1741 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N LYS D1759 " --> pdb=" O GLY D1562 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N GLY D1562 " --> pdb=" O LYS D1759 " (cutoff:3.500A) removed outlier: 7.052A 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: 3.640A pdb=" N GLY D1635 " --> pdb=" O VAL D1622 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ASP D1624 " --> pdb=" O LYS D1633 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N LYS D1633 " --> pdb=" O ASP D1624 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 1690 through 1691 removed outlier: 3.577A pdb=" N ILE D1690 " --> pdb=" O ARG D1699 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ARG D1699 " --> pdb=" O ILE D1690 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 1875 through 1879 removed outlier: 3.741A pdb=" N ASP D1853 " --> pdb=" O ILE D1862 " (cutoff:3.500A) removed outlier: 9.390A pdb=" N ALA D1864 " --> pdb=" O PRO D1851 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N GLY D1842 " --> pdb=" O LYS D1798 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N LYS D1798 " --> pdb=" O GLY D1842 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N PHE D1844 " --> pdb=" O ASN D1796 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N ASN D1796 " --> pdb=" O PHE D1844 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N GLU D1967 " --> pdb=" O TRP D1795 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N THR D1797 " --> pdb=" O LYS D1965 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N LYS D1965 " --> pdb=" O THR D1797 " (cutoff:3.500A) removed outlier: 5.046A pdb=" N ARG D1960 " --> pdb=" O LYS D1956 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N LYS D1956 " --> pdb=" O ARG D1960 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N MET D1962 " --> pdb=" O ALA D1954 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N ALA D1954 " --> pdb=" O MET D1962 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N MET D1946 " --> pdb=" O LEU D1970 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 1813 through 1820 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 1829 through 1830 current: chain 'D' and resid 1897 through 1905 Processing sheet with id=AC1, first strand: chain 'D' and resid 1909 through 1910 369 hydrogen bonds defined for protein. 990 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: 2.17 Time building geometry restraints manager: 0.92 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: 2559 1.33 - 1.45: 3605 1.45 - 1.57: 7886 1.57 - 1.70: 5 1.70 - 1.82: 93 Bond restraints: 14148 Sorted by residual: bond pdb=" C TYR D 820 " pdb=" N PRO D 821 " ideal model delta sigma weight residual 1.337 1.364 -0.027 9.80e-03 1.04e+04 7.69e+00 bond pdb=" O2 PSF D2012 " pdb=" P PSF D2012 " ideal model delta sigma weight residual 1.637 1.594 0.043 2.00e-02 2.50e+03 4.53e+00 bond pdb=" O2 PSF D2001 " pdb=" P PSF D2001 " ideal model delta sigma weight residual 1.637 1.595 0.042 2.00e-02 2.50e+03 4.45e+00 bond pdb=" O1 PSF D2012 " pdb=" P PSF D2012 " ideal model delta sigma weight residual 1.636 1.595 0.041 2.00e-02 2.50e+03 4.21e+00 bond pdb=" O1 PSF D2001 " pdb=" P PSF D2001 " ideal model delta sigma weight residual 1.636 1.596 0.040 2.00e-02 2.50e+03 3.97e+00 ... (remaining 14143 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.08: 18952 3.08 - 6.16: 182 6.16 - 9.24: 26 9.24 - 12.32: 5 12.32 - 15.40: 4 Bond angle restraints: 19169 Sorted by residual: angle pdb=" CB MET D1254 " pdb=" CG MET D1254 " pdb=" SD MET D1254 " ideal model delta sigma weight residual 112.70 128.10 -15.40 3.00e+00 1.11e-01 2.64e+01 angle pdb=" CB MET D1316 " pdb=" CG MET D1316 " pdb=" SD MET D1316 " ideal model delta sigma weight residual 112.70 127.58 -14.88 3.00e+00 1.11e-01 2.46e+01 angle pdb=" C GLN D1320 " pdb=" CA GLN D1320 " pdb=" CB GLN D1320 " ideal model delta sigma weight residual 116.54 110.87 5.67 1.15e+00 7.56e-01 2.43e+01 angle pdb=" CA ILE D1924 " pdb=" CB ILE D1924 " pdb=" CG1 ILE D1924 " ideal model delta sigma weight residual 110.40 118.60 -8.20 1.70e+00 3.46e-01 2.33e+01 angle pdb=" CA GLU D1449 " pdb=" CB GLU D1449 " pdb=" CG GLU D1449 " ideal model delta sigma weight residual 114.10 122.84 -8.74 2.00e+00 2.50e-01 1.91e+01 ... (remaining 19164 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.56: 7724 17.56 - 35.12: 651 35.12 - 52.69: 132 52.69 - 70.25: 47 70.25 - 87.81: 22 Dihedral angle restraints: 8576 sinusoidal: 3633 harmonic: 4943 Sorted by residual: dihedral pdb=" CA PHE D 885 " pdb=" C PHE D 885 " pdb=" N SER D 886 " pdb=" CA SER D 886 " ideal model delta harmonic sigma weight residual -180.00 -155.65 -24.35 0 5.00e+00 4.00e-02 2.37e+01 dihedral pdb=" CA PHE D1683 " pdb=" C PHE D1683 " pdb=" N LYS D1684 " pdb=" CA LYS D1684 " ideal model delta harmonic sigma weight residual -180.00 -155.87 -24.13 0 5.00e+00 4.00e-02 2.33e+01 dihedral pdb=" CA LYS D 884 " pdb=" C LYS D 884 " pdb=" N PHE D 885 " pdb=" CA PHE D 885 " ideal model delta harmonic sigma weight residual -180.00 -156.31 -23.69 0 5.00e+00 4.00e-02 2.24e+01 ... (remaining 8573 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 1369 0.041 - 0.083: 445 0.083 - 0.124: 184 0.124 - 0.166: 36 0.166 - 0.207: 9 Chirality restraints: 2043 Sorted by residual: chirality pdb=" CG LEU D 818 " pdb=" CB LEU D 818 " pdb=" CD1 LEU D 818 " pdb=" CD2 LEU D 818 " both_signs ideal model delta sigma weight residual False -2.59 -2.38 -0.21 2.00e-01 2.50e+01 1.07e+00 chirality pdb=" CG LEU D 708 " pdb=" CB LEU D 708 " pdb=" CD1 LEU D 708 " pdb=" CD2 LEU D 708 " both_signs ideal model delta sigma weight residual False -2.59 -2.39 -0.20 2.00e-01 2.50e+01 1.02e+00 chirality pdb=" CB ILE D1057 " pdb=" CA ILE D1057 " pdb=" CG1 ILE D1057 " pdb=" CG2 ILE D1057 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.19 2.00e-01 2.50e+01 9.26e-01 ... (remaining 2040 not shown) Planarity restraints: 2483 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE D1683 " -0.013 2.00e-02 2.50e+03 1.91e-02 6.41e+00 pdb=" CG PHE D1683 " 0.044 2.00e-02 2.50e+03 pdb=" CD1 PHE D1683 " -0.017 2.00e-02 2.50e+03 pdb=" CD2 PHE D1683 " -0.013 2.00e-02 2.50e+03 pdb=" CE1 PHE D1683 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE D1683 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE D1683 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D1697 " 0.194 9.50e-02 1.11e+02 8.74e-02 5.26e+00 pdb=" NE ARG D1697 " -0.016 2.00e-02 2.50e+03 pdb=" CZ ARG D1697 " 0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG D1697 " -0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG D1697 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA D1287 " 0.036 5.00e-02 4.00e+02 5.43e-02 4.73e+00 pdb=" N PRO D1288 " -0.094 5.00e-02 4.00e+02 pdb=" CA PRO D1288 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO D1288 " 0.030 5.00e-02 4.00e+02 ... (remaining 2480 not shown) Histogram of nonbonded interaction distances: 2.36 - 2.87: 4367 2.87 - 3.38: 12379 3.38 - 3.89: 23884 3.89 - 4.39: 26813 4.39 - 4.90: 45150 Nonbonded interactions: 112593 Sorted by model distance: nonbonded pdb=" O TYR D1625 " pdb="CA CA D2006 " model vdw 2.364 3.250 nonbonded pdb="CA CA D2007 " pdb=" O3 PSF D2012 " model vdw 2.370 3.250 nonbonded pdb=" OD2 ASP D1624 " pdb="CA CA D2007 " model vdw 2.377 3.250 nonbonded pdb=" O TRP D 445 " pdb="CA CA D2002 " model vdw 2.382 3.250 nonbonded pdb=" OD1 ASP D1569 " pdb="CA CA D2006 " model vdw 2.382 3.250 ... (remaining 112588 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=0.55 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: 2.640 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: 11.540 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 14148 Z= 0.197 Angle : 0.845 15.403 19169 Z= 0.455 Chirality : 0.050 0.207 2043 Planarity : 0.007 0.087 2483 Dihedral : 14.754 87.809 5386 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 2.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 0.86 % Allowed : 10.00 % Favored : 89.14 % 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 are not related in a simple way. whole: -1.25 (0.19), residues: 1681 helix: -1.66 (0.28), residues: 214 sheet: -0.33 (0.22), residues: 499 loop : -0.85 (0.18), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG D 230 TYR 0.027 0.002 TYR D1470 PHE 0.044 0.002 PHE D1683 TRP 0.020 0.002 TRP D1870 HIS 0.004 0.001 HIS D 223 Details of bonding type rmsd/Z covalent geometry : bond 0.00399 / 0.20 (14148) covalent geometry : angle 0.84472 / 0.45 (19169) hydrogen bonds : bond 0.21044 / 13.88 ( 369) hydrogen bonds : angle 8.49475 / 6.02 ( 990) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3362 Ramachandran restraints generated. 1681 Oldfield, 0 Emsley, 1681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3362 Ramachandran restraints generated. 1681 Oldfield, 0 Emsley, 1681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 191 time to evaluate : 0.472 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 223 HIS cc_start: 0.7863 (t70) cc_final: 0.7633 (t70) REVERT: D 232 ARG cc_start: 0.6519 (ppt170) cc_final: 0.6184 (ppt170) REVERT: D 293 HIS cc_start: 0.8864 (m170) cc_final: 0.8629 (m90) REVERT: D 348 LEU cc_start: 0.7600 (tp) cc_final: 0.7332 (tp) REVERT: D 518 ASP cc_start: 0.8684 (t0) cc_final: 0.8215 (t70) REVERT: D 522 GLU cc_start: 0.8906 (tt0) cc_final: 0.8644 (mp0) REVERT: D 527 LYS cc_start: 0.8549 (mptt) cc_final: 0.8164 (mptt) REVERT: D 668 GLN cc_start: 0.9252 (tt0) cc_final: 0.8936 (tt0) REVERT: D 783 GLU cc_start: 0.8809 (mm-30) cc_final: 0.8539 (tp30) REVERT: D 863 MET cc_start: 0.1745 (tpt) cc_final: 0.0826 (ptm) REVERT: D 870 MET cc_start: 0.3785 (mpp) cc_final: 0.2832 (pmm) REVERT: D 937 ASN cc_start: 0.8233 (m-40) cc_final: 0.7808 (m110) REVERT: D 980 TRP cc_start: 0.7591 (m100) cc_final: 0.6952 (m100) REVERT: D 1022 ARG cc_start: 0.8186 (ttt180) cc_final: 0.7943 (ttt180) REVERT: D 1026 LYS cc_start: 0.7063 (mtmm) cc_final: 0.6766 (mppt) REVERT: D 1382 GLN cc_start: 0.8283 (tm-30) cc_final: 0.7832 (tm130) REVERT: D 1496 ASP cc_start: 0.8667 (p0) cc_final: 0.8248 (p0) REVERT: D 1502 LYS cc_start: 0.8845 (mttp) cc_final: 0.8644 (mttm) REVERT: D 1519 GLU cc_start: 0.8454 (mt-10) cc_final: 0.8092 (mt-10) REVERT: D 1543 ARG cc_start: 0.7391 (mtm110) cc_final: 0.7064 (mtm110) REVERT: D 1581 THR cc_start: 0.8727 (m) cc_final: 0.8478 (p) REVERT: D 1636 GLU cc_start: 0.8032 (tt0) cc_final: 0.7719 (tm-30) REVERT: D 1658 GLU cc_start: 0.8645 (tt0) cc_final: 0.7926 (pt0) REVERT: D 1792 VAL cc_start: 0.8269 (t) cc_final: 0.7848 (t) REVERT: D 1848 PHE cc_start: 0.8351 (m-80) cc_final: 0.7779 (m-80) REVERT: D 1858 GLU cc_start: 0.8281 (mm-30) cc_final: 0.8069 (mm-30) outliers start: 13 outliers final: 5 residues processed: 201 average time/residue: 0.5348 time to fit residues: 117.6285 Evaluate side-chains 125 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 120 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 355 LEU Chi-restraints excluded: chain D residue 554 LEU Chi-restraints excluded: chain D residue 613 LEU Chi-restraints excluded: chain D residue 982 TYR Chi-restraints excluded: chain D residue 1510 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 98 optimal weight: 0.5980 chunk 107 optimal weight: 0.0770 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 30.0000 chunk 130 optimal weight: 8.9990 chunk 124 optimal weight: 30.0000 chunk 103 optimal weight: 6.9990 chunk 77 optimal weight: 9.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 5.9990 overall best weight: 1.3142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 338 ASN D1487 ASN D1541 GLN D1570 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.135341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.081067 restraints weight = 26160.589| |-----------------------------------------------------------------------------| r_work (start): 0.3157 rms_B_bonded: 3.24 r_work: 0.3006 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3039 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3039 r_free = 0.3039 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.55 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3039 r_free = 0.3039 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.71 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (10 function evaluations) r_final: 0.3039 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.1538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 14148 Z= 0.162 Angle : 0.559 7.806 19169 Z= 0.289 Chirality : 0.044 0.180 2043 Planarity : 0.004 0.038 2483 Dihedral : 7.661 139.951 1927 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 1.72 % Allowed : 12.58 % Favored : 85.70 % 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 are not related in a simple way. whole: -0.51 (0.19), residues: 1681 helix: -0.02 (0.33), residues: 215 sheet: -0.22 (0.22), residues: 512 loop : -0.40 (0.20), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D1791 TYR 0.013 0.001 TYR D 266 PHE 0.022 0.001 PHE D1751 TRP 0.017 0.001 TRP D1870 HIS 0.003 0.001 HIS D 581 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.16 (14148) covalent geometry : angle 0.55867 / 0.29 (19169) hydrogen bonds : bond 0.03686 / 2.49 ( 369) hydrogen bonds : angle 5.94006 / 4.20 ( 990) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3362 Ramachandran restraints generated. 1681 Oldfield, 0 Emsley, 1681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3362 Ramachandran restraints generated. 1681 Oldfield, 0 Emsley, 1681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 131 time to evaluate : 0.533 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 223 HIS cc_start: 0.7867 (t70) cc_final: 0.7632 (t70) REVERT: D 257 MET cc_start: 0.7306 (mmp) cc_final: 0.6839 (mmp) REVERT: D 286 PHE cc_start: 0.7761 (t80) cc_final: 0.7501 (t80) REVERT: D 293 HIS cc_start: 0.8802 (m170) cc_final: 0.8574 (m90) REVERT: D 518 ASP cc_start: 0.8764 (t0) cc_final: 0.8113 (t70) REVERT: D 527 LYS cc_start: 0.8527 (mptt) cc_final: 0.8026 (mptt) REVERT: D 783 GLU cc_start: 0.8793 (mm-30) cc_final: 0.8546 (tp30) REVERT: D 870 MET cc_start: 0.3234 (mpp) cc_final: 0.2262 (pmm) REVERT: D 929 GLU cc_start: 0.8285 (OUTLIER) cc_final: 0.8053 (pm20) REVERT: D 937 ASN cc_start: 0.8172 (m-40) cc_final: 0.7759 (m110) REVERT: D 980 TRP cc_start: 0.7405 (m100) cc_final: 0.6795 (m100) REVERT: D 1022 ARG cc_start: 0.7967 (ttt180) cc_final: 0.7739 (ttt180) REVERT: D 1026 LYS cc_start: 0.7183 (mtmm) cc_final: 0.6944 (mptt) REVERT: D 1382 GLN cc_start: 0.7833 (tm-30) cc_final: 0.7585 (tm130) REVERT: D 1519 GLU cc_start: 0.8375 (mt-10) cc_final: 0.7924 (mt-10) REVERT: D 1581 THR cc_start: 0.8784 (m) cc_final: 0.8383 (p) REVERT: D 1636 GLU cc_start: 0.8400 (tt0) cc_final: 0.8154 (tm-30) REVERT: D 1658 GLU cc_start: 0.8238 (tt0) cc_final: 0.8009 (pt0) REVERT: D 1858 GLU cc_start: 0.8273 (mm-30) cc_final: 0.8066 (mm-30) REVERT: D 1889 ASP cc_start: 0.6158 (OUTLIER) cc_final: 0.5758 (p0) outliers start: 26 outliers final: 9 residues processed: 149 average time/residue: 0.4504 time to fit residues: 74.7881 Evaluate side-chains 124 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 113 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 596 GLU Chi-restraints excluded: chain D residue 613 LEU Chi-restraints excluded: chain D residue 830 VAL Chi-restraints excluded: chain D residue 913 VAL Chi-restraints excluded: chain D residue 929 GLU Chi-restraints excluded: chain D residue 982 TYR Chi-restraints excluded: chain D residue 1230 SER Chi-restraints excluded: chain D residue 1290 LEU Chi-restraints excluded: chain D residue 1784 LYS Chi-restraints excluded: chain D residue 1849 VAL Chi-restraints excluded: chain D residue 1889 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 92 optimal weight: 1.9990 chunk 154 optimal weight: 50.0000 chunk 133 optimal weight: 0.9990 chunk 58 optimal weight: 1.9990 chunk 97 optimal weight: 0.8980 chunk 11 optimal weight: 0.5980 chunk 27 optimal weight: 0.5980 chunk 55 optimal weight: 0.9980 chunk 37 optimal weight: 0.9990 chunk 96 optimal weight: 0.3980 chunk 41 optimal weight: 0.2980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 338 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.136133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.082146 restraints weight = 26344.472| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 3.23 r_work: 0.3028 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3099 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3099 r_free = 0.3099 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.71 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3099 r_free = 0.3099 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.74 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (10 function evaluations) r_final: 0.3099 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.1723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 14148 Z= 0.101 Angle : 0.510 9.620 19169 Z= 0.262 Chirality : 0.043 0.167 2043 Planarity : 0.004 0.045 2483 Dihedral : 6.080 75.204 1920 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.32 % Allowed : 13.58 % Favored : 85.10 % 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 are not related in a simple way. whole: -0.18 (0.20), residues: 1681 helix: 0.63 (0.34), residues: 214 sheet: -0.10 (0.22), residues: 513 loop : -0.21 (0.20), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG D1396 TYR 0.012 0.001 TYR D 315 PHE 0.019 0.001 PHE D1683 TRP 0.016 0.001 TRP D1820 HIS 0.002 0.000 HIS D1018 Details of bonding type rmsd/Z covalent geometry : bond 0.00226 / 0.10 (14148) covalent geometry : angle 0.50969 / 0.26 (19169) hydrogen bonds : bond 0.03226 / 2.17 ( 369) hydrogen bonds : angle 5.42837 / 3.84 ( 990) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3362 Ramachandran restraints generated. 1681 Oldfield, 0 Emsley, 1681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3362 Ramachandran restraints generated. 1681 Oldfield, 0 Emsley, 1681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 123 time to evaluate : 0.407 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 223 HIS cc_start: 0.7881 (t70) cc_final: 0.7659 (t70) REVERT: D 232 ARG cc_start: 0.6696 (ppt170) cc_final: 0.6445 (ppt170) REVERT: D 293 HIS cc_start: 0.8781 (m170) cc_final: 0.8532 (m90) REVERT: D 356 ARG cc_start: 0.7869 (pmt170) cc_final: 0.7643 (pmt-80) REVERT: D 518 ASP cc_start: 0.8695 (t0) cc_final: 0.8013 (t70) REVERT: D 527 LYS cc_start: 0.8473 (mptt) cc_final: 0.8021 (mptt) REVERT: D 783 GLU cc_start: 0.8776 (mm-30) cc_final: 0.8463 (tp30) REVERT: D 870 MET cc_start: 0.3250 (mpp) cc_final: 0.2626 (pmm) REVERT: D 937 ASN cc_start: 0.8172 (m-40) cc_final: 0.7757 (m110) REVERT: D 980 TRP cc_start: 0.7405 (m100) cc_final: 0.6789 (m100) REVERT: D 1022 ARG cc_start: 0.7946 (ttt180) cc_final: 0.7732 (ttt180) REVERT: D 1026 LYS cc_start: 0.7104 (mtmm) cc_final: 0.6888 (mptt) REVERT: D 1292 MET cc_start: 0.8675 (ptm) cc_final: 0.8308 (ptm) REVERT: D 1382 GLN cc_start: 0.7882 (tm-30) cc_final: 0.7602 (tm130) REVERT: D 1450 ILE cc_start: 0.4144 (OUTLIER) cc_final: 0.3653 (tp) REVERT: D 1581 THR cc_start: 0.8776 (m) cc_final: 0.8355 (p) REVERT: D 1636 GLU cc_start: 0.8382 (tt0) cc_final: 0.8130 (tm-30) REVERT: D 1858 GLU cc_start: 0.8254 (mm-30) cc_final: 0.8039 (mm-30) outliers start: 20 outliers final: 7 residues processed: 137 average time/residue: 0.4097 time to fit residues: 62.7401 Evaluate side-chains 122 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 114 time to evaluate : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 355 LEU Chi-restraints excluded: chain D residue 396 ASP Chi-restraints excluded: chain D residue 424 VAL Chi-restraints excluded: chain D residue 433 SER Chi-restraints excluded: chain D residue 613 LEU Chi-restraints excluded: chain D residue 1290 LEU Chi-restraints excluded: chain D residue 1450 ILE Chi-restraints excluded: chain D residue 1970 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 35 optimal weight: 0.7980 chunk 167 optimal weight: 20.0000 chunk 87 optimal weight: 1.9990 chunk 12 optimal weight: 10.0000 chunk 152 optimal weight: 7.9990 chunk 40 optimal weight: 1.9990 chunk 111 optimal weight: 0.0770 chunk 95 optimal weight: 2.9990 chunk 45 optimal weight: 0.9990 chunk 88 optimal weight: 0.7980 chunk 77 optimal weight: 0.0370 overall best weight: 0.5418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 338 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.136422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.082503 restraints weight = 26334.664| |-----------------------------------------------------------------------------| r_work (start): 0.3187 rms_B_bonded: 3.24 r_work: 0.3035 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3106 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3106 r_free = 0.3106 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.74 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3106 r_free = 0.3106 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3106 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.1921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 14148 Z= 0.096 Angle : 0.494 9.649 19169 Z= 0.251 Chirality : 0.043 0.148 2043 Planarity : 0.003 0.044 2483 Dihedral : 5.546 75.367 1918 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 1.79 % Allowed : 13.51 % Favored : 84.70 % 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 are not related in a simple way. whole: 0.04 (0.20), residues: 1681 helix: 1.11 (0.35), residues: 214 sheet: -0.07 (0.22), residues: 527 loop : -0.07 (0.20), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG D1396 TYR 0.013 0.001 TYR D1558 PHE 0.023 0.001 PHE D1751 TRP 0.023 0.001 TRP D1820 HIS 0.002 0.000 HIS D1018 Details of bonding type rmsd/Z covalent geometry : bond 0.00215 / 0.10 (14148) covalent geometry : angle 0.49418 / 0.25 (19169) hydrogen bonds : bond 0.02940 / 1.99 ( 369) hydrogen bonds : angle 5.04481 / 3.56 ( 990) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3362 Ramachandran restraints generated. 1681 Oldfield, 0 Emsley, 1681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3362 Ramachandran restraints generated. 1681 Oldfield, 0 Emsley, 1681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 123 time to evaluate : 0.331 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 232 ARG cc_start: 0.6686 (ppt170) cc_final: 0.6437 (ppt170) REVERT: D 293 HIS cc_start: 0.8684 (m170) cc_final: 0.8430 (m90) REVERT: D 518 ASP cc_start: 0.8603 (t0) cc_final: 0.7913 (t70) REVERT: D 527 LYS cc_start: 0.8457 (mptt) cc_final: 0.8014 (mptt) REVERT: D 783 GLU cc_start: 0.8764 (mm-30) cc_final: 0.8476 (tp30) REVERT: D 870 MET cc_start: 0.3228 (mpp) cc_final: 0.2261 (pmm) REVERT: D 929 GLU cc_start: 0.8270 (OUTLIER) cc_final: 0.8058 (mp0) REVERT: D 932 ASP cc_start: 0.8178 (t0) cc_final: 0.7835 (t0) REVERT: D 937 ASN cc_start: 0.8227 (m-40) cc_final: 0.7827 (m110) REVERT: D 980 TRP cc_start: 0.7393 (m100) cc_final: 0.6796 (m100) REVERT: D 1026 LYS cc_start: 0.7093 (mtmm) cc_final: 0.6886 (mptt) REVERT: D 1292 MET cc_start: 0.8665 (ptm) cc_final: 0.8279 (ptm) REVERT: D 1382 GLN cc_start: 0.7947 (tm-30) cc_final: 0.7675 (tm130) REVERT: D 1450 ILE cc_start: 0.4132 (OUTLIER) cc_final: 0.3615 (tp) REVERT: D 1519 GLU cc_start: 0.8320 (mt-10) cc_final: 0.7836 (mt-10) REVERT: D 1581 THR cc_start: 0.8786 (m) cc_final: 0.8347 (p) REVERT: D 1636 GLU cc_start: 0.8391 (tt0) cc_final: 0.8141 (tm-30) REVERT: D 1791 ARG cc_start: 0.7416 (mmm-85) cc_final: 0.7210 (mmm-85) REVERT: D 1858 GLU cc_start: 0.8272 (mm-30) cc_final: 0.8059 (mm-30) outliers start: 27 outliers final: 12 residues processed: 145 average time/residue: 0.4169 time to fit residues: 67.5611 Evaluate side-chains 127 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 113 time to evaluate : 0.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 295 VAL Chi-restraints excluded: chain D residue 355 LEU Chi-restraints excluded: chain D residue 396 ASP Chi-restraints excluded: chain D residue 424 VAL Chi-restraints excluded: chain D residue 433 SER Chi-restraints excluded: chain D residue 596 GLU Chi-restraints excluded: chain D residue 613 LEU Chi-restraints excluded: chain D residue 929 GLU Chi-restraints excluded: chain D residue 982 TYR Chi-restraints excluded: chain D residue 1230 SER Chi-restraints excluded: chain D residue 1290 LEU Chi-restraints excluded: chain D residue 1450 ILE Chi-restraints excluded: chain D residue 1691 LEU Chi-restraints excluded: chain D residue 1698 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 9 optimal weight: 5.9990 chunk 11 optimal weight: 0.0170 chunk 117 optimal weight: 20.0000 chunk 102 optimal weight: 3.9990 chunk 86 optimal weight: 0.2980 chunk 101 optimal weight: 0.5980 chunk 15 optimal weight: 20.0000 chunk 75 optimal weight: 40.0000 chunk 38 optimal weight: 2.9990 chunk 29 optimal weight: 0.0370 chunk 12 optimal weight: 1.9990 overall best weight: 0.5898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 338 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.136486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.082107 restraints weight = 26462.175| |-----------------------------------------------------------------------------| r_work (start): 0.3188 rms_B_bonded: 3.25 r_work: 0.3037 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3071 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3071 r_free = 0.3071 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3071 r_free = 0.3071 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3071 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.2075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 14148 Z= 0.100 Angle : 0.496 11.815 19169 Z= 0.251 Chirality : 0.043 0.148 2043 Planarity : 0.003 0.048 2483 Dihedral : 5.320 75.296 1918 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.32 % Allowed : 14.70 % Favored : 83.97 % 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 are not related in a simple way. whole: 0.18 (0.20), residues: 1681 helix: 1.31 (0.35), residues: 214 sheet: 0.06 (0.22), residues: 520 loop : -0.02 (0.21), residues: 947 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG D1396 TYR 0.012 0.001 TYR D1558 PHE 0.025 0.001 PHE D1683 TRP 0.032 0.001 TRP D1820 HIS 0.002 0.000 HIS D1018 Details of bonding type rmsd/Z covalent geometry : bond 0.00223 / 0.10 (14148) covalent geometry : angle 0.49576 / 0.25 (19169) hydrogen bonds : bond 0.02852 / 1.93 ( 369) hydrogen bonds : angle 4.86262 / 3.43 ( 990) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3362 Ramachandran restraints generated. 1681 Oldfield, 0 Emsley, 1681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3362 Ramachandran restraints generated. 1681 Oldfield, 0 Emsley, 1681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 122 time to evaluate : 0.468 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 228 THR cc_start: 0.8487 (t) cc_final: 0.8263 (m) REVERT: D 232 ARG cc_start: 0.6679 (ppt170) cc_final: 0.6384 (ppt170) REVERT: D 293 HIS cc_start: 0.8601 (m170) cc_final: 0.8316 (m90) REVERT: D 518 ASP cc_start: 0.8615 (t0) cc_final: 0.7914 (t70) REVERT: D 527 LYS cc_start: 0.8442 (mptt) cc_final: 0.7992 (mptt) REVERT: D 783 GLU cc_start: 0.8768 (mm-30) cc_final: 0.8491 (tp30) REVERT: D 870 MET cc_start: 0.3170 (mpp) cc_final: 0.2181 (pmm) REVERT: D 937 ASN cc_start: 0.8268 (m-40) cc_final: 0.7878 (m110) REVERT: D 980 TRP cc_start: 0.7379 (m100) cc_final: 0.6748 (m100) REVERT: D 1292 MET cc_start: 0.8661 (ptm) cc_final: 0.8259 (ptm) REVERT: D 1382 GLN cc_start: 0.7959 (tm-30) cc_final: 0.7752 (tm130) REVERT: D 1450 ILE cc_start: 0.4156 (OUTLIER) cc_final: 0.3623 (tp) REVERT: D 1519 GLU cc_start: 0.8336 (mt-10) cc_final: 0.7875 (mt-10) REVERT: D 1581 THR cc_start: 0.8772 (m) cc_final: 0.8320 (p) REVERT: D 1636 GLU cc_start: 0.8423 (tt0) cc_final: 0.8206 (tm-30) REVERT: D 1686 PHE cc_start: 0.8318 (m-80) cc_final: 0.8108 (m-80) REVERT: D 1791 ARG cc_start: 0.7517 (mmm-85) cc_final: 0.7264 (mmm-85) REVERT: D 1848 PHE cc_start: 0.7967 (m-10) cc_final: 0.7720 (m-10) REVERT: D 1858 GLU cc_start: 0.8278 (mm-30) cc_final: 0.8063 (mm-30) REVERT: D 1868 HIS cc_start: 0.7879 (OUTLIER) cc_final: 0.7442 (p-80) outliers start: 20 outliers final: 10 residues processed: 139 average time/residue: 0.4214 time to fit residues: 65.8580 Evaluate side-chains 126 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 114 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 355 LEU Chi-restraints excluded: chain D residue 396 ASP Chi-restraints excluded: chain D residue 424 VAL Chi-restraints excluded: chain D residue 596 GLU Chi-restraints excluded: chain D residue 613 LEU Chi-restraints excluded: chain D residue 982 TYR Chi-restraints excluded: chain D residue 1290 LEU Chi-restraints excluded: chain D residue 1450 ILE Chi-restraints excluded: chain D residue 1698 ILE Chi-restraints excluded: chain D residue 1868 HIS Chi-restraints excluded: chain D residue 1970 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 35 optimal weight: 0.3980 chunk 75 optimal weight: 40.0000 chunk 146 optimal weight: 0.2980 chunk 96 optimal weight: 2.9990 chunk 67 optimal weight: 30.0000 chunk 98 optimal weight: 3.9990 chunk 94 optimal weight: 0.7980 chunk 110 optimal weight: 2.9990 chunk 113 optimal weight: 1.9990 chunk 42 optimal weight: 0.6980 chunk 14 optimal weight: 3.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 338 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.135972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.081202 restraints weight = 26270.531| |-----------------------------------------------------------------------------| r_work (start): 0.3172 rms_B_bonded: 3.25 r_work: 0.3021 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3056 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3056 r_free = 0.3056 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3056 r_free = 0.3056 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3056 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.2217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 14148 Z= 0.115 Angle : 0.495 9.303 19169 Z= 0.251 Chirality : 0.043 0.149 2043 Planarity : 0.003 0.054 2483 Dihedral : 5.242 75.667 1918 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.26 % Allowed : 15.23 % Favored : 83.51 % 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 are not related in a simple way. whole: 0.26 (0.20), residues: 1681 helix: 1.41 (0.35), residues: 214 sheet: 0.10 (0.22), residues: 533 loop : 0.02 (0.21), residues: 934 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG D1396 TYR 0.012 0.001 TYR D1558 PHE 0.024 0.001 PHE D1751 TRP 0.038 0.001 TRP D1820 HIS 0.002 0.000 HIS D 581 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 (14148) covalent geometry : angle 0.49464 / 0.25 (19169) hydrogen bonds : bond 0.02864 / 1.91 ( 369) hydrogen bonds : angle 4.78132 / 3.37 ( 990) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3362 Ramachandran restraints generated. 1681 Oldfield, 0 Emsley, 1681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3362 Ramachandran restraints generated. 1681 Oldfield, 0 Emsley, 1681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 121 time to evaluate : 0.415 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 228 THR cc_start: 0.8524 (t) cc_final: 0.8275 (m) REVERT: D 293 HIS cc_start: 0.8635 (m170) cc_final: 0.8366 (m90) REVERT: D 447 ARG cc_start: 0.8395 (OUTLIER) cc_final: 0.7458 (ttp80) REVERT: D 518 ASP cc_start: 0.8592 (t0) cc_final: 0.7883 (t70) REVERT: D 527 LYS cc_start: 0.8437 (mptt) cc_final: 0.7991 (mptt) REVERT: D 783 GLU cc_start: 0.8785 (mm-30) cc_final: 0.8492 (tp30) REVERT: D 870 MET cc_start: 0.3176 (mpp) cc_final: 0.2157 (pmm) REVERT: D 932 ASP cc_start: 0.8197 (t0) cc_final: 0.7848 (t0) REVERT: D 937 ASN cc_start: 0.8279 (m-40) cc_final: 0.7893 (m110) REVERT: D 980 TRP cc_start: 0.7386 (m100) cc_final: 0.6768 (m100) REVERT: D 1292 MET cc_start: 0.8641 (ptm) cc_final: 0.8252 (ptm) REVERT: D 1382 GLN cc_start: 0.7983 (tm-30) cc_final: 0.7773 (tm130) REVERT: D 1450 ILE cc_start: 0.4146 (OUTLIER) cc_final: 0.3654 (tp) REVERT: D 1519 GLU cc_start: 0.8353 (mt-10) cc_final: 0.7914 (mt-10) REVERT: D 1581 THR cc_start: 0.8777 (m) cc_final: 0.8342 (p) REVERT: D 1636 GLU cc_start: 0.8447 (tt0) cc_final: 0.8232 (tm-30) REVERT: D 1791 ARG cc_start: 0.7616 (mmm-85) cc_final: 0.7320 (mmm-85) REVERT: D 1848 PHE cc_start: 0.8028 (m-10) cc_final: 0.7727 (m-10) outliers start: 19 outliers final: 13 residues processed: 136 average time/residue: 0.4417 time to fit residues: 67.1556 Evaluate side-chains 127 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 112 time to evaluate : 0.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 286 PHE Chi-restraints excluded: chain D residue 339 ASP Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 355 LEU Chi-restraints excluded: chain D residue 396 ASP Chi-restraints excluded: chain D residue 424 VAL Chi-restraints excluded: chain D residue 447 ARG Chi-restraints excluded: chain D residue 596 GLU Chi-restraints excluded: chain D residue 613 LEU Chi-restraints excluded: chain D residue 959 ASP Chi-restraints excluded: chain D residue 982 TYR Chi-restraints excluded: chain D residue 1290 LEU Chi-restraints excluded: chain D residue 1450 ILE Chi-restraints excluded: chain D residue 1698 ILE Chi-restraints excluded: chain D residue 1970 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 21 optimal weight: 2.9990 chunk 9 optimal weight: 10.0000 chunk 82 optimal weight: 30.0000 chunk 29 optimal weight: 0.6980 chunk 49 optimal weight: 5.9990 chunk 91 optimal weight: 1.9990 chunk 75 optimal weight: 20.0000 chunk 87 optimal weight: 2.9990 chunk 160 optimal weight: 30.0000 chunk 154 optimal weight: 20.0000 chunk 142 optimal weight: 5.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 794 HIS D1652 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.132338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.076028 restraints weight = 26446.046| |-----------------------------------------------------------------------------| r_work (start): 0.3100 rms_B_bonded: 3.26 r_work: 0.2941 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2975 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2975 r_free = 0.2975 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2975 r_free = 0.2975 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.74 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2975 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.2647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.052 14148 Z= 0.293 Angle : 0.619 12.068 19169 Z= 0.315 Chirality : 0.047 0.170 2043 Planarity : 0.004 0.060 2483 Dihedral : 5.702 80.024 1918 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 1.85 % Allowed : 15.36 % Favored : 82.78 % 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 are not related in a simple way. whole: 0.12 (0.21), residues: 1681 helix: 0.85 (0.35), residues: 220 sheet: 0.08 (0.22), residues: 517 loop : 0.01 (0.21), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG D1396 TYR 0.018 0.002 TYR D 533 PHE 0.023 0.002 PHE D1683 TRP 0.042 0.001 TRP D1820 HIS 0.005 0.001 HIS D 581 Details of bonding type rmsd/Z covalent geometry : bond 0.00682 / 0.29 (14148) covalent geometry : angle 0.61853 / 0.32 (19169) hydrogen bonds : bond 0.03595 / 2.35 ( 369) hydrogen bonds : angle 5.27077 / 3.71 ( 990) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3362 Ramachandran restraints generated. 1681 Oldfield, 0 Emsley, 1681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3362 Ramachandran restraints generated. 1681 Oldfield, 0 Emsley, 1681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 114 time to evaluate : 0.474 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 447 ARG cc_start: 0.8502 (OUTLIER) cc_final: 0.7485 (ttp80) REVERT: D 518 ASP cc_start: 0.8643 (t0) cc_final: 0.8143 (t70) REVERT: D 527 LYS cc_start: 0.8450 (mptt) cc_final: 0.7986 (mptt) REVERT: D 613 LEU cc_start: 0.7309 (OUTLIER) cc_final: 0.7068 (pp) REVERT: D 783 GLU cc_start: 0.8767 (mm-30) cc_final: 0.8490 (tp30) REVERT: D 870 MET cc_start: 0.3357 (mpp) cc_final: 0.2240 (pmm) REVERT: D 932 ASP cc_start: 0.8254 (t0) cc_final: 0.7844 (t0) REVERT: D 937 ASN cc_start: 0.8228 (m-40) cc_final: 0.7849 (m110) REVERT: D 980 TRP cc_start: 0.7452 (m100) cc_final: 0.6805 (m100) REVERT: D 1382 GLN cc_start: 0.8012 (tm-30) cc_final: 0.7748 (tm130) REVERT: D 1396 ARG cc_start: 0.8288 (mmm160) cc_final: 0.8070 (mmm160) REVERT: D 1450 ILE cc_start: 0.4561 (OUTLIER) cc_final: 0.4179 (tt) REVERT: D 1543 ARG cc_start: 0.7410 (mtm110) cc_final: 0.6984 (mtm110) REVERT: D 1791 ARG cc_start: 0.7661 (mmm-85) cc_final: 0.7280 (mmm-85) REVERT: D 1848 PHE cc_start: 0.8088 (m-10) cc_final: 0.7671 (m-10) REVERT: D 1868 HIS cc_start: 0.7951 (OUTLIER) cc_final: 0.7173 (p90) outliers start: 28 outliers final: 14 residues processed: 136 average time/residue: 0.4537 time to fit residues: 69.0865 Evaluate side-chains 124 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 106 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 279 GLU Chi-restraints excluded: chain D residue 295 VAL Chi-restraints excluded: chain D residue 339 ASP Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 355 LEU Chi-restraints excluded: chain D residue 424 VAL Chi-restraints excluded: chain D residue 447 ARG Chi-restraints excluded: chain D residue 589 VAL Chi-restraints excluded: chain D residue 596 GLU Chi-restraints excluded: chain D residue 613 LEU Chi-restraints excluded: chain D residue 959 ASP Chi-restraints excluded: chain D residue 982 TYR Chi-restraints excluded: chain D residue 1230 SER Chi-restraints excluded: chain D residue 1290 LEU Chi-restraints excluded: chain D residue 1450 ILE Chi-restraints excluded: chain D residue 1698 ILE Chi-restraints excluded: chain D residue 1849 VAL Chi-restraints excluded: chain D residue 1868 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 129 optimal weight: 2.9990 chunk 145 optimal weight: 2.9990 chunk 148 optimal weight: 3.9990 chunk 104 optimal weight: 1.9990 chunk 102 optimal weight: 0.4980 chunk 51 optimal weight: 0.9980 chunk 71 optimal weight: 1.9990 chunk 118 optimal weight: 3.9990 chunk 88 optimal weight: 0.2980 chunk 86 optimal weight: 0.0370 chunk 167 optimal weight: 7.9990 overall best weight: 0.7660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1834 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.134732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.080098 restraints weight = 26222.837| |-----------------------------------------------------------------------------| r_work (start): 0.3133 rms_B_bonded: 3.22 r_work: 0.2980 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3017 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3017 r_free = 0.3017 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.74 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3017 r_free = 0.3017 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.73 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3017 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.2598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 14148 Z= 0.117 Angle : 0.531 11.355 19169 Z= 0.267 Chirality : 0.043 0.151 2043 Planarity : 0.003 0.040 2483 Dihedral : 5.438 74.376 1918 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.39 % Allowed : 16.23 % Favored : 82.38 % 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 are not related in a simple way. whole: 0.23 (0.21), residues: 1681 helix: 1.17 (0.35), residues: 220 sheet: 0.07 (0.22), residues: 512 loop : 0.07 (0.21), residues: 949 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D1396 TYR 0.012 0.001 TYR D1558 PHE 0.026 0.001 PHE D1751 TRP 0.034 0.001 TRP D1820 HIS 0.002 0.000 HIS D1062 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 (14148) covalent geometry : angle 0.53062 / 0.27 (19169) hydrogen bonds : bond 0.02944 / 1.97 ( 369) hydrogen bonds : angle 4.91593 / 3.49 ( 990) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3362 Ramachandran restraints generated. 1681 Oldfield, 0 Emsley, 1681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3362 Ramachandran restraints generated. 1681 Oldfield, 0 Emsley, 1681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 114 time to evaluate : 0.432 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 232 ARG cc_start: 0.6705 (ppt170) cc_final: 0.5990 (ppt170) REVERT: D 293 HIS cc_start: 0.8867 (m90) cc_final: 0.8581 (m90) REVERT: D 518 ASP cc_start: 0.8594 (t0) cc_final: 0.8102 (t70) REVERT: D 527 LYS cc_start: 0.8396 (mptt) cc_final: 0.7944 (mptt) REVERT: D 613 LEU cc_start: 0.7261 (OUTLIER) cc_final: 0.7045 (pp) REVERT: D 783 GLU cc_start: 0.8762 (mm-30) cc_final: 0.8554 (tp30) REVERT: D 870 MET cc_start: 0.3291 (mpp) cc_final: 0.2651 (pmm) REVERT: D 932 ASP cc_start: 0.8309 (t0) cc_final: 0.7933 (t0) REVERT: D 937 ASN cc_start: 0.8279 (m-40) cc_final: 0.7888 (m110) REVERT: D 980 TRP cc_start: 0.7467 (m100) cc_final: 0.6855 (m100) REVERT: D 1382 GLN cc_start: 0.8017 (tm-30) cc_final: 0.7742 (tm130) REVERT: D 1450 ILE cc_start: 0.4554 (OUTLIER) cc_final: 0.4181 (tt) REVERT: D 1543 ARG cc_start: 0.7326 (mtm110) cc_final: 0.6889 (mtm110) REVERT: D 1581 THR cc_start: 0.8781 (m) cc_final: 0.8279 (p) REVERT: D 1636 GLU cc_start: 0.8565 (OUTLIER) cc_final: 0.8335 (tm-30) REVERT: D 1791 ARG cc_start: 0.7631 (mmm-85) cc_final: 0.7299 (mmm-85) REVERT: D 1812 MET cc_start: 0.6481 (pp-130) cc_final: 0.4068 (ttt) REVERT: D 1848 PHE cc_start: 0.8080 (m-10) cc_final: 0.7670 (m-10) REVERT: D 1868 HIS cc_start: 0.7900 (OUTLIER) cc_final: 0.6954 (p90) REVERT: D 1870 TRP cc_start: 0.8016 (p90) cc_final: 0.7700 (p90) outliers start: 21 outliers final: 11 residues processed: 132 average time/residue: 0.4550 time to fit residues: 66.6650 Evaluate side-chains 124 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 109 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 279 GLU Chi-restraints excluded: chain D residue 286 PHE Chi-restraints excluded: chain D residue 295 VAL Chi-restraints excluded: chain D residue 355 LEU Chi-restraints excluded: chain D residue 424 VAL Chi-restraints excluded: chain D residue 589 VAL Chi-restraints excluded: chain D residue 596 GLU Chi-restraints excluded: chain D residue 613 LEU Chi-restraints excluded: chain D residue 982 TYR Chi-restraints excluded: chain D residue 1290 LEU Chi-restraints excluded: chain D residue 1450 ILE Chi-restraints excluded: chain D residue 1636 GLU Chi-restraints excluded: chain D residue 1698 ILE Chi-restraints excluded: chain D residue 1849 VAL Chi-restraints excluded: chain D residue 1868 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 116 optimal weight: 1.9990 chunk 156 optimal weight: 0.4980 chunk 49 optimal weight: 4.9990 chunk 46 optimal weight: 0.7980 chunk 67 optimal weight: 0.0170 chunk 74 optimal weight: 0.9980 chunk 134 optimal weight: 2.9990 chunk 162 optimal weight: 8.9990 chunk 140 optimal weight: 20.0000 chunk 11 optimal weight: 0.7980 chunk 82 optimal weight: 20.0000 overall best weight: 0.6218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 825 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.135412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.080462 restraints weight = 26617.327| |-----------------------------------------------------------------------------| r_work (start): 0.3187 rms_B_bonded: 3.26 r_work: 0.3029 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3059 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3059 r_free = 0.3059 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.73 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3059 r_free = 0.3059 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.74 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3059 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.2635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 14148 Z= 0.106 Angle : 0.530 14.011 19169 Z= 0.264 Chirality : 0.043 0.149 2043 Planarity : 0.004 0.064 2483 Dihedral : 5.213 72.383 1918 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.32 % Allowed : 16.69 % Favored : 81.99 % 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 are not related in a simple way. whole: 0.28 (0.21), residues: 1681 helix: 1.20 (0.35), residues: 227 sheet: 0.12 (0.22), residues: 508 loop : 0.09 (0.21), residues: 946 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG D1396 TYR 0.012 0.001 TYR D1558 PHE 0.028 0.001 PHE D1683 TRP 0.052 0.001 TRP D1820 HIS 0.002 0.000 HIS D1730 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.11 (14148) covalent geometry : angle 0.53002 / 0.26 (19169) hydrogen bonds : bond 0.02795 / 1.89 ( 369) hydrogen bonds : angle 4.72875 / 3.37 ( 990) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3362 Ramachandran restraints generated. 1681 Oldfield, 0 Emsley, 1681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3362 Ramachandran restraints generated. 1681 Oldfield, 0 Emsley, 1681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 118 time to evaluate : 0.375 Fit side-chains revert: symmetry clash REVERT: D 228 THR cc_start: 0.8599 (t) cc_final: 0.8342 (m) REVERT: D 293 HIS cc_start: 0.8943 (m90) cc_final: 0.8629 (m90) REVERT: D 301 LEU cc_start: 0.8381 (OUTLIER) cc_final: 0.8000 (mm) REVERT: D 518 ASP cc_start: 0.8557 (t0) cc_final: 0.7918 (t70) REVERT: D 527 LYS cc_start: 0.8373 (mptt) cc_final: 0.7931 (mptt) REVERT: D 783 GLU cc_start: 0.8789 (mm-30) cc_final: 0.8505 (tp30) REVERT: D 870 MET cc_start: 0.3353 (mpp) cc_final: 0.2708 (pmm) REVERT: D 937 ASN cc_start: 0.8304 (m-40) cc_final: 0.7912 (m110) REVERT: D 1382 GLN cc_start: 0.8021 (tm-30) cc_final: 0.7767 (tm130) REVERT: D 1450 ILE cc_start: 0.4580 (OUTLIER) cc_final: 0.4173 (tt) REVERT: D 1543 ARG cc_start: 0.7326 (mtm110) cc_final: 0.6877 (mtm110) REVERT: D 1581 THR cc_start: 0.8759 (m) cc_final: 0.8278 (p) REVERT: D 1636 GLU cc_start: 0.8508 (OUTLIER) cc_final: 0.8302 (tm-30) REVERT: D 1791 ARG cc_start: 0.7670 (mmm-85) cc_final: 0.7279 (mmm-85) REVERT: D 1812 MET cc_start: 0.6537 (pp-130) cc_final: 0.4162 (ttt) REVERT: D 1848 PHE cc_start: 0.8099 (m-10) cc_final: 0.7629 (m-10) REVERT: D 1868 HIS cc_start: 0.7913 (OUTLIER) cc_final: 0.6966 (p90) REVERT: D 1870 TRP cc_start: 0.8013 (p90) cc_final: 0.7689 (p90) outliers start: 20 outliers final: 12 residues processed: 135 average time/residue: 0.4338 time to fit residues: 65.3977 Evaluate side-chains 127 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 111 time to evaluate : 0.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 295 VAL Chi-restraints excluded: chain D residue 301 LEU Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 355 LEU Chi-restraints excluded: chain D residue 424 VAL Chi-restraints excluded: chain D residue 589 VAL Chi-restraints excluded: chain D residue 596 GLU Chi-restraints excluded: chain D residue 825 ASN Chi-restraints excluded: chain D residue 982 TYR Chi-restraints excluded: chain D residue 1129 VAL Chi-restraints excluded: chain D residue 1290 LEU Chi-restraints excluded: chain D residue 1450 ILE Chi-restraints excluded: chain D residue 1636 GLU Chi-restraints excluded: chain D residue 1698 ILE Chi-restraints excluded: chain D residue 1849 VAL Chi-restraints excluded: chain D residue 1868 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 23 optimal weight: 2.9990 chunk 50 optimal weight: 0.0040 chunk 155 optimal weight: 20.0000 chunk 43 optimal weight: 0.6980 chunk 62 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 2 optimal weight: 5.9990 chunk 31 optimal weight: 2.9990 chunk 96 optimal weight: 2.9990 chunk 111 optimal weight: 0.9990 chunk 59 optimal weight: 2.9990 overall best weight: 1.3398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.134374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.079041 restraints weight = 26499.058| |-----------------------------------------------------------------------------| r_work (start): 0.3153 rms_B_bonded: 3.26 r_work: 0.2996 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3046 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3046 r_free = 0.3046 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.74 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3046 r_free = 0.3046 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.73 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3046 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.2730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 14148 Z= 0.153 Angle : 0.545 13.089 19169 Z= 0.273 Chirality : 0.044 0.155 2043 Planarity : 0.003 0.037 2483 Dihedral : 5.161 70.651 1916 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 1.13 % Allowed : 16.69 % 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 are not related in a simple way. whole: 0.31 (0.21), residues: 1681 helix: 1.05 (0.35), residues: 227 sheet: 0.16 (0.22), residues: 512 loop : 0.14 (0.21), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D1396 TYR 0.013 0.001 TYR D1558 PHE 0.024 0.001 PHE D1751 TRP 0.040 0.001 TRP D1820 HIS 0.003 0.001 HIS D1730 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.15 (14148) covalent geometry : angle 0.54475 / 0.27 (19169) hydrogen bonds : bond 0.02961 / 1.97 ( 369) hydrogen bonds : angle 4.81542 / 3.43 ( 990) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3362 Ramachandran restraints generated. 1681 Oldfield, 0 Emsley, 1681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3362 Ramachandran restraints generated. 1681 Oldfield, 0 Emsley, 1681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 115 time to evaluate : 0.539 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 228 THR cc_start: 0.8582 (t) cc_final: 0.8314 (m) REVERT: D 293 HIS cc_start: 0.8938 (m90) cc_final: 0.8665 (m90) REVERT: D 301 LEU cc_start: 0.8353 (OUTLIER) cc_final: 0.7971 (mm) REVERT: D 518 ASP cc_start: 0.8551 (t0) cc_final: 0.8159 (t0) REVERT: D 527 LYS cc_start: 0.8395 (mptt) cc_final: 0.7949 (mptt) REVERT: D 783 GLU cc_start: 0.8761 (mm-30) cc_final: 0.8475 (tp30) REVERT: D 870 MET cc_start: 0.3397 (mpp) cc_final: 0.2723 (pmm) REVERT: D 937 ASN cc_start: 0.8326 (m-40) cc_final: 0.7937 (m110) REVERT: D 1022 ARG cc_start: 0.7829 (ttt180) cc_final: 0.7620 (ttt-90) REVERT: D 1382 GLN cc_start: 0.8007 (tm-30) cc_final: 0.7732 (tm130) REVERT: D 1450 ILE cc_start: 0.4711 (OUTLIER) cc_final: 0.4281 (tt) REVERT: D 1543 ARG cc_start: 0.7388 (mtm110) cc_final: 0.6918 (mtm110) REVERT: D 1581 THR cc_start: 0.8758 (m) cc_final: 0.8263 (p) REVERT: D 1636 GLU cc_start: 0.8561 (OUTLIER) cc_final: 0.8342 (tm-30) REVERT: D 1791 ARG cc_start: 0.7683 (mmm-85) cc_final: 0.7288 (mmm-85) REVERT: D 1848 PHE cc_start: 0.8130 (m-10) cc_final: 0.7655 (m-10) REVERT: D 1868 HIS cc_start: 0.7960 (OUTLIER) cc_final: 0.7015 (p90) REVERT: D 1870 TRP cc_start: 0.8016 (p90) cc_final: 0.7689 (p90) REVERT: D 1962 MET cc_start: 0.7189 (tpp) cc_final: 0.6922 (tpp) outliers start: 17 outliers final: 13 residues processed: 129 average time/residue: 0.4546 time to fit residues: 65.2415 Evaluate side-chains 126 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 109 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 286 PHE Chi-restraints excluded: chain D residue 295 VAL Chi-restraints excluded: chain D residue 301 LEU Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 355 LEU Chi-restraints excluded: chain D residue 424 VAL Chi-restraints excluded: chain D residue 589 VAL Chi-restraints excluded: chain D residue 596 GLU Chi-restraints excluded: chain D residue 982 TYR Chi-restraints excluded: chain D residue 1129 VAL Chi-restraints excluded: chain D residue 1290 LEU Chi-restraints excluded: chain D residue 1450 ILE Chi-restraints excluded: chain D residue 1636 GLU Chi-restraints excluded: chain D residue 1698 ILE Chi-restraints excluded: chain D residue 1849 VAL Chi-restraints excluded: chain D residue 1868 HIS Chi-restraints excluded: chain D residue 1927 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 52 optimal weight: 2.9990 chunk 134 optimal weight: 4.9990 chunk 159 optimal weight: 8.9990 chunk 123 optimal weight: 0.0970 chunk 139 optimal weight: 0.0270 chunk 23 optimal weight: 4.9990 chunk 164 optimal weight: 7.9990 chunk 19 optimal weight: 0.0370 chunk 88 optimal weight: 1.9990 chunk 149 optimal weight: 3.9990 chunk 156 optimal weight: 4.9990 overall best weight: 1.0318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 825 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.134762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.079584 restraints weight = 26515.866| |-----------------------------------------------------------------------------| r_work (start): 0.3169 rms_B_bonded: 3.26 r_work: 0.3010 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3055 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3055 r_free = 0.3055 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.73 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3055 r_free = 0.3055 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.74 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3055 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.2758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 14148 Z= 0.133 Angle : 0.540 12.685 19169 Z= 0.271 Chirality : 0.044 0.151 2043 Planarity : 0.003 0.037 2483 Dihedral : 5.103 66.634 1916 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 1.19 % Allowed : 16.75 % Favored : 82.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.29 (0.21), residues: 1681 helix: 0.97 (0.35), residues: 234 sheet: 0.16 (0.22), residues: 514 loop : 0.13 (0.21), residues: 933 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D1697 TYR 0.012 0.001 TYR D1558 PHE 0.028 0.001 PHE D1751 TRP 0.040 0.001 TRP D1820 HIS 0.005 0.001 HIS D1730 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.13 (14148) covalent geometry : angle 0.53956 / 0.27 (19169) hydrogen bonds : bond 0.02876 / 1.93 ( 369) hydrogen bonds : angle 4.82195 / 3.46 ( 990) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5177.81 seconds wall clock time: 88 minutes 36.14 seconds (5316.14 seconds total)