Starting phenix.real_space_refine on Thu Sep 18 04:32:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9h6x_51902/09_2025/9h6x_51902.cif Found real_map, /net/cci-nas-00/data/ceres_data/9h6x_51902/09_2025/9h6x_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_51902/09_2025/9h6x_51902.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9h6x_51902/09_2025/9h6x_51902.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9h6x_51902/09_2025/9h6x_51902.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9h6x_51902/09_2025/9h6x_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-2.0-5805/lib/python3.9/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, 70 Unusual residues: {' CA': 10, 'PSF': 2} Classifications: {'undetermined': 12} Link IDs: {None: 11} Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N PSF D2001 " occ=0.66 ... (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: 2.84, per 1000 atoms: 0.21 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: 0.86 Conformation dependent library (CDL) restraints added in 619.9 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.71 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: 2.67 Time building geometry restraints manager: 1.15 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 2.510 nonbonded pdb="CA CA D2007 " pdb=" O3 PSF D2012 " model vdw 2.370 2.510 nonbonded pdb=" OD2 ASP D1624 " pdb="CA CA D2007 " model vdw 2.377 2.510 nonbonded pdb=" O TRP D 445 " pdb="CA CA D2002 " model vdw 2.382 2.510 nonbonded pdb=" OD1 ASP D1569 " pdb="CA CA D2006 " model vdw 2.382 2.510 ... (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: 4.160 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: 0.270 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.740 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 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 aren 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 covalent geometry : bond 0.00399 (14148) covalent geometry : angle 0.84472 (19169) hydrogen bonds : bond 0.21044 ( 369) hydrogen bonds : angle 8.49475 ( 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 : 0.504 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: 0.8284 (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: 0.8352 (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: 0.6205 time to fit residues: 136.2300 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 : 0.570 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4051 r_free = 0.4051 target = 0.135284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.080889 restraints weight = 26115.702| |-----------------------------------------------------------------------------| r_work (start): 0.3150 rms_B_bonded: 3.24 r_work: 0.3000 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3072 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3072 r_free = 0.3072 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.55 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3072 r_free = 0.3072 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.69 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3072 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.1518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 14148 Z= 0.159 Angle : 0.552 7.602 19169 Z= 0.285 Chirality : 0.044 0.178 2043 Planarity : 0.004 0.038 2483 Dihedral : 7.229 138.645 1927 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.52 % Allowed : 12.52 % Favored : 85.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.54 (0.19), residues: 1681 helix: -0.15 (0.33), residues: 221 sheet: -0.18 (0.22), residues: 503 loop : -0.42 (0.19), residues: 957 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D1385 TYR 0.014 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 covalent geometry : bond 0.00363 (14148) covalent geometry : angle 0.55199 (19169) hydrogen bonds : bond 0.03615 ( 369) hydrogen bonds : angle 5.89371 ( 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 154 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 131 time to evaluate : 0.483 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 223 HIS cc_start: 0.7878 (t70) cc_final: 0.7645 (t70) REVERT: D 257 MET cc_start: 0.7309 (mmp) cc_final: 0.6831 (mmp) REVERT: D 286 PHE cc_start: 0.7777 (t80) cc_final: 0.7526 (t80) REVERT: D 293 HIS cc_start: 0.8817 (m170) cc_final: 0.8589 (m90) REVERT: D 518 ASP cc_start: 0.8755 (t0) cc_final: 0.8096 (t70) REVERT: D 527 LYS cc_start: 0.8528 (mptt) cc_final: 0.8027 (mptt) REVERT: D 783 GLU cc_start: 0.8785 (mm-30) cc_final: 0.8540 (tp30) REVERT: D 870 MET cc_start: 0.3276 (mpp) cc_final: 0.2291 (pmm) REVERT: D 929 GLU cc_start: 0.8301 (OUTLIER) cc_final: 0.7988 (mp0) REVERT: D 937 ASN cc_start: 0.8166 (m-40) cc_final: 0.7741 (m110) REVERT: D 980 TRP cc_start: 0.7410 (m100) cc_final: 0.6798 (m100) REVERT: D 1022 ARG cc_start: 0.7971 (ttt180) cc_final: 0.7742 (ttt180) REVERT: D 1026 LYS cc_start: 0.7201 (mtmm) cc_final: 0.6959 (mptt) REVERT: D 1292 MET cc_start: 0.8691 (ptm) cc_final: 0.8449 (ptm) REVERT: D 1382 GLN cc_start: 0.7839 (tm-30) cc_final: 0.7591 (tm130) REVERT: D 1543 ARG cc_start: 0.7191 (mtm110) cc_final: 0.6877 (mtm110) REVERT: D 1581 THR cc_start: 0.8793 (m) cc_final: 0.8388 (p) REVERT: D 1636 GLU cc_start: 0.8390 (tt0) cc_final: 0.8135 (tm-30) REVERT: D 1658 GLU cc_start: 0.8245 (tt0) cc_final: 0.8015 (pt0) REVERT: D 1858 GLU cc_start: 0.8269 (mm-30) cc_final: 0.8044 (mm-30) outliers start: 23 outliers final: 8 residues processed: 146 average time/residue: 0.5826 time to fit residues: 93.7177 Evaluate side-chains 124 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 115 time to evaluate : 0.533 ------------------------------------------------------------------------------- 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 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 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: 7.9990 chunk 133 optimal weight: 2.9990 chunk 58 optimal weight: 0.9980 chunk 97 optimal weight: 4.9990 chunk 11 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 55 optimal weight: 0.8980 chunk 37 optimal weight: 2.9990 chunk 96 optimal weight: 0.9980 chunk 41 optimal weight: 0.7980 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 338 ASN D1570 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.135488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.080417 restraints weight = 26443.034| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 3.27 r_work: 0.2997 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3070 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3070 r_free = 0.3070 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.69 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3070 r_free = 0.3070 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.71 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3070 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.1777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14148 Z= 0.122 Angle : 0.513 8.500 19169 Z= 0.262 Chirality : 0.043 0.162 2043 Planarity : 0.004 0.042 2483 Dihedral : 6.045 87.275 1920 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 1.39 % Allowed : 13.51 % 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 aren not related in a simple way. whole: -0.18 (0.20), residues: 1681 helix: 0.50 (0.34), residues: 220 sheet: -0.04 (0.22), residues: 502 loop : -0.22 (0.20), residues: 959 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D1396 TYR 0.012 0.001 TYR D1558 PHE 0.019 0.001 PHE D1683 TRP 0.017 0.001 TRP D1870 HIS 0.002 0.000 HIS D 581 Details of bonding type rmsd covalent geometry : bond 0.00276 (14148) covalent geometry : angle 0.51286 (19169) hydrogen bonds : bond 0.03276 ( 369) hydrogen bonds : angle 5.36750 ( 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: 21 poor density : 122 time to evaluate : 0.678 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 232 ARG cc_start: 0.6743 (ppt170) cc_final: 0.6487 (ppt170) REVERT: D 518 ASP cc_start: 0.8661 (t0) cc_final: 0.7976 (t70) REVERT: D 527 LYS cc_start: 0.8471 (mptt) cc_final: 0.8022 (mptt) REVERT: D 783 GLU cc_start: 0.8772 (mm-30) cc_final: 0.8514 (tp30) REVERT: D 870 MET cc_start: 0.3267 (mpp) cc_final: 0.2623 (pmm) REVERT: D 937 ASN cc_start: 0.8158 (m-40) cc_final: 0.7748 (m110) REVERT: D 980 TRP cc_start: 0.7413 (m100) cc_final: 0.6802 (m100) REVERT: D 1026 LYS cc_start: 0.7160 (mtmm) cc_final: 0.6938 (mptt) REVERT: D 1292 MET cc_start: 0.8704 (ptm) cc_final: 0.8353 (ptm) REVERT: D 1382 GLN cc_start: 0.7901 (tm-30) cc_final: 0.7614 (tm130) REVERT: D 1450 ILE cc_start: 0.4305 (OUTLIER) cc_final: 0.3800 (tp) REVERT: D 1519 GLU cc_start: 0.8329 (mt-10) cc_final: 0.7879 (mt-10) REVERT: D 1543 ARG cc_start: 0.7228 (mtm110) cc_final: 0.6899 (mtm110) REVERT: D 1581 THR cc_start: 0.8794 (m) cc_final: 0.8367 (p) REVERT: D 1636 GLU cc_start: 0.8385 (tt0) cc_final: 0.8104 (tm-30) REVERT: D 1658 GLU cc_start: 0.8335 (tt0) cc_final: 0.8098 (pt0) REVERT: D 1791 ARG cc_start: 0.7365 (mmm-85) cc_final: 0.7084 (mmm-85) REVERT: D 1848 PHE cc_start: 0.7859 (m-80) cc_final: 0.7574 (m-10) REVERT: D 1858 GLU cc_start: 0.8281 (mm-30) cc_final: 0.8072 (mm-30) outliers start: 21 outliers final: 7 residues processed: 137 average time/residue: 0.6093 time to fit residues: 92.5818 Evaluate side-chains 127 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 119 time to evaluate : 0.645 ------------------------------------------------------------------------------- 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 1784 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 35 optimal weight: 0.0370 chunk 167 optimal weight: 20.0000 chunk 87 optimal weight: 4.9990 chunk 12 optimal weight: 10.0000 chunk 152 optimal weight: 9.9990 chunk 40 optimal weight: 8.9990 chunk 111 optimal weight: 0.9990 chunk 95 optimal weight: 0.0010 chunk 45 optimal weight: 0.8980 chunk 88 optimal weight: 0.0980 chunk 77 optimal weight: 3.9990 overall best weight: 0.4066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 338 ASN D1570 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.136224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.082068 restraints weight = 26213.044| |-----------------------------------------------------------------------------| r_work (start): 0.3182 rms_B_bonded: 3.24 r_work: 0.3032 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3032 ------------------------------------------------------------------------------- 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 = 0.71 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3099 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.1911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 14148 Z= 0.090 Angle : 0.493 10.795 19169 Z= 0.249 Chirality : 0.043 0.147 2043 Planarity : 0.003 0.045 2483 Dihedral : 5.617 81.878 1918 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.85 % Allowed : 13.25 % Favored : 84.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.03 (0.20), residues: 1681 helix: 0.98 (0.35), residues: 220 sheet: -0.02 (0.22), residues: 517 loop : -0.09 (0.20), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG D1396 TYR 0.013 0.001 TYR D 288 PHE 0.026 0.001 PHE D 431 TRP 0.023 0.001 TRP D1820 HIS 0.002 0.000 HIS D1018 Details of bonding type rmsd covalent geometry : bond 0.00200 (14148) covalent geometry : angle 0.49264 (19169) hydrogen bonds : bond 0.02907 ( 369) hydrogen bonds : angle 5.01994 ( 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 156 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 128 time to evaluate : 0.594 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 232 ARG cc_start: 0.6686 (ppt170) cc_final: 0.6431 (ppt170) REVERT: D 293 HIS cc_start: 0.8879 (m90) cc_final: 0.8516 (m90) REVERT: D 518 ASP cc_start: 0.8596 (t0) cc_final: 0.7902 (t70) REVERT: D 527 LYS cc_start: 0.8426 (mptt) cc_final: 0.7976 (mptt) REVERT: D 783 GLU cc_start: 0.8761 (mm-30) cc_final: 0.8464 (tp30) REVERT: D 870 MET cc_start: 0.3225 (mpp) cc_final: 0.2251 (pmm) REVERT: D 929 GLU cc_start: 0.8295 (OUTLIER) cc_final: 0.8080 (mp0) REVERT: D 932 ASP cc_start: 0.8188 (t0) cc_final: 0.7857 (t0) REVERT: D 937 ASN cc_start: 0.8226 (m-40) cc_final: 0.7828 (m110) REVERT: D 980 TRP cc_start: 0.7410 (m100) cc_final: 0.6788 (m100) REVERT: D 1026 LYS cc_start: 0.6989 (mtmm) cc_final: 0.6789 (mptt) REVERT: D 1292 MET cc_start: 0.8695 (ptm) cc_final: 0.8298 (ptm) REVERT: D 1382 GLN cc_start: 0.7947 (tm-30) cc_final: 0.7669 (tm130) REVERT: D 1450 ILE cc_start: 0.4161 (OUTLIER) cc_final: 0.3640 (tp) REVERT: D 1519 GLU cc_start: 0.8329 (mt-10) cc_final: 0.7863 (mt-10) REVERT: D 1581 THR cc_start: 0.8791 (m) cc_final: 0.8348 (p) REVERT: D 1636 GLU cc_start: 0.8355 (tt0) cc_final: 0.8080 (tm-30) REVERT: D 1658 GLU cc_start: 0.8351 (tt0) cc_final: 0.8018 (pt0) REVERT: D 1791 ARG cc_start: 0.7479 (mmm-85) cc_final: 0.7155 (mmm-85) REVERT: D 1848 PHE cc_start: 0.7966 (m-80) cc_final: 0.7574 (m-10) REVERT: D 1858 GLU cc_start: 0.8274 (mm-30) cc_final: 0.8070 (mm-30) REVERT: D 1868 HIS cc_start: 0.7809 (OUTLIER) cc_final: 0.7083 (p-80) REVERT: D 1870 TRP cc_start: 0.7992 (p90) cc_final: 0.7620 (p90) outliers start: 28 outliers final: 10 residues processed: 150 average time/residue: 0.5557 time to fit residues: 92.9820 Evaluate side-chains 128 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 115 time to evaluate : 0.753 ------------------------------------------------------------------------------- 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 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 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 Chi-restraints excluded: chain D residue 1868 HIS Chi-restraints excluded: chain D residue 1970 LEU 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: 0.3980 chunk 117 optimal weight: 30.0000 chunk 102 optimal weight: 1.9990 chunk 86 optimal weight: 0.0030 chunk 101 optimal weight: 1.9990 chunk 15 optimal weight: 9.9990 chunk 75 optimal weight: 20.0000 chunk 38 optimal weight: 0.9980 chunk 29 optimal weight: 0.0170 chunk 12 optimal weight: 0.8980 overall best weight: 0.4628 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 338 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.136406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.082202 restraints weight = 26279.369| |-----------------------------------------------------------------------------| r_work (start): 0.3178 rms_B_bonded: 3.26 r_work: 0.3028 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3103 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3103 r_free = 0.3103 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 = 0.3103 r_free = 0.3103 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.72 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3103 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.2038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 14148 Z= 0.091 Angle : 0.483 8.470 19169 Z= 0.245 Chirality : 0.043 0.147 2043 Planarity : 0.003 0.051 2483 Dihedral : 5.371 76.920 1918 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.52 % Allowed : 14.04 % Favored : 84.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.22 (0.20), residues: 1681 helix: 1.37 (0.35), residues: 214 sheet: 0.09 (0.22), residues: 514 loop : -0.01 (0.21), residues: 953 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG D1396 TYR 0.013 0.001 TYR D1558 PHE 0.026 0.001 PHE D1683 TRP 0.032 0.001 TRP D1820 HIS 0.003 0.000 HIS D 293 Details of bonding type rmsd covalent geometry : bond 0.00204 (14148) covalent geometry : angle 0.48267 (19169) hydrogen bonds : bond 0.02774 ( 369) hydrogen bonds : angle 4.82449 ( 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 144 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 121 time to evaluate : 0.573 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 232 ARG cc_start: 0.6685 (ppt170) cc_final: 0.6390 (ppt170) REVERT: D 293 HIS cc_start: 0.8895 (m90) cc_final: 0.8489 (m90) REVERT: D 518 ASP cc_start: 0.8606 (t0) cc_final: 0.7904 (t70) REVERT: D 527 LYS cc_start: 0.8459 (mptt) cc_final: 0.8013 (mptt) REVERT: D 783 GLU cc_start: 0.8754 (mm-30) cc_final: 0.8441 (tp30) REVERT: D 784 LYS cc_start: 0.8759 (OUTLIER) cc_final: 0.8342 (ptmt) REVERT: D 870 MET cc_start: 0.3234 (mpp) cc_final: 0.2208 (pmm) REVERT: D 937 ASN cc_start: 0.8238 (m-40) cc_final: 0.7849 (m110) REVERT: D 980 TRP cc_start: 0.7387 (m100) cc_final: 0.6757 (m100) REVERT: D 1292 MET cc_start: 0.8697 (ptm) cc_final: 0.8284 (ptm) REVERT: D 1382 GLN cc_start: 0.7960 (tm-30) cc_final: 0.7733 (tm130) REVERT: D 1450 ILE cc_start: 0.4107 (OUTLIER) cc_final: 0.3588 (tp) REVERT: D 1519 GLU cc_start: 0.8326 (mt-10) cc_final: 0.7860 (mt-10) REVERT: D 1581 THR cc_start: 0.8794 (m) cc_final: 0.8370 (p) REVERT: D 1636 GLU cc_start: 0.8372 (tt0) cc_final: 0.8126 (tm-30) REVERT: D 1658 GLU cc_start: 0.8400 (tt0) cc_final: 0.8034 (pt0) REVERT: D 1686 PHE cc_start: 0.8314 (m-80) cc_final: 0.8106 (m-80) REVERT: D 1791 ARG cc_start: 0.7579 (mmm-85) cc_final: 0.7219 (mmm-85) REVERT: D 1848 PHE cc_start: 0.7964 (m-80) cc_final: 0.7525 (m-10) REVERT: D 1858 GLU cc_start: 0.8274 (mm-30) cc_final: 0.8047 (mm-30) outliers start: 23 outliers final: 12 residues processed: 140 average time/residue: 0.5802 time to fit residues: 90.2012 Evaluate side-chains 130 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 116 time to evaluate : 0.636 ------------------------------------------------------------------------------- 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 784 LYS 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 1784 LYS Chi-restraints excluded: chain D residue 1902 LEU 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: 0.7980 chunk 75 optimal weight: 20.0000 chunk 146 optimal weight: 7.9990 chunk 96 optimal weight: 3.9990 chunk 67 optimal weight: 8.9990 chunk 98 optimal weight: 0.2980 chunk 94 optimal weight: 2.9990 chunk 110 optimal weight: 2.9990 chunk 113 optimal weight: 0.7980 chunk 42 optimal weight: 0.5980 chunk 14 optimal weight: 4.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1570 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.135207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.080359 restraints weight = 26071.685| |-----------------------------------------------------------------------------| r_work (start): 0.3140 rms_B_bonded: 3.24 r_work: 0.2988 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3066 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3066 r_free = 0.3066 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.72 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3066 r_free = 0.3066 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.72 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3066 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.2233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 14148 Z= 0.135 Angle : 0.514 12.923 19169 Z= 0.258 Chirality : 0.043 0.152 2043 Planarity : 0.003 0.052 2483 Dihedral : 5.259 67.953 1918 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.46 % Allowed : 14.64 % Favored : 83.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.21 (0.21), residues: 1681 helix: 1.19 (0.35), residues: 220 sheet: 0.07 (0.22), residues: 531 loop : 0.04 (0.21), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG D1396 TYR 0.012 0.001 TYR D1558 PHE 0.024 0.001 PHE D1751 TRP 0.037 0.001 TRP D1820 HIS 0.003 0.001 HIS D 581 Details of bonding type rmsd covalent geometry : bond 0.00313 (14148) covalent geometry : angle 0.51429 (19169) hydrogen bonds : bond 0.02943 ( 369) hydrogen bonds : angle 4.82678 ( 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 141 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 119 time to evaluate : 0.609 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 228 THR cc_start: 0.8555 (t) cc_final: 0.8294 (m) REVERT: D 293 HIS cc_start: 0.8934 (m90) cc_final: 0.8526 (m90) REVERT: D 518 ASP cc_start: 0.8598 (t0) cc_final: 0.8135 (t70) REVERT: D 527 LYS cc_start: 0.8462 (mptt) cc_final: 0.8017 (mptt) REVERT: D 783 GLU cc_start: 0.8773 (mm-30) cc_final: 0.8477 (tp30) REVERT: D 870 MET cc_start: 0.3165 (mpp) cc_final: 0.2135 (pmm) REVERT: D 929 GLU cc_start: 0.8316 (OUTLIER) cc_final: 0.8114 (pm20) REVERT: D 932 ASP cc_start: 0.8246 (t0) cc_final: 0.7837 (t0) REVERT: D 937 ASN cc_start: 0.8257 (m-40) cc_final: 0.7864 (m110) REVERT: D 980 TRP cc_start: 0.7434 (m100) cc_final: 0.6796 (m100) REVERT: D 1292 MET cc_start: 0.8723 (ptm) cc_final: 0.8346 (ptm) REVERT: D 1382 GLN cc_start: 0.8019 (tm-30) cc_final: 0.7804 (tm130) REVERT: D 1450 ILE cc_start: 0.4227 (OUTLIER) cc_final: 0.3733 (tp) REVERT: D 1581 THR cc_start: 0.8791 (m) cc_final: 0.8354 (p) REVERT: D 1636 GLU cc_start: 0.8465 (tt0) cc_final: 0.8191 (tm-30) REVERT: D 1658 GLU cc_start: 0.8459 (tt0) cc_final: 0.8011 (pt0) REVERT: D 1791 ARG cc_start: 0.7631 (mmm-85) cc_final: 0.7239 (mmm-85) REVERT: D 1848 PHE cc_start: 0.8031 (m-80) cc_final: 0.7502 (m-10) REVERT: D 1868 HIS cc_start: 0.7840 (OUTLIER) cc_final: 0.6935 (p90) REVERT: D 1870 TRP cc_start: 0.7966 (p90) cc_final: 0.7685 (p90) outliers start: 22 outliers final: 12 residues processed: 138 average time/residue: 0.5551 time to fit residues: 85.6070 Evaluate side-chains 128 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 113 time to evaluate : 0.610 ------------------------------------------------------------------------------- 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 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 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 1698 ILE Chi-restraints excluded: chain D residue 1784 LYS Chi-restraints excluded: chain D residue 1849 VAL Chi-restraints excluded: chain D residue 1868 HIS 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: 9.9990 chunk 82 optimal weight: 20.0000 chunk 29 optimal weight: 0.6980 chunk 49 optimal weight: 4.9990 chunk 91 optimal weight: 2.9990 chunk 75 optimal weight: 20.0000 chunk 87 optimal weight: 0.9990 chunk 160 optimal weight: 40.0000 chunk 154 optimal weight: 20.0000 chunk 142 optimal weight: 3.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 794 HIS D1570 ASN D1652 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.133021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.077611 restraints weight = 26175.161| |-----------------------------------------------------------------------------| r_work (start): 0.3081 rms_B_bonded: 3.24 r_work: 0.2929 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2963 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2963 r_free = 0.2963 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.72 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2963 r_free = 0.2963 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.72 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2963 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.2535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 14148 Z= 0.242 Angle : 0.564 10.600 19169 Z= 0.288 Chirality : 0.045 0.157 2043 Planarity : 0.004 0.062 2483 Dihedral : 5.436 55.867 1918 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 1.72 % Allowed : 15.03 % Favored : 83.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.15 (0.21), residues: 1681 helix: 1.00 (0.35), residues: 220 sheet: 0.10 (0.22), residues: 523 loop : -0.02 (0.21), residues: 938 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG D1396 TYR 0.015 0.001 TYR D 533 PHE 0.025 0.001 PHE D1683 TRP 0.043 0.001 TRP D1820 HIS 0.004 0.001 HIS D 581 Details of bonding type rmsd covalent geometry : bond 0.00565 (14148) covalent geometry : angle 0.56409 (19169) hydrogen bonds : bond 0.03360 ( 369) hydrogen bonds : angle 5.08008 ( 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 143 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 117 time to evaluate : 0.591 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 293 HIS cc_start: 0.8879 (m90) cc_final: 0.8545 (m90) REVERT: D 447 ARG cc_start: 0.8637 (OUTLIER) cc_final: 0.7652 (ttp80) REVERT: D 518 ASP cc_start: 0.8625 (t0) cc_final: 0.8139 (t70) REVERT: D 527 LYS cc_start: 0.8439 (mptt) cc_final: 0.7992 (mptt) REVERT: D 613 LEU cc_start: 0.7262 (OUTLIER) cc_final: 0.7047 (pp) REVERT: D 783 GLU cc_start: 0.8782 (mm-30) cc_final: 0.8548 (tp30) REVERT: D 870 MET cc_start: 0.3336 (mpp) cc_final: 0.2250 (pmm) REVERT: D 932 ASP cc_start: 0.8278 (t0) cc_final: 0.7997 (t0) REVERT: D 937 ASN cc_start: 0.8266 (m-40) cc_final: 0.7877 (m110) REVERT: D 980 TRP cc_start: 0.7485 (m100) cc_final: 0.6899 (m100) REVERT: D 1382 GLN cc_start: 0.8024 (tm-30) cc_final: 0.7759 (tm130) REVERT: D 1450 ILE cc_start: 0.4562 (OUTLIER) cc_final: 0.4180 (tt) REVERT: D 1543 ARG cc_start: 0.7365 (mtm110) cc_final: 0.6939 (mtm110) REVERT: D 1636 GLU cc_start: 0.8565 (tt0) cc_final: 0.8247 (tm-30) REVERT: D 1658 GLU cc_start: 0.8496 (tt0) cc_final: 0.7905 (pt0) REVERT: D 1791 ARG cc_start: 0.7704 (mmm-85) cc_final: 0.7334 (mmm-85) REVERT: D 1848 PHE cc_start: 0.8065 (m-80) cc_final: 0.7706 (m-10) outliers start: 26 outliers final: 13 residues processed: 138 average time/residue: 0.5881 time to fit residues: 90.2049 Evaluate side-chains 128 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 112 time to evaluate : 0.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 295 VAL 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 1784 LYS Chi-restraints excluded: chain D residue 1849 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 129 optimal weight: 0.7980 chunk 145 optimal weight: 0.9980 chunk 148 optimal weight: 0.9990 chunk 104 optimal weight: 0.8980 chunk 102 optimal weight: 0.9990 chunk 51 optimal weight: 2.9990 chunk 71 optimal weight: 0.0010 chunk 118 optimal weight: 0.9990 chunk 88 optimal weight: 0.9980 chunk 86 optimal weight: 9.9990 chunk 167 optimal weight: 10.0000 overall best weight: 0.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D1570 ASN 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 = 0.134815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.079821 restraints weight = 26049.296| |-----------------------------------------------------------------------------| r_work (start): 0.3126 rms_B_bonded: 3.24 r_work: 0.2973 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.2973 ------------------------------------------------------------------------------- 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 = 0.72 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 = 0.72 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3055 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.2529 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 : 0.539 11.990 19169 Z= 0.268 Chirality : 0.043 0.150 2043 Planarity : 0.004 0.065 2483 Dihedral : 5.217 51.236 1918 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.26 % Allowed : 15.56 % Favored : 83.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.16 (0.21), residues: 1681 helix: 1.18 (0.35), residues: 221 sheet: 0.02 (0.22), residues: 519 loop : 0.00 (0.21), residues: 941 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG D1396 TYR 0.013 0.001 TYR D1558 PHE 0.027 0.001 PHE D1751 TRP 0.032 0.001 TRP D1820 HIS 0.002 0.000 HIS D1062 Details of bonding type rmsd covalent geometry : bond 0.00265 (14148) covalent geometry : angle 0.53900 (19169) hydrogen bonds : bond 0.02888 ( 369) hydrogen bonds : angle 4.86106 ( 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 136 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 117 time to evaluate : 0.581 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 293 HIS cc_start: 0.8901 (m90) cc_final: 0.8563 (m90) REVERT: D 518 ASP cc_start: 0.8589 (t0) cc_final: 0.8100 (t70) REVERT: D 527 LYS cc_start: 0.8369 (mptt) cc_final: 0.7922 (mptt) REVERT: D 783 GLU cc_start: 0.8768 (mm-30) cc_final: 0.8539 (tp30) REVERT: D 870 MET cc_start: 0.3266 (mpp) cc_final: 0.2633 (pmm) REVERT: D 929 GLU cc_start: 0.8334 (OUTLIER) cc_final: 0.8130 (pm20) REVERT: D 937 ASN cc_start: 0.8272 (m-40) cc_final: 0.7872 (m110) REVERT: D 1382 GLN cc_start: 0.8029 (tm-30) cc_final: 0.7778 (tm130) REVERT: D 1450 ILE cc_start: 0.4545 (OUTLIER) cc_final: 0.4159 (tt) REVERT: D 1543 ARG cc_start: 0.7304 (mtm110) cc_final: 0.6868 (mtm110) REVERT: D 1581 THR cc_start: 0.8765 (m) cc_final: 0.8279 (p) REVERT: D 1636 GLU cc_start: 0.8522 (tt0) cc_final: 0.8214 (tm-30) REVERT: D 1658 GLU cc_start: 0.8508 (tt0) cc_final: 0.7964 (pt0) REVERT: D 1791 ARG cc_start: 0.7667 (mmm-85) cc_final: 0.7316 (mmm-85) REVERT: D 1848 PHE cc_start: 0.8047 (m-80) cc_final: 0.7735 (m-10) REVERT: D 1868 HIS cc_start: 0.7876 (OUTLIER) cc_final: 0.7081 (p90) REVERT: D 1927 LEU cc_start: 0.4286 (OUTLIER) cc_final: 0.3817 (tm) outliers start: 19 outliers final: 11 residues processed: 133 average time/residue: 0.6080 time to fit residues: 89.6761 Evaluate side-chains 128 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 113 time to evaluate : 0.565 ------------------------------------------------------------------------------- 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 424 VAL Chi-restraints excluded: chain D residue 589 VAL Chi-restraints excluded: chain D residue 596 GLU Chi-restraints excluded: chain D residue 929 GLU 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 1784 LYS 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 116 optimal weight: 1.9990 chunk 156 optimal weight: 0.1980 chunk 49 optimal weight: 4.9990 chunk 46 optimal weight: 0.7980 chunk 67 optimal weight: 20.0000 chunk 74 optimal weight: 6.9990 chunk 134 optimal weight: 7.9990 chunk 162 optimal weight: 10.0000 chunk 140 optimal weight: 20.0000 chunk 11 optimal weight: 2.9990 chunk 82 optimal weight: 7.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D1824 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.132550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.076898 restraints weight = 26302.119| |-----------------------------------------------------------------------------| r_work (start): 0.3115 rms_B_bonded: 3.25 r_work: 0.2956 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2999 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2999 r_free = 0.2999 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.72 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2999 r_free = 0.2999 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.73 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2999 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.2740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 14148 Z= 0.228 Angle : 0.579 12.392 19169 Z= 0.293 Chirality : 0.045 0.156 2043 Planarity : 0.004 0.051 2483 Dihedral : 5.269 47.531 1916 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 1.19 % Allowed : 15.96 % Favored : 82.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.11 (0.21), residues: 1681 helix: 1.03 (0.35), residues: 221 sheet: 0.04 (0.21), residues: 536 loop : -0.04 (0.21), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D1396 TYR 0.014 0.001 TYR D 533 PHE 0.022 0.001 PHE D1683 TRP 0.047 0.001 TRP D1820 HIS 0.003 0.001 HIS D 581 Details of bonding type rmsd covalent geometry : bond 0.00530 (14148) covalent geometry : angle 0.57934 (19169) hydrogen bonds : bond 0.03274 ( 369) hydrogen bonds : angle 5.04462 ( 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 130 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 112 time to evaluate : 0.610 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 518 ASP cc_start: 0.8585 (t0) cc_final: 0.8077 (t70) REVERT: D 527 LYS cc_start: 0.8403 (mptt) cc_final: 0.7953 (mptt) REVERT: D 783 GLU cc_start: 0.8772 (mm-30) cc_final: 0.8532 (tp30) REVERT: D 870 MET cc_start: 0.3443 (mpp) cc_final: 0.2710 (pmm) REVERT: D 929 GLU cc_start: 0.8335 (OUTLIER) cc_final: 0.8125 (pm20) REVERT: D 937 ASN cc_start: 0.8260 (m-40) cc_final: 0.7874 (m110) REVERT: D 1382 GLN cc_start: 0.8004 (tm-30) cc_final: 0.7737 (tm130) REVERT: D 1450 ILE cc_start: 0.4760 (OUTLIER) cc_final: 0.4356 (tt) REVERT: D 1543 ARG cc_start: 0.7434 (mtm110) cc_final: 0.6955 (mtm110) REVERT: D 1658 GLU cc_start: 0.8524 (tt0) cc_final: 0.7896 (pt0) REVERT: D 1791 ARG cc_start: 0.7716 (mmm-85) cc_final: 0.7322 (mmm-85) REVERT: D 1848 PHE cc_start: 0.8051 (m-80) cc_final: 0.7681 (m-10) outliers start: 18 outliers final: 11 residues processed: 127 average time/residue: 0.6257 time to fit residues: 88.1124 Evaluate side-chains 118 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 105 time to evaluate : 0.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 295 VAL 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 929 GLU 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 1784 LYS Chi-restraints excluded: chain D residue 1849 VAL 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: 8.9990 chunk 155 optimal weight: 20.0000 chunk 43 optimal weight: 0.9980 chunk 62 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 2 optimal weight: 8.9990 chunk 31 optimal weight: 0.9990 chunk 96 optimal weight: 0.7980 chunk 111 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D1570 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.133677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.078586 restraints weight = 26134.689| |-----------------------------------------------------------------------------| r_work (start): 0.3101 rms_B_bonded: 3.23 r_work: 0.2947 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2988 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2988 r_free = 0.2988 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.73 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2988 r_free = 0.2988 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.72 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2988 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.2726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 14148 Z= 0.161 Angle : 0.568 12.686 19169 Z= 0.283 Chirality : 0.044 0.151 2043 Planarity : 0.003 0.037 2483 Dihedral : 5.187 45.150 1916 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 1.32 % Allowed : 16.09 % Favored : 82.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.15 (0.21), residues: 1681 helix: 1.11 (0.35), residues: 221 sheet: 0.04 (0.22), residues: 536 loop : 0.01 (0.22), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D1396 TYR 0.013 0.001 TYR D1558 PHE 0.025 0.001 PHE D1751 TRP 0.043 0.001 TRP D1820 HIS 0.003 0.001 HIS D1868 Details of bonding type rmsd covalent geometry : bond 0.00374 (14148) covalent geometry : angle 0.56817 (19169) hydrogen bonds : bond 0.03046 ( 369) hydrogen bonds : angle 4.94457 ( 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 131 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 111 time to evaluate : 0.604 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 232 ARG cc_start: 0.6721 (ppt170) cc_final: 0.6243 (ppt170) REVERT: D 293 HIS cc_start: 0.8899 (m90) cc_final: 0.8673 (m90) REVERT: D 518 ASP cc_start: 0.8566 (t0) cc_final: 0.8149 (t0) REVERT: D 527 LYS cc_start: 0.8405 (mptt) cc_final: 0.7961 (mptt) REVERT: D 783 GLU cc_start: 0.8767 (mm-30) cc_final: 0.8525 (tp30) REVERT: D 870 MET cc_start: 0.3369 (mpp) cc_final: 0.2701 (pmm) REVERT: D 929 GLU cc_start: 0.8340 (OUTLIER) cc_final: 0.8125 (pm20) REVERT: D 937 ASN cc_start: 0.8297 (m-40) cc_final: 0.7905 (m110) REVERT: D 1382 GLN cc_start: 0.8017 (tm-30) cc_final: 0.7748 (tm130) REVERT: D 1450 ILE cc_start: 0.4835 (OUTLIER) cc_final: 0.4408 (tt) REVERT: D 1543 ARG cc_start: 0.7427 (mtm110) cc_final: 0.6925 (mtm110) REVERT: D 1658 GLU cc_start: 0.8487 (tt0) cc_final: 0.8005 (pt0) REVERT: D 1791 ARG cc_start: 0.7747 (mmm-85) cc_final: 0.7377 (mmm-85) REVERT: D 1848 PHE cc_start: 0.8032 (m-80) cc_final: 0.7716 (m-10) outliers start: 20 outliers final: 11 residues processed: 127 average time/residue: 0.6168 time to fit residues: 87.0481 Evaluate side-chains 123 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 110 time to evaluate : 0.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 295 VAL 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 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 1698 ILE Chi-restraints excluded: chain D residue 1849 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 52 optimal weight: 3.9990 chunk 134 optimal weight: 2.9990 chunk 159 optimal weight: 9.9990 chunk 123 optimal weight: 0.9980 chunk 139 optimal weight: 0.4980 chunk 23 optimal weight: 4.9990 chunk 164 optimal weight: 7.9990 chunk 19 optimal weight: 0.0470 chunk 88 optimal weight: 0.9990 chunk 149 optimal weight: 4.9990 chunk 156 optimal weight: 0.9990 overall best weight: 0.7082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 825 ASN D1570 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.134747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.080074 restraints weight = 26172.259| |-----------------------------------------------------------------------------| r_work (start): 0.3133 rms_B_bonded: 3.24 r_work: 0.2980 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3018 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3018 r_free = 0.3018 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.72 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3018 r_free = 0.3018 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.73 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3018 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.2729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 14148 Z= 0.113 Angle : 0.542 13.588 19169 Z= 0.274 Chirality : 0.044 0.158 2043 Planarity : 0.003 0.039 2483 Dihedral : 5.026 43.793 1916 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.39 % Allowed : 15.83 % 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 aren not related in a simple way. whole: 0.16 (0.21), residues: 1681 helix: 1.12 (0.35), residues: 228 sheet: 0.07 (0.22), residues: 524 loop : -0.02 (0.21), residues: 929 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D1396 TYR 0.012 0.001 TYR D1558 PHE 0.029 0.001 PHE D1751 TRP 0.041 0.001 TRP D1820 HIS 0.003 0.001 HIS D1868 Details of bonding type rmsd covalent geometry : bond 0.00259 (14148) covalent geometry : angle 0.54160 (19169) hydrogen bonds : bond 0.02827 ( 369) hydrogen bonds : angle 4.82495 ( 990) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6945.08 seconds wall clock time: 118 minutes 52.06 seconds (7132.06 seconds total)