Starting phenix.real_space_refine on Thu Jul 2 22:35:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9p24_71158/07_2026/9p24_71158_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9p24_71158/07_2026/9p24_71158.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.48 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9p24_71158/07_2026/9p24_71158.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9p24_71158/07_2026/9p24_71158.map" model { file = "/net/cci-nas-00/data/ceres_data/9p24_71158/07_2026/9p24_71158_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9p24_71158/07_2026/9p24_71158_neut.cif" } resolution = 3.48 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= 0.001 sd= 0.022 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: 5 Type Number sf(0) Gaussians S 73 5.16 5 Na 1 4.78 5 C 6766 2.51 5 N 1624 2.21 5 O 1792 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10256 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 10104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1258, 10104 Classifications: {'peptide': 1258} Link IDs: {'PTRANS': 38, 'TRANS': 1219} Chain breaks: 4 Chain: "A" Number of atoms: 152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 151 Ad-hoc single atom residues: {' NA': 1} Unusual residues: {'9Z9': 1, 'NAG': 8} Classifications: {'undetermined': 9} Link IDs: {None: 8} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Time building chain proxies: 2.31, per 1000 atoms: 0.23 Number of scatterers: 10256 At special positions: 0 Unit cell: (115.072, 138.446, 134.85, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 73 16.00 Na 1 11.00 O 1792 8.00 N 1624 7.00 C 6766 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 280 " - pdb=" SG CYS A 335 " distance=2.03 Simple disulfide: pdb=" SG CYS A 326 " - pdb=" SG CYS A 341 " distance=2.03 Simple disulfide: pdb=" SG CYS A 906 " - pdb=" SG CYS A 915 " distance=2.03 Simple disulfide: pdb=" SG CYS A1363 " - pdb=" SG CYS A1384 " distance=2.03 Simple disulfide: pdb=" SG CYS A1728 " - pdb=" SG CYS A1742 " distance=2.03 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.13 Conformation dependent library (CDL) restraints added in 387.6 milliseconds 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2370 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 4 sheets defined 70.9% alpha, 1.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'A' and resid 17 through 37 removed outlier: 4.163A pdb=" N THR A 37 " --> pdb=" O ALA A 33 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 90 Processing helix chain 'A' and resid 118 through 130 removed outlier: 3.674A pdb=" N ALA A 123 " --> pdb=" O PRO A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 147 removed outlier: 3.588A pdb=" N MET A 135 " --> pdb=" O SER A 131 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N PHE A 147 " --> pdb=" O THR A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 179 removed outlier: 4.003A pdb=" N VAL A 160 " --> pdb=" O TRP A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 191 removed outlier: 3.549A pdb=" N ASP A 191 " --> pdb=" O PHE A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 210 removed outlier: 4.090A pdb=" N LEU A 196 " --> pdb=" O PRO A 192 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ASP A 197 " --> pdb=" O TRP A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 228 removed outlier: 3.682A pdb=" N LEU A 227 " --> pdb=" O VAL A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 250 removed outlier: 3.508A pdb=" N ILE A 239 " --> pdb=" O GLY A 235 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU A 250 " --> pdb=" O SER A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 270 removed outlier: 3.786A pdb=" N GLN A 270 " --> pdb=" O LEU A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 310 Processing helix chain 'A' and resid 348 through 352 Processing helix chain 'A' and resid 357 through 371 Processing helix chain 'A' and resid 373 through 385 removed outlier: 4.369A pdb=" N LEU A 377 " --> pdb=" O CYS A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 401 removed outlier: 4.242A pdb=" N PHE A 393 " --> pdb=" O TYR A 389 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N PHE A 398 " --> pdb=" O MET A 394 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N LEU A 399 " --> pdb=" O LEU A 395 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N SER A 401 " --> pdb=" O ILE A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 439 removed outlier: 3.600A pdb=" N ALA A 422 " --> pdb=" O GLU A 418 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N THR A 423 " --> pdb=" O GLN A 419 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLU A 431 " --> pdb=" O THR A 427 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LYS A 432 " --> pdb=" O GLU A 428 " (cutoff:3.500A) Processing helix chain 'A' and resid 703 through 715 Processing helix chain 'A' and resid 719 through 735 Processing helix chain 'A' and resid 742 through 776 removed outlier: 3.629A pdb=" N LEU A 749 " --> pdb=" O PHE A 745 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N LEU A 754 " --> pdb=" O GLN A 750 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N VAL A 755 " --> pdb=" O VAL A 751 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N PHE A 756 " --> pdb=" O GLY A 752 " (cutoff:3.500A) Proline residue: A 773 - end of helix Processing helix chain 'A' and resid 779 through 794 Processing helix chain 'A' and resid 804 through 821 removed outlier: 3.733A pdb=" N ARG A 811 " --> pdb=" O ARG A 808 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N LEU A 813 " --> pdb=" O PHE A 810 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N VAL A 815 " --> pdb=" O LEU A 812 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N SER A 821 " --> pdb=" O LEU A 818 " (cutoff:3.500A) Processing helix chain 'A' and resid 822 through 835 Processing helix chain 'A' and resid 842 through 861 removed outlier: 3.583A pdb=" N LEU A 846 " --> pdb=" O LEU A 842 " (cutoff:3.500A) Processing helix chain 'A' and resid 862 through 872 removed outlier: 3.738A pdb=" N TYR A 865 " --> pdb=" O GLY A 862 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N GLU A 867 " --> pdb=" O ASN A 864 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ASP A 870 " --> pdb=" O GLU A 867 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N SER A 871 " --> pdb=" O LEU A 868 " (cutoff:3.500A) Processing helix chain 'A' and resid 883 through 897 Processing helix chain 'A' and resid 900 through 911 removed outlier: 3.775A pdb=" N ASP A 905 " --> pdb=" O GLU A 901 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL A 909 " --> pdb=" O ASP A 905 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N GLY A 911 " --> pdb=" O MET A 907 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 943 removed outlier: 4.633A pdb=" N SER A 943 " --> pdb=" O LEU A 939 " (cutoff:3.500A) Processing helix chain 'A' and resid 958 through 971 Processing helix chain 'A' and resid 1189 through 1203 Processing helix chain 'A' and resid 1204 through 1221 removed outlier: 3.657A pdb=" N GLU A1208 " --> pdb=" O HIS A1204 " (cutoff:3.500A) Processing helix chain 'A' and resid 1222 through 1225 removed outlier: 3.908A pdb=" N GLU A1225 " --> pdb=" O LEU A1222 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1222 through 1225' Processing helix chain 'A' and resid 1235 through 1262 removed outlier: 3.658A pdb=" N LYS A1244 " --> pdb=" O GLU A1240 " (cutoff:3.500A) Processing helix chain 'A' and resid 1262 through 1267 Processing helix chain 'A' and resid 1269 through 1291 removed outlier: 3.936A pdb=" N TRP A1273 " --> pdb=" O ASN A1269 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU A1291 " --> pdb=" O VAL A1287 " (cutoff:3.500A) Processing helix chain 'A' and resid 1296 through 1304 removed outlier: 3.920A pdb=" N LYS A1300 " --> pdb=" O MET A1296 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N THR A1304 " --> pdb=" O LYS A1300 " (cutoff:3.500A) Processing helix chain 'A' and resid 1305 through 1315 Proline residue: A1310 - end of helix removed outlier: 3.527A pdb=" N ALA A1313 " --> pdb=" O PRO A1310 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N SER A1315 " --> pdb=" O ARG A1312 " (cutoff:3.500A) Processing helix chain 'A' and resid 1317 through 1329 removed outlier: 3.862A pdb=" N VAL A1323 " --> pdb=" O GLY A1319 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ASN A1325 " --> pdb=" O ARG A1321 " (cutoff:3.500A) Processing helix chain 'A' and resid 1331 through 1356 removed outlier: 4.055A pdb=" N ASN A1336 " --> pdb=" O PRO A1332 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N VAL A1337 " --> pdb=" O SER A1333 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ILE A1347 " --> pdb=" O ILE A1343 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N PHE A1348 " --> pdb=" O PHE A1344 " (cutoff:3.500A) Processing helix chain 'A' and resid 1380 through 1387 Processing helix chain 'A' and resid 1404 through 1417 removed outlier: 3.734A pdb=" N TYR A1409 " --> pdb=" O VAL A1405 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N LEU A1410 " --> pdb=" O GLY A1406 " (cutoff:3.500A) Processing helix chain 'A' and resid 1420 through 1430 removed outlier: 4.087A pdb=" N ILE A1424 " --> pdb=" O GLY A1420 " (cutoff:3.500A) Processing helix chain 'A' and resid 1443 through 1445 No H-bonds generated for 'chain 'A' and resid 1443 through 1445' Processing helix chain 'A' and resid 1446 through 1457 removed outlier: 4.117A pdb=" N PHE A1450 " --> pdb=" O MET A1446 " (cutoff:3.500A) Processing helix chain 'A' and resid 1459 through 1480 removed outlier: 3.582A pdb=" N LYS A1479 " --> pdb=" O GLN A1475 " (cutoff:3.500A) Processing helix chain 'A' and resid 1488 through 1503 removed outlier: 4.115A pdb=" N ALA A1497 " --> pdb=" O LYS A1493 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N MET A1498 " --> pdb=" O TYR A1494 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N LYS A1499 " --> pdb=" O TYR A1495 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N LYS A1500 " --> pdb=" O ASN A1496 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N SER A1503 " --> pdb=" O LYS A1499 " (cutoff:3.500A) Processing helix chain 'A' and resid 1518 through 1526 Processing helix chain 'A' and resid 1527 through 1546 removed outlier: 4.090A pdb=" N ASP A1531 " --> pdb=" O LYS A1527 " (cutoff:3.500A) Processing helix chain 'A' and resid 1553 through 1582 removed outlier: 3.507A pdb=" N ILE A1557 " --> pdb=" O SER A1553 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU A1582 " --> pdb=" O LYS A1578 " (cutoff:3.500A) Processing helix chain 'A' and resid 1591 through 1616 removed outlier: 3.547A pdb=" N ASP A1595 " --> pdb=" O TRP A1591 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N ILE A1611 " --> pdb=" O VAL A1607 " (cutoff:3.500A) Processing helix chain 'A' and resid 1618 through 1627 Processing helix chain 'A' and resid 1628 through 1631 Processing helix chain 'A' and resid 1633 through 1640 removed outlier: 3.591A pdb=" N ARG A1638 " --> pdb=" O ARG A1635 " (cutoff:3.500A) Processing helix chain 'A' and resid 1641 through 1654 Processing helix chain 'A' and resid 1654 through 1677 removed outlier: 3.808A pdb=" N ASN A1659 " --> pdb=" O PRO A1655 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N ILE A1660 " --> pdb=" O ALA A1656 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU A1663 " --> pdb=" O ASN A1659 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU A1664 " --> pdb=" O ILE A1660 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ALA A1677 " --> pdb=" O ILE A1673 " (cutoff:3.500A) Processing helix chain 'A' and resid 1696 through 1708 Processing helix chain 'A' and resid 1712 through 1718 removed outlier: 3.906A pdb=" N LEU A1716 " --> pdb=" O GLY A1712 " (cutoff:3.500A) Processing helix chain 'A' and resid 1744 through 1778 removed outlier: 4.036A pdb=" N GLY A1748 " --> pdb=" O SER A1744 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 92 through 93 Processing sheet with id=AA2, first strand: chain 'A' and resid 278 through 282 Processing sheet with id=AA3, first strand: chain 'A' and resid 295 through 296 Processing sheet with id=AA4, first strand: chain 'A' and resid 1361 through 1364 removed outlier: 3.626A pdb=" N ARG A1362 " --> pdb=" O THR A1396 " (cutoff:3.500A) 603 hydrogen bonds defined for protein. 1713 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: 1.83 Time building geometry restraints manager: 1.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1568 1.31 - 1.44: 2921 1.44 - 1.57: 5888 1.57 - 1.70: 0 1.70 - 1.83: 123 Bond restraints: 10500 Sorted by residual: bond pdb=" C7 NAG A2102 " pdb=" N2 NAG A2102 " ideal model delta sigma weight residual 1.346 1.453 -0.107 2.00e-02 2.50e+03 2.84e+01 bond pdb=" C7 NAG A2109 " pdb=" N2 NAG A2109 " ideal model delta sigma weight residual 1.346 1.452 -0.106 2.00e-02 2.50e+03 2.83e+01 bond pdb=" C7 NAG A2104 " pdb=" N2 NAG A2104 " ideal model delta sigma weight residual 1.346 1.452 -0.106 2.00e-02 2.50e+03 2.82e+01 bond pdb=" C7 NAG A2103 " pdb=" N2 NAG A2103 " ideal model delta sigma weight residual 1.346 1.452 -0.106 2.00e-02 2.50e+03 2.79e+01 bond pdb=" C7 NAG A2108 " pdb=" N2 NAG A2108 " ideal model delta sigma weight residual 1.346 1.451 -0.105 2.00e-02 2.50e+03 2.78e+01 ... (remaining 10495 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.59: 13889 1.59 - 3.18: 255 3.18 - 4.78: 60 4.78 - 6.37: 27 6.37 - 7.96: 9 Bond angle restraints: 14240 Sorted by residual: angle pdb=" N ILE A1334 " pdb=" CA ILE A1334 " pdb=" C ILE A1334 " ideal model delta sigma weight residual 112.96 108.59 4.37 1.00e+00 1.00e+00 1.91e+01 angle pdb=" C LEU A1772 " pdb=" N GLU A1773 " pdb=" CA GLU A1773 " ideal model delta sigma weight residual 120.44 115.90 4.54 1.36e+00 5.41e-01 1.12e+01 angle pdb=" N GLU A1773 " pdb=" CA GLU A1773 " pdb=" C GLU A1773 " ideal model delta sigma weight residual 111.14 107.62 3.52 1.08e+00 8.57e-01 1.06e+01 angle pdb=" CA GLN A1483 " pdb=" CB GLN A1483 " pdb=" CG GLN A1483 " ideal model delta sigma weight residual 114.10 120.19 -6.09 2.00e+00 2.50e-01 9.27e+00 angle pdb=" CB GLN A1483 " pdb=" CG GLN A1483 " pdb=" CD GLN A1483 " ideal model delta sigma weight residual 112.60 117.52 -4.92 1.70e+00 3.46e-01 8.37e+00 ... (remaining 14235 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.63: 5929 30.63 - 61.27: 394 61.27 - 91.90: 26 91.90 - 122.54: 3 122.54 - 153.17: 1 Dihedral angle restraints: 6353 sinusoidal: 2684 harmonic: 3669 Sorted by residual: dihedral pdb=" CB CYS A 326 " pdb=" SG CYS A 326 " pdb=" SG CYS A 341 " pdb=" CB CYS A 341 " ideal model delta sinusoidal sigma weight residual 93.00 175.14 -82.14 1 1.00e+01 1.00e-02 8.29e+01 dihedral pdb=" C21 9Z9 A2101 " pdb=" C22 9Z9 A2101 " pdb=" C23 9Z9 A2101 " pdb=" C24 9Z9 A2101 " ideal model delta sinusoidal sigma weight residual 77.99 -75.18 153.17 1 3.00e+01 1.11e-03 2.02e+01 dihedral pdb=" CB CYS A1728 " pdb=" SG CYS A1728 " pdb=" SG CYS A1742 " pdb=" CB CYS A1742 " ideal model delta sinusoidal sigma weight residual -86.00 -122.47 36.47 1 1.00e+01 1.00e-02 1.88e+01 ... (remaining 6350 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 1062 0.028 - 0.055: 354 0.055 - 0.083: 178 0.083 - 0.111: 54 0.111 - 0.138: 11 Chirality restraints: 1659 Sorted by residual: chirality pdb=" CA PRO A1298 " pdb=" N PRO A1298 " pdb=" C PRO A1298 " pdb=" CB PRO A1298 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.79e-01 chirality pdb=" CA PRO A1725 " pdb=" N PRO A1725 " pdb=" C PRO A1725 " pdb=" CB PRO A1725 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.01e-01 chirality pdb=" C2 NAG A2103 " pdb=" C1 NAG A2103 " pdb=" C3 NAG A2103 " pdb=" N2 NAG A2103 " both_signs ideal model delta sigma weight residual False -2.49 -2.62 0.12 2.00e-01 2.50e+01 3.88e-01 ... (remaining 1656 not shown) Planarity restraints: 1732 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA A 51 " 0.051 5.00e-02 4.00e+02 7.79e-02 9.70e+00 pdb=" N PRO A 52 " -0.135 5.00e-02 4.00e+02 pdb=" CA PRO A 52 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO A 52 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL A1597 " -0.010 2.00e-02 2.50e+03 2.09e-02 4.36e+00 pdb=" C VAL A1597 " 0.036 2.00e-02 2.50e+03 pdb=" O VAL A1597 " -0.014 2.00e-02 2.50e+03 pdb=" N VAL A1598 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A1600 " -0.010 2.00e-02 2.50e+03 2.03e-02 4.14e+00 pdb=" C ILE A1600 " 0.035 2.00e-02 2.50e+03 pdb=" O ILE A1600 " -0.013 2.00e-02 2.50e+03 pdb=" N LEU A1601 " -0.012 2.00e-02 2.50e+03 ... (remaining 1729 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.70: 192 2.70 - 3.25: 10038 3.25 - 3.80: 15103 3.80 - 4.35: 17761 4.35 - 4.90: 30348 Nonbonded interactions: 73442 Sorted by model distance: nonbonded pdb=" O PRO A 85 " pdb=" OG SER A 88 " model vdw 2.144 3.040 nonbonded pdb=" O MET A 203 " pdb=" OG1 THR A 207 " model vdw 2.231 3.040 nonbonded pdb=" OG SER A 115 " pdb=" O PHE A 117 " model vdw 2.258 3.040 nonbonded pdb=" O ASN A 275 " pdb=" OG SER A 384 " model vdw 2.287 3.040 nonbonded pdb=" O VAL A 806 " pdb=" OG SER A 809 " model vdw 2.298 3.040 ... (remaining 73437 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.850 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.260 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.060 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 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 0.107 10506 Z= 0.200 Angle : 0.596 7.960 14250 Z= 0.294 Chirality : 0.037 0.138 1659 Planarity : 0.004 0.078 1732 Dihedral : 18.298 153.170 3968 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 0.27 % Allowed : 31.76 % Favored : 67.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.73 (0.25), residues: 1248 helix: 1.63 (0.19), residues: 840 sheet: -2.57 (0.99), residues: 24 loop : -1.98 (0.30), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1626 TYR 0.016 0.001 TYR A1586 PHE 0.015 0.001 PHE A1751 TRP 0.014 0.001 TRP A 156 HIS 0.006 0.001 HIS A 118 Details of bonding type rmsd/Z covalent geometry : bond 0.00395 / 0.20 (10500) covalent geometry : angle 0.59511 / 0.29 (14240) SS BOND : bond 0.00210 / 0.10 ( 5) SS BOND : angle 1.31671 / 0.87 ( 10) hydrogen bonds : bond 0.12264 / 8.06 ( 603) hydrogen bonds : angle 4.41457 / 3.02 ( 1713) Misc. bond : bond 0.02407 / 1.27 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 146 time to evaluate : 0.373 Fit side-chains REVERT: A 774 TYR cc_start: 0.7662 (OUTLIER) cc_final: 0.7277 (t80) REVERT: A 1595 ASP cc_start: 0.7805 (m-30) cc_final: 0.7169 (m-30) outliers start: 3 outliers final: 0 residues processed: 148 average time/residue: 0.0775 time to fit residues: 17.5654 Evaluate side-chains 143 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 142 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 774 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 108 optimal weight: 3.9990 chunk 49 optimal weight: 0.9990 chunk 97 optimal weight: 6.9990 chunk 113 optimal weight: 2.9990 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 3.9990 chunk 123 optimal weight: 0.9980 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 10.0000 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 291 ASN A 406 ASN A1354 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.148377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.104494 restraints weight = 16762.425| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 3.22 r_work: 0.3145 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.0962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 10506 Z= 0.188 Angle : 0.571 8.114 14250 Z= 0.299 Chirality : 0.038 0.149 1659 Planarity : 0.004 0.062 1732 Dihedral : 8.224 145.432 1614 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 3.26 % Allowed : 29.77 % Favored : 66.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.81 (0.25), residues: 1248 helix: 1.76 (0.19), residues: 827 sheet: -2.95 (0.92), residues: 24 loop : -1.96 (0.30), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 367 TYR 0.018 0.001 TYR A1586 PHE 0.022 0.001 PHE A1751 TRP 0.016 0.001 TRP A1258 HIS 0.003 0.001 HIS A 118 Details of bonding type rmsd/Z covalent geometry : bond 0.00446 / 0.19 (10500) covalent geometry : angle 0.56914 / 0.30 (14240) SS BOND : bond 0.00401 / 0.19 ( 5) SS BOND : angle 1.69920 / 1.00 ( 10) hydrogen bonds : bond 0.06331 / 4.10 ( 603) hydrogen bonds : angle 3.72224 / 2.58 ( 1713) Misc. bond : bond 0.00102 / 0.05 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 145 time to evaluate : 0.368 Fit side-chains REVERT: A 96 LEU cc_start: 0.8314 (OUTLIER) cc_final: 0.7831 (tt) REVERT: A 346 GLU cc_start: 0.8587 (mt-10) cc_final: 0.8142 (pm20) REVERT: A 774 TYR cc_start: 0.8067 (OUTLIER) cc_final: 0.7433 (t80) REVERT: A 858 MET cc_start: 0.9130 (tmm) cc_final: 0.8895 (ttt) REVERT: A 1494 TYR cc_start: 0.7586 (OUTLIER) cc_final: 0.7347 (t80) outliers start: 36 outliers final: 19 residues processed: 169 average time/residue: 0.0786 time to fit residues: 20.4730 Evaluate side-chains 159 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 137 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 145 CYS Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 375 GLU Chi-restraints excluded: chain A residue 390 MET Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 759 ILE Chi-restraints excluded: chain A residue 774 TYR Chi-restraints excluded: chain A residue 776 TYR Chi-restraints excluded: chain A residue 793 LEU Chi-restraints excluded: chain A residue 1251 VAL Chi-restraints excluded: chain A residue 1343 ILE Chi-restraints excluded: chain A residue 1374 ASN Chi-restraints excluded: chain A residue 1494 TYR Chi-restraints excluded: chain A residue 1544 THR Chi-restraints excluded: chain A residue 1564 ASN Chi-restraints excluded: chain A residue 1572 THR Chi-restraints excluded: chain A residue 1763 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 58 optimal weight: 0.3980 chunk 17 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 14 optimal weight: 4.9990 chunk 21 optimal weight: 0.9990 chunk 46 optimal weight: 0.9990 chunk 120 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 90 optimal weight: 0.6980 chunk 61 optimal weight: 0.7980 chunk 118 optimal weight: 0.8980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 291 ASN A 834 ASN A 864 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.151663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.108004 restraints weight = 16740.549| |-----------------------------------------------------------------------------| r_work (start): 0.3323 rms_B_bonded: 3.24 r_work: 0.3190 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.0990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 10506 Z= 0.114 Angle : 0.498 8.837 14250 Z= 0.258 Chirality : 0.035 0.132 1659 Planarity : 0.004 0.051 1732 Dihedral : 7.503 143.048 1614 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 3.35 % Allowed : 29.95 % Favored : 66.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.03 (0.25), residues: 1248 helix: 1.94 (0.19), residues: 825 sheet: -3.23 (0.88), residues: 22 loop : -1.87 (0.30), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1626 TYR 0.015 0.001 TYR A1586 PHE 0.016 0.001 PHE A1751 TRP 0.013 0.001 TRP A 156 HIS 0.004 0.001 HIS A 118 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.11 (10500) covalent geometry : angle 0.49669 / 0.26 (14240) SS BOND : bond 0.00252 / 0.12 ( 5) SS BOND : angle 1.18623 / 0.66 ( 10) hydrogen bonds : bond 0.04930 / 3.17 ( 603) hydrogen bonds : angle 3.41907 / 2.36 ( 1713) Misc. bond : bond 0.00042 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 151 time to evaluate : 0.373 Fit side-chains REVERT: A 101 THR cc_start: 0.7383 (OUTLIER) cc_final: 0.7132 (p) REVERT: A 774 TYR cc_start: 0.8142 (OUTLIER) cc_final: 0.7442 (t80) REVERT: A 834 ASN cc_start: 0.8260 (OUTLIER) cc_final: 0.7959 (t0) REVERT: A 858 MET cc_start: 0.9102 (tmm) cc_final: 0.8848 (ttt) REVERT: A 1296 MET cc_start: 0.7259 (ptp) cc_final: 0.7057 (ptp) REVERT: A 1494 TYR cc_start: 0.7582 (OUTLIER) cc_final: 0.7332 (t80) REVERT: A 1626 ARG cc_start: 0.8212 (ttm-80) cc_final: 0.7890 (ttm110) outliers start: 37 outliers final: 21 residues processed: 170 average time/residue: 0.0808 time to fit residues: 20.7483 Evaluate side-chains 171 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 146 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 375 GLU Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 759 ILE Chi-restraints excluded: chain A residue 774 TYR Chi-restraints excluded: chain A residue 776 TYR Chi-restraints excluded: chain A residue 793 LEU Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 834 ASN Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 967 GLN Chi-restraints excluded: chain A residue 1259 VAL Chi-restraints excluded: chain A residue 1343 ILE Chi-restraints excluded: chain A residue 1363 CYS Chi-restraints excluded: chain A residue 1494 TYR Chi-restraints excluded: chain A residue 1544 THR Chi-restraints excluded: chain A residue 1564 ASN Chi-restraints excluded: chain A residue 1624 VAL Chi-restraints excluded: chain A residue 1696 THR Chi-restraints excluded: chain A residue 1708 THR Chi-restraints excluded: chain A residue 1759 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 26 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 chunk 96 optimal weight: 4.9990 chunk 53 optimal weight: 0.9980 chunk 63 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 88 optimal weight: 2.9990 chunk 1 optimal weight: 7.9990 chunk 38 optimal weight: 0.9990 chunk 18 optimal weight: 10.0000 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.149413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.105666 restraints weight = 16973.239| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 3.25 r_work: 0.3156 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.1212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10506 Z= 0.148 Angle : 0.528 8.172 14250 Z= 0.274 Chirality : 0.036 0.153 1659 Planarity : 0.004 0.048 1732 Dihedral : 7.257 140.731 1614 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.21 % Favored : 94.71 % Rotamer: Outliers : 3.71 % Allowed : 29.32 % Favored : 66.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.00 (0.25), residues: 1248 helix: 1.93 (0.19), residues: 827 sheet: -2.97 (0.91), residues: 24 loop : -1.94 (0.30), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 367 TYR 0.016 0.001 TYR A1586 PHE 0.049 0.001 PHE A1587 TRP 0.011 0.001 TRP A 156 HIS 0.003 0.001 HIS A 118 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.15 (10500) covalent geometry : angle 0.52655 / 0.27 (14240) SS BOND : bond 0.00328 / 0.15 ( 5) SS BOND : angle 1.45331 / 0.82 ( 10) hydrogen bonds : bond 0.05416 / 3.51 ( 603) hydrogen bonds : angle 3.48677 / 2.41 ( 1713) Misc. bond : bond 0.00034 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 148 time to evaluate : 0.424 Fit side-chains REVERT: A 96 LEU cc_start: 0.8280 (OUTLIER) cc_final: 0.7847 (tt) REVERT: A 101 THR cc_start: 0.7368 (OUTLIER) cc_final: 0.7029 (p) REVERT: A 219 ARG cc_start: 0.8178 (ttt-90) cc_final: 0.7939 (ttp80) REVERT: A 718 PHE cc_start: 0.7107 (p90) cc_final: 0.6867 (p90) REVERT: A 774 TYR cc_start: 0.8153 (OUTLIER) cc_final: 0.7345 (t80) REVERT: A 824 THR cc_start: 0.7961 (OUTLIER) cc_final: 0.7728 (m) REVERT: A 858 MET cc_start: 0.9103 (tmm) cc_final: 0.8896 (ttt) REVERT: A 1480 LEU cc_start: 0.7751 (tp) cc_final: 0.7296 (tt) REVERT: A 1494 TYR cc_start: 0.7586 (OUTLIER) cc_final: 0.7351 (t80) outliers start: 41 outliers final: 28 residues processed: 175 average time/residue: 0.0845 time to fit residues: 22.0638 Evaluate side-chains 173 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 140 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 375 GLU Chi-restraints excluded: chain A residue 382 LEU Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 759 ILE Chi-restraints excluded: chain A residue 774 TYR Chi-restraints excluded: chain A residue 776 TYR Chi-restraints excluded: chain A residue 793 LEU Chi-restraints excluded: chain A residue 824 THR Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 855 VAL Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 967 GLN Chi-restraints excluded: chain A residue 1251 VAL Chi-restraints excluded: chain A residue 1259 VAL Chi-restraints excluded: chain A residue 1343 ILE Chi-restraints excluded: chain A residue 1363 CYS Chi-restraints excluded: chain A residue 1374 ASN Chi-restraints excluded: chain A residue 1494 TYR Chi-restraints excluded: chain A residue 1544 THR Chi-restraints excluded: chain A residue 1564 ASN Chi-restraints excluded: chain A residue 1572 THR Chi-restraints excluded: chain A residue 1624 VAL Chi-restraints excluded: chain A residue 1696 THR Chi-restraints excluded: chain A residue 1708 THR Chi-restraints excluded: chain A residue 1759 SER Chi-restraints excluded: chain A residue 1763 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 67 optimal weight: 0.9980 chunk 119 optimal weight: 4.9990 chunk 83 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 77 optimal weight: 9.9990 chunk 34 optimal weight: 0.7980 chunk 59 optimal weight: 1.9990 chunk 4 optimal weight: 7.9990 chunk 97 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 47 optimal weight: 0.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 214 ASN A 291 ASN A1354 ASN A1507 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.148998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.105351 restraints weight = 16964.657| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 3.24 r_work: 0.3147 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.1377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10506 Z= 0.144 Angle : 0.530 7.324 14250 Z= 0.275 Chirality : 0.036 0.155 1659 Planarity : 0.004 0.047 1732 Dihedral : 6.927 130.654 1614 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.05 % Favored : 94.87 % Rotamer: Outliers : 5.16 % Allowed : 28.42 % Favored : 66.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.95 (0.25), residues: 1248 helix: 1.89 (0.19), residues: 833 sheet: -3.03 (0.91), residues: 24 loop : -2.02 (0.30), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1626 TYR 0.014 0.001 TYR A 378 PHE 0.019 0.001 PHE A1751 TRP 0.011 0.001 TRP A 156 HIS 0.003 0.001 HIS A 118 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.14 (10500) covalent geometry : angle 0.52929 / 0.27 (14240) SS BOND : bond 0.00323 / 0.15 ( 5) SS BOND : angle 1.42961 / 0.80 ( 10) hydrogen bonds : bond 0.05427 / 3.51 ( 603) hydrogen bonds : angle 3.49989 / 2.41 ( 1713) Misc. bond : bond 0.00027 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 143 time to evaluate : 0.373 Fit side-chains REVERT: A 34 ARG cc_start: 0.7303 (OUTLIER) cc_final: 0.7100 (mmp-170) REVERT: A 96 LEU cc_start: 0.8274 (OUTLIER) cc_final: 0.7820 (tt) REVERT: A 774 TYR cc_start: 0.8088 (OUTLIER) cc_final: 0.7291 (t80) REVERT: A 824 THR cc_start: 0.7970 (OUTLIER) cc_final: 0.7737 (m) REVERT: A 858 MET cc_start: 0.9113 (tmm) cc_final: 0.8903 (ttt) REVERT: A 1245 MET cc_start: 0.7662 (ttp) cc_final: 0.7071 (tmm) REVERT: A 1480 LEU cc_start: 0.7777 (tp) cc_final: 0.7202 (tt) REVERT: A 1494 TYR cc_start: 0.7548 (OUTLIER) cc_final: 0.7342 (t80) outliers start: 57 outliers final: 36 residues processed: 184 average time/residue: 0.0747 time to fit residues: 21.1090 Evaluate side-chains 183 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 142 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ARG Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 145 CYS Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 375 GLU Chi-restraints excluded: chain A residue 382 LEU Chi-restraints excluded: chain A residue 390 MET Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 759 ILE Chi-restraints excluded: chain A residue 774 TYR Chi-restraints excluded: chain A residue 776 TYR Chi-restraints excluded: chain A residue 793 LEU Chi-restraints excluded: chain A residue 824 THR Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 855 VAL Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 967 GLN Chi-restraints excluded: chain A residue 1251 VAL Chi-restraints excluded: chain A residue 1255 LEU Chi-restraints excluded: chain A residue 1259 VAL Chi-restraints excluded: chain A residue 1328 VAL Chi-restraints excluded: chain A residue 1343 ILE Chi-restraints excluded: chain A residue 1363 CYS Chi-restraints excluded: chain A residue 1494 TYR Chi-restraints excluded: chain A residue 1544 THR Chi-restraints excluded: chain A residue 1564 ASN Chi-restraints excluded: chain A residue 1572 THR Chi-restraints excluded: chain A residue 1595 ASP Chi-restraints excluded: chain A residue 1624 VAL Chi-restraints excluded: chain A residue 1696 THR Chi-restraints excluded: chain A residue 1708 THR Chi-restraints excluded: chain A residue 1759 SER Chi-restraints excluded: chain A residue 1763 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 31 optimal weight: 5.9990 chunk 50 optimal weight: 0.0040 chunk 79 optimal weight: 1.9990 chunk 113 optimal weight: 3.9990 chunk 47 optimal weight: 6.9990 chunk 19 optimal weight: 2.9990 chunk 90 optimal weight: 0.9990 chunk 69 optimal weight: 0.5980 chunk 43 optimal weight: 4.9990 chunk 68 optimal weight: 0.8980 chunk 98 optimal weight: 6.9990 overall best weight: 0.8996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 214 ASN A 283 ASN A 291 ASN A 834 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.151107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.107268 restraints weight = 17094.829| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 3.27 r_work: 0.3176 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.1441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10506 Z= 0.120 Angle : 0.518 9.630 14250 Z= 0.267 Chirality : 0.036 0.177 1659 Planarity : 0.004 0.046 1732 Dihedral : 6.495 108.040 1614 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.81 % Favored : 95.11 % Rotamer: Outliers : 3.71 % Allowed : 29.32 % Favored : 66.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.06 (0.25), residues: 1248 helix: 1.98 (0.19), residues: 831 sheet: -3.42 (0.86), residues: 22 loop : -1.94 (0.30), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A1626 TYR 0.012 0.001 TYR A1586 PHE 0.016 0.001 PHE A1751 TRP 0.016 0.001 TRP A 156 HIS 0.003 0.001 HIS A 118 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 (10500) covalent geometry : angle 0.51755 / 0.27 (14240) SS BOND : bond 0.00261 / 0.12 ( 5) SS BOND : angle 1.23188 / 0.68 ( 10) hydrogen bonds : bond 0.04756 / 3.06 ( 603) hydrogen bonds : angle 3.38945 / 2.33 ( 1713) Misc. bond : bond 0.00027 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 147 time to evaluate : 0.387 Fit side-chains REVERT: A 34 ARG cc_start: 0.7285 (OUTLIER) cc_final: 0.7084 (mmp-170) REVERT: A 101 THR cc_start: 0.7313 (OUTLIER) cc_final: 0.7096 (p) REVERT: A 195 TRP cc_start: 0.8099 (m-10) cc_final: 0.7641 (m-10) REVERT: A 774 TYR cc_start: 0.8059 (OUTLIER) cc_final: 0.7222 (t80) REVERT: A 824 THR cc_start: 0.7862 (OUTLIER) cc_final: 0.7620 (m) REVERT: A 834 ASN cc_start: 0.8310 (OUTLIER) cc_final: 0.8047 (t0) REVERT: A 858 MET cc_start: 0.9086 (tmm) cc_final: 0.8709 (ttt) REVERT: A 1253 GLU cc_start: 0.8160 (tt0) cc_final: 0.7725 (tt0) outliers start: 41 outliers final: 28 residues processed: 174 average time/residue: 0.0768 time to fit residues: 20.3855 Evaluate side-chains 173 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 140 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ARG Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 145 CYS Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 375 GLU Chi-restraints excluded: chain A residue 382 LEU Chi-restraints excluded: chain A residue 390 MET Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 759 ILE Chi-restraints excluded: chain A residue 774 TYR Chi-restraints excluded: chain A residue 776 TYR Chi-restraints excluded: chain A residue 793 LEU Chi-restraints excluded: chain A residue 824 THR Chi-restraints excluded: chain A residue 834 ASN Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 967 GLN Chi-restraints excluded: chain A residue 1255 LEU Chi-restraints excluded: chain A residue 1259 VAL Chi-restraints excluded: chain A residue 1328 VAL Chi-restraints excluded: chain A residue 1343 ILE Chi-restraints excluded: chain A residue 1363 CYS Chi-restraints excluded: chain A residue 1374 ASN Chi-restraints excluded: chain A residue 1544 THR Chi-restraints excluded: chain A residue 1564 ASN Chi-restraints excluded: chain A residue 1595 ASP Chi-restraints excluded: chain A residue 1611 ILE Chi-restraints excluded: chain A residue 1624 VAL Chi-restraints excluded: chain A residue 1696 THR Chi-restraints excluded: chain A residue 1759 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 69 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 chunk 7 optimal weight: 3.9990 chunk 97 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 22 optimal weight: 0.9990 chunk 18 optimal weight: 10.0000 chunk 54 optimal weight: 0.0040 chunk 124 optimal weight: 1.9990 chunk 99 optimal weight: 8.9990 chunk 96 optimal weight: 0.8980 overall best weight: 0.7798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 214 ASN A 291 ASN A 834 ASN A1354 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.151655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.107987 restraints weight = 16862.241| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 3.21 r_work: 0.3188 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.1501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 10506 Z= 0.115 Angle : 0.529 11.343 14250 Z= 0.270 Chirality : 0.036 0.163 1659 Planarity : 0.004 0.046 1732 Dihedral : 6.320 103.463 1614 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.05 % Favored : 94.87 % Rotamer: Outliers : 3.71 % Allowed : 30.14 % Favored : 66.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.16 (0.25), residues: 1248 helix: 2.06 (0.19), residues: 825 sheet: -3.54 (0.88), residues: 22 loop : -1.83 (0.30), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1626 TYR 0.012 0.001 TYR A1586 PHE 0.015 0.001 PHE A1751 TRP 0.014 0.001 TRP A 156 HIS 0.003 0.001 HIS A 118 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.12 (10500) covalent geometry : angle 0.52762 / 0.27 (14240) SS BOND : bond 0.00384 / 0.19 ( 5) SS BOND : angle 1.40145 / 0.71 ( 10) hydrogen bonds : bond 0.04632 / 2.98 ( 603) hydrogen bonds : angle 3.37233 / 2.31 ( 1713) Misc. bond : bond 0.00024 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 147 time to evaluate : 0.221 Fit side-chains REVERT: A 195 TRP cc_start: 0.8112 (m-10) cc_final: 0.7691 (m-10) REVERT: A 774 TYR cc_start: 0.8057 (OUTLIER) cc_final: 0.7240 (t80) REVERT: A 824 THR cc_start: 0.7844 (OUTLIER) cc_final: 0.7615 (m) REVERT: A 834 ASN cc_start: 0.8277 (OUTLIER) cc_final: 0.8067 (t0) REVERT: A 1245 MET cc_start: 0.7497 (ttp) cc_final: 0.6887 (tmm) REVERT: A 1253 GLU cc_start: 0.8096 (tt0) cc_final: 0.7667 (tt0) REVERT: A 1480 LEU cc_start: 0.7664 (tp) cc_final: 0.7305 (tt) outliers start: 41 outliers final: 32 residues processed: 173 average time/residue: 0.0738 time to fit residues: 19.5583 Evaluate side-chains 176 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 141 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 145 CYS Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 214 ASN Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 375 GLU Chi-restraints excluded: chain A residue 382 LEU Chi-restraints excluded: chain A residue 390 MET Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 759 ILE Chi-restraints excluded: chain A residue 774 TYR Chi-restraints excluded: chain A residue 776 TYR Chi-restraints excluded: chain A residue 793 LEU Chi-restraints excluded: chain A residue 824 THR Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 834 ASN Chi-restraints excluded: chain A residue 967 GLN Chi-restraints excluded: chain A residue 1255 LEU Chi-restraints excluded: chain A residue 1259 VAL Chi-restraints excluded: chain A residue 1328 VAL Chi-restraints excluded: chain A residue 1343 ILE Chi-restraints excluded: chain A residue 1363 CYS Chi-restraints excluded: chain A residue 1374 ASN Chi-restraints excluded: chain A residue 1544 THR Chi-restraints excluded: chain A residue 1564 ASN Chi-restraints excluded: chain A residue 1595 ASP Chi-restraints excluded: chain A residue 1611 ILE Chi-restraints excluded: chain A residue 1624 VAL Chi-restraints excluded: chain A residue 1696 THR Chi-restraints excluded: chain A residue 1759 SER Chi-restraints excluded: chain A residue 1761 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 82 optimal weight: 0.6980 chunk 56 optimal weight: 0.9980 chunk 115 optimal weight: 1.9990 chunk 112 optimal weight: 0.5980 chunk 111 optimal weight: 3.9990 chunk 68 optimal weight: 0.9980 chunk 37 optimal weight: 0.9980 chunk 44 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 101 optimal weight: 0.9990 chunk 35 optimal weight: 2.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 214 ASN A 291 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.151678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.107995 restraints weight = 16900.303| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 3.22 r_work: 0.3187 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.1549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10506 Z= 0.119 Angle : 0.536 10.625 14250 Z= 0.273 Chirality : 0.036 0.171 1659 Planarity : 0.004 0.046 1732 Dihedral : 6.225 99.269 1614 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.97 % Favored : 94.95 % Rotamer: Outliers : 3.80 % Allowed : 30.23 % Favored : 65.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.18 (0.25), residues: 1248 helix: 2.08 (0.19), residues: 825 sheet: -3.53 (0.89), residues: 22 loop : -1.83 (0.30), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1626 TYR 0.012 0.001 TYR A 378 PHE 0.055 0.001 PHE A1587 TRP 0.013 0.001 TRP A 156 HIS 0.003 0.001 HIS A 118 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 (10500) covalent geometry : angle 0.53449 / 0.27 (14240) SS BOND : bond 0.00314 / 0.16 ( 5) SS BOND : angle 1.56676 / 0.79 ( 10) hydrogen bonds : bond 0.04638 / 2.99 ( 603) hydrogen bonds : angle 3.36796 / 2.31 ( 1713) Misc. bond : bond 0.00023 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 142 time to evaluate : 0.306 Fit side-chains REVERT: A 189 LEU cc_start: 0.7788 (OUTLIER) cc_final: 0.7340 (mm) REVERT: A 195 TRP cc_start: 0.8129 (m-10) cc_final: 0.7675 (m-10) REVERT: A 774 TYR cc_start: 0.8038 (OUTLIER) cc_final: 0.7223 (t80) REVERT: A 824 THR cc_start: 0.7880 (OUTLIER) cc_final: 0.7651 (m) REVERT: A 1245 MET cc_start: 0.7504 (ttp) cc_final: 0.6878 (tmm) REVERT: A 1253 GLU cc_start: 0.8100 (tt0) cc_final: 0.7671 (tt0) REVERT: A 1480 LEU cc_start: 0.7634 (tp) cc_final: 0.7241 (tt) outliers start: 42 outliers final: 33 residues processed: 168 average time/residue: 0.0740 time to fit residues: 19.0860 Evaluate side-chains 174 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 138 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 145 CYS Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 375 GLU Chi-restraints excluded: chain A residue 382 LEU Chi-restraints excluded: chain A residue 390 MET Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 759 ILE Chi-restraints excluded: chain A residue 774 TYR Chi-restraints excluded: chain A residue 776 TYR Chi-restraints excluded: chain A residue 793 LEU Chi-restraints excluded: chain A residue 824 THR Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 855 VAL Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 967 GLN Chi-restraints excluded: chain A residue 1255 LEU Chi-restraints excluded: chain A residue 1259 VAL Chi-restraints excluded: chain A residue 1328 VAL Chi-restraints excluded: chain A residue 1343 ILE Chi-restraints excluded: chain A residue 1363 CYS Chi-restraints excluded: chain A residue 1544 THR Chi-restraints excluded: chain A residue 1564 ASN Chi-restraints excluded: chain A residue 1595 ASP Chi-restraints excluded: chain A residue 1624 VAL Chi-restraints excluded: chain A residue 1651 MET Chi-restraints excluded: chain A residue 1696 THR Chi-restraints excluded: chain A residue 1708 THR Chi-restraints excluded: chain A residue 1759 SER Chi-restraints excluded: chain A residue 1761 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 60 optimal weight: 2.9990 chunk 64 optimal weight: 0.6980 chunk 40 optimal weight: 3.9990 chunk 56 optimal weight: 0.7980 chunk 122 optimal weight: 0.8980 chunk 55 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 37 optimal weight: 0.7980 chunk 35 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 108 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 214 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.152346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.108645 restraints weight = 16829.606| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 3.22 r_work: 0.3195 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.1607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 10506 Z= 0.113 Angle : 0.524 10.149 14250 Z= 0.265 Chirality : 0.036 0.189 1659 Planarity : 0.004 0.046 1732 Dihedral : 6.077 94.363 1614 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.73 % Favored : 95.19 % Rotamer: Outliers : 3.53 % Allowed : 30.59 % Favored : 65.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.17 (0.25), residues: 1248 helix: 2.06 (0.19), residues: 833 sheet: -3.50 (0.90), residues: 22 loop : -1.93 (0.30), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1626 TYR 0.011 0.001 TYR A 378 PHE 0.031 0.001 PHE A 188 TRP 0.019 0.001 TRP A 156 HIS 0.003 0.001 HIS A 118 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.11 (10500) covalent geometry : angle 0.52300 / 0.27 (14240) SS BOND : bond 0.00332 / 0.16 ( 5) SS BOND : angle 1.23139 / 0.64 ( 10) hydrogen bonds : bond 0.04395 / 2.83 ( 603) hydrogen bonds : angle 3.33099 / 2.29 ( 1713) Misc. bond : bond 0.00022 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 139 time to evaluate : 0.373 Fit side-chains REVERT: A 189 LEU cc_start: 0.7747 (OUTLIER) cc_final: 0.7243 (mm) REVERT: A 195 TRP cc_start: 0.8087 (m-10) cc_final: 0.7620 (m-10) REVERT: A 774 TYR cc_start: 0.8041 (OUTLIER) cc_final: 0.7197 (t80) REVERT: A 824 THR cc_start: 0.7841 (OUTLIER) cc_final: 0.7596 (m) REVERT: A 1245 MET cc_start: 0.7487 (ttp) cc_final: 0.6854 (tmm) REVERT: A 1253 GLU cc_start: 0.8038 (tt0) cc_final: 0.7607 (tt0) REVERT: A 1480 LEU cc_start: 0.7538 (tp) cc_final: 0.7145 (tt) outliers start: 39 outliers final: 33 residues processed: 163 average time/residue: 0.0749 time to fit residues: 18.7863 Evaluate side-chains 172 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 136 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 145 CYS Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 375 GLU Chi-restraints excluded: chain A residue 382 LEU Chi-restraints excluded: chain A residue 390 MET Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 759 ILE Chi-restraints excluded: chain A residue 774 TYR Chi-restraints excluded: chain A residue 776 TYR Chi-restraints excluded: chain A residue 793 LEU Chi-restraints excluded: chain A residue 824 THR Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 855 VAL Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 967 GLN Chi-restraints excluded: chain A residue 1255 LEU Chi-restraints excluded: chain A residue 1259 VAL Chi-restraints excluded: chain A residue 1328 VAL Chi-restraints excluded: chain A residue 1343 ILE Chi-restraints excluded: chain A residue 1363 CYS Chi-restraints excluded: chain A residue 1544 THR Chi-restraints excluded: chain A residue 1564 ASN Chi-restraints excluded: chain A residue 1595 ASP Chi-restraints excluded: chain A residue 1624 VAL Chi-restraints excluded: chain A residue 1651 MET Chi-restraints excluded: chain A residue 1696 THR Chi-restraints excluded: chain A residue 1708 THR Chi-restraints excluded: chain A residue 1759 SER Chi-restraints excluded: chain A residue 1761 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 119 optimal weight: 4.9990 chunk 38 optimal weight: 0.8980 chunk 59 optimal weight: 0.5980 chunk 116 optimal weight: 0.5980 chunk 89 optimal weight: 0.5980 chunk 99 optimal weight: 0.8980 chunk 68 optimal weight: 0.9980 chunk 104 optimal weight: 1.9990 chunk 67 optimal weight: 4.9990 chunk 24 optimal weight: 0.7980 chunk 98 optimal weight: 6.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 214 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.153108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.109303 restraints weight = 16624.697| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 3.24 r_work: 0.3201 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.1667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 10506 Z= 0.111 Angle : 0.538 10.425 14250 Z= 0.272 Chirality : 0.036 0.186 1659 Planarity : 0.004 0.046 1732 Dihedral : 5.973 90.360 1614 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.49 % Favored : 95.43 % Rotamer: Outliers : 3.44 % Allowed : 30.59 % Favored : 65.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.19 (0.25), residues: 1248 helix: 2.06 (0.19), residues: 835 sheet: -3.39 (0.96), residues: 22 loop : -1.91 (0.30), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A1626 TYR 0.010 0.001 TYR A1586 PHE 0.029 0.001 PHE A 188 TRP 0.018 0.001 TRP A 156 HIS 0.003 0.001 HIS A 118 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.11 (10500) covalent geometry : angle 0.53777 / 0.27 (14240) SS BOND : bond 0.00292 / 0.15 ( 5) SS BOND : angle 1.10639 / 0.58 ( 10) hydrogen bonds : bond 0.04275 / 2.76 ( 603) hydrogen bonds : angle 3.29886 / 2.27 ( 1713) Misc. bond : bond 0.00021 / 0.01 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 139 time to evaluate : 0.379 Fit side-chains REVERT: A 189 LEU cc_start: 0.7793 (OUTLIER) cc_final: 0.7334 (mm) REVERT: A 195 TRP cc_start: 0.8099 (m-10) cc_final: 0.7602 (m-10) REVERT: A 715 MET cc_start: 0.5241 (tpt) cc_final: 0.4675 (ttp) REVERT: A 774 TYR cc_start: 0.8001 (OUTLIER) cc_final: 0.7154 (t80) REVERT: A 824 THR cc_start: 0.7867 (OUTLIER) cc_final: 0.7618 (m) REVERT: A 1245 MET cc_start: 0.7505 (ttp) cc_final: 0.6884 (tmm) REVERT: A 1253 GLU cc_start: 0.8065 (tt0) cc_final: 0.7634 (tt0) REVERT: A 1480 LEU cc_start: 0.7564 (tp) cc_final: 0.7159 (tt) outliers start: 38 outliers final: 33 residues processed: 162 average time/residue: 0.0736 time to fit residues: 18.4283 Evaluate side-chains 172 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 136 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 145 CYS Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 375 GLU Chi-restraints excluded: chain A residue 382 LEU Chi-restraints excluded: chain A residue 390 MET Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 759 ILE Chi-restraints excluded: chain A residue 774 TYR Chi-restraints excluded: chain A residue 793 LEU Chi-restraints excluded: chain A residue 824 THR Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 855 VAL Chi-restraints excluded: chain A residue 967 GLN Chi-restraints excluded: chain A residue 1255 LEU Chi-restraints excluded: chain A residue 1259 VAL Chi-restraints excluded: chain A residue 1328 VAL Chi-restraints excluded: chain A residue 1343 ILE Chi-restraints excluded: chain A residue 1363 CYS Chi-restraints excluded: chain A residue 1544 THR Chi-restraints excluded: chain A residue 1564 ASN Chi-restraints excluded: chain A residue 1595 ASP Chi-restraints excluded: chain A residue 1611 ILE Chi-restraints excluded: chain A residue 1624 VAL Chi-restraints excluded: chain A residue 1651 MET Chi-restraints excluded: chain A residue 1696 THR Chi-restraints excluded: chain A residue 1708 THR Chi-restraints excluded: chain A residue 1759 SER Chi-restraints excluded: chain A residue 1761 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 36 optimal weight: 0.8980 chunk 43 optimal weight: 5.9990 chunk 11 optimal weight: 2.9990 chunk 115 optimal weight: 0.7980 chunk 47 optimal weight: 6.9990 chunk 116 optimal weight: 0.3980 chunk 55 optimal weight: 2.9990 chunk 105 optimal weight: 0.9980 chunk 107 optimal weight: 3.9990 chunk 67 optimal weight: 4.9990 chunk 60 optimal weight: 1.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 214 ASN A1734 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.151561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.107515 restraints weight = 16890.379| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 3.26 r_work: 0.3177 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.1764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10506 Z= 0.128 Angle : 0.559 10.463 14250 Z= 0.284 Chirality : 0.036 0.176 1659 Planarity : 0.004 0.047 1732 Dihedral : 5.983 87.591 1614 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.97 % Favored : 94.95 % Rotamer: Outliers : 3.53 % Allowed : 30.68 % Favored : 65.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.08 (0.25), residues: 1248 helix: 1.99 (0.19), residues: 841 sheet: -3.49 (0.94), residues: 22 loop : -2.04 (0.30), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1626 TYR 0.012 0.001 TYR A 378 PHE 0.016 0.001 PHE A1751 TRP 0.018 0.001 TRP A 156 HIS 0.002 0.001 HIS A 118 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 (10500) covalent geometry : angle 0.55856 / 0.28 (14240) SS BOND : bond 0.00333 / 0.17 ( 5) SS BOND : angle 1.30008 / 0.69 ( 10) hydrogen bonds : bond 0.04742 / 3.07 ( 603) hydrogen bonds : angle 3.35792 / 2.30 ( 1713) Misc. bond : bond 0.00012 / 0.01 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2345.59 seconds wall clock time: 40 minutes 58.92 seconds (2458.92 seconds total)