Starting phenix.real_space_refine on Wed Feb 4 08:47:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ith_60865/02_2026/9ith_60865.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ith_60865/02_2026/9ith_60865.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ith_60865/02_2026/9ith_60865.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ith_60865/02_2026/9ith_60865.map" model { file = "/net/cci-nas-00/data/ceres_data/9ith_60865/02_2026/9ith_60865.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ith_60865/02_2026/9ith_60865.cif" } resolution = 3.4 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: 4 Type Number sf(0) Gaussians S 73 5.16 5 C 6232 2.51 5 N 1470 2.21 5 O 1649 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 48 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9424 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 9237 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1151, 9237 Classifications: {'peptide': 1151} Link IDs: {'PTRANS': 30, 'TRANS': 1120} Chain breaks: 2 Chain: "A" Number of atoms: 187 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 187 Unusual residues: {'9SR': 1, '9Z9': 1, 'NAG': 9} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Time building chain proxies: 2.27, per 1000 atoms: 0.24 Number of scatterers: 9424 At special positions: 0 Unit cell: (128.738, 123.283, 106.918, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 73 16.00 O 1649 8.00 N 1470 7.00 C 6232 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 326 " distance=2.02 Simple disulfide: pdb=" SG CYS A 335 " - 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=2.04 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 Links applied NAG-ASN " NAG A2101 " - " ASN A 283 " " NAG A2102 " - " ASN A 288 " " NAG A2103 " - " ASN A 291 " " NAG A2104 " - " ASN A 318 " " NAG A2105 " - " ASN A 328 " " NAG A2106 " - " ASN A1365 " " NAG A2107 " - " ASN A1374 " " NAG A2108 " - " ASN A1380 " " NAG A2109 " - " ASN A1388 " Time building additional restraints: 0.76 Conformation dependent library (CDL) restraints added in 486.7 milliseconds 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2166 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 3 sheets defined 74.7% alpha, 1.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing helix chain 'A' and resid 120 through 130 removed outlier: 3.884A pdb=" N HIS A 130 " --> pdb=" O LYS A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 149 removed outlier: 3.925A pdb=" N ASN A 134 " --> pdb=" O HIS A 130 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ALA A 149 " --> pdb=" O CYS A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 180 Processing helix chain 'A' and resid 192 through 210 removed outlier: 4.184A pdb=" N LEU A 196 " --> pdb=" O PRO A 192 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ASP A 197 " --> pdb=" O TRP A 193 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N VAL A 210 " --> pdb=" O THR A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 227 Processing helix chain 'A' and resid 228 through 233 removed outlier: 3.695A pdb=" N VAL A 232 " --> pdb=" O LYS A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 250 removed outlier: 3.774A pdb=" N LYS A 237 " --> pdb=" O ILE A 233 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N THR A 238 " --> pdb=" O SER A 234 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ILE A 244 " --> pdb=" O VAL A 240 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL A 247 " --> pdb=" O LEU A 243 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LYS A 248 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LYS A 249 " --> pdb=" O GLN A 245 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU A 250 " --> pdb=" O SER A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 272 Processing helix chain 'A' and resid 303 through 308 Processing helix chain 'A' and resid 348 through 352 removed outlier: 3.563A pdb=" N TYR A 352 " --> pdb=" O ASP A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 370 removed outlier: 3.542A pdb=" N ALA A 364 " --> pdb=" O TRP A 360 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N LEU A 365 " --> pdb=" O ALA A 361 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N LEU A 368 " --> pdb=" O ALA A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 386 removed outlier: 3.843A pdb=" N LEU A 377 " --> pdb=" O CYS A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 400 removed outlier: 3.980A pdb=" N PHE A 393 " --> pdb=" O TYR A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 429 Processing helix chain 'A' and resid 702 through 715 removed outlier: 3.611A pdb=" N ILE A 706 " --> pdb=" O LEU A 702 " (cutoff:3.500A) Processing helix chain 'A' and resid 716 through 735 Processing helix chain 'A' and resid 742 through 771 removed outlier: 3.650A pdb=" N LEU A 754 " --> pdb=" O GLN A 750 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N VAL A 755 " --> pdb=" O VAL A 751 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N PHE A 760 " --> pdb=" O PHE A 756 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LEU A 771 " --> pdb=" O LYS A 767 " (cutoff:3.500A) Processing helix chain 'A' and resid 772 through 777 Processing helix chain 'A' and resid 782 through 797 removed outlier: 3.607A pdb=" N ILE A 788 " --> pdb=" O PHE A 784 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU A 796 " --> pdb=" O SER A 792 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLY A 797 " --> pdb=" O LEU A 793 " (cutoff:3.500A) Processing helix chain 'A' and resid 805 through 810 Processing helix chain 'A' and resid 811 through 820 removed outlier: 3.962A pdb=" N LYS A 820 " --> pdb=" O LYS A 817 " (cutoff:3.500A) Processing helix chain 'A' and resid 822 through 838 Processing helix chain 'A' and resid 839 through 862 removed outlier: 4.158A pdb=" N THR A 843 " --> pdb=" O LEU A 839 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU A 844 " --> pdb=" O GLY A 840 " (cutoff:3.500A) Processing helix chain 'A' and resid 863 through 867 Processing helix chain 'A' and resid 883 through 896 Processing helix chain 'A' and resid 899 through 911 removed outlier: 3.550A pdb=" N MET A 903 " --> pdb=" O TRP A 899 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ASP A 905 " --> pdb=" O GLU A 901 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N GLU A 908 " --> pdb=" O TRP A 904 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N VAL A 909 " --> pdb=" O ASP A 905 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLY A 911 " --> pdb=" O MET A 907 " (cutoff:3.500A) Processing helix chain 'A' and resid 911 through 919 removed outlier: 3.686A pdb=" N CYS A 915 " --> pdb=" O GLY A 911 " (cutoff:3.500A) Processing helix chain 'A' and resid 920 through 944 removed outlier: 3.684A pdb=" N SER A 941 " --> pdb=" O LEU A 937 " (cutoff:3.500A) Processing helix chain 'A' and resid 1190 through 1204 removed outlier: 3.881A pdb=" N LYS A1196 " --> pdb=" O TRP A1192 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ILE A1201 " --> pdb=" O THR A1197 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N VAL A1202 " --> pdb=" O CYS A1198 " (cutoff:3.500A) Processing helix chain 'A' and resid 1204 through 1221 removed outlier: 4.040A pdb=" N GLU A1208 " --> pdb=" O HIS A1204 " (cutoff:3.500A) Processing helix chain 'A' and resid 1222 through 1225 Processing helix chain 'A' and resid 1232 through 1269 removed outlier: 3.629A pdb=" N VAL A1237 " --> pdb=" O LYS A1233 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N LEU A1238 " --> pdb=" O THR A1234 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLU A1240 " --> pdb=" O LYS A1236 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N PHE A1263 " --> pdb=" O VAL A1259 " (cutoff:3.500A) removed outlier: 8.924A pdb=" N LYS A1264 " --> pdb=" O ALA A1260 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LYS A1265 " --> pdb=" O TYR A1261 " (cutoff:3.500A) Processing helix chain 'A' and resid 1271 through 1291 removed outlier: 3.863A pdb=" N ASP A1275 " --> pdb=" O TRP A1271 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU A1291 " --> pdb=" O VAL A1287 " (cutoff:3.500A) Processing helix chain 'A' and resid 1298 through 1303 removed outlier: 3.569A pdb=" N ARG A1303 " --> pdb=" O ILE A1299 " (cutoff:3.500A) Processing helix chain 'A' and resid 1304 through 1311 removed outlier: 3.795A pdb=" N ALA A1307 " --> pdb=" O THR A1304 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU A1308 " --> pdb=" O LEU A1305 " (cutoff:3.500A) Proline residue: A1310 - end of helix Processing helix chain 'A' and resid 1312 through 1317 removed outlier: 4.267A pdb=" N ARG A1316 " --> pdb=" O ARG A1312 " (cutoff:3.500A) Processing helix chain 'A' and resid 1317 through 1330 removed outlier: 3.531A pdb=" N ALA A1330 " --> pdb=" O ALA A1326 " (cutoff:3.500A) Processing helix chain 'A' and resid 1330 through 1357 removed outlier: 3.581A pdb=" N ASN A1336 " --> pdb=" O PRO A1332 " (cutoff:3.500A) Processing helix chain 'A' and resid 1380 through 1385 Processing helix chain 'A' and resid 1404 through 1418 removed outlier: 3.805A pdb=" N LEU A1410 " --> pdb=" O GLY A1406 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ALA A1411 " --> pdb=" O ALA A1407 " (cutoff:3.500A) Processing helix chain 'A' and resid 1420 through 1429 removed outlier: 3.861A 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 1480 removed outlier: 3.583A pdb=" N PHE A1450 " --> pdb=" O MET A1446 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N PHE A1460 " --> pdb=" O PHE A1456 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N THR A1461 " --> pdb=" O GLY A1457 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LYS A1478 " --> pdb=" O ASN A1474 " (cutoff:3.500A) Processing helix chain 'A' and resid 1488 through 1502 removed outlier: 3.565A pdb=" N LYS A1493 " --> pdb=" O GLU A1489 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N TYR A1494 " --> pdb=" O GLU A1490 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N GLY A1502 " --> pdb=" O MET A1498 " (cutoff:3.500A) Processing helix chain 'A' and resid 1521 through 1526 Processing helix chain 'A' and resid 1527 through 1546 Processing helix chain 'A' and resid 1553 through 1579 Processing helix chain 'A' and resid 1586 through 1590 removed outlier: 4.002A pdb=" N ASN A1589 " --> pdb=" O TYR A1586 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N SER A1590 " --> pdb=" O PHE A1587 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1586 through 1590' Processing helix chain 'A' and resid 1591 through 1608 removed outlier: 3.545A pdb=" N PHE A1596 " --> pdb=" O ASN A1592 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N VAL A1597 " --> pdb=" O ILE A1593 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N VAL A1598 " --> pdb=" O PHE A1594 " (cutoff:3.500A) Processing helix chain 'A' and resid 1609 through 1615 removed outlier: 4.236A pdb=" N ILE A1612 " --> pdb=" O SER A1609 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLN A1613 " --> pdb=" O ASP A1610 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LYS A1614 " --> pdb=" O ILE A1611 " (cutoff:3.500A) Processing helix chain 'A' and resid 1617 through 1627 removed outlier: 4.062A pdb=" N LEU A1621 " --> pdb=" O PHE A1617 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N PHE A1622 " --> pdb=" O SER A1618 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ARG A1623 " --> pdb=" O PRO A1619 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N VAL A1624 " --> pdb=" O THR A1620 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ILE A1625 " --> pdb=" O LEU A1621 " (cutoff:3.500A) Processing helix chain 'A' and resid 1629 through 1634 removed outlier: 3.949A pdb=" N ILE A1633 " --> pdb=" O ARG A1629 " (cutoff:3.500A) Processing helix chain 'A' and resid 1635 through 1638 removed outlier: 3.848A pdb=" N ARG A1638 " --> pdb=" O ARG A1635 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1635 through 1638' Processing helix chain 'A' and resid 1640 through 1679 removed outlier: 4.003A pdb=" N LEU A1650 " --> pdb=" O LEU A1646 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N MET A1651 " --> pdb=" O LEU A1647 " (cutoff:3.500A) Proline residue: A1655 - end of helix Processing helix chain 'A' and resid 1696 through 1708 Processing helix chain 'A' and resid 1712 through 1721 removed outlier: 3.745A pdb=" N LEU A1716 " --> pdb=" O GLY A1712 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LEU A1717 " --> pdb=" O TRP A1713 " (cutoff:3.500A) Proline residue: A1719 - end of helix Processing helix chain 'A' and resid 1744 through 1778 removed outlier: 3.870A pdb=" N LEU A1750 " --> pdb=" O ALA A1746 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ILE A1757 " --> pdb=" O THR A1753 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 279 through 282 Processing sheet with id=AA2, first strand: chain 'A' and resid 294 through 295 Processing sheet with id=AA3, first strand: chain 'A' and resid 1361 through 1364 557 hydrogen bonds defined for protein. 1605 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: 1.50 Time building geometry restraints manager: 1.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.28: 1438 1.28 - 1.42: 2676 1.42 - 1.56: 5410 1.56 - 1.69: 12 1.69 - 1.83: 121 Bond restraints: 9657 Sorted by residual: bond pdb=" C13 9SR A2110 " pdb=" N14 9SR A2110 " ideal model delta sigma weight residual 1.281 1.500 -0.219 2.00e-02 2.50e+03 1.19e+02 bond pdb=" CA ALA A 332 " pdb=" C ALA A 332 " ideal model delta sigma weight residual 1.524 1.402 0.121 1.23e-02 6.61e+03 9.73e+01 bond pdb=" CA CYS A 341 " pdb=" C CYS A 341 " ideal model delta sigma weight residual 1.524 1.399 0.125 1.27e-02 6.20e+03 9.61e+01 bond pdb=" CA LEU A1721 " pdb=" C LEU A1721 " ideal model delta sigma weight residual 1.523 1.401 0.122 1.34e-02 5.57e+03 8.35e+01 bond pdb=" CA ALA A 735 " pdb=" C ALA A 735 " ideal model delta sigma weight residual 1.531 1.432 0.100 1.12e-02 7.97e+03 7.90e+01 ... (remaining 9652 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.75: 11629 2.75 - 5.50: 1157 5.50 - 8.25: 236 8.25 - 11.00: 77 11.00 - 13.74: 19 Bond angle restraints: 13118 Sorted by residual: angle pdb=" N ILE A 900 " pdb=" CA ILE A 900 " pdb=" C ILE A 900 " ideal model delta sigma weight residual 110.72 124.46 -13.74 1.01e+00 9.80e-01 1.85e+02 angle pdb=" N MET A 903 " pdb=" CA MET A 903 " pdb=" C MET A 903 " ideal model delta sigma weight residual 111.28 98.06 13.22 1.09e+00 8.42e-01 1.47e+02 angle pdb=" N TRP A 703 " pdb=" CA TRP A 703 " pdb=" C TRP A 703 " ideal model delta sigma weight residual 111.28 98.14 13.14 1.09e+00 8.42e-01 1.45e+02 angle pdb=" N TRP A1440 " pdb=" CA TRP A1440 " pdb=" C TRP A1440 " ideal model delta sigma weight residual 111.07 123.57 -12.50 1.07e+00 8.73e-01 1.37e+02 angle pdb=" N TRP A1591 " pdb=" CA TRP A1591 " pdb=" C TRP A1591 " ideal model delta sigma weight residual 113.18 99.45 13.73 1.33e+00 5.65e-01 1.07e+02 ... (remaining 13113 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.99: 5374 22.99 - 45.97: 432 45.97 - 68.96: 67 68.96 - 91.94: 12 91.94 - 114.93: 1 Dihedral angle restraints: 5886 sinusoidal: 2529 harmonic: 3357 Sorted by residual: dihedral pdb=" CB CYS A1363 " pdb=" SG CYS A1363 " pdb=" SG CYS A1384 " pdb=" CB CYS A1384 " ideal model delta sinusoidal sigma weight residual -86.00 -162.31 76.31 1 1.00e+01 1.00e-02 7.33e+01 dihedral pdb=" CB CYS A 280 " pdb=" SG CYS A 280 " pdb=" SG CYS A 326 " pdb=" CB CYS A 326 " ideal model delta sinusoidal sigma weight residual -86.00 -159.18 73.18 1 1.00e+01 1.00e-02 6.82e+01 dihedral pdb=" C THR A 902 " pdb=" N THR A 902 " pdb=" CA THR A 902 " pdb=" CB THR A 902 " ideal model delta harmonic sigma weight residual -122.00 -139.49 17.49 0 2.50e+00 1.60e-01 4.89e+01 ... (remaining 5883 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.259: 1385 0.259 - 0.519: 151 0.519 - 0.778: 11 0.778 - 1.037: 4 1.037 - 1.297: 1 Chirality restraints: 1552 Sorted by residual: chirality pdb=" C1 NAG A2109 " pdb=" ND2 ASN A1388 " pdb=" C2 NAG A2109 " pdb=" O5 NAG A2109 " both_signs ideal model delta sigma weight residual False -2.40 -1.10 -1.30 2.00e-01 2.50e+01 4.20e+01 chirality pdb=" C1 NAG A2103 " pdb=" ND2 ASN A 291 " pdb=" C2 NAG A2103 " pdb=" O5 NAG A2103 " both_signs ideal model delta sigma weight residual False -2.40 -1.42 -0.98 2.00e-01 2.50e+01 2.41e+01 chirality pdb=" CA ASP A1690 " pdb=" N ASP A1690 " pdb=" C ASP A1690 " pdb=" CB ASP A1690 " both_signs ideal model delta sigma weight residual False 2.51 1.57 0.94 2.00e-01 2.50e+01 2.21e+01 ... (remaining 1549 not shown) Planarity restraints: 1587 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A2107 " 0.319 2.00e-02 2.50e+03 2.69e-01 9.02e+02 pdb=" C7 NAG A2107 " -0.083 2.00e-02 2.50e+03 pdb=" C8 NAG A2107 " 0.187 2.00e-02 2.50e+03 pdb=" N2 NAG A2107 " -0.464 2.00e-02 2.50e+03 pdb=" O7 NAG A2107 " 0.041 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A2105 " -0.292 2.00e-02 2.50e+03 2.48e-01 7.69e+02 pdb=" C7 NAG A2105 " 0.077 2.00e-02 2.50e+03 pdb=" C8 NAG A2105 " -0.180 2.00e-02 2.50e+03 pdb=" N2 NAG A2105 " 0.428 2.00e-02 2.50e+03 pdb=" O7 NAG A2105 " -0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A2108 " 0.281 2.00e-02 2.50e+03 2.34e-01 6.85e+02 pdb=" C7 NAG A2108 " -0.075 2.00e-02 2.50e+03 pdb=" C8 NAG A2108 " 0.185 2.00e-02 2.50e+03 pdb=" N2 NAG A2108 " -0.394 2.00e-02 2.50e+03 pdb=" O7 NAG A2108 " 0.003 2.00e-02 2.50e+03 ... (remaining 1584 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.82: 3434 2.82 - 3.34: 9413 3.34 - 3.86: 14732 3.86 - 4.38: 17930 4.38 - 4.90: 28733 Nonbonded interactions: 74242 Sorted by model distance: nonbonded pdb=" O SER A 910 " pdb=" OG SER A 910 " model vdw 2.306 3.040 nonbonded pdb=" O ARG A 190 " pdb=" NH1 ARG A 190 " model vdw 2.321 3.120 nonbonded pdb=" N ASN A1693 " pdb=" O ASN A1693 " model vdw 2.325 2.496 nonbonded pdb=" N MET A1446 " pdb=" N TYR A1447 " model vdw 2.361 2.560 nonbonded pdb=" N ILE A1485 " pdb=" O ILE A1485 " model vdw 2.364 2.496 ... (remaining 74237 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: 0.850 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: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.310 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 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:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 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 : 0.020 0.219 9671 Z= 1.476 Angle : 1.953 18.955 13155 Z= 1.326 Chirality : 0.161 1.297 1552 Planarity : 0.018 0.269 1578 Dihedral : 15.811 114.927 3705 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.35 % Allowed : 5.94 % Favored : 93.71 % Rotamer: Outliers : 4.05 % Allowed : 18.95 % Favored : 77.00 % Cbeta Deviations : 2.95 % 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: -0.82 (0.24), residues: 1145 helix: 0.30 (0.18), residues: 763 sheet: -2.70 (1.11), residues: 22 loop : -2.17 (0.30), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 340 TYR 0.034 0.004 TYR A 307 PHE 0.041 0.003 PHE A 919 TRP 0.030 0.003 TRP A1713 HIS 0.027 0.003 HIS A 880 Details of bonding type rmsd covalent geometry : bond 0.02014 ( 9657) covalent geometry : angle 1.91272 (13118) SS BOND : bond 0.00584 ( 5) SS BOND : angle 2.24619 ( 10) hydrogen bonds : bond 0.23929 ( 557) hydrogen bonds : angle 8.51139 ( 1605) link_NAG-ASN : bond 0.02217 ( 9) link_NAG-ASN : angle 8.87860 ( 27) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 231 time to evaluate : 0.285 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 LEU cc_start: 0.5915 (OUTLIER) cc_final: 0.5652 (tm) REVERT: A 135 MET cc_start: 0.6810 (tpt) cc_final: 0.6581 (mmm) REVERT: A 205 TYR cc_start: 0.6382 (OUTLIER) cc_final: 0.5581 (t80) REVERT: A 375 GLU cc_start: 0.8283 (OUTLIER) cc_final: 0.7938 (pp20) REVERT: A 398 PHE cc_start: 0.8282 (t80) cc_final: 0.6906 (m-10) REVERT: A 419 GLN cc_start: 0.8042 (OUTLIER) cc_final: 0.7428 (pp30) REVERT: A 784 PHE cc_start: 0.7912 (t80) cc_final: 0.7589 (t80) REVERT: A 790 ILE cc_start: 0.7949 (OUTLIER) cc_final: 0.7721 (mm) REVERT: A 903 MET cc_start: 0.8484 (mtp) cc_final: 0.8277 (mtt) REVERT: A 909 VAL cc_start: 0.8968 (OUTLIER) cc_final: 0.8745 (m) REVERT: A 1206 TRP cc_start: 0.6923 (OUTLIER) cc_final: 0.6497 (t60) REVERT: A 1320 MET cc_start: 0.7841 (mtm) cc_final: 0.7602 (mtp) REVERT: A 1449 TYR cc_start: 0.8605 (t80) cc_final: 0.8404 (t80) REVERT: A 1472 ASN cc_start: 0.8701 (t0) cc_final: 0.8496 (t0) REVERT: A 1671 TYR cc_start: 0.7911 (m-80) cc_final: 0.7603 (m-80) REVERT: A 1696 THR cc_start: 0.9183 (t) cc_final: 0.8855 (m) outliers start: 41 outliers final: 17 residues processed: 260 average time/residue: 0.0726 time to fit residues: 28.3882 Evaluate side-chains 202 residues out of total 1013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 178 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 205 TYR Chi-restraints excluded: chain A residue 336 PRO Chi-restraints excluded: chain A residue 375 GLU Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain A residue 419 GLN Chi-restraints excluded: chain A residue 707 LYS Chi-restraints excluded: chain A residue 742 THR Chi-restraints excluded: chain A residue 764 MET Chi-restraints excluded: chain A residue 790 ILE Chi-restraints excluded: chain A residue 806 VAL Chi-restraints excluded: chain A residue 811 ARG Chi-restraints excluded: chain A residue 848 ILE Chi-restraints excluded: chain A residue 906 CYS Chi-restraints excluded: chain A residue 909 VAL Chi-restraints excluded: chain A residue 931 LEU Chi-restraints excluded: chain A residue 937 LEU Chi-restraints excluded: chain A residue 1206 TRP Chi-restraints excluded: chain A residue 1286 LEU Chi-restraints excluded: chain A residue 1328 VAL Chi-restraints excluded: chain A residue 1625 ILE Chi-restraints excluded: chain A residue 1750 LEU Chi-restraints excluded: chain A residue 1758 ILE Chi-restraints excluded: chain A residue 1777 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 108 optimal weight: 0.0870 chunk 49 optimal weight: 0.7980 chunk 97 optimal weight: 0.9980 chunk 113 optimal weight: 1.9990 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 chunk 100 optimal weight: 0.9990 overall best weight: 0.7558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 144 ASN A 313 ASN A 834 ASN A 859 GLN A 886 HIS A1439 GLN A1507 GLN A1558 ASN A1592 ASN A1678 ASN A1774 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.170761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.136312 restraints weight = 12908.711| |-----------------------------------------------------------------------------| r_work (start): 0.3670 rms_B_bonded: 2.13 r_work: 0.3533 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3409 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.2299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 9671 Z= 0.175 Angle : 0.783 14.737 13155 Z= 0.398 Chirality : 0.047 0.466 1552 Planarity : 0.005 0.086 1578 Dihedral : 8.158 64.856 1632 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.02 % Favored : 95.81 % Rotamer: Outliers : 4.34 % Allowed : 19.84 % Favored : 75.81 % 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: -0.29 (0.24), residues: 1145 helix: 0.73 (0.18), residues: 771 sheet: -2.88 (1.04), residues: 22 loop : -2.05 (0.29), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 282 TYR 0.020 0.002 TYR A 416 PHE 0.024 0.002 PHE A 164 TRP 0.015 0.002 TRP A1440 HIS 0.006 0.002 HIS A 886 Details of bonding type rmsd covalent geometry : bond 0.00339 ( 9657) covalent geometry : angle 0.72631 (13118) SS BOND : bond 0.01163 ( 5) SS BOND : angle 3.15621 ( 10) hydrogen bonds : bond 0.06263 ( 557) hydrogen bonds : angle 5.00860 ( 1605) link_NAG-ASN : bond 0.00940 ( 9) link_NAG-ASN : angle 6.23076 ( 27) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 216 time to evaluate : 0.247 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 LEU cc_start: 0.5811 (OUTLIER) cc_final: 0.5528 (tm) REVERT: A 135 MET cc_start: 0.6873 (tpt) cc_final: 0.6506 (mmm) REVERT: A 156 TRP cc_start: 0.6847 (p90) cc_final: 0.6246 (t-100) REVERT: A 168 TYR cc_start: 0.8055 (m-80) cc_final: 0.7547 (m-80) REVERT: A 172 SER cc_start: 0.8724 (m) cc_final: 0.8350 (p) REVERT: A 270 GLN cc_start: 0.8663 (OUTLIER) cc_final: 0.7565 (mt0) REVERT: A 375 GLU cc_start: 0.8509 (OUTLIER) cc_final: 0.8248 (pp20) REVERT: A 784 PHE cc_start: 0.7740 (t80) cc_final: 0.7035 (t80) REVERT: A 898 GLU cc_start: 0.8072 (OUTLIER) cc_final: 0.7503 (mt-10) REVERT: A 902 THR cc_start: 0.8891 (OUTLIER) cc_final: 0.8681 (p) REVERT: A 905 ASP cc_start: 0.8375 (t0) cc_final: 0.8037 (m-30) REVERT: A 923 MET cc_start: 0.8683 (ttm) cc_final: 0.8452 (ttm) REVERT: A 1206 TRP cc_start: 0.6486 (OUTLIER) cc_final: 0.5980 (t60) REVERT: A 1252 LEU cc_start: 0.8561 (tt) cc_final: 0.8157 (mt) REVERT: A 1253 GLU cc_start: 0.8123 (tp30) cc_final: 0.7914 (tp30) REVERT: A 1320 MET cc_start: 0.7816 (mtm) cc_final: 0.7521 (mtp) REVERT: A 1472 ASN cc_start: 0.8557 (t0) cc_final: 0.8319 (t0) REVERT: A 1542 MET cc_start: 0.8335 (ttt) cc_final: 0.7998 (ttp) REVERT: A 1592 ASN cc_start: 0.7428 (OUTLIER) cc_final: 0.7218 (t0) REVERT: A 1654 LEU cc_start: 0.7859 (mt) cc_final: 0.7587 (mt) REVERT: A 1671 TYR cc_start: 0.8406 (m-80) cc_final: 0.8163 (m-80) REVERT: A 1696 THR cc_start: 0.9163 (t) cc_final: 0.8885 (m) outliers start: 44 outliers final: 17 residues processed: 245 average time/residue: 0.0715 time to fit residues: 26.2975 Evaluate side-chains 195 residues out of total 1013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 171 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 148 MET Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 270 GLN Chi-restraints excluded: chain A residue 375 GLU Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain A residue 729 LEU Chi-restraints excluded: chain A residue 785 ASP Chi-restraints excluded: chain A residue 898 GLU Chi-restraints excluded: chain A residue 902 THR Chi-restraints excluded: chain A residue 906 CYS Chi-restraints excluded: chain A residue 1206 TRP Chi-restraints excluded: chain A residue 1268 THR Chi-restraints excluded: chain A residue 1272 CYS Chi-restraints excluded: chain A residue 1286 LEU Chi-restraints excluded: chain A residue 1328 VAL Chi-restraints excluded: chain A residue 1485 ILE Chi-restraints excluded: chain A residue 1486 PHE Chi-restraints excluded: chain A residue 1592 ASN Chi-restraints excluded: chain A residue 1701 MET Chi-restraints excluded: chain A residue 1714 ASP Chi-restraints excluded: chain A residue 1758 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 17 optimal weight: 3.9990 chunk 111 optimal weight: 4.9990 chunk 89 optimal weight: 6.9990 chunk 88 optimal weight: 7.9990 chunk 78 optimal weight: 0.7980 chunk 45 optimal weight: 2.9990 chunk 58 optimal weight: 0.9980 chunk 41 optimal weight: 0.0000 chunk 84 optimal weight: 1.9990 chunk 7 optimal weight: 7.9990 chunk 10 optimal weight: 0.7980 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 778 GLN A1518 GLN A1592 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.171417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.137290 restraints weight = 12919.099| |-----------------------------------------------------------------------------| r_work (start): 0.3680 rms_B_bonded: 2.23 r_work: 0.3525 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3402 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3402 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.2921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9671 Z= 0.142 Angle : 0.666 14.011 13155 Z= 0.336 Chirality : 0.044 0.445 1552 Planarity : 0.004 0.072 1578 Dihedral : 6.872 62.044 1597 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.67 % Favored : 96.24 % Rotamer: Outliers : 4.54 % Allowed : 22.11 % Favored : 73.35 % 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: 0.04 (0.24), residues: 1145 helix: 0.94 (0.19), residues: 763 sheet: -3.08 (0.97), residues: 22 loop : -1.72 (0.30), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 340 TYR 0.019 0.002 TYR A 205 PHE 0.018 0.001 PHE A1594 TRP 0.012 0.001 TRP A1206 HIS 0.004 0.001 HIS A 738 Details of bonding type rmsd covalent geometry : bond 0.00298 ( 9657) covalent geometry : angle 0.61669 (13118) SS BOND : bond 0.00897 ( 5) SS BOND : angle 2.04450 ( 10) hydrogen bonds : bond 0.04946 ( 557) hydrogen bonds : angle 4.64002 ( 1605) link_NAG-ASN : bond 0.00939 ( 9) link_NAG-ASN : angle 5.46118 ( 27) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 190 time to evaluate : 0.403 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 132 LEU cc_start: 0.5815 (OUTLIER) cc_final: 0.5517 (tm) REVERT: A 135 MET cc_start: 0.6931 (tpt) cc_final: 0.6715 (mmm) REVERT: A 168 TYR cc_start: 0.8153 (m-80) cc_final: 0.7824 (m-80) REVERT: A 172 SER cc_start: 0.8700 (m) cc_final: 0.8307 (p) REVERT: A 270 GLN cc_start: 0.8622 (OUTLIER) cc_final: 0.7506 (mt0) REVERT: A 365 LEU cc_start: 0.8746 (OUTLIER) cc_final: 0.8520 (tt) REVERT: A 375 GLU cc_start: 0.8649 (OUTLIER) cc_final: 0.8342 (pp20) REVERT: A 729 LEU cc_start: 0.8156 (OUTLIER) cc_final: 0.7953 (mm) REVERT: A 753 ASN cc_start: 0.8207 (p0) cc_final: 0.7367 (m-40) REVERT: A 784 PHE cc_start: 0.7537 (t80) cc_final: 0.6967 (t80) REVERT: A 898 GLU cc_start: 0.8014 (OUTLIER) cc_final: 0.7449 (mt-10) REVERT: A 905 ASP cc_start: 0.8441 (OUTLIER) cc_final: 0.8080 (m-30) REVERT: A 1206 TRP cc_start: 0.6410 (OUTLIER) cc_final: 0.5868 (t60) REVERT: A 1320 MET cc_start: 0.7702 (mtm) cc_final: 0.7482 (mtp) REVERT: A 1422 MET cc_start: 0.8692 (tpp) cc_final: 0.8229 (mmm) REVERT: A 1472 ASN cc_start: 0.8579 (t0) cc_final: 0.8191 (t0) REVERT: A 1517 TYR cc_start: 0.5133 (OUTLIER) cc_final: 0.4430 (m-80) REVERT: A 1542 MET cc_start: 0.8539 (ttt) cc_final: 0.8136 (ttp) REVERT: A 1654 LEU cc_start: 0.7824 (mt) cc_final: 0.7410 (mt) REVERT: A 1671 TYR cc_start: 0.8404 (m-80) cc_final: 0.8119 (m-80) REVERT: A 1773 GLU cc_start: 0.8447 (mm-30) cc_final: 0.7959 (mm-30) outliers start: 46 outliers final: 25 residues processed: 223 average time/residue: 0.0698 time to fit residues: 23.9062 Evaluate side-chains 197 residues out of total 1013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 163 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 148 MET Chi-restraints excluded: chain A residue 186 PHE Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 270 GLN Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 375 GLU Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain A residue 729 LEU Chi-restraints excluded: chain A residue 778 GLN Chi-restraints excluded: chain A residue 842 LEU Chi-restraints excluded: chain A residue 898 GLU Chi-restraints excluded: chain A residue 905 ASP Chi-restraints excluded: chain A residue 906 CYS Chi-restraints excluded: chain A residue 913 SER Chi-restraints excluded: chain A residue 1206 TRP Chi-restraints excluded: chain A residue 1239 LEU Chi-restraints excluded: chain A residue 1268 THR Chi-restraints excluded: chain A residue 1271 TRP Chi-restraints excluded: chain A residue 1272 CYS Chi-restraints excluded: chain A residue 1286 LEU Chi-restraints excluded: chain A residue 1338 LEU Chi-restraints excluded: chain A residue 1485 ILE Chi-restraints excluded: chain A residue 1486 PHE Chi-restraints excluded: chain A residue 1517 TYR Chi-restraints excluded: chain A residue 1701 MET Chi-restraints excluded: chain A residue 1758 ILE Chi-restraints excluded: chain A residue 1761 LEU Chi-restraints excluded: chain A residue 1771 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 18 optimal weight: 3.9990 chunk 42 optimal weight: 6.9990 chunk 29 optimal weight: 3.9990 chunk 83 optimal weight: 3.9990 chunk 75 optimal weight: 3.9990 chunk 66 optimal weight: 8.9990 chunk 38 optimal weight: 10.0000 chunk 84 optimal weight: 0.9980 chunk 99 optimal weight: 0.9990 chunk 6 optimal weight: 0.8980 chunk 98 optimal weight: 0.9980 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1592 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.169126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.132941 restraints weight = 13009.042| |-----------------------------------------------------------------------------| r_work (start): 0.3628 rms_B_bonded: 2.36 r_work: 0.3485 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3357 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.3149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 9671 Z= 0.163 Angle : 0.667 13.982 13155 Z= 0.335 Chirality : 0.044 0.422 1552 Planarity : 0.004 0.064 1578 Dihedral : 6.711 59.952 1596 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.58 % Favored : 96.33 % Rotamer: Outliers : 4.94 % Allowed : 23.49 % Favored : 71.57 % 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: 0.01 (0.24), residues: 1145 helix: 0.94 (0.19), residues: 765 sheet: -3.12 (0.88), residues: 22 loop : -1.81 (0.30), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 340 TYR 0.018 0.002 TYR A 205 PHE 0.015 0.001 PHE A 164 TRP 0.016 0.001 TRP A 156 HIS 0.004 0.001 HIS A 738 Details of bonding type rmsd covalent geometry : bond 0.00375 ( 9657) covalent geometry : angle 0.61930 (13118) SS BOND : bond 0.01005 ( 5) SS BOND : angle 1.98752 ( 10) hydrogen bonds : bond 0.04775 ( 557) hydrogen bonds : angle 4.60137 ( 1605) link_NAG-ASN : bond 0.00896 ( 9) link_NAG-ASN : angle 5.36176 ( 27) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 173 time to evaluate : 0.303 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 132 LEU cc_start: 0.5962 (OUTLIER) cc_final: 0.5644 (tm) REVERT: A 135 MET cc_start: 0.6998 (tpt) cc_final: 0.6766 (mmm) REVERT: A 172 SER cc_start: 0.8734 (m) cc_final: 0.8307 (p) REVERT: A 270 GLN cc_start: 0.8643 (OUTLIER) cc_final: 0.7547 (mt0) REVERT: A 375 GLU cc_start: 0.8700 (OUTLIER) cc_final: 0.8392 (pp20) REVERT: A 378 TYR cc_start: 0.8746 (OUTLIER) cc_final: 0.7875 (t80) REVERT: A 729 LEU cc_start: 0.8218 (OUTLIER) cc_final: 0.7998 (mm) REVERT: A 753 ASN cc_start: 0.8077 (p0) cc_final: 0.7307 (m-40) REVERT: A 784 PHE cc_start: 0.7602 (t80) cc_final: 0.7029 (t80) REVERT: A 816 PHE cc_start: 0.7814 (m-80) cc_final: 0.7573 (m-80) REVERT: A 825 LEU cc_start: 0.8451 (OUTLIER) cc_final: 0.7804 (tt) REVERT: A 898 GLU cc_start: 0.8048 (OUTLIER) cc_final: 0.7368 (mt-10) REVERT: A 905 ASP cc_start: 0.8586 (OUTLIER) cc_final: 0.8211 (m-30) REVERT: A 1206 TRP cc_start: 0.6174 (OUTLIER) cc_final: 0.5615 (t60) REVERT: A 1335 MET cc_start: 0.7997 (mmp) cc_final: 0.7794 (mmm) REVERT: A 1342 LEU cc_start: 0.8949 (OUTLIER) cc_final: 0.8698 (mm) REVERT: A 1422 MET cc_start: 0.8691 (tpp) cc_final: 0.8405 (mmm) REVERT: A 1472 ASN cc_start: 0.8669 (t0) cc_final: 0.8289 (t0) REVERT: A 1517 TYR cc_start: 0.5253 (OUTLIER) cc_final: 0.4706 (m-80) REVERT: A 1542 MET cc_start: 0.8628 (ttt) cc_final: 0.8305 (ttp) REVERT: A 1654 LEU cc_start: 0.7822 (mt) cc_final: 0.7309 (mt) REVERT: A 1671 TYR cc_start: 0.8453 (m-80) cc_final: 0.8173 (m-80) outliers start: 50 outliers final: 32 residues processed: 211 average time/residue: 0.0684 time to fit residues: 22.3544 Evaluate side-chains 206 residues out of total 1013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 163 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 148 MET Chi-restraints excluded: chain A residue 186 PHE Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 270 GLN Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 375 GLU Chi-restraints excluded: chain A residue 378 TYR Chi-restraints excluded: chain A residue 390 MET Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain A residue 729 LEU Chi-restraints excluded: chain A residue 825 LEU Chi-restraints excluded: chain A residue 835 SER Chi-restraints excluded: chain A residue 842 LEU Chi-restraints excluded: chain A residue 843 THR Chi-restraints excluded: chain A residue 898 GLU Chi-restraints excluded: chain A residue 905 ASP Chi-restraints excluded: chain A residue 906 CYS Chi-restraints excluded: chain A residue 913 SER Chi-restraints excluded: chain A residue 1206 TRP Chi-restraints excluded: chain A residue 1239 LEU Chi-restraints excluded: chain A residue 1268 THR Chi-restraints excluded: chain A residue 1269 ASN Chi-restraints excluded: chain A residue 1271 TRP Chi-restraints excluded: chain A residue 1272 CYS Chi-restraints excluded: chain A residue 1286 LEU Chi-restraints excluded: chain A residue 1328 VAL Chi-restraints excluded: chain A residue 1338 LEU Chi-restraints excluded: chain A residue 1342 LEU Chi-restraints excluded: chain A residue 1396 THR Chi-restraints excluded: chain A residue 1485 ILE Chi-restraints excluded: chain A residue 1495 TYR Chi-restraints excluded: chain A residue 1517 TYR Chi-restraints excluded: chain A residue 1758 ILE Chi-restraints excluded: chain A residue 1761 LEU Chi-restraints excluded: chain A residue 1771 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 55 optimal weight: 0.0170 chunk 33 optimal weight: 5.9990 chunk 102 optimal weight: 4.9990 chunk 73 optimal weight: 5.9990 chunk 92 optimal weight: 3.9990 chunk 41 optimal weight: 9.9990 chunk 51 optimal weight: 2.9990 chunk 1 optimal weight: 10.0000 chunk 50 optimal weight: 0.7980 chunk 71 optimal weight: 3.9990 chunk 94 optimal weight: 10.0000 overall best weight: 2.3624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 347 ASN A1774 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.166125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.130793 restraints weight = 13023.153| |-----------------------------------------------------------------------------| r_work (start): 0.3597 rms_B_bonded: 2.20 r_work: 0.3452 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3329 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.3330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.086 9671 Z= 0.201 Angle : 0.700 14.176 13155 Z= 0.351 Chirality : 0.045 0.452 1552 Planarity : 0.004 0.062 1578 Dihedral : 6.750 59.295 1596 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.54 % Favored : 95.37 % Rotamer: Outliers : 5.73 % Allowed : 22.61 % Favored : 71.67 % 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: -0.18 (0.24), residues: 1145 helix: 0.81 (0.19), residues: 771 sheet: -3.22 (0.83), residues: 22 loop : -1.97 (0.30), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 340 TYR 0.028 0.002 TYR A 168 PHE 0.017 0.002 PHE A 164 TRP 0.012 0.002 TRP A1206 HIS 0.004 0.001 HIS A 738 Details of bonding type rmsd covalent geometry : bond 0.00468 ( 9657) covalent geometry : angle 0.65480 (13118) SS BOND : bond 0.00793 ( 5) SS BOND : angle 1.54307 ( 10) hydrogen bonds : bond 0.05008 ( 557) hydrogen bonds : angle 4.66193 ( 1605) link_NAG-ASN : bond 0.00900 ( 9) link_NAG-ASN : angle 5.42856 ( 27) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 172 time to evaluate : 0.338 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 132 LEU cc_start: 0.5986 (OUTLIER) cc_final: 0.5695 (tm) REVERT: A 135 MET cc_start: 0.7054 (tpt) cc_final: 0.6818 (mmm) REVERT: A 168 TYR cc_start: 0.8227 (m-80) cc_final: 0.7749 (m-80) REVERT: A 172 SER cc_start: 0.8727 (m) cc_final: 0.8237 (p) REVERT: A 205 TYR cc_start: 0.5764 (OUTLIER) cc_final: 0.5396 (t80) REVERT: A 270 GLN cc_start: 0.8694 (OUTLIER) cc_final: 0.7660 (mt0) REVERT: A 375 GLU cc_start: 0.8732 (OUTLIER) cc_final: 0.8462 (pp20) REVERT: A 378 TYR cc_start: 0.8809 (OUTLIER) cc_final: 0.7693 (t80) REVERT: A 784 PHE cc_start: 0.7567 (t80) cc_final: 0.6930 (t80) REVERT: A 801 MET cc_start: 0.5066 (pmm) cc_final: 0.4064 (mmm) REVERT: A 905 ASP cc_start: 0.8572 (OUTLIER) cc_final: 0.8249 (m-30) REVERT: A 1206 TRP cc_start: 0.6287 (OUTLIER) cc_final: 0.5816 (t60) REVERT: A 1308 LEU cc_start: 0.8911 (OUTLIER) cc_final: 0.8670 (mt) REVERT: A 1335 MET cc_start: 0.7952 (mmp) cc_final: 0.7711 (mmm) REVERT: A 1342 LEU cc_start: 0.8978 (OUTLIER) cc_final: 0.8770 (mm) REVERT: A 1403 ASP cc_start: 0.8600 (m-30) cc_final: 0.8390 (m-30) REVERT: A 1422 MET cc_start: 0.8703 (tpp) cc_final: 0.8372 (mmm) REVERT: A 1517 TYR cc_start: 0.5254 (OUTLIER) cc_final: 0.4838 (m-80) REVERT: A 1542 MET cc_start: 0.8656 (ttt) cc_final: 0.8368 (ttp) outliers start: 58 outliers final: 38 residues processed: 212 average time/residue: 0.0721 time to fit residues: 23.6317 Evaluate side-chains 209 residues out of total 1013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 161 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 148 MET Chi-restraints excluded: chain A residue 186 PHE Chi-restraints excluded: chain A residue 205 TYR Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 270 GLN Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 375 GLU Chi-restraints excluded: chain A residue 378 TYR Chi-restraints excluded: chain A residue 390 MET Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain A residue 729 LEU Chi-restraints excluded: chain A residue 835 SER Chi-restraints excluded: chain A residue 842 LEU Chi-restraints excluded: chain A residue 843 THR Chi-restraints excluded: chain A residue 905 ASP Chi-restraints excluded: chain A residue 906 CYS Chi-restraints excluded: chain A residue 913 SER Chi-restraints excluded: chain A residue 1206 TRP Chi-restraints excluded: chain A residue 1238 LEU Chi-restraints excluded: chain A residue 1239 LEU Chi-restraints excluded: chain A residue 1268 THR Chi-restraints excluded: chain A residue 1269 ASN Chi-restraints excluded: chain A residue 1271 TRP Chi-restraints excluded: chain A residue 1272 CYS Chi-restraints excluded: chain A residue 1286 LEU Chi-restraints excluded: chain A residue 1308 LEU Chi-restraints excluded: chain A residue 1328 VAL Chi-restraints excluded: chain A residue 1338 LEU Chi-restraints excluded: chain A residue 1342 LEU Chi-restraints excluded: chain A residue 1382 SER Chi-restraints excluded: chain A residue 1396 THR Chi-restraints excluded: chain A residue 1485 ILE Chi-restraints excluded: chain A residue 1486 PHE Chi-restraints excluded: chain A residue 1517 TYR Chi-restraints excluded: chain A residue 1602 SER Chi-restraints excluded: chain A residue 1714 ASP Chi-restraints excluded: chain A residue 1723 THR Chi-restraints excluded: chain A residue 1758 ILE Chi-restraints excluded: chain A residue 1761 LEU Chi-restraints excluded: chain A residue 1770 ILE Chi-restraints excluded: chain A residue 1771 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 103 optimal weight: 4.9990 chunk 80 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 chunk 107 optimal weight: 0.9980 chunk 20 optimal weight: 6.9990 chunk 52 optimal weight: 0.8980 chunk 85 optimal weight: 8.9990 chunk 11 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 chunk 65 optimal weight: 10.0000 chunk 59 optimal weight: 5.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.167134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.131731 restraints weight = 12904.019| |-----------------------------------------------------------------------------| r_work (start): 0.3606 rms_B_bonded: 1.98 r_work: 0.3461 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3341 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.3526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 9671 Z= 0.178 Angle : 0.683 13.951 13155 Z= 0.341 Chirality : 0.044 0.435 1552 Planarity : 0.004 0.057 1578 Dihedral : 6.548 59.557 1596 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.19 % Favored : 95.72 % Rotamer: Outliers : 6.02 % Allowed : 24.09 % Favored : 69.89 % 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: -0.08 (0.24), residues: 1145 helix: 0.90 (0.19), residues: 769 sheet: -3.22 (0.83), residues: 22 loop : -1.95 (0.30), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1316 TYR 0.016 0.002 TYR A 416 PHE 0.021 0.001 PHE A1530 TRP 0.015 0.001 TRP A 156 HIS 0.004 0.001 HIS A 738 Details of bonding type rmsd covalent geometry : bond 0.00415 ( 9657) covalent geometry : angle 0.63493 (13118) SS BOND : bond 0.00988 ( 5) SS BOND : angle 2.88411 ( 10) hydrogen bonds : bond 0.04650 ( 557) hydrogen bonds : angle 4.58220 ( 1605) link_NAG-ASN : bond 0.00898 ( 9) link_NAG-ASN : angle 5.29836 ( 27) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 165 time to evaluate : 0.275 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 132 LEU cc_start: 0.6028 (OUTLIER) cc_final: 0.5778 (tm) REVERT: A 135 MET cc_start: 0.7061 (tpt) cc_final: 0.6832 (mmm) REVERT: A 168 TYR cc_start: 0.8265 (m-80) cc_final: 0.7908 (m-80) REVERT: A 172 SER cc_start: 0.8709 (m) cc_final: 0.8244 (p) REVERT: A 270 GLN cc_start: 0.8651 (OUTLIER) cc_final: 0.7616 (mt0) REVERT: A 375 GLU cc_start: 0.8731 (OUTLIER) cc_final: 0.8491 (pp20) REVERT: A 378 TYR cc_start: 0.8777 (OUTLIER) cc_final: 0.7631 (t80) REVERT: A 417 GLU cc_start: 0.8061 (tm-30) cc_final: 0.7742 (tm-30) REVERT: A 700 CYS cc_start: 0.6723 (OUTLIER) cc_final: 0.6304 (p) REVERT: A 784 PHE cc_start: 0.7527 (t80) cc_final: 0.6882 (t80) REVERT: A 801 MET cc_start: 0.5324 (pmm) cc_final: 0.4146 (mmm) REVERT: A 905 ASP cc_start: 0.8588 (OUTLIER) cc_final: 0.8314 (m-30) REVERT: A 1206 TRP cc_start: 0.6182 (OUTLIER) cc_final: 0.5710 (t60) REVERT: A 1308 LEU cc_start: 0.8899 (OUTLIER) cc_final: 0.8639 (mt) REVERT: A 1335 MET cc_start: 0.7876 (mmp) cc_final: 0.7627 (mmm) REVERT: A 1422 MET cc_start: 0.8700 (tpp) cc_final: 0.8363 (mmm) REVERT: A 1472 ASN cc_start: 0.8779 (t0) cc_final: 0.8419 (t0) REVERT: A 1542 MET cc_start: 0.8674 (ttt) cc_final: 0.8395 (ttp) REVERT: A 1772 LEU cc_start: 0.8240 (OUTLIER) cc_final: 0.7977 (mp) outliers start: 61 outliers final: 38 residues processed: 208 average time/residue: 0.0703 time to fit residues: 22.6403 Evaluate side-chains 206 residues out of total 1013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 159 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 148 MET Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 186 PHE Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 270 GLN Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 375 GLU Chi-restraints excluded: chain A residue 378 TYR Chi-restraints excluded: chain A residue 390 MET Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain A residue 700 CYS Chi-restraints excluded: chain A residue 835 SER Chi-restraints excluded: chain A residue 842 LEU Chi-restraints excluded: chain A residue 843 THR Chi-restraints excluded: chain A residue 905 ASP Chi-restraints excluded: chain A residue 906 CYS Chi-restraints excluded: chain A residue 910 SER Chi-restraints excluded: chain A residue 913 SER Chi-restraints excluded: chain A residue 1206 TRP Chi-restraints excluded: chain A residue 1238 LEU Chi-restraints excluded: chain A residue 1239 LEU Chi-restraints excluded: chain A residue 1268 THR Chi-restraints excluded: chain A residue 1269 ASN Chi-restraints excluded: chain A residue 1271 TRP Chi-restraints excluded: chain A residue 1272 CYS Chi-restraints excluded: chain A residue 1286 LEU Chi-restraints excluded: chain A residue 1308 LEU Chi-restraints excluded: chain A residue 1338 LEU Chi-restraints excluded: chain A residue 1382 SER Chi-restraints excluded: chain A residue 1396 THR Chi-restraints excluded: chain A residue 1485 ILE Chi-restraints excluded: chain A residue 1486 PHE Chi-restraints excluded: chain A residue 1602 SER Chi-restraints excluded: chain A residue 1714 ASP Chi-restraints excluded: chain A residue 1723 THR Chi-restraints excluded: chain A residue 1761 LEU Chi-restraints excluded: chain A residue 1770 ILE Chi-restraints excluded: chain A residue 1771 ILE Chi-restraints excluded: chain A residue 1772 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 71 optimal weight: 0.7980 chunk 88 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 79 optimal weight: 0.6980 chunk 65 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 1 optimal weight: 9.9990 chunk 87 optimal weight: 7.9990 chunk 4 optimal weight: 0.8980 chunk 42 optimal weight: 0.9990 chunk 39 optimal weight: 6.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 371 GLN A1475 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.169584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.134907 restraints weight = 12904.541| |-----------------------------------------------------------------------------| r_work (start): 0.3653 rms_B_bonded: 1.90 r_work: 0.3517 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3398 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.3744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 9671 Z= 0.135 Angle : 0.645 13.641 13155 Z= 0.319 Chirality : 0.043 0.398 1552 Planarity : 0.004 0.057 1578 Dihedral : 6.168 59.948 1594 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.10 % Favored : 95.81 % Rotamer: Outliers : 5.13 % Allowed : 25.67 % Favored : 69.20 % 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: 0.19 (0.25), residues: 1145 helix: 1.10 (0.19), residues: 764 sheet: -2.90 (0.83), residues: 20 loop : -1.81 (0.30), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1316 TYR 0.017 0.001 TYR A 168 PHE 0.017 0.001 PHE A1530 TRP 0.015 0.001 TRP A 156 HIS 0.004 0.001 HIS A 738 Details of bonding type rmsd covalent geometry : bond 0.00304 ( 9657) covalent geometry : angle 0.59902 (13118) SS BOND : bond 0.00736 ( 5) SS BOND : angle 2.37953 ( 10) hydrogen bonds : bond 0.04292 ( 557) hydrogen bonds : angle 4.42771 ( 1605) link_NAG-ASN : bond 0.00934 ( 9) link_NAG-ASN : angle 5.10321 ( 27) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 176 time to evaluate : 0.362 Fit side-chains revert: symmetry clash REVERT: A 132 LEU cc_start: 0.5957 (OUTLIER) cc_final: 0.5713 (tm) REVERT: A 135 MET cc_start: 0.6968 (tpt) cc_final: 0.6743 (mmm) REVERT: A 168 TYR cc_start: 0.8219 (m-80) cc_final: 0.7862 (m-80) REVERT: A 172 SER cc_start: 0.8640 (m) cc_final: 0.8174 (p) REVERT: A 270 GLN cc_start: 0.8564 (OUTLIER) cc_final: 0.7506 (mt0) REVERT: A 282 ARG cc_start: 0.8659 (mtm180) cc_final: 0.8443 (mtp180) REVERT: A 378 TYR cc_start: 0.8722 (OUTLIER) cc_final: 0.7538 (t80) REVERT: A 417 GLU cc_start: 0.7992 (tm-30) cc_final: 0.7677 (tm-30) REVERT: A 700 CYS cc_start: 0.6640 (OUTLIER) cc_final: 0.6188 (p) REVERT: A 784 PHE cc_start: 0.7496 (t80) cc_final: 0.6910 (t80) REVERT: A 801 MET cc_start: 0.5247 (pmm) cc_final: 0.4256 (mmm) REVERT: A 816 PHE cc_start: 0.7502 (m-80) cc_final: 0.7300 (m-80) REVERT: A 905 ASP cc_start: 0.8507 (OUTLIER) cc_final: 0.8232 (m-30) REVERT: A 1320 MET cc_start: 0.7518 (mtm) cc_final: 0.7294 (mtp) REVERT: A 1335 MET cc_start: 0.7781 (mmp) cc_final: 0.7504 (mmm) REVERT: A 1422 MET cc_start: 0.8657 (tpp) cc_final: 0.8188 (mmm) REVERT: A 1472 ASN cc_start: 0.8709 (t0) cc_final: 0.8366 (t0) REVERT: A 1499 LYS cc_start: 0.8222 (tmmt) cc_final: 0.7783 (tmmt) REVERT: A 1542 MET cc_start: 0.8687 (ttt) cc_final: 0.8441 (ttp) REVERT: A 1671 TYR cc_start: 0.8325 (m-80) cc_final: 0.7849 (m-80) REVERT: A 1772 LEU cc_start: 0.8170 (OUTLIER) cc_final: 0.7891 (mp) outliers start: 52 outliers final: 32 residues processed: 213 average time/residue: 0.0723 time to fit residues: 23.8136 Evaluate side-chains 205 residues out of total 1013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 167 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 270 GLN Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 378 TYR Chi-restraints excluded: chain A residue 390 MET Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain A residue 700 CYS Chi-restraints excluded: chain A residue 839 LEU Chi-restraints excluded: chain A residue 842 LEU Chi-restraints excluded: chain A residue 843 THR Chi-restraints excluded: chain A residue 905 ASP Chi-restraints excluded: chain A residue 906 CYS Chi-restraints excluded: chain A residue 1206 TRP Chi-restraints excluded: chain A residue 1238 LEU Chi-restraints excluded: chain A residue 1239 LEU Chi-restraints excluded: chain A residue 1269 ASN Chi-restraints excluded: chain A residue 1271 TRP Chi-restraints excluded: chain A residue 1272 CYS Chi-restraints excluded: chain A residue 1286 LEU Chi-restraints excluded: chain A residue 1328 VAL Chi-restraints excluded: chain A residue 1338 LEU Chi-restraints excluded: chain A residue 1382 SER Chi-restraints excluded: chain A residue 1396 THR Chi-restraints excluded: chain A residue 1486 PHE Chi-restraints excluded: chain A residue 1602 SER Chi-restraints excluded: chain A residue 1714 ASP Chi-restraints excluded: chain A residue 1723 THR Chi-restraints excluded: chain A residue 1761 LEU Chi-restraints excluded: chain A residue 1771 ILE Chi-restraints excluded: chain A residue 1772 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 35 optimal weight: 8.9990 chunk 33 optimal weight: 5.9990 chunk 43 optimal weight: 0.9990 chunk 19 optimal weight: 6.9990 chunk 76 optimal weight: 4.9990 chunk 12 optimal weight: 0.8980 chunk 104 optimal weight: 2.9990 chunk 78 optimal weight: 0.1980 chunk 87 optimal weight: 1.9990 chunk 41 optimal weight: 20.0000 chunk 81 optimal weight: 3.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 708 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.168778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.132307 restraints weight = 12876.583| |-----------------------------------------------------------------------------| r_work (start): 0.3618 rms_B_bonded: 2.31 r_work: 0.3474 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3347 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.3850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9671 Z= 0.148 Angle : 0.658 13.721 13155 Z= 0.323 Chirality : 0.043 0.405 1552 Planarity : 0.004 0.054 1578 Dihedral : 5.975 60.859 1591 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.10 % Favored : 95.81 % Rotamer: Outliers : 4.94 % Allowed : 25.96 % Favored : 69.10 % 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: 0.11 (0.25), residues: 1145 helix: 1.01 (0.19), residues: 774 sheet: -2.78 (0.86), residues: 20 loop : -1.86 (0.30), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1316 TYR 0.026 0.002 TYR A1375 PHE 0.017 0.001 PHE A1596 TRP 0.014 0.001 TRP A 156 HIS 0.004 0.001 HIS A 738 Details of bonding type rmsd covalent geometry : bond 0.00337 ( 9657) covalent geometry : angle 0.61460 (13118) SS BOND : bond 0.00632 ( 5) SS BOND : angle 1.87572 ( 10) hydrogen bonds : bond 0.04323 ( 557) hydrogen bonds : angle 4.38592 ( 1605) link_NAG-ASN : bond 0.00905 ( 9) link_NAG-ASN : angle 5.09678 ( 27) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 175 time to evaluate : 0.373 Fit side-chains revert: symmetry clash REVERT: A 132 LEU cc_start: 0.5957 (OUTLIER) cc_final: 0.5727 (tm) REVERT: A 135 MET cc_start: 0.6986 (tpt) cc_final: 0.6758 (mmm) REVERT: A 168 TYR cc_start: 0.8235 (m-80) cc_final: 0.7921 (m-80) REVERT: A 172 SER cc_start: 0.8668 (m) cc_final: 0.8212 (p) REVERT: A 270 GLN cc_start: 0.8576 (OUTLIER) cc_final: 0.7516 (mt0) REVERT: A 378 TYR cc_start: 0.8770 (OUTLIER) cc_final: 0.7601 (t80) REVERT: A 417 GLU cc_start: 0.8007 (tm-30) cc_final: 0.7669 (tm-30) REVERT: A 418 GLU cc_start: 0.7621 (tm-30) cc_final: 0.7338 (tm-30) REVERT: A 700 CYS cc_start: 0.6625 (OUTLIER) cc_final: 0.6141 (p) REVERT: A 711 LYS cc_start: 0.7426 (mmmt) cc_final: 0.7189 (tppp) REVERT: A 784 PHE cc_start: 0.7501 (t80) cc_final: 0.6909 (t80) REVERT: A 801 MET cc_start: 0.5171 (pmm) cc_final: 0.4357 (mmm) REVERT: A 898 GLU cc_start: 0.8012 (OUTLIER) cc_final: 0.7259 (mt-10) REVERT: A 905 ASP cc_start: 0.8608 (OUTLIER) cc_final: 0.8342 (m-30) REVERT: A 1320 MET cc_start: 0.7581 (mtm) cc_final: 0.7343 (mtp) REVERT: A 1335 MET cc_start: 0.7995 (mmp) cc_final: 0.7710 (mmm) REVERT: A 1422 MET cc_start: 0.8734 (tpp) cc_final: 0.8110 (mmm) REVERT: A 1472 ASN cc_start: 0.8805 (t0) cc_final: 0.8457 (t0) REVERT: A 1499 LYS cc_start: 0.8174 (tmmt) cc_final: 0.7744 (tmmt) REVERT: A 1542 MET cc_start: 0.8778 (ttt) cc_final: 0.8542 (ttp) REVERT: A 1652 MET cc_start: 0.7454 (mmm) cc_final: 0.7166 (mmt) REVERT: A 1671 TYR cc_start: 0.8423 (m-80) cc_final: 0.7988 (m-80) REVERT: A 1772 LEU cc_start: 0.8230 (OUTLIER) cc_final: 0.7922 (mp) outliers start: 50 outliers final: 36 residues processed: 211 average time/residue: 0.0727 time to fit residues: 23.5236 Evaluate side-chains 211 residues out of total 1013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 168 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 148 MET Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 270 GLN Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 378 TYR Chi-restraints excluded: chain A residue 390 MET Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain A residue 700 CYS Chi-restraints excluded: chain A residue 710 VAL Chi-restraints excluded: chain A residue 726 CYS Chi-restraints excluded: chain A residue 783 ILE Chi-restraints excluded: chain A residue 835 SER Chi-restraints excluded: chain A residue 842 LEU Chi-restraints excluded: chain A residue 843 THR Chi-restraints excluded: chain A residue 898 GLU Chi-restraints excluded: chain A residue 905 ASP Chi-restraints excluded: chain A residue 906 CYS Chi-restraints excluded: chain A residue 913 SER Chi-restraints excluded: chain A residue 1206 TRP Chi-restraints excluded: chain A residue 1238 LEU Chi-restraints excluded: chain A residue 1271 TRP Chi-restraints excluded: chain A residue 1272 CYS Chi-restraints excluded: chain A residue 1286 LEU Chi-restraints excluded: chain A residue 1328 VAL Chi-restraints excluded: chain A residue 1338 LEU Chi-restraints excluded: chain A residue 1382 SER Chi-restraints excluded: chain A residue 1396 THR Chi-restraints excluded: chain A residue 1486 PHE Chi-restraints excluded: chain A residue 1602 SER Chi-restraints excluded: chain A residue 1714 ASP Chi-restraints excluded: chain A residue 1761 LEU Chi-restraints excluded: chain A residue 1771 ILE Chi-restraints excluded: chain A residue 1772 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 68 optimal weight: 0.9990 chunk 61 optimal weight: 4.9990 chunk 69 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 114 optimal weight: 4.9990 chunk 113 optimal weight: 0.9990 chunk 40 optimal weight: 0.0570 chunk 77 optimal weight: 4.9990 chunk 94 optimal weight: 0.6980 chunk 36 optimal weight: 6.9990 chunk 56 optimal weight: 4.9990 overall best weight: 0.9504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.171068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.134737 restraints weight = 12816.150| |-----------------------------------------------------------------------------| r_work (start): 0.3650 rms_B_bonded: 2.27 r_work: 0.3504 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3379 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.4016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9671 Z= 0.130 Angle : 0.652 13.451 13155 Z= 0.319 Chirality : 0.042 0.384 1552 Planarity : 0.004 0.056 1578 Dihedral : 5.830 60.685 1591 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.02 % Favored : 95.90 % Rotamer: Outliers : 4.34 % Allowed : 25.96 % Favored : 69.69 % 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: 0.43 (0.25), residues: 1145 helix: 1.24 (0.19), residues: 754 sheet: -2.89 (0.82), residues: 20 loop : -1.51 (0.31), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1316 TYR 0.025 0.002 TYR A1375 PHE 0.025 0.001 PHE A 164 TRP 0.013 0.001 TRP A 156 HIS 0.004 0.001 HIS A 738 Details of bonding type rmsd covalent geometry : bond 0.00283 ( 9657) covalent geometry : angle 0.60657 (13118) SS BOND : bond 0.00936 ( 5) SS BOND : angle 3.05828 ( 10) hydrogen bonds : bond 0.04063 ( 557) hydrogen bonds : angle 4.29485 ( 1605) link_NAG-ASN : bond 0.00942 ( 9) link_NAG-ASN : angle 4.96882 ( 27) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 174 time to evaluate : 0.353 Fit side-chains revert: symmetry clash REVERT: A 132 LEU cc_start: 0.5945 (OUTLIER) cc_final: 0.5701 (tm) REVERT: A 135 MET cc_start: 0.6975 (tpt) cc_final: 0.6747 (mmm) REVERT: A 168 TYR cc_start: 0.8212 (m-80) cc_final: 0.7990 (m-80) REVERT: A 172 SER cc_start: 0.8647 (m) cc_final: 0.8213 (p) REVERT: A 270 GLN cc_start: 0.8559 (OUTLIER) cc_final: 0.7507 (mt0) REVERT: A 375 GLU cc_start: 0.8713 (OUTLIER) cc_final: 0.8416 (pp20) REVERT: A 378 TYR cc_start: 0.8746 (OUTLIER) cc_final: 0.7551 (t80) REVERT: A 417 GLU cc_start: 0.8010 (tm-30) cc_final: 0.7679 (tm-30) REVERT: A 418 GLU cc_start: 0.7654 (tm-30) cc_final: 0.7401 (tm-30) REVERT: A 700 CYS cc_start: 0.6701 (OUTLIER) cc_final: 0.6266 (p) REVERT: A 711 LYS cc_start: 0.7412 (mmmt) cc_final: 0.7182 (tppp) REVERT: A 764 MET cc_start: 0.7086 (tpt) cc_final: 0.6728 (tpt) REVERT: A 784 PHE cc_start: 0.7441 (t80) cc_final: 0.6872 (t80) REVERT: A 801 MET cc_start: 0.5226 (pmm) cc_final: 0.4140 (mmm) REVERT: A 816 PHE cc_start: 0.7489 (m-80) cc_final: 0.7248 (m-80) REVERT: A 905 ASP cc_start: 0.8556 (OUTLIER) cc_final: 0.8293 (m-30) REVERT: A 1196 LYS cc_start: 0.8001 (tppt) cc_final: 0.7556 (pptt) REVERT: A 1335 MET cc_start: 0.7877 (mmp) cc_final: 0.7604 (mmm) REVERT: A 1422 MET cc_start: 0.8690 (tpp) cc_final: 0.8226 (mmm) REVERT: A 1472 ASN cc_start: 0.8764 (t0) cc_final: 0.8416 (t0) REVERT: A 1492 LYS cc_start: 0.7002 (OUTLIER) cc_final: 0.6288 (tptt) REVERT: A 1499 LYS cc_start: 0.8117 (tmmt) cc_final: 0.7694 (tmmt) REVERT: A 1542 MET cc_start: 0.8768 (ttt) cc_final: 0.8531 (ttp) REVERT: A 1652 MET cc_start: 0.7462 (mmm) cc_final: 0.7174 (mmt) REVERT: A 1671 TYR cc_start: 0.8330 (m-80) cc_final: 0.7887 (m-80) REVERT: A 1772 LEU cc_start: 0.8157 (OUTLIER) cc_final: 0.7837 (mp) outliers start: 44 outliers final: 31 residues processed: 206 average time/residue: 0.0769 time to fit residues: 24.3991 Evaluate side-chains 203 residues out of total 1013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 164 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 270 GLN Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 375 GLU Chi-restraints excluded: chain A residue 378 TYR Chi-restraints excluded: chain A residue 390 MET Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain A residue 700 CYS Chi-restraints excluded: chain A residue 710 VAL Chi-restraints excluded: chain A residue 729 LEU Chi-restraints excluded: chain A residue 783 ILE Chi-restraints excluded: chain A residue 835 SER Chi-restraints excluded: chain A residue 842 LEU Chi-restraints excluded: chain A residue 843 THR Chi-restraints excluded: chain A residue 905 ASP Chi-restraints excluded: chain A residue 906 CYS Chi-restraints excluded: chain A residue 913 SER Chi-restraints excluded: chain A residue 1206 TRP Chi-restraints excluded: chain A residue 1238 LEU Chi-restraints excluded: chain A residue 1272 CYS Chi-restraints excluded: chain A residue 1328 VAL Chi-restraints excluded: chain A residue 1338 LEU Chi-restraints excluded: chain A residue 1382 SER Chi-restraints excluded: chain A residue 1396 THR Chi-restraints excluded: chain A residue 1486 PHE Chi-restraints excluded: chain A residue 1492 LYS Chi-restraints excluded: chain A residue 1602 SER Chi-restraints excluded: chain A residue 1714 ASP Chi-restraints excluded: chain A residue 1723 THR Chi-restraints excluded: chain A residue 1761 LEU Chi-restraints excluded: chain A residue 1772 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 75 optimal weight: 10.0000 chunk 29 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 36 optimal weight: 8.9990 chunk 56 optimal weight: 3.9990 chunk 51 optimal weight: 0.6980 chunk 97 optimal weight: 3.9990 chunk 5 optimal weight: 0.9980 chunk 32 optimal weight: 6.9990 chunk 92 optimal weight: 5.9990 chunk 48 optimal weight: 3.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 753 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.167453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.131907 restraints weight = 12921.282| |-----------------------------------------------------------------------------| r_work (start): 0.3617 rms_B_bonded: 2.32 r_work: 0.3457 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3329 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.3993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9671 Z= 0.184 Angle : 0.708 13.917 13155 Z= 0.348 Chirality : 0.045 0.422 1552 Planarity : 0.004 0.055 1578 Dihedral : 6.039 62.683 1589 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.45 % Favored : 95.46 % Rotamer: Outliers : 4.54 % Allowed : 26.46 % Favored : 69.00 % 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: -0.02 (0.25), residues: 1145 helix: 0.94 (0.19), residues: 774 sheet: -3.06 (0.81), residues: 20 loop : -2.00 (0.31), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 340 TYR 0.028 0.002 TYR A1375 PHE 0.025 0.002 PHE A 164 TRP 0.013 0.001 TRP A 899 HIS 0.004 0.001 HIS A 738 Details of bonding type rmsd covalent geometry : bond 0.00429 ( 9657) covalent geometry : angle 0.66239 (13118) SS BOND : bond 0.00696 ( 5) SS BOND : angle 3.34246 ( 10) hydrogen bonds : bond 0.04545 ( 557) hydrogen bonds : angle 4.42826 ( 1605) link_NAG-ASN : bond 0.00880 ( 9) link_NAG-ASN : angle 5.16965 ( 27) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 164 time to evaluate : 0.309 Fit side-chains revert: symmetry clash REVERT: A 132 LEU cc_start: 0.5876 (OUTLIER) cc_final: 0.5629 (tm) REVERT: A 135 MET cc_start: 0.7037 (tpt) cc_final: 0.6811 (mmm) REVERT: A 168 TYR cc_start: 0.8236 (m-80) cc_final: 0.7967 (m-80) REVERT: A 172 SER cc_start: 0.8698 (m) cc_final: 0.8236 (p) REVERT: A 270 GLN cc_start: 0.8595 (OUTLIER) cc_final: 0.7527 (mt0) REVERT: A 375 GLU cc_start: 0.8772 (OUTLIER) cc_final: 0.8485 (pp20) REVERT: A 378 TYR cc_start: 0.8792 (OUTLIER) cc_final: 0.7586 (t80) REVERT: A 417 GLU cc_start: 0.8049 (tm-30) cc_final: 0.7703 (tm-30) REVERT: A 418 GLU cc_start: 0.7608 (tm-30) cc_final: 0.7317 (tm-30) REVERT: A 700 CYS cc_start: 0.6713 (OUTLIER) cc_final: 0.6286 (p) REVERT: A 744 GLU cc_start: 0.5022 (OUTLIER) cc_final: 0.4540 (mt-10) REVERT: A 784 PHE cc_start: 0.7509 (t80) cc_final: 0.6873 (t80) REVERT: A 801 MET cc_start: 0.5315 (pmm) cc_final: 0.4173 (mmm) REVERT: A 816 PHE cc_start: 0.7655 (m-80) cc_final: 0.7422 (m-80) REVERT: A 905 ASP cc_start: 0.8653 (OUTLIER) cc_final: 0.8385 (m-30) REVERT: A 1196 LYS cc_start: 0.7999 (tppt) cc_final: 0.7593 (pptt) REVERT: A 1308 LEU cc_start: 0.8922 (OUTLIER) cc_final: 0.8643 (mt) REVERT: A 1335 MET cc_start: 0.8000 (mmp) cc_final: 0.7751 (mmm) REVERT: A 1422 MET cc_start: 0.8728 (tpp) cc_final: 0.8391 (mmm) REVERT: A 1472 ASN cc_start: 0.8834 (t0) cc_final: 0.8472 (t0) REVERT: A 1492 LYS cc_start: 0.7005 (OUTLIER) cc_final: 0.5928 (tptt) REVERT: A 1499 LYS cc_start: 0.8134 (tmmt) cc_final: 0.7680 (tmmt) REVERT: A 1542 MET cc_start: 0.8721 (ttt) cc_final: 0.8471 (ttp) REVERT: A 1652 MET cc_start: 0.7498 (mmm) cc_final: 0.7137 (mmt) REVERT: A 1772 LEU cc_start: 0.8275 (OUTLIER) cc_final: 0.7945 (mp) REVERT: A 1773 GLU cc_start: 0.8038 (tp30) cc_final: 0.7815 (tp30) outliers start: 46 outliers final: 32 residues processed: 201 average time/residue: 0.0711 time to fit residues: 22.3740 Evaluate side-chains 204 residues out of total 1013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 162 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 270 GLN Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 375 GLU Chi-restraints excluded: chain A residue 378 TYR Chi-restraints excluded: chain A residue 390 MET Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain A residue 700 CYS Chi-restraints excluded: chain A residue 710 VAL Chi-restraints excluded: chain A residue 726 CYS Chi-restraints excluded: chain A residue 729 LEU Chi-restraints excluded: chain A residue 744 GLU Chi-restraints excluded: chain A residue 812 LEU Chi-restraints excluded: chain A residue 835 SER Chi-restraints excluded: chain A residue 842 LEU Chi-restraints excluded: chain A residue 843 THR Chi-restraints excluded: chain A residue 905 ASP Chi-restraints excluded: chain A residue 913 SER Chi-restraints excluded: chain A residue 1206 TRP Chi-restraints excluded: chain A residue 1208 GLU Chi-restraints excluded: chain A residue 1238 LEU Chi-restraints excluded: chain A residue 1271 TRP Chi-restraints excluded: chain A residue 1272 CYS Chi-restraints excluded: chain A residue 1308 LEU Chi-restraints excluded: chain A residue 1328 VAL Chi-restraints excluded: chain A residue 1338 LEU Chi-restraints excluded: chain A residue 1382 SER Chi-restraints excluded: chain A residue 1396 THR Chi-restraints excluded: chain A residue 1486 PHE Chi-restraints excluded: chain A residue 1492 LYS Chi-restraints excluded: chain A residue 1602 SER Chi-restraints excluded: chain A residue 1714 ASP Chi-restraints excluded: chain A residue 1723 THR Chi-restraints excluded: chain A residue 1771 ILE Chi-restraints excluded: chain A residue 1772 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 52 optimal weight: 0.6980 chunk 90 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 49 optimal weight: 0.0050 chunk 57 optimal weight: 2.9990 chunk 22 optimal weight: 0.6980 chunk 104 optimal weight: 3.9990 chunk 107 optimal weight: 0.7980 overall best weight: 0.8396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 803 ASN ** 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 = 0.4079 r_free = 0.4079 target = 0.171710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.135355 restraints weight = 12683.114| |-----------------------------------------------------------------------------| r_work (start): 0.3656 rms_B_bonded: 2.30 r_work: 0.3514 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3389 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.4186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9671 Z= 0.126 Angle : 0.648 13.258 13155 Z= 0.316 Chirality : 0.042 0.382 1552 Planarity : 0.004 0.053 1578 Dihedral : 5.703 61.010 1588 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.45 % Favored : 95.46 % Rotamer: Outliers : 3.65 % Allowed : 27.54 % Favored : 68.81 % 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: 0.36 (0.25), residues: 1145 helix: 1.25 (0.19), residues: 754 sheet: -3.06 (0.79), residues: 20 loop : -1.70 (0.31), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 340 TYR 0.023 0.002 TYR A1375 PHE 0.016 0.001 PHE A1530 TRP 0.015 0.001 TRP A 899 HIS 0.004 0.001 HIS A 738 Details of bonding type rmsd covalent geometry : bond 0.00274 ( 9657) covalent geometry : angle 0.60488 (13118) SS BOND : bond 0.00549 ( 5) SS BOND : angle 2.56444 ( 10) hydrogen bonds : bond 0.03967 ( 557) hydrogen bonds : angle 4.25293 ( 1605) link_NAG-ASN : bond 0.00956 ( 9) link_NAG-ASN : angle 4.94896 ( 27) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2744.30 seconds wall clock time: 47 minutes 40.10 seconds (2860.10 seconds total)