Starting phenix.real_space_refine on Fri Sep 11 12:12:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6kzp_0792/09_2026/6kzp_0792.cif Found real_map, /net/cci-nas-00/data/ceres_data/6kzp_0792/09_2026/6kzp_0792.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6kzp_0792/09_2026/6kzp_0792.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6kzp_0792/09_2026/6kzp_0792.map" model { file = "/net/cci-nas-00/data/ceres_data/6kzp_0792/09_2026/6kzp_0792.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6kzp_0792/09_2026/6kzp_0792.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6kzp_0792/09_2026/6kzp_0792.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6kzp_0792/09_2026/6kzp_0792.cif" } resolution = 3.1 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: 8 Type Number sf(0) Gaussians Ca 2 9.91 5 P 5 5.49 5 S 65 5.16 5 Cl 1 4.86 5 C 5694 2.51 5 N 1336 2.21 5 O 1453 1.98 5 F 1 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8557 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 8159 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1014, 8159 Classifications: {'peptide': 1014} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 28, 'TRANS': 985} Chain breaks: 10 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "A" Number of atoms: 398 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 398 Unusual residues: {' CA': 2, '3PE': 8, 'DZR': 1, 'NAG': 4, 'Y01': 3} Classifications: {'undetermined': 18} Link IDs: {None: 17} Unresolved non-hydrogen bonds: 203 Unresolved non-hydrogen angles: 225 Unresolved non-hydrogen dihedrals: 166 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'3PE:plan-1': 3, '3PE:plan-2': 3} Unresolved non-hydrogen planarities: 22 Time building chain proxies: 1.85, per 1000 atoms: 0.22 Number of scatterers: 8557 At special positions: 0 Unit cell: (108.009, 121.101, 104.736, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Ca 2 19.99 Cl 1 17.00 S 65 16.00 P 5 15.00 F 1 9.00 O 1453 8.00 N 1336 7.00 C 5694 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 241 " - pdb=" SG CYS A 282 " distance=2.04 Simple disulfide: pdb=" SG CYS A 271 " - pdb=" SG CYS A 323 " distance=2.03 Simple disulfide: pdb=" SG CYS A1418 " - pdb=" SG CYS A1432 " distance=2.03 Simple disulfide: pdb=" SG CYS A1747 " - pdb=" SG CYS A1753 " distance=2.02 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 A2303 " - " ASN A 246 " " NAG A2304 " - " ASN A 322 " " NAG A2305 " - " ASN A1425 " " NAG A2306 " - " ASN A1428 " Time building additional restraints: 0.71 Conformation dependent library (CDL) restraints added in 238.9 milliseconds 1984 Ramachandran restraints generated. 992 Oldfield, 0 Emsley, 992 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1924 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 2 sheets defined 78.6% alpha, 1.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 Creating SS restraints... Processing helix chain 'A' and resid 80 through 100 removed outlier: 3.971A pdb=" N GLU A 84 " --> pdb=" O ASN A 80 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ARG A 85 " --> pdb=" O PRO A 81 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N MET A 88 " --> pdb=" O GLU A 84 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU A 89 " --> pdb=" O ARG A 85 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N VAL A 90 " --> pdb=" O ILE A 86 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N MET A 100 " --> pdb=" O VAL A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 136 Processing helix chain 'A' and resid 151 through 172 removed outlier: 3.853A pdb=" N VAL A 160 " --> pdb=" O ASP A 156 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLU A 166 " --> pdb=" O ALA A 162 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU A 171 " --> pdb=" O TYR A 167 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N GLN A 172 " --> pdb=" O SER A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 188 Proline residue: A 187 - end of helix Processing helix chain 'A' and resid 189 through 194 removed outlier: 3.674A pdb=" N ARG A 193 " --> pdb=" O ARG A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 208 removed outlier: 3.737A pdb=" N ILE A 199 " --> pdb=" O PRO A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 234 removed outlier: 3.607A pdb=" N LEU A 215 " --> pdb=" O LEU A 211 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N PHE A 220 " --> pdb=" O LEU A 216 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLY A 229 " --> pdb=" O PHE A 225 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ALA A 234 " --> pdb=" O VAL A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 285 removed outlier: 3.938A pdb=" N VAL A 285 " --> pdb=" O CYS A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 320 removed outlier: 4.187A pdb=" N GLN A 318 " --> pdb=" O ASN A 315 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N TYR A 320 " --> pdb=" O ASN A 317 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 334 Processing helix chain 'A' and resid 339 through 352 removed outlier: 3.507A pdb=" N TRP A 344 " --> pdb=" O ILE A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 367 removed outlier: 3.781A pdb=" N ILE A 359 " --> pdb=" O GLY A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 370 No H-bonds generated for 'chain 'A' and resid 368 through 370' Processing helix chain 'A' and resid 371 through 382 removed outlier: 3.743A pdb=" N PHE A 375 " --> pdb=" O ASN A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 405 removed outlier: 3.604A pdb=" N LEU A 391 " --> pdb=" O ILE A 387 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE A 394 " --> pdb=" O CYS A 390 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N SER A 399 " --> pdb=" O ALA A 395 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLN A 403 " --> pdb=" O SER A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 743 through 761 removed outlier: 3.556A pdb=" N MET A 750 " --> pdb=" O GLY A 746 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE A 751 " --> pdb=" O ARG A 747 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LEU A 754 " --> pdb=" O MET A 750 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ASN A 756 " --> pdb=" O ALA A 752 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N MET A 760 " --> pdb=" O ASN A 756 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLY A 761 " --> pdb=" O THR A 757 " (cutoff:3.500A) Processing helix chain 'A' and resid 769 through 796 removed outlier: 3.546A pdb=" N LEU A 795 " --> pdb=" O LEU A 791 " (cutoff:3.500A) Processing helix chain 'A' and resid 798 through 803 removed outlier: 3.525A pdb=" N ILE A 803 " --> pdb=" O PRO A 799 " (cutoff:3.500A) Processing helix chain 'A' and resid 805 through 823 removed outlier: 3.841A pdb=" N ILE A 809 " --> pdb=" O ASN A 805 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N PHE A 810 " --> pdb=" O PRO A 806 " (cutoff:3.500A) Processing helix chain 'A' and resid 832 through 836 removed outlier: 3.619A pdb=" N PHE A 836 " --> pdb=" O VAL A 832 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 832 through 836' Processing helix chain 'A' and resid 837 through 845 removed outlier: 3.538A pdb=" N ARG A 840 " --> pdb=" O ARG A 837 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU A 844 " --> pdb=" O VAL A 841 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N VAL A 845 " --> pdb=" O LEU A 842 " (cutoff:3.500A) Processing helix chain 'A' and resid 849 through 865 removed outlier: 3.593A pdb=" N MET A 859 " --> pdb=" O LEU A 855 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N MET A 862 " --> pdb=" O LEU A 858 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ASP A 863 " --> pdb=" O MET A 859 " (cutoff:3.500A) Processing helix chain 'A' and resid 865 through 887 removed outlier: 3.532A pdb=" N LEU A 871 " --> pdb=" O THR A 867 " (cutoff:3.500A) Processing helix chain 'A' and resid 909 through 921 removed outlier: 3.643A pdb=" N THR A 915 " --> pdb=" O TRP A 911 " (cutoff:3.500A) Processing helix chain 'A' and resid 924 through 936 removed outlier: 3.708A pdb=" N VAL A 928 " --> pdb=" O ASP A 924 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASN A 931 " --> pdb=" O LYS A 927 " (cutoff:3.500A) Processing helix chain 'A' and resid 937 through 939 No H-bonds generated for 'chain 'A' and resid 937 through 939' Processing helix chain 'A' and resid 940 through 953 removed outlier: 4.223A pdb=" N PHE A 944 " --> pdb=" O ALA A 940 " (cutoff:3.500A) Processing helix chain 'A' and resid 954 through 968 removed outlier: 3.717A pdb=" N LEU A 959 " --> pdb=" O LEU A 955 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLN A 968 " --> pdb=" O VAL A 964 " (cutoff:3.500A) Processing helix chain 'A' and resid 1243 through 1252 removed outlier: 3.605A pdb=" N ARG A1248 " --> pdb=" O LEU A1244 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ILE A1249 " --> pdb=" O LEU A1245 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ILE A1250 " --> pdb=" O CYS A1246 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N THR A1251 " --> pdb=" O HIS A1247 " (cutoff:3.500A) Processing helix chain 'A' and resid 1252 through 1272 removed outlier: 4.135A pdb=" N ASP A1256 " --> pdb=" O HIS A1252 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N HIS A1257 " --> pdb=" O LYS A1253 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N VAL A1259 " --> pdb=" O PHE A1255 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N LEU A1260 " --> pdb=" O ASP A1256 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE A1268 " --> pdb=" O PHE A1264 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N THR A1269 " --> pdb=" O LEU A1265 " (cutoff:3.500A) Processing helix chain 'A' and resid 1283 through 1309 removed outlier: 3.612A pdb=" N ASN A1291 " --> pdb=" O LEU A1287 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N TYR A1292 " --> pdb=" O THR A1288 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N VAL A1297 " --> pdb=" O ILE A1293 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N LYS A1305 " --> pdb=" O GLU A1301 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N VAL A1307 " --> pdb=" O THR A1303 " (cutoff:3.500A) Processing helix chain 'A' and resid 1322 through 1344 removed outlier: 3.503A pdb=" N VAL A1331 " --> pdb=" O ASP A1327 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ILE A1336 " --> pdb=" O LEU A1332 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ILE A1338 " --> pdb=" O SER A1334 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N SER A1344 " --> pdb=" O VAL A1340 " (cutoff:3.500A) Processing helix chain 'A' and resid 1350 through 1362 removed outlier: 3.895A pdb=" N VAL A1356 " --> pdb=" O GLY A1352 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N LEU A1357 " --> pdb=" O MET A1353 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU A1359 " --> pdb=" O ARG A1355 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N THR A1362 " --> pdb=" O ARG A1358 " (cutoff:3.500A) Processing helix chain 'A' and resid 1363 through 1366 Processing helix chain 'A' and resid 1367 through 1372 removed outlier: 3.954A pdb=" N ARG A1371 " --> pdb=" O ARG A1367 " (cutoff:3.500A) Processing helix chain 'A' and resid 1372 through 1386 removed outlier: 3.658A pdb=" N VAL A1378 " --> pdb=" O GLY A1374 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU A1386 " --> pdb=" O LEU A1382 " (cutoff:3.500A) Processing helix chain 'A' and resid 1389 through 1412 removed outlier: 3.690A pdb=" N ILE A1401 " --> pdb=" O CYS A1397 " (cutoff:3.500A) Processing helix chain 'A' and resid 1428 through 1436 removed outlier: 3.809A pdb=" N CYS A1432 " --> pdb=" O ASN A1428 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ALA A1433 " --> pdb=" O LYS A1429 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA A1435 " --> pdb=" O ASP A1431 " (cutoff:3.500A) Processing helix chain 'A' and resid 1448 through 1461 removed outlier: 3.720A pdb=" N MET A1454 " --> pdb=" O GLY A1450 " (cutoff:3.500A) Processing helix chain 'A' and resid 1464 through 1475 removed outlier: 3.887A pdb=" N ILE A1468 " --> pdb=" O GLY A1464 " (cutoff:3.500A) Processing helix chain 'A' and resid 1487 through 1489 No H-bonds generated for 'chain 'A' and resid 1487 through 1489' Processing helix chain 'A' and resid 1490 through 1518 removed outlier: 3.709A pdb=" N SER A1496 " --> pdb=" O LEU A1492 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLU A1515 " --> pdb=" O GLY A1511 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N HIS A1518 " --> pdb=" O VAL A1514 " (cutoff:3.500A) Processing helix chain 'A' and resid 1590 through 1607 removed outlier: 3.687A pdb=" N GLY A1596 " --> pdb=" O LEU A1592 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N VAL A1603 " --> pdb=" O GLY A1599 " (cutoff:3.500A) Processing helix chain 'A' and resid 1613 through 1643 removed outlier: 3.513A pdb=" N LEU A1620 " --> pdb=" O LEU A1616 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LYS A1621 " --> pdb=" O ASP A1617 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N THR A1628 " --> pdb=" O ASN A1624 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL A1629 " --> pdb=" O TYR A1625 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ILE A1630 " --> pdb=" O ILE A1626 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLU A1634 " --> pdb=" O ILE A1630 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ALA A1641 " --> pdb=" O PHE A1637 " (cutoff:3.500A) Processing helix chain 'A' and resid 1645 through 1650 removed outlier: 3.553A pdb=" N ASP A1650 " --> pdb=" O ARG A1646 " (cutoff:3.500A) Processing helix chain 'A' and resid 1651 through 1668 removed outlier: 3.647A pdb=" N ALA A1658 " --> pdb=" O GLN A1654 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N THR A1668 " --> pdb=" O ILE A1664 " (cutoff:3.500A) Processing helix chain 'A' and resid 1669 through 1676 removed outlier: 3.919A pdb=" N GLU A1673 " --> pdb=" O LEU A1669 " (cutoff:3.500A) Processing helix chain 'A' and resid 1681 through 1692 removed outlier: 3.894A pdb=" N ILE A1685 " --> pdb=" O ASN A1681 " (cutoff:3.500A) Processing helix chain 'A' and resid 1693 through 1700 removed outlier: 3.514A pdb=" N VAL A1696 " --> pdb=" O ILE A1693 " (cutoff:3.500A) Processing helix chain 'A' and resid 1703 through 1716 removed outlier: 3.597A pdb=" N ALA A1708 " --> pdb=" O VAL A1704 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU A1709 " --> pdb=" O GLY A1705 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N THR A1712 " --> pdb=" O ALA A1708 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N VAL A1713 " --> pdb=" O LEU A1709 " (cutoff:3.500A) Processing helix chain 'A' and resid 1716 through 1743 Processing helix chain 'A' and resid 1764 through 1777 Processing helix chain 'A' and resid 1780 through 1789 removed outlier: 3.746A pdb=" N ILE A1784 " --> pdb=" O ASN A1780 " (cutoff:3.500A) Processing helix chain 'A' and resid 1800 through 1832 Proline residue: A1805 - end of helix removed outlier: 3.588A pdb=" N PHE A1817 " --> pdb=" O LEU A1813 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LYS A1829 " --> pdb=" O ALA A1825 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 239 through 242 Processing sheet with id=AA2, first strand: chain 'A' and resid 1416 through 1419 removed outlier: 3.523A pdb=" N ARG A1438 " --> pdb=" O GLN A1419 " (cutoff:3.500A) 485 hydrogen bonds defined for protein. 1407 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: 1.53 Time building geometry restraints manager: 0.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1286 1.31 - 1.43: 2335 1.43 - 1.56: 4958 1.56 - 1.69: 43 1.69 - 1.82: 113 Bond restraints: 8735 Sorted by residual: bond pdb=" CAI Y01 A2317 " pdb=" CAZ Y01 A2317 " ideal model delta sigma weight residual 1.332 1.689 -0.357 2.00e-02 2.50e+03 3.18e+02 bond pdb=" CAI Y01 A2318 " pdb=" CAZ Y01 A2318 " ideal model delta sigma weight residual 1.332 1.688 -0.356 2.00e-02 2.50e+03 3.16e+02 bond pdb=" CAI Y01 A2316 " pdb=" CAZ Y01 A2316 " ideal model delta sigma weight residual 1.332 1.682 -0.350 2.00e-02 2.50e+03 3.07e+02 bond pdb=" CAP Y01 A2317 " pdb=" CAQ Y01 A2317 " ideal model delta sigma weight residual 1.541 1.728 -0.187 2.00e-02 2.50e+03 8.72e+01 bond pdb=" CAP Y01 A2318 " pdb=" CAQ Y01 A2318 " ideal model delta sigma weight residual 1.541 1.726 -0.185 2.00e-02 2.50e+03 8.57e+01 ... (remaining 8730 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.79: 11619 4.79 - 9.57: 171 9.57 - 14.36: 11 14.36 - 19.14: 0 19.14 - 23.93: 5 Bond angle restraints: 11806 Sorted by residual: angle pdb=" O12 3PE A2308 " pdb=" P 3PE A2308 " pdb=" O14 3PE A2308 " ideal model delta sigma weight residual 123.79 99.86 23.93 3.00e+00 1.11e-01 6.36e+01 angle pdb=" O12 3PE A2315 " pdb=" P 3PE A2315 " pdb=" O14 3PE A2315 " ideal model delta sigma weight residual 123.79 100.79 23.00 3.00e+00 1.11e-01 5.88e+01 angle pdb=" O12 3PE A2311 " pdb=" P 3PE A2311 " pdb=" O14 3PE A2311 " ideal model delta sigma weight residual 123.79 101.04 22.75 3.00e+00 1.11e-01 5.75e+01 angle pdb=" O12 3PE A2313 " pdb=" P 3PE A2313 " pdb=" O14 3PE A2313 " ideal model delta sigma weight residual 123.79 101.05 22.74 3.00e+00 1.11e-01 5.74e+01 angle pdb=" O12 3PE A2309 " pdb=" P 3PE A2309 " pdb=" O14 3PE A2309 " ideal model delta sigma weight residual 123.79 101.99 21.80 3.00e+00 1.11e-01 5.28e+01 ... (remaining 11801 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.82: 4766 21.82 - 43.64: 255 43.64 - 65.45: 55 65.45 - 87.27: 7 87.27 - 109.09: 4 Dihedral angle restraints: 5087 sinusoidal: 2133 harmonic: 2954 Sorted by residual: dihedral pdb=" CB CYS A1418 " pdb=" SG CYS A1418 " pdb=" SG CYS A1432 " pdb=" CB CYS A1432 " ideal model delta sinusoidal sigma weight residual -86.00 -152.47 66.47 1 1.00e+01 1.00e-02 5.77e+01 dihedral pdb=" N GLU A 769 " pdb=" C GLU A 769 " pdb=" CA GLU A 769 " pdb=" CB GLU A 769 " ideal model delta harmonic sigma weight residual 122.80 135.02 -12.22 0 2.50e+00 1.60e-01 2.39e+01 dihedral pdb=" CA ASP A 907 " pdb=" C ASP A 907 " pdb=" N SER A 908 " pdb=" CA SER A 908 " ideal model delta harmonic sigma weight residual 180.00 156.64 23.36 0 5.00e+00 4.00e-02 2.18e+01 ... (remaining 5084 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.143: 1325 0.143 - 0.285: 42 0.285 - 0.428: 13 0.428 - 0.570: 0 0.570 - 0.713: 3 Chirality restraints: 1383 Sorted by residual: chirality pdb=" CBI Y01 A2317 " pdb=" CAU Y01 A2317 " pdb=" CBE Y01 A2317 " pdb=" CBG Y01 A2317 " both_signs ideal model delta sigma weight residual False 2.94 2.22 0.71 2.00e-01 2.50e+01 1.27e+01 chirality pdb=" CBI Y01 A2318 " pdb=" CAU Y01 A2318 " pdb=" CBE Y01 A2318 " pdb=" CBG Y01 A2318 " both_signs ideal model delta sigma weight residual False 2.94 2.30 0.64 2.00e-01 2.50e+01 1.01e+01 chirality pdb=" CBI Y01 A2316 " pdb=" CAU Y01 A2316 " pdb=" CBE Y01 A2316 " pdb=" CBG Y01 A2316 " both_signs ideal model delta sigma weight residual False 2.94 2.30 0.63 2.00e-01 2.50e+01 1.01e+01 ... (remaining 1380 not shown) Planarity restraints: 1418 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS A1387 " -0.067 5.00e-02 4.00e+02 1.02e-01 1.65e+01 pdb=" N PRO A1388 " 0.176 5.00e-02 4.00e+02 pdb=" CA PRO A1388 " -0.055 5.00e-02 4.00e+02 pdb=" CD PRO A1388 " -0.054 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A1717 " -0.066 5.00e-02 4.00e+02 1.00e-01 1.61e+01 pdb=" N PRO A1718 " 0.174 5.00e-02 4.00e+02 pdb=" CA PRO A1718 " -0.054 5.00e-02 4.00e+02 pdb=" CD PRO A1718 " -0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG A1364 " -0.057 5.00e-02 4.00e+02 8.67e-02 1.20e+01 pdb=" N PRO A1365 " 0.150 5.00e-02 4.00e+02 pdb=" CA PRO A1365 " -0.048 5.00e-02 4.00e+02 pdb=" CD PRO A1365 " -0.045 5.00e-02 4.00e+02 ... (remaining 1415 not shown) Histogram of nonbonded interaction distances: 2.39 - 2.89: 3114 2.89 - 3.39: 8267 3.39 - 3.90: 13070 3.90 - 4.40: 15585 4.40 - 4.90: 25812 Nonbonded interactions: 65848 Sorted by model distance: nonbonded pdb=" O PHE A1403 " pdb=" OH TYR A1493 " model vdw 2.390 3.040 nonbonded pdb=" O SER A1810 " pdb=" OG1 THR A1814 " model vdw 2.430 3.040 nonbonded pdb=" O21 3PE A2311 " pdb=" O31 3PE A2311 " model vdw 2.443 2.432 nonbonded pdb=" O5 NAG A2304 " pdb=" O6 NAG A2304 " model vdw 2.446 2.432 nonbonded pdb=" C12 DZR A2307 " pdb=" O14 3PE A2313 " model vdw 2.458 3.440 ... (remaining 65843 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 8.720 Find NCS groups from input model: 0.040 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: 0.010 Load rotamer database and sin/cos tables:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 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 : 0.013 0.357 8743 Z= 0.650 Angle : 1.457 23.926 11826 Z= 0.706 Chirality : 0.077 0.713 1383 Planarity : 0.009 0.102 1414 Dihedral : 14.131 109.089 3151 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.30 % Allowed : 3.33 % Favored : 96.37 % Rotamer: Outliers : 2.44 % Allowed : 6.87 % Favored : 90.69 % Cbeta Deviations : 0.10 % 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: -4.53 (0.21), residues: 992 helix: -3.17 (0.15), residues: 694 sheet: -4.04 (1.35), residues: 12 loop : -1.83 (0.31), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A1441 TYR 0.029 0.004 TYR A 320 PHE 0.046 0.004 PHE A1403 TRP 0.034 0.004 TRP A 233 HIS 0.009 0.002 HIS A 765 Details of bonding type rmsd/Z covalent geometry : bond 0.01327 / 0.65 ( 8735) covalent geometry : angle 1.45373 / 0.71 (11806) SS BOND : bond 0.00577 / 0.29 ( 4) SS BOND : angle 2.36643 / 2.06 ( 8) hydrogen bonds : bond 0.31391 / 20.50 ( 485) hydrogen bonds : angle 9.68840 / 6.83 ( 1407) link_NAG-ASN : bond 0.00830 / 0.43 ( 4) link_NAG-ASN : angle 2.92919 / 2.21 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1984 Ramachandran restraints generated. 992 Oldfield, 0 Emsley, 992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1984 Ramachandran restraints generated. 992 Oldfield, 0 Emsley, 992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 225 time to evaluate : 0.298 Fit side-chains REVERT: A 85 ARG cc_start: 0.7488 (mtt90) cc_final: 0.6958 (mtm180) REVERT: A 92 LEU cc_start: 0.7718 (mm) cc_final: 0.7331 (mp) REVERT: A 118 GLN cc_start: 0.7981 (tt0) cc_final: 0.7134 (tp40) REVERT: A 122 ASP cc_start: 0.5882 (m-30) cc_final: 0.5528 (m-30) REVERT: A 128 PHE cc_start: 0.7973 (m-80) cc_final: 0.7764 (m-10) REVERT: A 183 ARG cc_start: 0.7343 (ptt180) cc_final: 0.7106 (ptt90) REVERT: A 213 ASN cc_start: 0.8189 (m-40) cc_final: 0.7963 (m-40) REVERT: A 263 ASN cc_start: 0.7574 (p0) cc_final: 0.7064 (p0) REVERT: A 835 THR cc_start: 0.8265 (m) cc_final: 0.7917 (p) REVERT: A 859 MET cc_start: 0.6816 (mmt) cc_final: 0.6366 (ptp) REVERT: A 884 MET cc_start: 0.8700 (mtp) cc_final: 0.8477 (mtp) REVERT: A 1243 ARG cc_start: 0.7632 (ttt-90) cc_final: 0.7379 (ttt-90) REVERT: A 1383 MET cc_start: 0.7876 (mmt) cc_final: 0.7586 (mmm) REVERT: A 1651 ARG cc_start: 0.6399 (tpp-160) cc_final: 0.5771 (ttp-170) REVERT: A 1719 GLN cc_start: 0.7512 (tp40) cc_final: 0.7166 (tm-30) REVERT: A 1725 LEU cc_start: 0.8218 (tt) cc_final: 0.7831 (mt) outliers start: 22 outliers final: 10 residues processed: 240 average time/residue: 0.0969 time to fit residues: 31.0935 Evaluate side-chains 178 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 168 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 809 ILE Chi-restraints excluded: chain A residue 1350 ILE Chi-restraints excluded: chain A residue 1366 LEU Chi-restraints excluded: chain A residue 1381 THR Chi-restraints excluded: chain A residue 1476 VAL Chi-restraints excluded: chain A residue 1630 ILE Chi-restraints excluded: chain A residue 1687 ILE Chi-restraints excluded: chain A residue 1789 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 0.7980 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.5980 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 6.9990 chunk 100 optimal weight: 0.5980 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 0.6980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 80 ASN ** A 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 805 ASN A 864 ASN A 918 GLN A 957 ASN A1252 HIS A1391 ASN A1624 ASN A1649 GLN A1675 ASN A1681 ASN A1722 ASN A1751 HIS A1780 ASN A1821 ASN A1835 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.154930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.120613 restraints weight = 10669.017| |-----------------------------------------------------------------------------| r_work (start): 0.3193 rms_B_bonded: 1.64 r_work: 0.3011 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2883 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.2617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8743 Z= 0.146 Angle : 0.675 9.547 11826 Z= 0.332 Chirality : 0.043 0.284 1383 Planarity : 0.006 0.074 1414 Dihedral : 12.222 109.414 1276 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 3.10 % Allowed : 11.20 % Favored : 85.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.17 (0.23), residues: 992 helix: -1.09 (0.17), residues: 735 sheet: -3.41 (1.41), residues: 12 loop : -1.89 (0.33), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A1645 TYR 0.017 0.002 TYR A1437 PHE 0.015 0.002 PHE A 868 TRP 0.011 0.001 TRP A 911 HIS 0.003 0.001 HIS A1751 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.15 ( 8735) covalent geometry : angle 0.67073 / 0.33 (11806) SS BOND : bond 0.00277 / 0.14 ( 4) SS BOND : angle 1.21385 / 0.89 ( 8) hydrogen bonds : bond 0.05870 / 3.77 ( 485) hydrogen bonds : angle 4.75141 / 3.26 ( 1407) link_NAG-ASN : bond 0.00415 / 0.22 ( 4) link_NAG-ASN : angle 2.31827 / 1.65 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1984 Ramachandran restraints generated. 992 Oldfield, 0 Emsley, 992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1984 Ramachandran restraints generated. 992 Oldfield, 0 Emsley, 992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 189 time to evaluate : 0.317 Fit side-chains REVERT: A 85 ARG cc_start: 0.7855 (mtt90) cc_final: 0.7074 (mtm180) REVERT: A 92 LEU cc_start: 0.7423 (mm) cc_final: 0.7192 (mp) REVERT: A 118 GLN cc_start: 0.8025 (tt0) cc_final: 0.6960 (tp-100) REVERT: A 122 ASP cc_start: 0.6032 (m-30) cc_final: 0.5675 (m-30) REVERT: A 156 ASP cc_start: 0.8064 (t0) cc_final: 0.7741 (m-30) REVERT: A 183 ARG cc_start: 0.7728 (ptt180) cc_final: 0.7481 (ptt90) REVERT: A 251 LEU cc_start: 0.7412 (OUTLIER) cc_final: 0.7150 (mt) REVERT: A 808 ASN cc_start: 0.8164 (m-40) cc_final: 0.7068 (m110) REVERT: A 835 THR cc_start: 0.8629 (m) cc_final: 0.8292 (p) REVERT: A 844 LEU cc_start: 0.7984 (OUTLIER) cc_final: 0.7770 (mm) REVERT: A 859 MET cc_start: 0.6886 (mmt) cc_final: 0.5948 (ptp) REVERT: A 1243 ARG cc_start: 0.7180 (ttt-90) cc_final: 0.6929 (ttt-90) REVERT: A 1283 GLU cc_start: 0.7871 (tt0) cc_final: 0.7504 (tt0) REVERT: A 1349 LYS cc_start: 0.3834 (tptt) cc_final: 0.3563 (tptt) REVERT: A 1353 MET cc_start: 0.7987 (tmm) cc_final: 0.7446 (tpp) REVERT: A 1383 MET cc_start: 0.8268 (mmt) cc_final: 0.7798 (mmm) REVERT: A 1431 ASP cc_start: 0.8026 (t0) cc_final: 0.7695 (t0) REVERT: A 1645 ARG cc_start: 0.7351 (ttt90) cc_final: 0.6734 (tpm170) REVERT: A 1651 ARG cc_start: 0.6182 (tpp-160) cc_final: 0.5158 (ttt180) REVERT: A 1689 ARG cc_start: 0.7540 (tpp80) cc_final: 0.6836 (ttp80) REVERT: A 1789 LEU cc_start: 0.8646 (OUTLIER) cc_final: 0.8441 (pp) REVERT: A 1828 MET cc_start: 0.8041 (OUTLIER) cc_final: 0.7785 (mmm) outliers start: 28 outliers final: 14 residues processed: 207 average time/residue: 0.0942 time to fit residues: 26.5017 Evaluate side-chains 180 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 162 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 809 ILE Chi-restraints excluded: chain A residue 844 LEU Chi-restraints excluded: chain A residue 867 THR Chi-restraints excluded: chain A residue 872 LEU Chi-restraints excluded: chain A residue 1297 VAL Chi-restraints excluded: chain A residue 1337 ASP Chi-restraints excluded: chain A residue 1476 VAL Chi-restraints excluded: chain A residue 1501 VAL Chi-restraints excluded: chain A residue 1630 ILE Chi-restraints excluded: chain A residue 1632 VAL Chi-restraints excluded: chain A residue 1687 ILE Chi-restraints excluded: chain A residue 1789 LEU Chi-restraints excluded: chain A residue 1828 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 37 optimal weight: 0.0970 chunk 38 optimal weight: 0.2980 chunk 90 optimal weight: 0.5980 chunk 4 optimal weight: 2.9990 chunk 21 optimal weight: 4.9990 chunk 13 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 36 optimal weight: 3.9990 chunk 58 optimal weight: 0.9980 chunk 84 optimal weight: 3.9990 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 231 GLN A 371 ASN A1719 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.155801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.122049 restraints weight = 10463.584| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 1.58 r_work: 0.3020 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2888 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.3185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8743 Z= 0.121 Angle : 0.610 9.533 11826 Z= 0.292 Chirality : 0.043 0.512 1383 Planarity : 0.005 0.065 1414 Dihedral : 10.855 107.934 1269 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 3.22 % Allowed : 13.19 % Favored : 83.59 % 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: -0.46 (0.25), residues: 992 helix: 0.26 (0.19), residues: 738 sheet: -2.89 (1.47), residues: 12 loop : -1.69 (0.35), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 283 TYR 0.013 0.001 TYR A1437 PHE 0.014 0.001 PHE A 868 TRP 0.008 0.001 TRP A 152 HIS 0.001 0.000 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 ( 8735) covalent geometry : angle 0.60564 / 0.29 (11806) SS BOND : bond 0.00263 / 0.13 ( 4) SS BOND : angle 0.97774 / 0.72 ( 8) hydrogen bonds : bond 0.04401 / 2.83 ( 485) hydrogen bonds : angle 4.17002 / 2.86 ( 1407) link_NAG-ASN : bond 0.00935 / 0.49 ( 4) link_NAG-ASN : angle 2.16380 / 1.64 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1984 Ramachandran restraints generated. 992 Oldfield, 0 Emsley, 992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1984 Ramachandran restraints generated. 992 Oldfield, 0 Emsley, 992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 171 time to evaluate : 0.351 Fit side-chains REVERT: A 85 ARG cc_start: 0.7811 (mtt90) cc_final: 0.6959 (mtm180) REVERT: A 92 LEU cc_start: 0.7273 (mm) cc_final: 0.7048 (mp) REVERT: A 122 ASP cc_start: 0.6074 (m-30) cc_final: 0.5692 (m-30) REVERT: A 216 LEU cc_start: 0.8619 (OUTLIER) cc_final: 0.8161 (tt) REVERT: A 231 GLN cc_start: 0.8817 (mm110) cc_final: 0.8603 (mm-40) REVERT: A 246 ASN cc_start: 0.7111 (m110) cc_final: 0.6874 (m-40) REVERT: A 251 LEU cc_start: 0.7414 (OUTLIER) cc_final: 0.7141 (mt) REVERT: A 275 ARG cc_start: 0.7105 (mtp85) cc_final: 0.6848 (mtm-85) REVERT: A 400 GLU cc_start: 0.7805 (tp30) cc_final: 0.7297 (tt0) REVERT: A 808 ASN cc_start: 0.8108 (m-40) cc_final: 0.7018 (m110) REVERT: A 848 LEU cc_start: 0.7325 (OUTLIER) cc_final: 0.7015 (pp) REVERT: A 859 MET cc_start: 0.6802 (mmt) cc_final: 0.5875 (ptp) REVERT: A 1243 ARG cc_start: 0.6967 (ttt-90) cc_final: 0.6730 (ttt-90) REVERT: A 1283 GLU cc_start: 0.7755 (tt0) cc_final: 0.7515 (tt0) REVERT: A 1353 MET cc_start: 0.7816 (tmm) cc_final: 0.7394 (tpp) REVERT: A 1355 ARG cc_start: 0.6498 (mtm180) cc_final: 0.6248 (mtm180) REVERT: A 1389 ILE cc_start: 0.8237 (OUTLIER) cc_final: 0.7842 (pp) REVERT: A 1651 ARG cc_start: 0.6327 (tpp-160) cc_final: 0.5230 (tmm160) REVERT: A 1689 ARG cc_start: 0.7540 (tpp80) cc_final: 0.6829 (ttp80) REVERT: A 1692 ARG cc_start: 0.8202 (ttm170) cc_final: 0.8002 (ttm170) outliers start: 29 outliers final: 14 residues processed: 189 average time/residue: 0.1065 time to fit residues: 26.9494 Evaluate side-chains 179 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 161 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 751 ILE Chi-restraints excluded: chain A residue 757 THR Chi-restraints excluded: chain A residue 848 LEU Chi-restraints excluded: chain A residue 867 THR Chi-restraints excluded: chain A residue 1254 MET Chi-restraints excluded: chain A residue 1377 LEU Chi-restraints excluded: chain A residue 1389 ILE Chi-restraints excluded: chain A residue 1476 VAL Chi-restraints excluded: chain A residue 1501 VAL Chi-restraints excluded: chain A residue 1630 ILE Chi-restraints excluded: chain A residue 1687 ILE Chi-restraints excluded: chain A residue 1761 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 42 optimal weight: 1.9990 chunk 90 optimal weight: 0.8980 chunk 69 optimal weight: 2.9990 chunk 98 optimal weight: 0.0970 chunk 34 optimal weight: 0.8980 chunk 73 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 57 optimal weight: 4.9990 chunk 72 optimal weight: 0.7980 overall best weight: 0.7378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.155020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.121066 restraints weight = 10614.464| |-----------------------------------------------------------------------------| r_work (start): 0.3195 rms_B_bonded: 1.61 r_work: 0.3002 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2872 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.3426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8743 Z= 0.126 Angle : 0.582 9.603 11826 Z= 0.281 Chirality : 0.043 0.448 1383 Planarity : 0.005 0.065 1414 Dihedral : 10.144 102.031 1265 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 3.22 % Allowed : 14.86 % Favored : 81.93 % 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: 0.25 (0.26), residues: 992 helix: 0.84 (0.19), residues: 741 sheet: -2.47 (1.45), residues: 12 loop : -1.72 (0.35), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 283 TYR 0.012 0.001 TYR A 374 PHE 0.018 0.001 PHE A 127 TRP 0.007 0.001 TRP A 911 HIS 0.001 0.001 HIS A1442 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 ( 8735) covalent geometry : angle 0.57798 / 0.28 (11806) SS BOND : bond 0.00286 / 0.14 ( 4) SS BOND : angle 0.96712 / 0.75 ( 8) hydrogen bonds : bond 0.04236 / 2.71 ( 485) hydrogen bonds : angle 4.06636 / 2.80 ( 1407) link_NAG-ASN : bond 0.00897 / 0.47 ( 4) link_NAG-ASN : angle 2.07577 / 1.40 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1984 Ramachandran restraints generated. 992 Oldfield, 0 Emsley, 992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1984 Ramachandran restraints generated. 992 Oldfield, 0 Emsley, 992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 160 time to evaluate : 0.307 Fit side-chains REVERT: A 85 ARG cc_start: 0.7773 (mtt90) cc_final: 0.7004 (mtm180) REVERT: A 92 LEU cc_start: 0.7346 (mm) cc_final: 0.7056 (mp) REVERT: A 122 ASP cc_start: 0.6106 (m-30) cc_final: 0.5720 (m-30) REVERT: A 216 LEU cc_start: 0.8645 (OUTLIER) cc_final: 0.8147 (tt) REVERT: A 231 GLN cc_start: 0.8790 (mm110) cc_final: 0.8579 (mm-40) REVERT: A 251 LEU cc_start: 0.7425 (OUTLIER) cc_final: 0.7143 (mt) REVERT: A 400 GLU cc_start: 0.7867 (tp30) cc_final: 0.7242 (tt0) REVERT: A 808 ASN cc_start: 0.8136 (m-40) cc_final: 0.7250 (m110) REVERT: A 848 LEU cc_start: 0.7179 (OUTLIER) cc_final: 0.6883 (pp) REVERT: A 859 MET cc_start: 0.6700 (mmt) cc_final: 0.5763 (ptp) REVERT: A 1353 MET cc_start: 0.7790 (tmm) cc_final: 0.7426 (tpp) REVERT: A 1355 ARG cc_start: 0.6590 (mtm180) cc_final: 0.6341 (mtm180) REVERT: A 1387 LYS cc_start: 0.7957 (mtpp) cc_final: 0.7222 (mttt) REVERT: A 1389 ILE cc_start: 0.8240 (OUTLIER) cc_final: 0.7847 (pp) REVERT: A 1651 ARG cc_start: 0.6348 (tpp-160) cc_final: 0.5196 (tmm160) outliers start: 29 outliers final: 18 residues processed: 177 average time/residue: 0.1075 time to fit residues: 25.5462 Evaluate side-chains 174 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 152 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 328 HIS Chi-restraints excluded: chain A residue 757 THR Chi-restraints excluded: chain A residue 792 LEU Chi-restraints excluded: chain A residue 835 THR Chi-restraints excluded: chain A residue 848 LEU Chi-restraints excluded: chain A residue 867 THR Chi-restraints excluded: chain A residue 872 LEU Chi-restraints excluded: chain A residue 1254 MET Chi-restraints excluded: chain A residue 1385 SER Chi-restraints excluded: chain A residue 1389 ILE Chi-restraints excluded: chain A residue 1476 VAL Chi-restraints excluded: chain A residue 1501 VAL Chi-restraints excluded: chain A residue 1604 THR Chi-restraints excluded: chain A residue 1630 ILE Chi-restraints excluded: chain A residue 1632 VAL Chi-restraints excluded: chain A residue 1761 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 68 optimal weight: 4.9990 chunk 55 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 chunk 86 optimal weight: 0.0170 chunk 84 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 chunk 67 optimal weight: 1.9990 chunk 85 optimal weight: 6.9990 chunk 59 optimal weight: 0.5980 chunk 70 optimal weight: 0.6980 chunk 41 optimal weight: 1.9990 overall best weight: 0.8220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1487 ASN A1719 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.154650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.119295 restraints weight = 10592.255| |-----------------------------------------------------------------------------| r_work (start): 0.3172 rms_B_bonded: 1.79 r_work: 0.2978 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2845 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.3546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8743 Z= 0.131 Angle : 0.583 9.628 11826 Z= 0.281 Chirality : 0.043 0.412 1383 Planarity : 0.004 0.064 1414 Dihedral : 9.817 100.467 1263 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 3.22 % Allowed : 16.41 % Favored : 80.38 % 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: 0.59 (0.27), residues: 992 helix: 1.11 (0.19), residues: 742 sheet: -2.17 (1.49), residues: 12 loop : -1.68 (0.35), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 283 TYR 0.012 0.001 TYR A 374 PHE 0.014 0.001 PHE A 868 TRP 0.007 0.001 TRP A 911 HIS 0.001 0.001 HIS A1609 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.13 ( 8735) covalent geometry : angle 0.57840 / 0.28 (11806) SS BOND : bond 0.00316 / 0.16 ( 4) SS BOND : angle 0.96622 / 0.77 ( 8) hydrogen bonds : bond 0.04186 / 2.67 ( 485) hydrogen bonds : angle 4.02567 / 2.77 ( 1407) link_NAG-ASN : bond 0.00831 / 0.44 ( 4) link_NAG-ASN : angle 2.16248 / 1.49 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1984 Ramachandran restraints generated. 992 Oldfield, 0 Emsley, 992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1984 Ramachandran restraints generated. 992 Oldfield, 0 Emsley, 992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 157 time to evaluate : 0.345 Fit side-chains REVERT: A 85 ARG cc_start: 0.7726 (mtt90) cc_final: 0.6787 (mtt90) REVERT: A 92 LEU cc_start: 0.7361 (mm) cc_final: 0.7087 (mp) REVERT: A 122 ASP cc_start: 0.6120 (m-30) cc_final: 0.5723 (m-30) REVERT: A 216 LEU cc_start: 0.8702 (OUTLIER) cc_final: 0.8149 (tt) REVERT: A 251 LEU cc_start: 0.7428 (OUTLIER) cc_final: 0.7116 (mt) REVERT: A 263 ASN cc_start: 0.7565 (p0) cc_final: 0.7144 (p0) REVERT: A 400 GLU cc_start: 0.7895 (tp30) cc_final: 0.7025 (mt-10) REVERT: A 808 ASN cc_start: 0.8164 (m-40) cc_final: 0.7083 (m110) REVERT: A 811 ASP cc_start: 0.6966 (t0) cc_final: 0.6591 (t70) REVERT: A 839 MET cc_start: 0.7519 (mtp) cc_final: 0.7256 (mtm) REVERT: A 848 LEU cc_start: 0.7188 (OUTLIER) cc_final: 0.6864 (pp) REVERT: A 859 MET cc_start: 0.6588 (mmt) cc_final: 0.5706 (ttp) REVERT: A 1260 LEU cc_start: 0.8112 (OUTLIER) cc_final: 0.7894 (tt) REVERT: A 1353 MET cc_start: 0.7498 (tmm) cc_final: 0.7154 (tpp) REVERT: A 1389 ILE cc_start: 0.8252 (OUTLIER) cc_final: 0.7840 (pp) REVERT: A 1651 ARG cc_start: 0.6389 (tpp-160) cc_final: 0.5170 (tmm160) REVERT: A 1728 MET cc_start: 0.8379 (OUTLIER) cc_final: 0.8079 (mmt) outliers start: 29 outliers final: 19 residues processed: 176 average time/residue: 0.0960 time to fit residues: 23.3338 Evaluate side-chains 174 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 149 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 328 HIS Chi-restraints excluded: chain A residue 757 THR Chi-restraints excluded: chain A residue 792 LEU Chi-restraints excluded: chain A residue 848 LEU Chi-restraints excluded: chain A residue 867 THR Chi-restraints excluded: chain A residue 872 LEU Chi-restraints excluded: chain A residue 1254 MET Chi-restraints excluded: chain A residue 1260 LEU Chi-restraints excluded: chain A residue 1377 LEU Chi-restraints excluded: chain A residue 1385 SER Chi-restraints excluded: chain A residue 1389 ILE Chi-restraints excluded: chain A residue 1476 VAL Chi-restraints excluded: chain A residue 1501 VAL Chi-restraints excluded: chain A residue 1604 THR Chi-restraints excluded: chain A residue 1630 ILE Chi-restraints excluded: chain A residue 1632 VAL Chi-restraints excluded: chain A residue 1687 ILE Chi-restraints excluded: chain A residue 1728 MET Chi-restraints excluded: chain A residue 1761 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 70 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 62 optimal weight: 0.0870 chunk 12 optimal weight: 0.7980 chunk 42 optimal weight: 0.9990 chunk 97 optimal weight: 0.7980 chunk 36 optimal weight: 10.0000 chunk 35 optimal weight: 3.9990 chunk 90 optimal weight: 0.8980 chunk 54 optimal weight: 0.6980 chunk 45 optimal weight: 0.5980 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.157765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.122922 restraints weight = 10503.997| |-----------------------------------------------------------------------------| r_work (start): 0.3197 rms_B_bonded: 1.76 r_work: 0.3004 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2873 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.3754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8743 Z= 0.111 Angle : 0.551 9.592 11826 Z= 0.266 Chirality : 0.041 0.388 1383 Planarity : 0.004 0.064 1414 Dihedral : 9.426 95.305 1263 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 2.66 % Allowed : 17.41 % Favored : 79.93 % 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: 0.96 (0.27), residues: 992 helix: 1.38 (0.19), residues: 744 sheet: -1.85 (1.58), residues: 12 loop : -1.59 (0.36), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1774 TYR 0.010 0.001 TYR A 374 PHE 0.020 0.001 PHE A 127 TRP 0.006 0.001 TRP A1465 HIS 0.001 0.000 HIS A1609 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.11 ( 8735) covalent geometry : angle 0.54729 / 0.27 (11806) SS BOND : bond 0.00262 / 0.13 ( 4) SS BOND : angle 0.82867 / 0.65 ( 8) hydrogen bonds : bond 0.03762 / 2.40 ( 485) hydrogen bonds : angle 3.88763 / 2.69 ( 1407) link_NAG-ASN : bond 0.00801 / 0.42 ( 4) link_NAG-ASN : angle 2.01981 / 1.37 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1984 Ramachandran restraints generated. 992 Oldfield, 0 Emsley, 992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1984 Ramachandran restraints generated. 992 Oldfield, 0 Emsley, 992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 151 time to evaluate : 0.327 Fit side-chains REVERT: A 85 ARG cc_start: 0.7702 (mtt90) cc_final: 0.6772 (mtt90) REVERT: A 92 LEU cc_start: 0.7368 (mm) cc_final: 0.7116 (mp) REVERT: A 122 ASP cc_start: 0.6119 (m-30) cc_final: 0.5722 (m-30) REVERT: A 216 LEU cc_start: 0.8687 (OUTLIER) cc_final: 0.8138 (tt) REVERT: A 251 LEU cc_start: 0.7407 (OUTLIER) cc_final: 0.7071 (mt) REVERT: A 263 ASN cc_start: 0.7542 (p0) cc_final: 0.7120 (p0) REVERT: A 400 GLU cc_start: 0.7856 (tp30) cc_final: 0.7093 (mt-10) REVERT: A 839 MET cc_start: 0.7509 (mtp) cc_final: 0.7187 (mtm) REVERT: A 859 MET cc_start: 0.6571 (mmt) cc_final: 0.5664 (ttt) REVERT: A 1353 MET cc_start: 0.7474 (tmm) cc_final: 0.7161 (tpp) REVERT: A 1389 ILE cc_start: 0.8223 (OUTLIER) cc_final: 0.7832 (pp) REVERT: A 1651 ARG cc_start: 0.6397 (tpp-160) cc_final: 0.5151 (tmm160) REVERT: A 1728 MET cc_start: 0.8428 (OUTLIER) cc_final: 0.8107 (mmt) outliers start: 24 outliers final: 17 residues processed: 164 average time/residue: 0.0952 time to fit residues: 21.5711 Evaluate side-chains 167 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 146 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 328 HIS Chi-restraints excluded: chain A residue 757 THR Chi-restraints excluded: chain A residue 867 THR Chi-restraints excluded: chain A residue 872 LEU Chi-restraints excluded: chain A residue 1254 MET Chi-restraints excluded: chain A residue 1377 LEU Chi-restraints excluded: chain A residue 1389 ILE Chi-restraints excluded: chain A residue 1476 VAL Chi-restraints excluded: chain A residue 1501 VAL Chi-restraints excluded: chain A residue 1592 LEU Chi-restraints excluded: chain A residue 1604 THR Chi-restraints excluded: chain A residue 1630 ILE Chi-restraints excluded: chain A residue 1632 VAL Chi-restraints excluded: chain A residue 1687 ILE Chi-restraints excluded: chain A residue 1728 MET Chi-restraints excluded: chain A residue 1761 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 24 optimal weight: 0.6980 chunk 53 optimal weight: 0.2980 chunk 48 optimal weight: 0.9980 chunk 85 optimal weight: 0.6980 chunk 20 optimal weight: 0.0030 chunk 74 optimal weight: 2.9990 chunk 31 optimal weight: 0.0060 chunk 87 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 35 optimal weight: 7.9990 chunk 70 optimal weight: 1.9990 overall best weight: 0.3406 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1266 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.160176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.126289 restraints weight = 10565.173| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 1.65 r_work: 0.3051 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2922 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.4018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 8743 Z= 0.096 Angle : 0.527 9.523 11826 Z= 0.254 Chirality : 0.040 0.368 1383 Planarity : 0.004 0.065 1414 Dihedral : 8.955 89.421 1263 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 2.77 % Allowed : 17.29 % Favored : 79.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.40 (0.27), residues: 992 helix: 1.70 (0.20), residues: 746 sheet: -1.74 (1.61), residues: 12 loop : -1.45 (0.37), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 283 TYR 0.008 0.001 TYR A 374 PHE 0.016 0.001 PHE A 123 TRP 0.006 0.001 TRP A 925 HIS 0.001 0.000 HIS A1280 Details of bonding type rmsd/Z covalent geometry : bond 0.00205 / 0.10 ( 8735) covalent geometry : angle 0.52329 / 0.25 (11806) SS BOND : bond 0.00214 / 0.11 ( 4) SS BOND : angle 0.68313 / 0.52 ( 8) hydrogen bonds : bond 0.03296 / 2.12 ( 485) hydrogen bonds : angle 3.72792 / 2.59 ( 1407) link_NAG-ASN : bond 0.00754 / 0.40 ( 4) link_NAG-ASN : angle 1.94661 / 1.31 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1984 Ramachandran restraints generated. 992 Oldfield, 0 Emsley, 992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1984 Ramachandran restraints generated. 992 Oldfield, 0 Emsley, 992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 151 time to evaluate : 0.319 Fit side-chains REVERT: A 85 ARG cc_start: 0.7697 (mtt90) cc_final: 0.6777 (mtt90) REVERT: A 92 LEU cc_start: 0.7294 (mm) cc_final: 0.7037 (mp) REVERT: A 121 ASP cc_start: 0.7449 (t70) cc_final: 0.7160 (t70) REVERT: A 122 ASP cc_start: 0.6112 (m-30) cc_final: 0.5627 (m-30) REVERT: A 216 LEU cc_start: 0.8645 (OUTLIER) cc_final: 0.8141 (tt) REVERT: A 251 LEU cc_start: 0.7179 (OUTLIER) cc_final: 0.6859 (mt) REVERT: A 400 GLU cc_start: 0.7907 (tp30) cc_final: 0.7095 (mt-10) REVERT: A 808 ASN cc_start: 0.8074 (m-40) cc_final: 0.6992 (m110) REVERT: A 859 MET cc_start: 0.6453 (mmt) cc_final: 0.5529 (ttt) REVERT: A 1353 MET cc_start: 0.7408 (tmm) cc_final: 0.7100 (tpp) REVERT: A 1389 ILE cc_start: 0.8160 (OUTLIER) cc_final: 0.7798 (pp) REVERT: A 1431 ASP cc_start: 0.8371 (t0) cc_final: 0.8055 (m-30) REVERT: A 1651 ARG cc_start: 0.6305 (tpp-160) cc_final: 0.5050 (tmm160) REVERT: A 1669 LEU cc_start: 0.8049 (OUTLIER) cc_final: 0.7644 (tt) REVERT: A 1728 MET cc_start: 0.8403 (OUTLIER) cc_final: 0.8038 (mmt) outliers start: 25 outliers final: 13 residues processed: 166 average time/residue: 0.0973 time to fit residues: 22.1940 Evaluate side-chains 158 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 140 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 164 MET Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 867 THR Chi-restraints excluded: chain A residue 872 LEU Chi-restraints excluded: chain A residue 873 MET Chi-restraints excluded: chain A residue 1377 LEU Chi-restraints excluded: chain A residue 1389 ILE Chi-restraints excluded: chain A residue 1476 VAL Chi-restraints excluded: chain A residue 1501 VAL Chi-restraints excluded: chain A residue 1592 LEU Chi-restraints excluded: chain A residue 1604 THR Chi-restraints excluded: chain A residue 1630 ILE Chi-restraints excluded: chain A residue 1669 LEU Chi-restraints excluded: chain A residue 1728 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 11 optimal weight: 0.8980 chunk 76 optimal weight: 0.8980 chunk 41 optimal weight: 3.9990 chunk 19 optimal weight: 0.9990 chunk 51 optimal weight: 0.2980 chunk 60 optimal weight: 0.7980 chunk 13 optimal weight: 1.9990 chunk 78 optimal weight: 3.9990 chunk 30 optimal weight: 0.8980 chunk 100 optimal weight: 1.9990 chunk 93 optimal weight: 8.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 918 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.159471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.123246 restraints weight = 10453.074| |-----------------------------------------------------------------------------| r_work (start): 0.3175 rms_B_bonded: 1.87 r_work: 0.2983 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2846 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.3899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8743 Z= 0.125 Angle : 0.577 10.996 11826 Z= 0.275 Chirality : 0.042 0.380 1383 Planarity : 0.004 0.062 1414 Dihedral : 9.186 91.354 1263 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.33 % Allowed : 17.41 % Favored : 80.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.36 (0.27), residues: 992 helix: 1.68 (0.19), residues: 744 sheet: -1.44 (1.71), residues: 12 loop : -1.50 (0.37), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1692 TYR 0.012 0.001 TYR A 374 PHE 0.020 0.001 PHE A 127 TRP 0.008 0.001 TRP A 911 HIS 0.002 0.001 HIS A1609 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.12 ( 8735) covalent geometry : angle 0.57298 / 0.27 (11806) SS BOND : bond 0.00296 / 0.15 ( 4) SS BOND : angle 0.89701 / 0.74 ( 8) hydrogen bonds : bond 0.03948 / 2.53 ( 485) hydrogen bonds : angle 3.86982 / 2.69 ( 1407) link_NAG-ASN : bond 0.00794 / 0.42 ( 4) link_NAG-ASN : angle 2.07190 / 1.40 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1984 Ramachandran restraints generated. 992 Oldfield, 0 Emsley, 992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1984 Ramachandran restraints generated. 992 Oldfield, 0 Emsley, 992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 145 time to evaluate : 0.338 Fit side-chains REVERT: A 85 ARG cc_start: 0.7663 (mtt90) cc_final: 0.6736 (mtt90) REVERT: A 92 LEU cc_start: 0.7335 (mm) cc_final: 0.7011 (mp) REVERT: A 122 ASP cc_start: 0.6134 (m-30) cc_final: 0.5733 (m-30) REVERT: A 216 LEU cc_start: 0.8661 (OUTLIER) cc_final: 0.8103 (tt) REVERT: A 251 LEU cc_start: 0.7407 (OUTLIER) cc_final: 0.7046 (mt) REVERT: A 400 GLU cc_start: 0.7900 (tp30) cc_final: 0.7062 (mt-10) REVERT: A 808 ASN cc_start: 0.8179 (m-40) cc_final: 0.7181 (m110) REVERT: A 839 MET cc_start: 0.7602 (mtp) cc_final: 0.7269 (mtm) REVERT: A 859 MET cc_start: 0.6526 (mmt) cc_final: 0.5617 (ttt) REVERT: A 1353 MET cc_start: 0.7472 (tmm) cc_final: 0.7140 (tpp) REVERT: A 1389 ILE cc_start: 0.8186 (OUTLIER) cc_final: 0.7768 (pp) REVERT: A 1431 ASP cc_start: 0.8385 (t0) cc_final: 0.8029 (m-30) REVERT: A 1651 ARG cc_start: 0.6340 (tpp-160) cc_final: 0.5035 (tmm160) REVERT: A 1669 LEU cc_start: 0.8011 (OUTLIER) cc_final: 0.7588 (tt) outliers start: 21 outliers final: 14 residues processed: 156 average time/residue: 0.0947 time to fit residues: 20.3524 Evaluate side-chains 160 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 142 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 867 THR Chi-restraints excluded: chain A residue 872 LEU Chi-restraints excluded: chain A residue 873 MET Chi-restraints excluded: chain A residue 1377 LEU Chi-restraints excluded: chain A residue 1385 SER Chi-restraints excluded: chain A residue 1389 ILE Chi-restraints excluded: chain A residue 1476 VAL Chi-restraints excluded: chain A residue 1501 VAL Chi-restraints excluded: chain A residue 1604 THR Chi-restraints excluded: chain A residue 1630 ILE Chi-restraints excluded: chain A residue 1669 LEU Chi-restraints excluded: chain A residue 1687 ILE Chi-restraints excluded: chain A residue 1706 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 86 optimal weight: 0.9990 chunk 18 optimal weight: 2.9990 chunk 71 optimal weight: 0.5980 chunk 87 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 42 optimal weight: 0.8980 chunk 38 optimal weight: 0.5980 chunk 96 optimal weight: 0.8980 chunk 1 optimal weight: 3.9990 chunk 37 optimal weight: 0.6980 chunk 61 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 918 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.157535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.122595 restraints weight = 10508.471| |-----------------------------------------------------------------------------| r_work (start): 0.3192 rms_B_bonded: 1.76 r_work: 0.2997 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2869 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.3967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8743 Z= 0.118 Angle : 0.565 9.921 11826 Z= 0.270 Chirality : 0.041 0.380 1383 Planarity : 0.004 0.062 1414 Dihedral : 9.149 90.023 1263 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 2.22 % Allowed : 17.41 % Favored : 80.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.44 (0.27), residues: 992 helix: 1.73 (0.19), residues: 744 sheet: -1.36 (1.76), residues: 12 loop : -1.46 (0.37), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1774 TYR 0.012 0.001 TYR A 374 PHE 0.016 0.001 PHE A 123 TRP 0.006 0.001 TRP A1465 HIS 0.001 0.000 HIS A1609 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 ( 8735) covalent geometry : angle 0.56131 / 0.27 (11806) SS BOND : bond 0.00269 / 0.14 ( 4) SS BOND : angle 0.81342 / 0.66 ( 8) hydrogen bonds : bond 0.03813 / 2.44 ( 485) hydrogen bonds : angle 3.85518 / 2.68 ( 1407) link_NAG-ASN : bond 0.00791 / 0.42 ( 4) link_NAG-ASN : angle 2.08432 / 1.41 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1984 Ramachandran restraints generated. 992 Oldfield, 0 Emsley, 992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1984 Ramachandran restraints generated. 992 Oldfield, 0 Emsley, 992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 144 time to evaluate : 0.335 Fit side-chains REVERT: A 85 ARG cc_start: 0.7690 (mtt90) cc_final: 0.6605 (mtm180) REVERT: A 92 LEU cc_start: 0.7338 (mm) cc_final: 0.7043 (mp) REVERT: A 122 ASP cc_start: 0.6128 (m-30) cc_final: 0.5723 (m-30) REVERT: A 216 LEU cc_start: 0.8656 (OUTLIER) cc_final: 0.8131 (tt) REVERT: A 251 LEU cc_start: 0.7392 (OUTLIER) cc_final: 0.7035 (mt) REVERT: A 400 GLU cc_start: 0.7980 (tp30) cc_final: 0.7045 (mt-10) REVERT: A 808 ASN cc_start: 0.8192 (m-40) cc_final: 0.7194 (m110) REVERT: A 839 MET cc_start: 0.7564 (mtp) cc_final: 0.7240 (mtm) REVERT: A 859 MET cc_start: 0.6491 (mmt) cc_final: 0.5588 (ttt) REVERT: A 1353 MET cc_start: 0.7506 (tmm) cc_final: 0.7179 (tpp) REVERT: A 1389 ILE cc_start: 0.8194 (OUTLIER) cc_final: 0.7800 (pp) REVERT: A 1431 ASP cc_start: 0.8365 (t0) cc_final: 0.8024 (m-30) REVERT: A 1651 ARG cc_start: 0.6410 (tpp-160) cc_final: 0.5046 (tmm160) REVERT: A 1669 LEU cc_start: 0.8035 (OUTLIER) cc_final: 0.7616 (tt) REVERT: A 1689 ARG cc_start: 0.8275 (tpp80) cc_final: 0.7474 (tpt90) REVERT: A 1728 MET cc_start: 0.8426 (OUTLIER) cc_final: 0.8141 (mmt) outliers start: 20 outliers final: 14 residues processed: 155 average time/residue: 0.1036 time to fit residues: 21.9141 Evaluate side-chains 160 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 141 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 164 MET Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 867 THR Chi-restraints excluded: chain A residue 872 LEU Chi-restraints excluded: chain A residue 873 MET Chi-restraints excluded: chain A residue 1377 LEU Chi-restraints excluded: chain A residue 1385 SER Chi-restraints excluded: chain A residue 1389 ILE Chi-restraints excluded: chain A residue 1476 VAL Chi-restraints excluded: chain A residue 1501 VAL Chi-restraints excluded: chain A residue 1604 THR Chi-restraints excluded: chain A residue 1630 ILE Chi-restraints excluded: chain A residue 1669 LEU Chi-restraints excluded: chain A residue 1706 MET Chi-restraints excluded: chain A residue 1728 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 1 optimal weight: 3.9990 chunk 89 optimal weight: 2.9990 chunk 5 optimal weight: 6.9990 chunk 55 optimal weight: 3.9990 chunk 67 optimal weight: 0.6980 chunk 78 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 15 optimal weight: 0.7980 chunk 24 optimal weight: 0.6980 chunk 8 optimal weight: 1.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.155775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.120502 restraints weight = 10467.885| |-----------------------------------------------------------------------------| r_work (start): 0.3175 rms_B_bonded: 1.74 r_work: 0.2983 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2851 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.3848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8743 Z= 0.151 Angle : 0.615 10.584 11826 Z= 0.294 Chirality : 0.043 0.388 1383 Planarity : 0.005 0.061 1414 Dihedral : 9.631 93.320 1263 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.88 % Allowed : 16.85 % Favored : 80.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.21 (0.27), residues: 992 helix: 1.57 (0.19), residues: 743 sheet: -1.23 (1.79), residues: 12 loop : -1.55 (0.37), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 834 TYR 0.014 0.002 TYR A 374 PHE 0.016 0.001 PHE A 868 TRP 0.008 0.001 TRP A 911 HIS 0.002 0.001 HIS A1442 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.15 ( 8735) covalent geometry : angle 0.61123 / 0.29 (11806) SS BOND : bond 0.00374 / 0.19 ( 4) SS BOND : angle 1.00966 / 0.85 ( 8) hydrogen bonds : bond 0.04367 / 2.79 ( 485) hydrogen bonds : angle 4.01680 / 2.78 ( 1407) link_NAG-ASN : bond 0.00852 / 0.45 ( 4) link_NAG-ASN : angle 2.17013 / 1.45 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1984 Ramachandran restraints generated. 992 Oldfield, 0 Emsley, 992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1984 Ramachandran restraints generated. 992 Oldfield, 0 Emsley, 992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 145 time to evaluate : 0.326 Fit side-chains REVERT: A 85 ARG cc_start: 0.7807 (mtt90) cc_final: 0.6718 (mtm180) REVERT: A 92 LEU cc_start: 0.7410 (mm) cc_final: 0.7065 (mp) REVERT: A 118 GLN cc_start: 0.8017 (tt0) cc_final: 0.6889 (tp-100) REVERT: A 122 ASP cc_start: 0.6198 (m-30) cc_final: 0.5802 (m-30) REVERT: A 216 LEU cc_start: 0.8675 (OUTLIER) cc_final: 0.8118 (tt) REVERT: A 251 LEU cc_start: 0.7412 (OUTLIER) cc_final: 0.7074 (mt) REVERT: A 400 GLU cc_start: 0.7946 (tp30) cc_final: 0.7032 (mt-10) REVERT: A 808 ASN cc_start: 0.8133 (m-40) cc_final: 0.7170 (m110) REVERT: A 839 MET cc_start: 0.7577 (mtp) cc_final: 0.7344 (mtm) REVERT: A 859 MET cc_start: 0.6547 (mmt) cc_final: 0.5748 (ttt) REVERT: A 1353 MET cc_start: 0.7561 (tmm) cc_final: 0.7238 (tpp) REVERT: A 1389 ILE cc_start: 0.8276 (OUTLIER) cc_final: 0.7870 (pp) REVERT: A 1651 ARG cc_start: 0.6337 (tpp-160) cc_final: 0.4872 (tmm160) REVERT: A 1669 LEU cc_start: 0.8035 (OUTLIER) cc_final: 0.7624 (tt) REVERT: A 1689 ARG cc_start: 0.8273 (tpp80) cc_final: 0.7448 (tpt90) REVERT: A 1728 MET cc_start: 0.8397 (OUTLIER) cc_final: 0.8153 (mmt) outliers start: 26 outliers final: 17 residues processed: 158 average time/residue: 0.0969 time to fit residues: 21.1867 Evaluate side-chains 165 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 143 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 867 THR Chi-restraints excluded: chain A residue 872 LEU Chi-restraints excluded: chain A residue 873 MET Chi-restraints excluded: chain A residue 1377 LEU Chi-restraints excluded: chain A residue 1385 SER Chi-restraints excluded: chain A residue 1389 ILE Chi-restraints excluded: chain A residue 1476 VAL Chi-restraints excluded: chain A residue 1501 VAL Chi-restraints excluded: chain A residue 1604 THR Chi-restraints excluded: chain A residue 1630 ILE Chi-restraints excluded: chain A residue 1667 ILE Chi-restraints excluded: chain A residue 1669 LEU Chi-restraints excluded: chain A residue 1687 ILE Chi-restraints excluded: chain A residue 1706 MET Chi-restraints excluded: chain A residue 1728 MET Chi-restraints excluded: chain A residue 1761 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 68 optimal weight: 4.9990 chunk 25 optimal weight: 0.5980 chunk 43 optimal weight: 1.9990 chunk 48 optimal weight: 0.7980 chunk 55 optimal weight: 2.9990 chunk 29 optimal weight: 6.9990 chunk 97 optimal weight: 0.0370 chunk 13 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 54 optimal weight: 0.7980 chunk 89 optimal weight: 2.9990 overall best weight: 0.8460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 918 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.156583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.121259 restraints weight = 10433.456| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 1.73 r_work: 0.2983 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2852 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.3926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8743 Z= 0.132 Angle : 0.590 10.075 11826 Z= 0.282 Chirality : 0.042 0.382 1383 Planarity : 0.004 0.061 1414 Dihedral : 9.555 92.988 1263 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 2.66 % Allowed : 17.41 % Favored : 79.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.31 (0.27), residues: 992 helix: 1.64 (0.19), residues: 744 sheet: -1.11 (1.83), residues: 12 loop : -1.51 (0.37), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 834 TYR 0.012 0.001 TYR A 374 PHE 0.014 0.001 PHE A 868 TRP 0.007 0.001 TRP A 911 HIS 0.002 0.001 HIS A1609 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.13 ( 8735) covalent geometry : angle 0.58637 / 0.28 (11806) SS BOND : bond 0.00322 / 0.16 ( 4) SS BOND : angle 0.87375 / 0.72 ( 8) hydrogen bonds : bond 0.04085 / 2.61 ( 485) hydrogen bonds : angle 3.96250 / 2.75 ( 1407) link_NAG-ASN : bond 0.00830 / 0.44 ( 4) link_NAG-ASN : angle 2.18194 / 1.47 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2703.55 seconds wall clock time: 46 minutes 52.41 seconds (2812.41 seconds total)