Starting phenix.real_space_refine on Tue Mar 3 23:34:51 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6kzp_0792/03_2026/6kzp_0792.cif Found real_map, /net/cci-nas-00/data/ceres_data/6kzp_0792/03_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 { model { file = "/net/cci-nas-00/data/ceres_data/6kzp_0792/03_2026/6kzp_0792.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6kzp_0792/03_2026/6kzp_0792.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6kzp_0792/03_2026/6kzp_0792.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6kzp_0792/03_2026/6kzp_0792.map" } 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-dev-5986/lib/python3.9/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: 214 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: 1.87, 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: 0.60 Conformation dependent library (CDL) restraints added in 201.4 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: 0.22 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: 1.29 Time building geometry restraints manager: 0.81 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 - 24.94: 5057 24.94 - 49.88: 289 49.88 - 74.83: 52 74.83 - 99.77: 2 99.77 - 124.71: 11 Dihedral angle restraints: 5411 sinusoidal: 2457 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 5408 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: 2.840 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 8.490 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.280 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 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 : 16.067 124.710 3475 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 covalent geometry : bond 0.01327 ( 8735) covalent geometry : angle 1.45373 (11806) SS BOND : bond 0.00577 ( 4) SS BOND : angle 2.36643 ( 8) hydrogen bonds : bond 0.31391 ( 485) hydrogen bonds : angle 9.68840 ( 1407) link_NAG-ASN : bond 0.00830 ( 4) link_NAG-ASN : angle 2.92919 ( 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 : 0.282 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: 0.1009 time to fit residues: 32.0940 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 : 0.279 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3755 r_free = 0.3755 target = 0.157007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.122806 restraints weight = 10632.118| |-----------------------------------------------------------------------------| r_work (start): 0.3200 rms_B_bonded: 1.67 r_work: 0.3014 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2888 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.2696 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= 0.145 Angle : 0.672 9.538 11826 Z= 0.330 Chirality : 0.043 0.273 1383 Planarity : 0.006 0.073 1414 Dihedral : 14.737 101.969 1600 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 2.99 % Allowed : 11.64 % Favored : 85.37 % 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: 736 sheet: -3.41 (1.41), residues: 12 loop : -1.87 (0.33), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A1645 TYR 0.017 0.002 TYR A1437 PHE 0.016 0.002 PHE A 868 TRP 0.010 0.001 TRP A 911 HIS 0.003 0.001 HIS A1751 Details of bonding type rmsd covalent geometry : bond 0.00321 ( 8735) covalent geometry : angle 0.66634 (11806) SS BOND : bond 0.00264 ( 4) SS BOND : angle 1.19611 ( 8) hydrogen bonds : bond 0.05591 ( 485) hydrogen bonds : angle 4.71456 ( 1407) link_NAG-ASN : bond 0.00420 ( 4) link_NAG-ASN : angle 2.60723 ( 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 215 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 188 time to evaluate : 0.319 Fit side-chains REVERT: A 85 ARG cc_start: 0.7839 (mtt90) cc_final: 0.7065 (mtm180) REVERT: A 92 LEU cc_start: 0.7415 (mm) cc_final: 0.7183 (mp) REVERT: A 118 GLN cc_start: 0.8028 (tt0) cc_final: 0.6961 (tp-100) REVERT: A 122 ASP cc_start: 0.6040 (m-30) cc_final: 0.5680 (m-30) REVERT: A 156 ASP cc_start: 0.8065 (t0) cc_final: 0.7761 (m-30) REVERT: A 183 ARG cc_start: 0.7732 (ptt180) cc_final: 0.7491 (ptt90) REVERT: A 251 LEU cc_start: 0.7361 (OUTLIER) cc_final: 0.7116 (mt) REVERT: A 808 ASN cc_start: 0.8163 (m-40) cc_final: 0.7079 (m110) REVERT: A 835 THR cc_start: 0.8638 (m) cc_final: 0.8305 (p) REVERT: A 844 LEU cc_start: 0.7997 (OUTLIER) cc_final: 0.7777 (mm) REVERT: A 859 MET cc_start: 0.6902 (mmt) cc_final: 0.5972 (ptp) REVERT: A 1243 ARG cc_start: 0.7193 (ttt-90) cc_final: 0.6950 (ttt-90) REVERT: A 1283 GLU cc_start: 0.7879 (tt0) cc_final: 0.7518 (tt0) REVERT: A 1349 LYS cc_start: 0.3881 (tptt) cc_final: 0.3602 (tptt) REVERT: A 1353 MET cc_start: 0.7967 (tmm) cc_final: 0.7436 (tpp) REVERT: A 1383 MET cc_start: 0.8237 (mmt) cc_final: 0.7758 (mmm) REVERT: A 1431 ASP cc_start: 0.8013 (t0) cc_final: 0.7684 (t0) REVERT: A 1645 ARG cc_start: 0.7324 (ttt90) cc_final: 0.6715 (tpm170) REVERT: A 1651 ARG cc_start: 0.6194 (tpp-160) cc_final: 0.5162 (ttt180) REVERT: A 1689 ARG cc_start: 0.7540 (tpp80) cc_final: 0.6854 (ttp80) REVERT: A 1828 MET cc_start: 0.7995 (OUTLIER) cc_final: 0.7772 (mmm) outliers start: 27 outliers final: 14 residues processed: 205 average time/residue: 0.0952 time to fit residues: 26.4033 Evaluate side-chains 177 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 160 time to evaluate : 0.313 ------------------------------------------------------------------------------- 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 1828 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 37 optimal weight: 1.9990 chunk 38 optimal weight: 0.0870 chunk 90 optimal weight: 0.8980 chunk 4 optimal weight: 2.9990 chunk 21 optimal weight: 4.9990 chunk 13 optimal weight: 0.9980 chunk 47 optimal weight: 2.9990 chunk 45 optimal weight: 0.7980 chunk 36 optimal weight: 6.9990 chunk 58 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 overall best weight: 0.9560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 231 GLN ** A 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1719 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.153928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.119037 restraints weight = 10477.608| |-----------------------------------------------------------------------------| r_work (start): 0.3171 rms_B_bonded: 1.70 r_work: 0.2981 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2851 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.3064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8743 Z= 0.151 Angle : 0.652 9.669 11826 Z= 0.313 Chirality : 0.044 0.346 1383 Planarity : 0.005 0.066 1414 Dihedral : 13.642 96.130 1591 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 3.88 % Allowed : 12.64 % Favored : 83.48 % 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: -0.70 (0.25), residues: 992 helix: 0.10 (0.19), residues: 739 sheet: -2.82 (1.48), residues: 12 loop : -1.83 (0.34), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 283 TYR 0.013 0.002 TYR A1437 PHE 0.018 0.002 PHE A 868 TRP 0.009 0.001 TRP A 911 HIS 0.002 0.001 HIS A 328 Details of bonding type rmsd covalent geometry : bond 0.00352 ( 8735) covalent geometry : angle 0.64792 (11806) SS BOND : bond 0.00341 ( 4) SS BOND : angle 1.15582 ( 8) hydrogen bonds : bond 0.04980 ( 485) hydrogen bonds : angle 4.33413 ( 1407) link_NAG-ASN : bond 0.01498 ( 4) link_NAG-ASN : angle 2.10583 ( 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 202 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 167 time to evaluate : 0.390 Fit side-chains REVERT: A 85 ARG cc_start: 0.7823 (mtt90) cc_final: 0.6993 (mtm180) REVERT: A 92 LEU cc_start: 0.7366 (mm) cc_final: 0.7125 (mp) REVERT: A 118 GLN cc_start: 0.8011 (tt0) cc_final: 0.6920 (tp-100) REVERT: A 122 ASP cc_start: 0.6084 (m-30) cc_final: 0.5708 (m-30) REVERT: A 216 LEU cc_start: 0.8633 (OUTLIER) cc_final: 0.8144 (tt) REVERT: A 251 LEU cc_start: 0.7481 (OUTLIER) cc_final: 0.7219 (mt) REVERT: A 275 ARG cc_start: 0.7112 (mtp85) cc_final: 0.6847 (mtm-85) REVERT: A 400 GLU cc_start: 0.7867 (tp30) cc_final: 0.7342 (tt0) REVERT: A 808 ASN cc_start: 0.8191 (m-40) cc_final: 0.7094 (m110) REVERT: A 848 LEU cc_start: 0.7257 (OUTLIER) cc_final: 0.6893 (pp) REVERT: A 859 MET cc_start: 0.6861 (mmt) cc_final: 0.5919 (ptp) REVERT: A 1243 ARG cc_start: 0.7036 (ttt-90) cc_final: 0.6767 (ttt-90) REVERT: A 1283 GLU cc_start: 0.7803 (tt0) cc_final: 0.7549 (tt0) REVERT: A 1349 LYS cc_start: 0.4077 (tptt) cc_final: 0.3748 (tptp) REVERT: A 1353 MET cc_start: 0.7868 (tmm) cc_final: 0.7466 (tpp) REVERT: A 1383 MET cc_start: 0.8274 (mmt) cc_final: 0.8015 (mmm) REVERT: A 1389 ILE cc_start: 0.8253 (OUTLIER) cc_final: 0.7866 (pp) REVERT: A 1651 ARG cc_start: 0.6388 (tpp-160) cc_final: 0.5258 (tmm160) REVERT: A 1689 ARG cc_start: 0.7540 (tpp80) cc_final: 0.6811 (ttp80) REVERT: A 1789 LEU cc_start: 0.8667 (OUTLIER) cc_final: 0.8410 (pp) outliers start: 35 outliers final: 17 residues processed: 190 average time/residue: 0.1011 time to fit residues: 25.5680 Evaluate side-chains 181 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 159 time to evaluate : 0.282 ------------------------------------------------------------------------------- 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 743 LYS Chi-restraints excluded: chain A residue 751 ILE 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 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 1632 VAL Chi-restraints excluded: chain A residue 1687 ILE Chi-restraints excluded: chain A residue 1761 THR Chi-restraints excluded: chain A residue 1789 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 42 optimal weight: 0.7980 chunk 90 optimal weight: 0.8980 chunk 69 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 62 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 chunk 72 optimal weight: 0.5980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 371 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.151979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.116925 restraints weight = 10638.382| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 1.69 r_work: 0.2981 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2852 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.3304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8743 Z= 0.150 Angle : 0.623 9.685 11826 Z= 0.298 Chirality : 0.043 0.273 1383 Planarity : 0.005 0.065 1414 Dihedral : 12.761 91.525 1589 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 3.55 % Allowed : 14.97 % Favored : 81.49 % 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: 0.13 (0.26), residues: 992 helix: 0.71 (0.19), residues: 730 sheet: -2.40 (1.48), residues: 12 loop : -1.46 (0.36), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 283 TYR 0.013 0.002 TYR A 374 PHE 0.018 0.002 PHE A 127 TRP 0.008 0.001 TRP A 911 HIS 0.002 0.001 HIS A1442 Details of bonding type rmsd covalent geometry : bond 0.00355 ( 8735) covalent geometry : angle 0.61507 (11806) SS BOND : bond 0.00339 ( 4) SS BOND : angle 1.06089 ( 8) hydrogen bonds : bond 0.04620 ( 485) hydrogen bonds : angle 4.20670 ( 1407) link_NAG-ASN : bond 0.00787 ( 4) link_NAG-ASN : angle 3.01338 ( 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 190 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 158 time to evaluate : 0.300 Fit side-chains REVERT: A 85 ARG cc_start: 0.7792 (mtt90) cc_final: 0.6980 (mtm180) REVERT: A 92 LEU cc_start: 0.7351 (mm) cc_final: 0.7075 (mp) REVERT: A 122 ASP cc_start: 0.6128 (m-30) cc_final: 0.5745 (m-30) REVERT: A 216 LEU cc_start: 0.8677 (OUTLIER) cc_final: 0.8146 (tt) REVERT: A 251 LEU cc_start: 0.7376 (OUTLIER) cc_final: 0.7113 (mt) REVERT: A 263 ASN cc_start: 0.7679 (p0) cc_final: 0.7154 (p0) REVERT: A 400 GLU cc_start: 0.7859 (tp30) cc_final: 0.7341 (tt0) REVERT: A 808 ASN cc_start: 0.8183 (m-40) cc_final: 0.7364 (m110) REVERT: A 839 MET cc_start: 0.7611 (mtp) cc_final: 0.7393 (mtm) REVERT: A 848 LEU cc_start: 0.7403 (OUTLIER) cc_final: 0.6913 (pp) REVERT: A 859 MET cc_start: 0.6926 (mmt) cc_final: 0.5969 (ptp) REVERT: A 1260 LEU cc_start: 0.8162 (OUTLIER) cc_final: 0.7939 (tt) REVERT: A 1283 GLU cc_start: 0.7748 (tt0) cc_final: 0.7513 (tt0) REVERT: A 1353 MET cc_start: 0.7852 (tmm) cc_final: 0.7482 (tpp) REVERT: A 1387 LYS cc_start: 0.7974 (mtpp) cc_final: 0.7243 (mttt) REVERT: A 1389 ILE cc_start: 0.8232 (OUTLIER) cc_final: 0.7845 (pp) REVERT: A 1651 ARG cc_start: 0.6415 (tpp-160) cc_final: 0.5193 (tmm160) REVERT: A 1689 ARG cc_start: 0.7620 (tpp80) cc_final: 0.6909 (ttp80) REVERT: A 1789 LEU cc_start: 0.8724 (OUTLIER) cc_final: 0.8491 (pp) outliers start: 32 outliers final: 18 residues processed: 176 average time/residue: 0.1053 time to fit residues: 24.5239 Evaluate side-chains 174 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 150 time to evaluate : 0.289 ------------------------------------------------------------------------------- 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 743 LYS 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 1260 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 1687 ILE Chi-restraints excluded: chain A residue 1761 THR Chi-restraints excluded: chain A residue 1789 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 68 optimal weight: 5.9990 chunk 55 optimal weight: 0.9990 chunk 44 optimal weight: 1.9990 chunk 86 optimal weight: 0.7980 chunk 84 optimal weight: 2.9990 chunk 38 optimal weight: 0.1980 chunk 67 optimal weight: 0.0030 chunk 85 optimal weight: 3.9990 chunk 59 optimal weight: 0.5980 chunk 70 optimal weight: 0.8980 chunk 41 optimal weight: 0.8980 overall best weight: 0.4990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1266 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.156025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.120849 restraints weight = 10578.260| |-----------------------------------------------------------------------------| r_work (start): 0.3191 rms_B_bonded: 1.76 r_work: 0.3003 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2876 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.3586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 8743 Z= 0.108 Angle : 0.561 9.643 11826 Z= 0.269 Chirality : 0.041 0.258 1383 Planarity : 0.004 0.064 1414 Dihedral : 12.060 85.040 1589 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.88 % Allowed : 15.41 % Favored : 81.71 % 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: 0.78 (0.27), residues: 992 helix: 1.20 (0.19), residues: 733 sheet: -2.33 (1.46), residues: 12 loop : -1.29 (0.36), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 283 TYR 0.010 0.001 TYR A 374 PHE 0.010 0.001 PHE A 868 TRP 0.007 0.001 TRP A1465 HIS 0.001 0.000 HIS A1609 Details of bonding type rmsd covalent geometry : bond 0.00237 ( 8735) covalent geometry : angle 0.55616 (11806) SS BOND : bond 0.00220 ( 4) SS BOND : angle 0.74552 ( 8) hydrogen bonds : bond 0.03788 ( 485) hydrogen bonds : angle 3.94472 ( 1407) link_NAG-ASN : bond 0.00642 ( 4) link_NAG-ASN : angle 2.24752 ( 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 192 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 166 time to evaluate : 0.270 Fit side-chains REVERT: A 85 ARG cc_start: 0.7742 (mtt90) cc_final: 0.6822 (mtt90) REVERT: A 92 LEU cc_start: 0.7345 (mm) cc_final: 0.7083 (mp) REVERT: A 122 ASP cc_start: 0.6104 (m-30) cc_final: 0.5714 (m-30) REVERT: A 216 LEU cc_start: 0.8636 (OUTLIER) cc_final: 0.8067 (tt) REVERT: A 231 GLN cc_start: 0.8787 (mm110) cc_final: 0.8508 (mm-40) REVERT: A 251 LEU cc_start: 0.7391 (OUTLIER) cc_final: 0.7101 (mt) REVERT: A 263 ASN cc_start: 0.7555 (p0) cc_final: 0.7137 (p0) REVERT: A 400 GLU cc_start: 0.7868 (tp30) cc_final: 0.7199 (tt0) REVERT: A 808 ASN cc_start: 0.8114 (m-40) cc_final: 0.7271 (m110) REVERT: A 839 MET cc_start: 0.7511 (mtp) cc_final: 0.7262 (mtm) REVERT: A 848 LEU cc_start: 0.7181 (OUTLIER) cc_final: 0.6850 (pp) REVERT: A 859 MET cc_start: 0.6675 (mmt) cc_final: 0.5737 (ptp) REVERT: A 1353 MET cc_start: 0.7563 (tmm) cc_final: 0.7199 (tpp) REVERT: A 1387 LYS cc_start: 0.7895 (mtpp) cc_final: 0.7149 (mttt) REVERT: A 1389 ILE cc_start: 0.8205 (OUTLIER) cc_final: 0.7824 (pp) REVERT: A 1651 ARG cc_start: 0.6357 (tpp-160) cc_final: 0.5095 (tmm160) REVERT: A 1689 ARG cc_start: 0.7629 (tpp80) cc_final: 0.6910 (ttp80) REVERT: A 1728 MET cc_start: 0.8397 (OUTLIER) cc_final: 0.8086 (mmt) outliers start: 26 outliers final: 13 residues processed: 181 average time/residue: 0.0976 time to fit residues: 23.6452 Evaluate side-chains 173 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 155 time to evaluate : 0.229 ------------------------------------------------------------------------------- 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 790 MET Chi-restraints excluded: chain A residue 848 LEU Chi-restraints excluded: chain A residue 867 THR 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 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: 0.8980 chunk 26 optimal weight: 0.6980 chunk 62 optimal weight: 0.6980 chunk 12 optimal weight: 0.8980 chunk 42 optimal weight: 0.5980 chunk 97 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 54 optimal weight: 0.2980 chunk 45 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1719 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.155767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.120994 restraints weight = 10523.734| |-----------------------------------------------------------------------------| r_work (start): 0.3198 rms_B_bonded: 1.70 r_work: 0.3019 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2885 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.3761 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= 0.111 Angle : 0.556 9.622 11826 Z= 0.267 Chirality : 0.041 0.258 1383 Planarity : 0.004 0.064 1414 Dihedral : 11.525 77.787 1587 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 2.77 % Allowed : 17.18 % Favored : 80.04 % 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: 1.14 (0.27), residues: 992 helix: 1.48 (0.19), residues: 734 sheet: -2.06 (1.51), residues: 12 loop : -1.26 (0.36), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1774 TYR 0.011 0.001 TYR A 374 PHE 0.019 0.001 PHE A 127 TRP 0.006 0.001 TRP A1465 HIS 0.002 0.000 HIS A1609 Details of bonding type rmsd covalent geometry : bond 0.00251 ( 8735) covalent geometry : angle 0.55289 (11806) SS BOND : bond 0.00256 ( 4) SS BOND : angle 0.83698 ( 8) hydrogen bonds : bond 0.03770 ( 485) hydrogen bonds : angle 3.86809 ( 1407) link_NAG-ASN : bond 0.00435 ( 4) link_NAG-ASN : angle 1.93044 ( 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 184 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 159 time to evaluate : 0.296 Fit side-chains REVERT: A 85 ARG cc_start: 0.7688 (mtt90) cc_final: 0.6578 (mtm180) REVERT: A 92 LEU cc_start: 0.7355 (mm) cc_final: 0.7100 (mp) REVERT: A 122 ASP cc_start: 0.6111 (m-30) cc_final: 0.5721 (m-30) REVERT: A 216 LEU cc_start: 0.8667 (OUTLIER) cc_final: 0.8126 (tt) REVERT: A 231 GLN cc_start: 0.8790 (mm110) cc_final: 0.8516 (mm-40) REVERT: A 251 LEU cc_start: 0.7388 (OUTLIER) cc_final: 0.7068 (mt) REVERT: A 263 ASN cc_start: 0.7711 (p0) cc_final: 0.7184 (p0) REVERT: A 400 GLU cc_start: 0.7895 (tp30) cc_final: 0.7046 (mt-10) REVERT: A 808 ASN cc_start: 0.8115 (m-40) cc_final: 0.7147 (m110) REVERT: A 859 MET cc_start: 0.6642 (mmt) cc_final: 0.5698 (ttp) REVERT: A 1353 MET cc_start: 0.7508 (tmm) cc_final: 0.7181 (tpp) REVERT: A 1389 ILE cc_start: 0.8162 (OUTLIER) cc_final: 0.7773 (pp) REVERT: A 1651 ARG cc_start: 0.6415 (tpp-160) cc_final: 0.5120 (tmm160) REVERT: A 1689 ARG cc_start: 0.7613 (tpp80) cc_final: 0.6912 (ttp80) REVERT: A 1728 MET cc_start: 0.8421 (OUTLIER) cc_final: 0.8102 (mmt) outliers start: 25 outliers final: 17 residues processed: 173 average time/residue: 0.0946 time to fit residues: 22.0840 Evaluate side-chains 173 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 152 time to evaluate : 0.285 ------------------------------------------------------------------------------- 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 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 328 HIS Chi-restraints excluded: chain A residue 790 MET 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 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 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: 0.7980 chunk 53 optimal weight: 0.7980 chunk 48 optimal weight: 0.7980 chunk 85 optimal weight: 0.7980 chunk 20 optimal weight: 0.0770 chunk 74 optimal weight: 0.5980 chunk 31 optimal weight: 0.9980 chunk 87 optimal weight: 0.8980 chunk 22 optimal weight: 2.9990 chunk 35 optimal weight: 10.0000 chunk 70 optimal weight: 1.9990 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3755 r_free = 0.3755 target = 0.157545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.122609 restraints weight = 10553.283| |-----------------------------------------------------------------------------| r_work (start): 0.3194 rms_B_bonded: 1.79 r_work: 0.3003 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2872 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.3835 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= 0.113 Angle : 0.559 9.629 11826 Z= 0.268 Chirality : 0.041 0.261 1383 Planarity : 0.004 0.064 1414 Dihedral : 11.273 78.086 1587 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.99 % Allowed : 17.74 % Favored : 79.27 % 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: 1.34 (0.27), residues: 992 helix: 1.62 (0.20), residues: 735 sheet: -1.70 (1.63), residues: 12 loop : -1.23 (0.37), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 283 TYR 0.011 0.001 TYR A 374 PHE 0.011 0.001 PHE A 868 TRP 0.006 0.001 TRP A1465 HIS 0.002 0.000 HIS A1609 Details of bonding type rmsd covalent geometry : bond 0.00258 ( 8735) covalent geometry : angle 0.55584 (11806) SS BOND : bond 0.00269 ( 4) SS BOND : angle 0.84580 ( 8) hydrogen bonds : bond 0.03772 ( 485) hydrogen bonds : angle 3.85397 ( 1407) link_NAG-ASN : bond 0.00384 ( 4) link_NAG-ASN : angle 1.82749 ( 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 181 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 154 time to evaluate : 0.275 Fit side-chains REVERT: A 85 ARG cc_start: 0.7763 (mtt90) cc_final: 0.6678 (mtm180) REVERT: A 92 LEU cc_start: 0.7383 (mm) cc_final: 0.7095 (mp) REVERT: A 121 ASP cc_start: 0.7413 (t70) cc_final: 0.7133 (t70) REVERT: A 122 ASP cc_start: 0.6128 (m-30) cc_final: 0.5650 (m-30) REVERT: A 216 LEU cc_start: 0.8671 (OUTLIER) cc_final: 0.8154 (tt) REVERT: A 231 GLN cc_start: 0.8811 (mm110) cc_final: 0.8550 (mm-40) REVERT: A 251 LEU cc_start: 0.7416 (OUTLIER) cc_final: 0.7075 (mt) REVERT: A 263 ASN cc_start: 0.7514 (p0) cc_final: 0.7098 (p0) REVERT: A 400 GLU cc_start: 0.7900 (tp30) cc_final: 0.7069 (mt-10) REVERT: A 808 ASN cc_start: 0.8091 (m-40) cc_final: 0.7099 (m110) REVERT: A 839 MET cc_start: 0.7576 (mtp) cc_final: 0.7253 (mtm) REVERT: A 859 MET cc_start: 0.6579 (mmt) cc_final: 0.5661 (ttt) REVERT: A 1289 LEU cc_start: 0.8242 (OUTLIER) cc_final: 0.7024 (tt) REVERT: A 1353 MET cc_start: 0.7492 (tmm) cc_final: 0.7173 (tpp) REVERT: A 1389 ILE cc_start: 0.8174 (OUTLIER) cc_final: 0.7785 (pp) REVERT: A 1651 ARG cc_start: 0.6338 (tpp-160) cc_final: 0.5016 (tmm160) REVERT: A 1689 ARG cc_start: 0.7595 (tpp80) cc_final: 0.6925 (ttp80) REVERT: A 1728 MET cc_start: 0.8450 (OUTLIER) cc_final: 0.8127 (mmt) outliers start: 27 outliers final: 17 residues processed: 168 average time/residue: 0.0935 time to fit residues: 21.4451 Evaluate side-chains 172 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 150 time to evaluate : 0.222 ------------------------------------------------------------------------------- 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 790 MET 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 1254 MET Chi-restraints excluded: chain A residue 1289 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 1728 MET Chi-restraints excluded: chain A residue 1761 THR 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: 0.5980 chunk 41 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 51 optimal weight: 0.0050 chunk 60 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 chunk 78 optimal weight: 3.9990 chunk 30 optimal weight: 4.9990 chunk 100 optimal weight: 0.5980 chunk 93 optimal weight: 6.9990 overall best weight: 0.8196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 918 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1487 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.156364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.121135 restraints weight = 10415.539| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 1.79 r_work: 0.2985 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2852 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.3837 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= 0.131 Angle : 0.591 11.329 11826 Z= 0.282 Chirality : 0.042 0.267 1383 Planarity : 0.004 0.061 1414 Dihedral : 11.052 78.374 1587 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 3.22 % Allowed : 17.41 % Favored : 79.38 % 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: 1.30 (0.27), residues: 992 helix: 1.61 (0.19), residues: 734 sheet: -1.33 (1.75), residues: 12 loop : -1.27 (0.37), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1774 TYR 0.012 0.001 TYR A 374 PHE 0.020 0.001 PHE A 127 TRP 0.007 0.001 TRP A 911 HIS 0.002 0.001 HIS A1609 Details of bonding type rmsd covalent geometry : bond 0.00307 ( 8735) covalent geometry : angle 0.58796 (11806) SS BOND : bond 0.00319 ( 4) SS BOND : angle 0.92675 ( 8) hydrogen bonds : bond 0.04115 ( 485) hydrogen bonds : angle 3.93884 ( 1407) link_NAG-ASN : bond 0.00365 ( 4) link_NAG-ASN : angle 1.83063 ( 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 182 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 153 time to evaluate : 0.210 Fit side-chains REVERT: A 85 ARG cc_start: 0.7756 (mtt90) cc_final: 0.6686 (mtm180) REVERT: A 92 LEU cc_start: 0.7412 (mm) cc_final: 0.7113 (mp) REVERT: A 122 ASP cc_start: 0.6147 (m-30) cc_final: 0.5756 (m-30) REVERT: A 216 LEU cc_start: 0.8659 (OUTLIER) cc_final: 0.8105 (tt) REVERT: A 231 GLN cc_start: 0.8811 (mm110) cc_final: 0.8588 (mm-40) REVERT: A 251 LEU cc_start: 0.7444 (OUTLIER) cc_final: 0.7109 (mt) REVERT: A 263 ASN cc_start: 0.7589 (p0) cc_final: 0.7091 (p0) REVERT: A 400 GLU cc_start: 0.7945 (tp30) cc_final: 0.7098 (mt-10) REVERT: A 839 MET cc_start: 0.7515 (mtp) cc_final: 0.7259 (mtm) REVERT: A 859 MET cc_start: 0.6603 (mmt) cc_final: 0.5695 (ttt) REVERT: A 1289 LEU cc_start: 0.8365 (OUTLIER) cc_final: 0.7123 (tt) REVERT: A 1353 MET cc_start: 0.7574 (tmm) cc_final: 0.7255 (tpp) REVERT: A 1387 LYS cc_start: 0.7931 (mtpp) cc_final: 0.7209 (mttt) REVERT: A 1389 ILE cc_start: 0.8233 (OUTLIER) cc_final: 0.7842 (pp) REVERT: A 1651 ARG cc_start: 0.6283 (tpp-160) cc_final: 0.5002 (tmm160) REVERT: A 1669 LEU cc_start: 0.8001 (OUTLIER) cc_final: 0.7599 (tt) REVERT: A 1728 MET cc_start: 0.8414 (OUTLIER) cc_final: 0.8134 (mmt) outliers start: 29 outliers final: 19 residues processed: 169 average time/residue: 0.0844 time to fit residues: 19.7261 Evaluate side-chains 175 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 150 time to evaluate : 0.313 ------------------------------------------------------------------------------- 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 357 VAL Chi-restraints excluded: chain A residue 790 MET 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 1254 MET Chi-restraints excluded: chain A residue 1289 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 1669 LEU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 86 optimal weight: 0.0010 chunk 18 optimal weight: 0.5980 chunk 71 optimal weight: 0.0070 chunk 87 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 42 optimal weight: 0.5980 chunk 38 optimal weight: 0.8980 chunk 96 optimal weight: 0.5980 chunk 1 optimal weight: 0.5980 chunk 37 optimal weight: 4.9990 chunk 61 optimal weight: 0.8980 overall best weight: 0.3604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 918 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.151308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.116197 restraints weight = 10473.325| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 1.67 r_work: 0.3083 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2952 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.4080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8743 Z= 0.099 Angle : 0.537 9.563 11826 Z= 0.259 Chirality : 0.039 0.252 1383 Planarity : 0.004 0.062 1414 Dihedral : 10.595 77.967 1587 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.33 % Allowed : 18.18 % Favored : 79.49 % 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: 1.66 (0.27), residues: 992 helix: 1.87 (0.20), residues: 736 sheet: -1.37 (1.76), residues: 12 loop : -1.17 (0.37), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 834 TYR 0.009 0.001 TYR A 374 PHE 0.010 0.001 PHE A 101 TRP 0.007 0.001 TRP A 925 HIS 0.001 0.000 HIS A1609 Details of bonding type rmsd covalent geometry : bond 0.00213 ( 8735) covalent geometry : angle 0.53480 (11806) SS BOND : bond 0.00194 ( 4) SS BOND : angle 0.67261 ( 8) hydrogen bonds : bond 0.03443 ( 485) hydrogen bonds : angle 3.75092 ( 1407) link_NAG-ASN : bond 0.00320 ( 4) link_NAG-ASN : angle 1.59810 ( 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 171 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 150 time to evaluate : 0.306 Fit side-chains REVERT: A 85 ARG cc_start: 0.7634 (mtt90) cc_final: 0.6525 (mtm180) REVERT: A 92 LEU cc_start: 0.7094 (mm) cc_final: 0.6830 (mp) REVERT: A 122 ASP cc_start: 0.5947 (m-30) cc_final: 0.5534 (m-30) REVERT: A 216 LEU cc_start: 0.8437 (OUTLIER) cc_final: 0.7850 (tt) REVERT: A 251 LEU cc_start: 0.7407 (OUTLIER) cc_final: 0.7040 (mt) REVERT: A 400 GLU cc_start: 0.7805 (tp30) cc_final: 0.6962 (mt-10) REVERT: A 839 MET cc_start: 0.7363 (mtp) cc_final: 0.6966 (mtm) REVERT: A 859 MET cc_start: 0.6323 (mmt) cc_final: 0.5390 (ttt) REVERT: A 1353 MET cc_start: 0.7419 (tmm) cc_final: 0.7093 (tpp) REVERT: A 1389 ILE cc_start: 0.7954 (OUTLIER) cc_final: 0.7576 (pp) REVERT: A 1431 ASP cc_start: 0.8275 (t0) cc_final: 0.7943 (m-30) REVERT: A 1651 ARG cc_start: 0.6073 (tpp-160) cc_final: 0.4793 (tmm160) REVERT: A 1669 LEU cc_start: 0.7868 (OUTLIER) cc_final: 0.7468 (tt) REVERT: A 1728 MET cc_start: 0.8286 (OUTLIER) cc_final: 0.7964 (mmt) outliers start: 21 outliers final: 15 residues processed: 162 average time/residue: 0.0891 time to fit residues: 20.1257 Evaluate side-chains 163 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 143 time to evaluate : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 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 357 VAL Chi-restraints excluded: chain A residue 790 MET Chi-restraints excluded: chain A residue 822 ILE 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 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 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 1 optimal weight: 2.9990 chunk 89 optimal weight: 4.9990 chunk 5 optimal weight: 0.9980 chunk 55 optimal weight: 0.9980 chunk 67 optimal weight: 0.0170 chunk 78 optimal weight: 3.9990 chunk 65 optimal weight: 0.5980 chunk 11 optimal weight: 0.7980 chunk 15 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 8 optimal weight: 0.0870 overall best weight: 0.4996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.154186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.120303 restraints weight = 10398.218| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 1.57 r_work: 0.3114 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2987 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.4100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8743 Z= 0.105 Angle : 0.544 9.626 11826 Z= 0.262 Chirality : 0.040 0.258 1383 Planarity : 0.004 0.062 1414 Dihedral : 10.527 77.955 1587 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 2.33 % Allowed : 18.07 % Favored : 79.60 % 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: 1.75 (0.27), residues: 992 helix: 1.92 (0.19), residues: 736 sheet: -1.33 (1.78), residues: 12 loop : -1.09 (0.38), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 834 TYR 0.010 0.001 TYR A 374 PHE 0.022 0.001 PHE A 127 TRP 0.006 0.001 TRP A 925 HIS 0.002 0.000 HIS A1609 Details of bonding type rmsd covalent geometry : bond 0.00234 ( 8735) covalent geometry : angle 0.54201 (11806) SS BOND : bond 0.00222 ( 4) SS BOND : angle 0.73529 ( 8) hydrogen bonds : bond 0.03587 ( 485) hydrogen bonds : angle 3.76196 ( 1407) link_NAG-ASN : bond 0.00328 ( 4) link_NAG-ASN : angle 1.51399 ( 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 163 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 142 time to evaluate : 0.308 Fit side-chains REVERT: A 85 ARG cc_start: 0.7788 (mtt90) cc_final: 0.6654 (mtm180) REVERT: A 92 LEU cc_start: 0.7211 (mm) cc_final: 0.6936 (mp) REVERT: A 121 ASP cc_start: 0.7296 (t70) cc_final: 0.6985 (t70) REVERT: A 122 ASP cc_start: 0.6056 (m-30) cc_final: 0.5557 (m-30) REVERT: A 216 LEU cc_start: 0.8542 (OUTLIER) cc_final: 0.7991 (tt) REVERT: A 400 GLU cc_start: 0.7823 (tp30) cc_final: 0.7023 (mt-10) REVERT: A 839 MET cc_start: 0.7368 (mtp) cc_final: 0.6982 (mtm) REVERT: A 859 MET cc_start: 0.6332 (mmt) cc_final: 0.5412 (ttt) REVERT: A 1353 MET cc_start: 0.7395 (tmm) cc_final: 0.7081 (tpp) REVERT: A 1387 LYS cc_start: 0.7817 (mtpp) cc_final: 0.7052 (mttt) REVERT: A 1389 ILE cc_start: 0.8033 (OUTLIER) cc_final: 0.7658 (pp) REVERT: A 1431 ASP cc_start: 0.8295 (t0) cc_final: 0.7983 (m-30) REVERT: A 1651 ARG cc_start: 0.6150 (tpp-160) cc_final: 0.4874 (tmm160) REVERT: A 1669 LEU cc_start: 0.7945 (OUTLIER) cc_final: 0.7543 (tt) REVERT: A 1689 ARG cc_start: 0.8201 (tpp80) cc_final: 0.7418 (tpt90) REVERT: A 1728 MET cc_start: 0.8279 (OUTLIER) cc_final: 0.7973 (mmt) outliers start: 21 outliers final: 15 residues processed: 154 average time/residue: 0.0857 time to fit residues: 18.4360 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 : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 790 MET 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 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 1698 LYS 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: 3.9990 chunk 25 optimal weight: 0.8980 chunk 43 optimal weight: 1.9990 chunk 48 optimal weight: 0.6980 chunk 55 optimal weight: 3.9990 chunk 29 optimal weight: 7.9990 chunk 97 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 54 optimal weight: 0.6980 chunk 89 optimal weight: 2.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.154649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.118716 restraints weight = 10434.269| |-----------------------------------------------------------------------------| r_work (start): 0.3141 rms_B_bonded: 1.86 r_work: 0.2949 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2815 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.3860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8743 Z= 0.172 Angle : 0.634 10.932 11826 Z= 0.305 Chirality : 0.044 0.279 1383 Planarity : 0.005 0.061 1414 Dihedral : 11.260 78.348 1587 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.66 % Allowed : 17.96 % Favored : 79.38 % 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: 1.10 (0.27), residues: 992 helix: 1.48 (0.19), residues: 743 sheet: -1.20 (1.79), residues: 12 loop : -1.55 (0.37), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 834 TYR 0.014 0.002 TYR A 374 PHE 0.016 0.002 PHE A 868 TRP 0.010 0.001 TRP A 911 HIS 0.002 0.001 HIS A1609 Details of bonding type rmsd covalent geometry : bond 0.00419 ( 8735) covalent geometry : angle 0.63132 (11806) SS BOND : bond 0.00432 ( 4) SS BOND : angle 1.10798 ( 8) hydrogen bonds : bond 0.04678 ( 485) hydrogen bonds : angle 4.08961 ( 1407) link_NAG-ASN : bond 0.00457 ( 4) link_NAG-ASN : angle 1.74138 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2464.98 seconds wall clock time: 42 minutes 36.38 seconds (2556.38 seconds total)