Starting phenix.real_space_refine on Thu Feb 13 19:15:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6kzp_0792/02_2025/6kzp_0792.cif Found real_map, /net/cci-nas-00/data/ceres_data/6kzp_0792/02_2025/6kzp_0792.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6kzp_0792/02_2025/6kzp_0792.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6kzp_0792/02_2025/6kzp_0792.map" model { file = "/net/cci-nas-00/data/ceres_data/6kzp_0792/02_2025/6kzp_0792.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6kzp_0792/02_2025/6kzp_0792.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: {'GLN:plan1': 1, 'ASP:plan': 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: 5.95, per 1000 atoms: 0.70 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: 2.22 Conformation dependent library (CDL) restraints added in 949.7 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: 0.84 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: 2.71 Time building geometry restraints manager: 2.44 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: 5.760 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: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 21.430 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.660 ------------------------------------------------------------------------------- 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 8735 Z= 0.807 Angle : 1.454 23.926 11806 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.034 0.004 TRP A 233 HIS 0.009 0.002 HIS A 765 PHE 0.046 0.004 PHE A1403 TYR 0.029 0.004 TYR A 320 ARG 0.012 0.001 ARG A1441 *********************** 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 : 0.908 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: 0.2428 time to fit residues: 76.9373 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 : 0.961 ------------------------------------------------------------------------------- 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 85 optimal weight: 0.0670 chunk 76 optimal weight: 0.6980 chunk 42 optimal weight: 0.6980 chunk 26 optimal weight: 0.6980 chunk 51 optimal weight: 6.9990 chunk 40 optimal weight: 1.9990 chunk 79 optimal weight: 0.7980 chunk 30 optimal weight: 0.9980 chunk 48 optimal weight: 0.8980 chunk 58 optimal weight: 0.7980 chunk 91 optimal weight: 0.7980 overall best weight: 0.5918 ------------------------------------------------------------------------------- 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 A1442 HIS 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: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.157875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.123702 restraints weight = 10531.988| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 1.70 r_work: 0.3025 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2896 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.2766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8735 Z= 0.184 Angle : 0.654 9.490 11806 Z= 0.324 Chirality : 0.042 0.276 1383 Planarity : 0.006 0.072 1414 Dihedral : 14.611 97.219 1600 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 2.88 % Allowed : 11.64 % Favored : 85.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.06 (0.23), residues: 992 helix: -1.01 (0.17), residues: 736 sheet: -3.39 (1.42), residues: 12 loop : -1.85 (0.33), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 911 HIS 0.003 0.001 HIS A1751 PHE 0.014 0.001 PHE A1731 TYR 0.017 0.002 TYR A1437 ARG 0.005 0.001 ARG A1645 *********************** 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 213 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 187 time to evaluate : 0.967 Fit side-chains REVERT: A 83 PHE cc_start: 0.7065 (t80) cc_final: 0.6806 (t80) REVERT: A 85 ARG cc_start: 0.7817 (mtt90) cc_final: 0.7034 (mtm180) REVERT: A 92 LEU cc_start: 0.7366 (mm) cc_final: 0.7150 (mp) REVERT: A 118 GLN cc_start: 0.8005 (tt0) cc_final: 0.6904 (tp-100) REVERT: A 122 ASP cc_start: 0.6025 (m-30) cc_final: 0.5660 (m-30) REVERT: A 183 ARG cc_start: 0.7717 (ptt180) cc_final: 0.7465 (ptt90) REVERT: A 251 LEU cc_start: 0.7360 (OUTLIER) cc_final: 0.7111 (mt) REVERT: A 808 ASN cc_start: 0.8132 (m-40) cc_final: 0.7041 (m110) REVERT: A 835 THR cc_start: 0.8639 (m) cc_final: 0.8305 (p) REVERT: A 844 LEU cc_start: 0.7987 (OUTLIER) cc_final: 0.7734 (mm) REVERT: A 859 MET cc_start: 0.6868 (mmt) cc_final: 0.5919 (ptp) REVERT: A 1243 ARG cc_start: 0.7125 (ttt-90) cc_final: 0.6897 (ttt-90) REVERT: A 1283 GLU cc_start: 0.7876 (tt0) cc_final: 0.7511 (tt0) REVERT: A 1321 SER cc_start: 0.7423 (t) cc_final: 0.7218 (p) REVERT: A 1349 LYS cc_start: 0.3921 (tptt) cc_final: 0.3646 (tptt) REVERT: A 1353 MET cc_start: 0.7932 (tmm) cc_final: 0.7388 (tpp) REVERT: A 1383 MET cc_start: 0.8233 (mmt) cc_final: 0.7739 (mmm) REVERT: A 1431 ASP cc_start: 0.8042 (t0) cc_final: 0.7695 (t0) REVERT: A 1645 ARG cc_start: 0.7289 (ttt90) cc_final: 0.6691 (tpm170) REVERT: A 1651 ARG cc_start: 0.6142 (tpp-160) cc_final: 0.5128 (ttt180) REVERT: A 1689 ARG cc_start: 0.7567 (tpp80) cc_final: 0.7326 (mmm160) REVERT: A 1828 MET cc_start: 0.8017 (OUTLIER) cc_final: 0.7771 (mmm) outliers start: 26 outliers final: 13 residues processed: 204 average time/residue: 0.2237 time to fit residues: 61.1109 Evaluate side-chains 180 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 164 time to evaluate : 0.985 ------------------------------------------------------------------------------- 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 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 51 optimal weight: 0.5980 chunk 68 optimal weight: 9.9990 chunk 58 optimal weight: 1.9990 chunk 8 optimal weight: 7.9990 chunk 38 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 46 optimal weight: 0.0470 chunk 83 optimal weight: 0.9990 chunk 30 optimal weight: 0.5980 chunk 10 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 overall best weight: 0.5880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 371 ASN A1719 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.156114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.121799 restraints weight = 10621.857| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 1.68 r_work: 0.3021 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2890 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.3196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8735 Z= 0.169 Angle : 0.607 9.606 11806 Z= 0.291 Chirality : 0.042 0.317 1383 Planarity : 0.005 0.066 1414 Dihedral : 13.107 94.066 1591 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 3.22 % Allowed : 13.53 % Favored : 83.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.25), residues: 992 helix: 0.29 (0.19), residues: 737 sheet: -2.85 (1.47), residues: 12 loop : -1.73 (0.34), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 911 HIS 0.001 0.000 HIS A 328 PHE 0.014 0.001 PHE A 868 TYR 0.012 0.001 TYR A1437 ARG 0.005 0.000 ARG A 283 *********************** 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 199 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 170 time to evaluate : 1.060 Fit side-chains REVERT: A 85 ARG cc_start: 0.7813 (mtt90) cc_final: 0.6953 (mtm180) REVERT: A 92 LEU cc_start: 0.7293 (mm) cc_final: 0.7060 (mp) REVERT: A 118 GLN cc_start: 0.7980 (tt0) cc_final: 0.6833 (tp-100) REVERT: A 122 ASP cc_start: 0.6087 (m-30) cc_final: 0.5708 (m-30) REVERT: A 216 LEU cc_start: 0.8600 (OUTLIER) cc_final: 0.8150 (tt) REVERT: A 251 LEU cc_start: 0.7466 (OUTLIER) cc_final: 0.7209 (mt) REVERT: A 275 ARG cc_start: 0.7132 (mtp85) cc_final: 0.6861 (mtm-85) REVERT: A 400 GLU cc_start: 0.7845 (tp30) cc_final: 0.7323 (tt0) REVERT: A 808 ASN cc_start: 0.8132 (m-40) cc_final: 0.7205 (m110) REVERT: A 848 LEU cc_start: 0.7376 (OUTLIER) cc_final: 0.7084 (pp) REVERT: A 859 MET cc_start: 0.6784 (mmt) cc_final: 0.5866 (ptp) REVERT: A 1243 ARG cc_start: 0.7010 (ttt-90) cc_final: 0.6778 (ttt-90) REVERT: A 1283 GLU cc_start: 0.7745 (tt0) cc_final: 0.7507 (tt0) REVERT: A 1353 MET cc_start: 0.7788 (tmm) cc_final: 0.7393 (tpp) REVERT: A 1355 ARG cc_start: 0.6546 (mtm180) cc_final: 0.6293 (mtm180) REVERT: A 1389 ILE cc_start: 0.8240 (OUTLIER) cc_final: 0.7842 (pp) REVERT: A 1651 ARG cc_start: 0.6309 (tpp-160) cc_final: 0.5215 (tmm160) REVERT: A 1692 ARG cc_start: 0.8216 (ttm170) cc_final: 0.7908 (ttm170) REVERT: A 1789 LEU cc_start: 0.8698 (OUTLIER) cc_final: 0.8474 (pp) outliers start: 29 outliers final: 12 residues processed: 189 average time/residue: 0.2427 time to fit residues: 60.6607 Evaluate side-chains 173 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 156 time to evaluate : 1.066 ------------------------------------------------------------------------------- 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 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 1389 ILE Chi-restraints excluded: chain A residue 1476 VAL Chi-restraints excluded: chain A residue 1501 VAL Chi-restraints excluded: chain A residue 1630 ILE Chi-restraints excluded: chain A residue 1687 ILE Chi-restraints excluded: chain A residue 1761 THR 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 44 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 chunk 68 optimal weight: 4.9990 chunk 83 optimal weight: 0.2980 chunk 30 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 chunk 46 optimal weight: 0.8980 chunk 10 optimal weight: 2.9990 chunk 69 optimal weight: 0.7980 chunk 89 optimal weight: 4.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1451 GLN A1719 GLN A1782 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.152120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.116428 restraints weight = 10477.978| |-----------------------------------------------------------------------------| r_work (start): 0.3137 rms_B_bonded: 1.76 r_work: 0.2947 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2814 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.3276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 8735 Z= 0.291 Angle : 0.665 9.785 11806 Z= 0.320 Chirality : 0.046 0.333 1383 Planarity : 0.005 0.064 1414 Dihedral : 13.207 90.824 1589 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 3.33 % Allowed : 14.97 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.26), residues: 992 helix: 0.55 (0.19), residues: 740 sheet: -2.35 (1.47), residues: 12 loop : -1.87 (0.34), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 911 HIS 0.002 0.001 HIS A1280 PHE 0.020 0.002 PHE A 868 TYR 0.015 0.002 TYR A 370 ARG 0.005 0.001 ARG A 283 *********************** 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 187 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 157 time to evaluate : 0.986 Fit side-chains REVERT: A 85 ARG cc_start: 0.7732 (mtt90) cc_final: 0.6776 (mtt90) REVERT: A 92 LEU cc_start: 0.7328 (mm) cc_final: 0.7015 (mp) REVERT: A 118 GLN cc_start: 0.8036 (tt0) cc_final: 0.6953 (tp-100) REVERT: A 122 ASP cc_start: 0.6162 (m-30) cc_final: 0.5779 (m-30) REVERT: A 216 LEU cc_start: 0.8674 (OUTLIER) cc_final: 0.8123 (tt) REVERT: A 251 LEU cc_start: 0.7430 (OUTLIER) cc_final: 0.7167 (mt) REVERT: A 400 GLU cc_start: 0.7814 (tp30) cc_final: 0.7286 (tt0) REVERT: A 808 ASN cc_start: 0.8237 (m-40) cc_final: 0.7290 (m110) REVERT: A 811 ASP cc_start: 0.7047 (t0) cc_final: 0.6696 (t70) REVERT: A 839 MET cc_start: 0.7616 (mtp) cc_final: 0.7394 (mtm) REVERT: A 848 LEU cc_start: 0.7389 (OUTLIER) cc_final: 0.6941 (pp) REVERT: A 859 MET cc_start: 0.6844 (mmt) cc_final: 0.5915 (ptp) REVERT: A 1283 GLU cc_start: 0.7739 (tt0) cc_final: 0.7507 (tt0) REVERT: A 1353 MET cc_start: 0.7834 (tmm) cc_final: 0.7456 (tpp) REVERT: A 1389 ILE cc_start: 0.8266 (OUTLIER) cc_final: 0.7867 (pp) REVERT: A 1651 ARG cc_start: 0.6469 (tpp-160) cc_final: 0.5236 (tmm160) REVERT: A 1789 LEU cc_start: 0.8744 (OUTLIER) cc_final: 0.8489 (pp) outliers start: 30 outliers final: 19 residues processed: 174 average time/residue: 0.2498 time to fit residues: 57.6207 Evaluate side-chains 173 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 149 time to evaluate : 0.867 ------------------------------------------------------------------------------- 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 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 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 1668 THR 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 92 optimal weight: 0.7980 chunk 57 optimal weight: 3.9990 chunk 91 optimal weight: 0.7980 chunk 72 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 78 optimal weight: 0.9990 chunk 95 optimal weight: 0.6980 chunk 64 optimal weight: 2.9990 chunk 83 optimal weight: 4.9990 chunk 25 optimal weight: 1.9990 chunk 77 optimal weight: 0.8980 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 = 0.3737 r_free = 0.3737 target = 0.155904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.121113 restraints weight = 10437.526| |-----------------------------------------------------------------------------| r_work (start): 0.3174 rms_B_bonded: 1.71 r_work: 0.2981 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2851 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.3504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8735 Z= 0.196 Angle : 0.592 9.710 11806 Z= 0.285 Chirality : 0.042 0.275 1383 Planarity : 0.004 0.063 1414 Dihedral : 12.622 80.484 1589 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 3.44 % Allowed : 15.85 % Favored : 80.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.26), residues: 992 helix: 0.91 (0.19), residues: 741 sheet: -2.13 (1.49), residues: 12 loop : -1.73 (0.35), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1465 HIS 0.001 0.000 HIS A1609 PHE 0.014 0.001 PHE A 868 TYR 0.011 0.001 TYR A 374 ARG 0.006 0.000 ARG A 283 *********************** 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 183 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 152 time to evaluate : 0.979 Fit side-chains REVERT: A 85 ARG cc_start: 0.7741 (mtt90) cc_final: 0.6886 (mtm180) REVERT: A 92 LEU cc_start: 0.7372 (mm) cc_final: 0.7084 (mp) REVERT: A 122 ASP cc_start: 0.6134 (m-30) cc_final: 0.5744 (m-30) REVERT: A 216 LEU cc_start: 0.8688 (OUTLIER) cc_final: 0.8162 (tt) REVERT: A 251 LEU cc_start: 0.7450 (OUTLIER) cc_final: 0.7173 (mt) REVERT: A 263 ASN cc_start: 0.7663 (p0) cc_final: 0.7142 (p0) REVERT: A 400 GLU cc_start: 0.7914 (tp30) cc_final: 0.7239 (tt0) REVERT: A 808 ASN cc_start: 0.8177 (m-40) cc_final: 0.7405 (m110) REVERT: A 839 MET cc_start: 0.7572 (mtp) cc_final: 0.7355 (mtm) REVERT: A 848 LEU cc_start: 0.7215 (OUTLIER) cc_final: 0.6883 (pp) REVERT: A 859 MET cc_start: 0.6829 (mmt) cc_final: 0.5862 (ptp) REVERT: A 1353 MET cc_start: 0.7575 (tmm) cc_final: 0.7231 (tpp) REVERT: A 1387 LYS cc_start: 0.7941 (mtpp) cc_final: 0.7210 (mttt) REVERT: A 1389 ILE cc_start: 0.8219 (OUTLIER) cc_final: 0.7839 (pp) REVERT: A 1651 ARG cc_start: 0.6464 (tpp-160) cc_final: 0.5169 (tmm160) REVERT: A 1789 LEU cc_start: 0.8747 (OUTLIER) cc_final: 0.8529 (pp) outliers start: 31 outliers final: 17 residues processed: 170 average time/residue: 0.2336 time to fit residues: 53.1122 Evaluate side-chains 169 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 147 time to evaluate : 0.891 ------------------------------------------------------------------------------- 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 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 1604 THR Chi-restraints excluded: chain A residue 1630 ILE Chi-restraints excluded: chain A residue 1698 LYS Chi-restraints excluded: chain A residue 1728 MET Chi-restraints excluded: chain A residue 1761 THR Chi-restraints excluded: chain A residue 1789 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 84 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 chunk 57 optimal weight: 0.3980 chunk 82 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 chunk 62 optimal weight: 0.6980 chunk 48 optimal weight: 0.6980 chunk 73 optimal weight: 0.5980 chunk 24 optimal weight: 0.6980 chunk 90 optimal weight: 2.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1266 ASN A1487 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.155543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.120448 restraints weight = 10443.488| |-----------------------------------------------------------------------------| r_work (start): 0.3188 rms_B_bonded: 1.73 r_work: 0.3004 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2879 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.3768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8735 Z= 0.166 Angle : 0.565 9.608 11806 Z= 0.271 Chirality : 0.041 0.257 1383 Planarity : 0.004 0.064 1414 Dihedral : 11.826 78.372 1587 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 3.10 % Allowed : 17.07 % Favored : 79.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.27), residues: 992 helix: 1.32 (0.20), residues: 742 sheet: -1.88 (1.55), residues: 12 loop : -1.65 (0.35), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 152 HIS 0.002 0.000 HIS A1609 PHE 0.021 0.001 PHE A 127 TYR 0.010 0.001 TYR A 374 ARG 0.007 0.000 ARG A 834 *********************** 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 185 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 157 time to evaluate : 0.856 Fit side-chains REVERT: A 85 ARG cc_start: 0.7705 (mtt90) cc_final: 0.6819 (mtm180) REVERT: A 92 LEU cc_start: 0.7342 (mm) cc_final: 0.7087 (mp) REVERT: A 121 ASP cc_start: 0.7372 (t70) cc_final: 0.7116 (t70) REVERT: A 122 ASP cc_start: 0.6105 (m-30) cc_final: 0.5629 (m-30) REVERT: A 216 LEU cc_start: 0.8618 (OUTLIER) cc_final: 0.8075 (tt) REVERT: A 251 LEU cc_start: 0.7382 (OUTLIER) cc_final: 0.7062 (mt) REVERT: A 263 ASN cc_start: 0.7550 (p0) cc_final: 0.7138 (p0) REVERT: A 400 GLU cc_start: 0.7891 (tp30) cc_final: 0.7095 (mt-10) REVERT: A 808 ASN cc_start: 0.8205 (m-40) cc_final: 0.7288 (m110) REVERT: A 839 MET cc_start: 0.7484 (mtp) cc_final: 0.7237 (mtm) REVERT: A 848 LEU cc_start: 0.7185 (OUTLIER) cc_final: 0.6907 (pp) REVERT: A 859 MET cc_start: 0.6713 (mmt) cc_final: 0.5737 (ttp) REVERT: A 1243 ARG cc_start: 0.7171 (ttt-90) cc_final: 0.6885 (ttt180) REVERT: A 1353 MET cc_start: 0.7596 (tmm) cc_final: 0.7262 (tpp) REVERT: A 1389 ILE cc_start: 0.8187 (OUTLIER) cc_final: 0.7801 (pp) REVERT: A 1651 ARG cc_start: 0.6320 (tpp-160) cc_final: 0.5041 (tmm160) REVERT: A 1728 MET cc_start: 0.8412 (OUTLIER) cc_final: 0.8131 (mmt) outliers start: 28 outliers final: 16 residues processed: 172 average time/residue: 0.2167 time to fit residues: 50.8055 Evaluate side-chains 172 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 151 time to evaluate : 0.979 ------------------------------------------------------------------------------- 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 792 LEU 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 1668 THR 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 55 optimal weight: 3.9990 chunk 12 optimal weight: 0.9980 chunk 42 optimal weight: 0.9980 chunk 52 optimal weight: 0.0170 chunk 75 optimal weight: 0.5980 chunk 31 optimal weight: 1.9990 chunk 2 optimal weight: 0.0870 chunk 61 optimal weight: 0.8980 chunk 26 optimal weight: 0.6980 chunk 53 optimal weight: 0.9990 chunk 73 optimal weight: 0.8980 overall best weight: 0.4596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 918 GLN A1719 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.158301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.123530 restraints weight = 10581.221| |-----------------------------------------------------------------------------| r_work (start): 0.3206 rms_B_bonded: 1.72 r_work: 0.3028 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2899 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.3926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 8735 Z= 0.145 Angle : 0.548 10.302 11806 Z= 0.262 Chirality : 0.040 0.257 1383 Planarity : 0.004 0.061 1414 Dihedral : 11.035 78.035 1587 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.22 % Allowed : 18.18 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.27), residues: 992 helix: 1.53 (0.20), residues: 746 sheet: -1.58 (1.63), residues: 12 loop : -1.55 (0.36), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 152 HIS 0.001 0.000 HIS A1280 PHE 0.012 0.001 PHE A 128 TYR 0.010 0.001 TYR A 374 ARG 0.006 0.000 ARG A 834 *********************** 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 174 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 154 time to evaluate : 0.972 Fit side-chains REVERT: A 85 ARG cc_start: 0.7748 (mtt90) cc_final: 0.6876 (mtm180) REVERT: A 92 LEU cc_start: 0.7315 (mm) cc_final: 0.7086 (mp) REVERT: A 121 ASP cc_start: 0.7392 (t70) cc_final: 0.7106 (t70) REVERT: A 122 ASP cc_start: 0.6139 (m-30) cc_final: 0.5659 (m-30) REVERT: A 251 LEU cc_start: 0.7390 (OUTLIER) cc_final: 0.7052 (mt) REVERT: A 263 ASN cc_start: 0.7433 (p0) cc_final: 0.7013 (p0) REVERT: A 400 GLU cc_start: 0.7896 (tp30) cc_final: 0.7108 (mt-10) REVERT: A 808 ASN cc_start: 0.8053 (m-40) cc_final: 0.7065 (m110) REVERT: A 839 MET cc_start: 0.7507 (mtp) cc_final: 0.7158 (mtm) REVERT: A 859 MET cc_start: 0.6656 (mmt) cc_final: 0.5664 (ttt) REVERT: A 1243 ARG cc_start: 0.7079 (ttt-90) cc_final: 0.6855 (ttt180) REVERT: A 1353 MET cc_start: 0.7549 (tmm) cc_final: 0.7210 (tpp) REVERT: A 1389 ILE cc_start: 0.8140 (OUTLIER) cc_final: 0.7746 (pp) REVERT: A 1651 ARG cc_start: 0.6359 (tpp-160) cc_final: 0.5061 (tmm160) REVERT: A 1728 MET cc_start: 0.8392 (OUTLIER) cc_final: 0.8073 (mmt) outliers start: 20 outliers final: 14 residues processed: 164 average time/residue: 0.2215 time to fit residues: 49.8302 Evaluate side-chains 165 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 148 time to evaluate : 0.939 ------------------------------------------------------------------------------- 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 164 MET Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 867 THR Chi-restraints excluded: chain A residue 872 LEU Chi-restraints excluded: chain A residue 873 MET Chi-restraints excluded: chain A residue 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 1604 THR Chi-restraints excluded: chain A residue 1630 ILE Chi-restraints excluded: chain A residue 1698 LYS Chi-restraints excluded: chain A residue 1728 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 46 optimal weight: 0.8980 chunk 76 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 chunk 38 optimal weight: 0.0980 chunk 29 optimal weight: 7.9990 chunk 93 optimal weight: 8.9990 chunk 24 optimal weight: 0.6980 chunk 43 optimal weight: 1.9990 chunk 8 optimal weight: 0.5980 chunk 25 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.3736 r_free = 0.3736 target = 0.156146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.120690 restraints weight = 10596.297| |-----------------------------------------------------------------------------| r_work (start): 0.3192 rms_B_bonded: 1.78 r_work: 0.3003 rms_B_bonded: 2.75 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: 0.8085 moved from start: 0.3952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8735 Z= 0.166 Angle : 0.562 9.619 11806 Z= 0.270 Chirality : 0.041 0.262 1383 Planarity : 0.004 0.061 1414 Dihedral : 10.912 78.039 1587 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 2.55 % Allowed : 18.07 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.27), residues: 992 helix: 1.61 (0.19), residues: 744 sheet: -1.55 (1.64), residues: 12 loop : -1.57 (0.36), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A1465 HIS 0.001 0.000 HIS A1609 PHE 0.012 0.001 PHE A 128 TYR 0.011 0.001 TYR A 374 ARG 0.008 0.000 ARG A 283 *********************** 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 174 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 151 time to evaluate : 0.849 Fit side-chains REVERT: A 85 ARG cc_start: 0.7738 (mtt90) cc_final: 0.6638 (mtm180) REVERT: A 92 LEU cc_start: 0.7379 (mm) cc_final: 0.7081 (mp) REVERT: A 122 ASP cc_start: 0.6141 (m-30) cc_final: 0.5749 (m-30) REVERT: A 216 LEU cc_start: 0.8671 (OUTLIER) cc_final: 0.8131 (tt) REVERT: A 251 LEU cc_start: 0.7365 (OUTLIER) cc_final: 0.7021 (mt) REVERT: A 263 ASN cc_start: 0.7705 (p0) cc_final: 0.7179 (p0) REVERT: A 400 GLU cc_start: 0.7928 (tp30) cc_final: 0.7128 (mt-10) REVERT: A 839 MET cc_start: 0.7541 (mtp) cc_final: 0.7188 (mtm) REVERT: A 859 MET cc_start: 0.6638 (mmt) cc_final: 0.5673 (ttt) REVERT: A 1243 ARG cc_start: 0.7091 (ttt-90) cc_final: 0.6849 (ttt180) REVERT: A 1353 MET cc_start: 0.7538 (tmm) cc_final: 0.7218 (tpp) REVERT: A 1389 ILE cc_start: 0.8161 (OUTLIER) cc_final: 0.7759 (pp) REVERT: A 1431 ASP cc_start: 0.8356 (OUTLIER) cc_final: 0.8026 (m-30) REVERT: A 1651 ARG cc_start: 0.6355 (tpp-160) cc_final: 0.5102 (tmm160) REVERT: A 1669 LEU cc_start: 0.8034 (OUTLIER) cc_final: 0.7609 (tt) REVERT: A 1728 MET cc_start: 0.8460 (OUTLIER) cc_final: 0.8168 (mmt) outliers start: 23 outliers final: 16 residues processed: 163 average time/residue: 0.2236 time to fit residues: 49.0073 Evaluate side-chains 169 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 147 time to evaluate : 0.925 ------------------------------------------------------------------------------- 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 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 1377 LEU Chi-restraints excluded: chain A residue 1385 SER Chi-restraints excluded: chain A residue 1389 ILE Chi-restraints excluded: chain A residue 1431 ASP 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 31 optimal weight: 2.9990 chunk 35 optimal weight: 7.9990 chunk 32 optimal weight: 0.0470 chunk 65 optimal weight: 0.6980 chunk 98 optimal weight: 0.2980 chunk 67 optimal weight: 0.0980 chunk 11 optimal weight: 0.7980 chunk 84 optimal weight: 0.6980 chunk 30 optimal weight: 0.9990 chunk 71 optimal weight: 0.8980 chunk 55 optimal weight: 1.9990 overall best weight: 0.3678 ------------------------------------------------------------------------------- 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 = 0.3779 r_free = 0.3779 target = 0.159816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.124659 restraints weight = 10609.049| |-----------------------------------------------------------------------------| r_work (start): 0.3222 rms_B_bonded: 1.77 r_work: 0.3034 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2903 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.4120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 8735 Z= 0.134 Angle : 0.536 9.561 11806 Z= 0.258 Chirality : 0.039 0.253 1383 Planarity : 0.004 0.061 1414 Dihedral : 10.552 77.830 1587 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.53 (0.27), residues: 992 helix: 1.82 (0.20), residues: 746 sheet: -1.64 (1.64), residues: 12 loop : -1.50 (0.37), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 152 HIS 0.001 0.000 HIS A1609 PHE 0.011 0.001 PHE A 101 TYR 0.009 0.001 TYR A 374 ARG 0.008 0.000 ARG A 283 *********************** 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 174 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 153 time to evaluate : 0.887 Fit side-chains REVERT: A 85 ARG cc_start: 0.7691 (mtt90) cc_final: 0.6594 (mtm180) REVERT: A 92 LEU cc_start: 0.7320 (mm) cc_final: 0.7066 (mp) REVERT: A 121 ASP cc_start: 0.7390 (t70) cc_final: 0.7091 (t70) REVERT: A 122 ASP cc_start: 0.6147 (m-30) cc_final: 0.5653 (m-30) REVERT: A 216 LEU cc_start: 0.8653 (OUTLIER) cc_final: 0.8136 (tt) REVERT: A 251 LEU cc_start: 0.7195 (OUTLIER) cc_final: 0.6948 (mt) REVERT: A 400 GLU cc_start: 0.7944 (tp30) cc_final: 0.7084 (mt-10) REVERT: A 769 GLU cc_start: 0.7180 (tt0) cc_final: 0.6776 (tm-30) REVERT: A 790 MET cc_start: 0.7069 (ttp) cc_final: 0.6817 (ttp) REVERT: A 839 MET cc_start: 0.7497 (mtp) cc_final: 0.7137 (mtm) REVERT: A 859 MET cc_start: 0.6509 (mmt) cc_final: 0.5590 (ttt) REVERT: A 1243 ARG cc_start: 0.7111 (ttt-90) cc_final: 0.6901 (ttt180) REVERT: A 1353 MET cc_start: 0.7447 (tmm) cc_final: 0.7128 (tpp) REVERT: A 1389 ILE cc_start: 0.8135 (OUTLIER) cc_final: 0.7747 (pp) REVERT: A 1431 ASP cc_start: 0.8361 (OUTLIER) cc_final: 0.8077 (m-30) REVERT: A 1651 ARG cc_start: 0.6337 (tpp-160) cc_final: 0.5078 (tmm160) REVERT: A 1669 LEU cc_start: 0.8043 (OUTLIER) cc_final: 0.7581 (tt) REVERT: A 1728 MET cc_start: 0.8431 (OUTLIER) cc_final: 0.8104 (mmt) outliers start: 21 outliers final: 13 residues processed: 166 average time/residue: 0.2318 time to fit residues: 52.2774 Evaluate side-chains 164 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 145 time to evaluate : 0.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 164 MET Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 867 THR Chi-restraints excluded: chain A residue 872 LEU Chi-restraints excluded: chain A residue 873 MET Chi-restraints excluded: chain A residue 1377 LEU Chi-restraints excluded: chain A residue 1385 SER Chi-restraints excluded: chain A residue 1389 ILE Chi-restraints excluded: chain A residue 1431 ASP 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 1728 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 82 optimal weight: 0.0670 chunk 24 optimal weight: 1.9990 chunk 70 optimal weight: 0.9990 chunk 77 optimal weight: 0.0570 chunk 54 optimal weight: 0.1980 chunk 21 optimal weight: 3.9990 chunk 18 optimal weight: 0.9980 chunk 96 optimal weight: 0.5980 chunk 79 optimal weight: 0.8980 chunk 50 optimal weight: 0.0370 chunk 48 optimal weight: 0.5980 overall best weight: 0.1914 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1653 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.161561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.127107 restraints weight = 10585.373| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 1.74 r_work: 0.3097 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2968 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.4427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 8735 Z= 0.117 Angle : 0.517 9.530 11806 Z= 0.249 Chirality : 0.038 0.248 1383 Planarity : 0.004 0.061 1414 Dihedral : 10.000 77.875 1587 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.88 % Allowed : 18.51 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.03 (0.28), residues: 992 helix: 2.14 (0.20), residues: 737 sheet: -1.49 (1.71), residues: 12 loop : -1.05 (0.38), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 152 HIS 0.001 0.000 HIS A1830 PHE 0.017 0.001 PHE A 123 TYR 0.007 0.001 TYR A1807 ARG 0.004 0.000 ARG A 834 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1984 Ramachandran restraints generated. 992 Oldfield, 0 Emsley, 992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1984 Ramachandran restraints generated. 992 Oldfield, 0 Emsley, 992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 154 time to evaluate : 0.896 Fit side-chains REVERT: A 85 ARG cc_start: 0.7449 (mtt90) cc_final: 0.6641 (mtm180) REVERT: A 92 LEU cc_start: 0.7270 (mm) cc_final: 0.7002 (mp) REVERT: A 121 ASP cc_start: 0.7535 (t70) cc_final: 0.7257 (t70) REVERT: A 122 ASP cc_start: 0.6078 (m-30) cc_final: 0.5652 (m-30) REVERT: A 216 LEU cc_start: 0.8600 (OUTLIER) cc_final: 0.8091 (tt) REVERT: A 251 LEU cc_start: 0.7146 (OUTLIER) cc_final: 0.6890 (mt) REVERT: A 400 GLU cc_start: 0.7929 (tp30) cc_final: 0.7097 (mt-10) REVERT: A 769 GLU cc_start: 0.7214 (tt0) cc_final: 0.6803 (tm-30) REVERT: A 808 ASN cc_start: 0.7991 (m-40) cc_final: 0.5833 (t0) REVERT: A 859 MET cc_start: 0.6179 (mmt) cc_final: 0.5268 (ttt) REVERT: A 1353 MET cc_start: 0.7465 (tmm) cc_final: 0.7108 (tpp) REVERT: A 1383 MET cc_start: 0.7649 (mmm) cc_final: 0.7030 (mmp) REVERT: A 1389 ILE cc_start: 0.7977 (OUTLIER) cc_final: 0.7567 (pp) REVERT: A 1431 ASP cc_start: 0.8338 (t0) cc_final: 0.8001 (m-30) REVERT: A 1651 ARG cc_start: 0.6277 (tpp-160) cc_final: 0.5057 (tmm160) REVERT: A 1669 LEU cc_start: 0.8056 (OUTLIER) cc_final: 0.7577 (tt) REVERT: A 1728 MET cc_start: 0.8430 (OUTLIER) cc_final: 0.8059 (mmt) outliers start: 17 outliers final: 11 residues processed: 166 average time/residue: 0.2270 time to fit residues: 50.8151 Evaluate side-chains 160 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 144 time to evaluate : 0.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 164 MET Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 867 THR Chi-restraints excluded: chain A residue 872 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 1604 THR Chi-restraints excluded: chain A residue 1630 ILE Chi-restraints excluded: chain A residue 1669 LEU Chi-restraints excluded: chain A residue 1728 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 28 optimal weight: 4.9990 chunk 59 optimal weight: 3.9990 chunk 69 optimal weight: 0.9980 chunk 10 optimal weight: 0.9980 chunk 44 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 48 optimal weight: 0.0770 chunk 64 optimal weight: 0.9980 chunk 18 optimal weight: 2.9990 chunk 93 optimal weight: 8.9990 chunk 9 optimal weight: 2.9990 overall best weight: 1.0140 ------------------------------------------------------------------------------- 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 = 0.3743 r_free = 0.3743 target = 0.156440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.121299 restraints weight = 10620.802| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 1.69 r_work: 0.2991 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2861 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.4041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8735 Z= 0.229 Angle : 0.604 9.754 11806 Z= 0.291 Chirality : 0.042 0.272 1383 Planarity : 0.004 0.061 1414 Dihedral : 10.758 78.218 1587 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.00 % Allowed : 18.63 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.44 (0.27), residues: 992 helix: 1.74 (0.19), residues: 744 sheet: -1.49 (1.67), residues: 12 loop : -1.47 (0.37), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 911 HIS 0.002 0.001 HIS A1609 PHE 0.017 0.001 PHE A 128 TYR 0.014 0.002 TYR A 374 ARG 0.004 0.000 ARG A 834 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5394.07 seconds wall clock time: 96 minutes 8.63 seconds (5768.63 seconds total)