Starting phenix.real_space_refine on Sun Jul 27 11:10:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6kzp_0792/07_2025/6kzp_0792.cif Found real_map, /net/cci-nas-00/data/ceres_data/6kzp_0792/07_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_0792/07_2025/6kzp_0792.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6kzp_0792/07_2025/6kzp_0792.map" model { file = "/net/cci-nas-00/data/ceres_data/6kzp_0792/07_2025/6kzp_0792.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6kzp_0792/07_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-5711/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: 6.60, per 1000 atoms: 0.77 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: 2.67 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 1.22 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: 3.66 Time building geometry restraints manager: 3.05 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: 23.360 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: 0.010 Extract box with map and model: 0.460 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 28.380 Find NCS groups from input model: 0.100 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: 0.000 Load rotamer database and sin/cos tables:3.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.950 ------------------------------------------------------------------------------- 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 (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 Details of bonding type rmsd link_NAG-ASN : bond 0.00830 ( 4) link_NAG-ASN : angle 2.92919 ( 12) hydrogen bonds : bond 0.31391 ( 485) hydrogen bonds : angle 9.68840 ( 1407) SS BOND : bond 0.00577 ( 4) SS BOND : angle 2.36643 ( 8) covalent geometry : bond 0.01327 ( 8735) covalent geometry : angle 1.45373 (11806) *********************** 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 : 1.010 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: 0.3241 time to fit residues: 102.2843 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 : 1.164 ------------------------------------------------------------------------------- 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 = 0.123701 restraints weight = 10531.988| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 1.70 r_work: 0.3027 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2897 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 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 8743 Z= 0.136 Angle : 0.660 9.490 11826 Z= 0.325 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 Details of bonding type rmsd link_NAG-ASN : bond 0.00411 ( 4) link_NAG-ASN : angle 2.64829 ( 12) hydrogen bonds : bond 0.05203 ( 485) hydrogen bonds : angle 4.63996 ( 1407) SS BOND : bond 0.00243 ( 4) SS BOND : angle 1.17716 ( 8) covalent geometry : bond 0.00293 ( 8735) covalent geometry : angle 0.65447 (11806) *********************** 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 : 1.033 Fit side-chains REVERT: A 83 PHE cc_start: 0.7072 (t80) cc_final: 0.6813 (t80) REVERT: A 85 ARG cc_start: 0.7828 (mtt90) cc_final: 0.7051 (mtm180) REVERT: A 92 LEU cc_start: 0.7377 (mm) cc_final: 0.7163 (mp) REVERT: A 118 GLN cc_start: 0.8015 (tt0) cc_final: 0.6915 (tp-100) REVERT: A 122 ASP cc_start: 0.6030 (m-30) cc_final: 0.5666 (m-30) REVERT: A 183 ARG cc_start: 0.7723 (ptt180) cc_final: 0.7477 (ptt90) REVERT: A 251 LEU cc_start: 0.7355 (OUTLIER) cc_final: 0.7106 (mt) REVERT: A 808 ASN cc_start: 0.8145 (m-40) cc_final: 0.7059 (m110) REVERT: A 835 THR cc_start: 0.8638 (m) cc_final: 0.8306 (p) REVERT: A 844 LEU cc_start: 0.7991 (OUTLIER) cc_final: 0.7741 (mm) REVERT: A 859 MET cc_start: 0.6872 (mmt) cc_final: 0.5932 (ptp) REVERT: A 1243 ARG cc_start: 0.7137 (ttt-90) cc_final: 0.6908 (ttt-90) REVERT: A 1283 GLU cc_start: 0.7872 (tt0) cc_final: 0.7512 (tt0) REVERT: A 1321 SER cc_start: 0.7419 (t) cc_final: 0.7216 (p) REVERT: A 1349 LYS cc_start: 0.3952 (tptt) cc_final: 0.3677 (tptt) REVERT: A 1353 MET cc_start: 0.7948 (tmm) cc_final: 0.7405 (tpp) REVERT: A 1383 MET cc_start: 0.8237 (mmt) cc_final: 0.7743 (mmm) REVERT: A 1431 ASP cc_start: 0.8036 (t0) cc_final: 0.7693 (t0) REVERT: A 1645 ARG cc_start: 0.7295 (ttt90) cc_final: 0.6708 (tpm170) REVERT: A 1651 ARG cc_start: 0.6158 (tpp-160) cc_final: 0.5147 (ttt180) REVERT: A 1689 ARG cc_start: 0.7574 (tpp80) cc_final: 0.7333 (mmm160) REVERT: A 1828 MET cc_start: 0.8014 (OUTLIER) cc_final: 0.7765 (mmm) outliers start: 26 outliers final: 13 residues processed: 204 average time/residue: 0.2676 time to fit residues: 73.1227 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 : 1.435 ------------------------------------------------------------------------------- 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: 0.8980 chunk 68 optimal weight: 9.9990 chunk 58 optimal weight: 1.9990 chunk 8 optimal weight: 0.5980 chunk 38 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 46 optimal weight: 0.3980 chunk 83 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.3729 r_free = 0.3729 target = 0.155179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.120427 restraints weight = 10623.356| |-----------------------------------------------------------------------------| r_work (start): 0.3194 rms_B_bonded: 1.72 r_work: 0.3001 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2868 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.3117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8743 Z= 0.131 Angle : 0.628 9.613 11826 Z= 0.300 Chirality : 0.043 0.344 1383 Planarity : 0.005 0.065 1414 Dihedral : 13.394 94.787 1591 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 3.33 % Allowed : 13.41 % 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: -0.55 (0.25), residues: 992 helix: 0.21 (0.19), residues: 737 sheet: -2.83 (1.47), residues: 12 loop : -1.75 (0.34), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 911 HIS 0.001 0.000 HIS A 328 PHE 0.015 0.001 PHE A 868 TYR 0.012 0.001 TYR A1437 ARG 0.005 0.000 ARG A 283 Details of bonding type rmsd link_NAG-ASN : bond 0.01269 ( 4) link_NAG-ASN : angle 2.00098 ( 12) hydrogen bonds : bond 0.04647 ( 485) hydrogen bonds : angle 4.24590 ( 1407) SS BOND : bond 0.00291 ( 4) SS BOND : angle 1.05035 ( 8) covalent geometry : bond 0.00295 ( 8735) covalent geometry : angle 0.62485 (11806) *********************** 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: 30 poor density : 169 time to evaluate : 0.886 Fit side-chains REVERT: A 85 ARG cc_start: 0.7797 (mtt90) cc_final: 0.6930 (mtm180) REVERT: A 92 LEU cc_start: 0.7313 (mm) cc_final: 0.7074 (mp) REVERT: A 118 GLN cc_start: 0.7998 (tt0) cc_final: 0.6868 (tp-100) REVERT: A 122 ASP cc_start: 0.6077 (m-30) cc_final: 0.5699 (m-30) REVERT: A 216 LEU cc_start: 0.8612 (OUTLIER) cc_final: 0.8141 (tt) REVERT: A 251 LEU cc_start: 0.7470 (OUTLIER) cc_final: 0.7197 (mt) REVERT: A 275 ARG cc_start: 0.7160 (mtp85) cc_final: 0.6876 (mtm-85) REVERT: A 400 GLU cc_start: 0.7876 (tp30) cc_final: 0.7329 (tt0) REVERT: A 808 ASN cc_start: 0.8140 (m-40) cc_final: 0.7034 (m110) REVERT: A 848 LEU cc_start: 0.7360 (OUTLIER) cc_final: 0.7068 (pp) REVERT: A 859 MET cc_start: 0.6840 (mmt) cc_final: 0.5900 (ptp) REVERT: A 1243 ARG cc_start: 0.6962 (ttt-90) cc_final: 0.6715 (ttt-90) REVERT: A 1283 GLU cc_start: 0.7780 (tt0) cc_final: 0.7523 (tt0) REVERT: A 1321 SER cc_start: 0.7424 (t) cc_final: 0.7204 (p) REVERT: A 1353 MET cc_start: 0.7792 (tmm) cc_final: 0.7383 (tpp) REVERT: A 1355 ARG cc_start: 0.6587 (mtm180) cc_final: 0.6326 (mtm180) REVERT: A 1389 ILE cc_start: 0.8229 (OUTLIER) cc_final: 0.7840 (pp) REVERT: A 1651 ARG cc_start: 0.6320 (tpp-160) cc_final: 0.5219 (tmm160) REVERT: A 1692 ARG cc_start: 0.8206 (ttm170) cc_final: 0.7974 (ttm170) REVERT: A 1789 LEU cc_start: 0.8697 (OUTLIER) cc_final: 0.8460 (pp) outliers start: 30 outliers final: 14 residues processed: 188 average time/residue: 0.2374 time to fit residues: 59.2563 Evaluate side-chains 182 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 163 time to evaluate : 0.966 ------------------------------------------------------------------------------- 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 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 44 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 chunk 68 optimal weight: 6.9990 chunk 83 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 chunk 46 optimal weight: 0.6980 chunk 10 optimal weight: 0.9980 chunk 69 optimal weight: 0.8980 chunk 89 optimal weight: 0.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1451 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.153119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.117858 restraints weight = 10504.900| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 1.73 r_work: 0.2971 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2840 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.3309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8743 Z= 0.161 Angle : 0.635 9.728 11826 Z= 0.304 Chirality : 0.044 0.278 1383 Planarity : 0.005 0.064 1414 Dihedral : 12.854 91.057 1589 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 3.77 % Allowed : 14.19 % Favored : 82.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.13 (0.26), residues: 992 helix: 0.70 (0.19), residues: 730 sheet: -2.44 (1.45), residues: 12 loop : -1.44 (0.36), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 911 HIS 0.002 0.001 HIS A 328 PHE 0.018 0.002 PHE A 868 TYR 0.014 0.002 TYR A 374 ARG 0.005 0.000 ARG A 283 Details of bonding type rmsd link_NAG-ASN : bond 0.00845 ( 4) link_NAG-ASN : angle 2.71773 ( 12) hydrogen bonds : bond 0.04795 ( 485) hydrogen bonds : angle 4.23676 ( 1407) SS BOND : bond 0.00366 ( 4) SS BOND : angle 1.11498 ( 8) covalent geometry : bond 0.00384 ( 8735) covalent geometry : angle 0.62908 (11806) *********************** 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 191 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 157 time to evaluate : 1.098 Fit side-chains REVERT: A 85 ARG cc_start: 0.7768 (mtt90) cc_final: 0.6838 (mtt90) REVERT: A 92 LEU cc_start: 0.7300 (mm) cc_final: 0.7004 (mp) REVERT: A 118 GLN cc_start: 0.8011 (tt0) cc_final: 0.6887 (tp-100) REVERT: A 122 ASP cc_start: 0.6109 (m-30) cc_final: 0.5728 (m-30) REVERT: A 216 LEU cc_start: 0.8667 (OUTLIER) cc_final: 0.8127 (tt) REVERT: A 251 LEU cc_start: 0.7458 (OUTLIER) cc_final: 0.7208 (mt) REVERT: A 400 GLU cc_start: 0.7788 (tp30) cc_final: 0.7272 (tt0) REVERT: A 808 ASN cc_start: 0.8172 (m-40) cc_final: 0.7166 (m110) REVERT: A 811 ASP cc_start: 0.6972 (t0) cc_final: 0.6614 (t70) REVERT: A 839 MET cc_start: 0.7582 (mtp) cc_final: 0.7352 (mtm) REVERT: A 848 LEU cc_start: 0.7384 (OUTLIER) cc_final: 0.6932 (pp) REVERT: A 859 MET cc_start: 0.6804 (mmt) cc_final: 0.5871 (ptp) REVERT: A 1283 GLU cc_start: 0.7730 (tt0) cc_final: 0.7509 (tt0) REVERT: A 1321 SER cc_start: 0.7484 (t) cc_final: 0.7271 (p) REVERT: A 1353 MET cc_start: 0.7813 (tmm) cc_final: 0.7432 (tpp) REVERT: A 1387 LYS cc_start: 0.7950 (mtpp) cc_final: 0.7216 (mttt) REVERT: A 1389 ILE cc_start: 0.8249 (OUTLIER) cc_final: 0.7850 (pp) REVERT: A 1651 ARG cc_start: 0.6384 (tpp-160) cc_final: 0.5164 (tmm160) REVERT: A 1789 LEU cc_start: 0.8720 (OUTLIER) cc_final: 0.8474 (pp) outliers start: 34 outliers final: 22 residues processed: 176 average time/residue: 0.2319 time to fit residues: 54.4767 Evaluate side-chains 178 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 151 time to evaluate : 0.881 ------------------------------------------------------------------------------- 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 1385 SER Chi-restraints excluded: chain A residue 1389 ILE Chi-restraints excluded: chain A residue 1476 VAL Chi-restraints excluded: chain A residue 1501 VAL Chi-restraints excluded: chain A residue 1604 THR Chi-restraints excluded: chain A residue 1630 ILE Chi-restraints excluded: chain A residue 1632 VAL Chi-restraints excluded: chain A residue 1668 THR Chi-restraints excluded: chain A residue 1687 ILE Chi-restraints excluded: chain A residue 1698 LYS Chi-restraints excluded: chain A residue 1700 LEU 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 92 optimal weight: 2.9990 chunk 57 optimal weight: 4.9990 chunk 91 optimal weight: 0.7980 chunk 72 optimal weight: 0.8980 chunk 22 optimal weight: 2.9990 chunk 78 optimal weight: 0.9990 chunk 95 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1719 GLN A1782 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.150830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.116077 restraints weight = 10510.691| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 1.65 r_work: 0.3121 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2999 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.3406 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= 0.181 Angle : 0.653 9.822 11826 Z= 0.313 Chirality : 0.045 0.281 1383 Planarity : 0.005 0.063 1414 Dihedral : 12.626 85.220 1589 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 3.88 % Allowed : 15.96 % Favored : 80.16 % 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: 0.23 (0.26), residues: 992 helix: 0.78 (0.19), residues: 731 sheet: -2.10 (1.51), residues: 12 loop : -1.44 (0.36), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 911 HIS 0.003 0.001 HIS A1609 PHE 0.018 0.002 PHE A 868 TYR 0.015 0.002 TYR A 370 ARG 0.006 0.001 ARG A1774 Details of bonding type rmsd link_NAG-ASN : bond 0.00556 ( 4) link_NAG-ASN : angle 2.31905 ( 12) hydrogen bonds : bond 0.04937 ( 485) hydrogen bonds : angle 4.28217 ( 1407) SS BOND : bond 0.00434 ( 4) SS BOND : angle 1.19154 ( 8) covalent geometry : bond 0.00440 ( 8735) covalent geometry : angle 0.64902 (11806) *********************** 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 189 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 154 time to evaluate : 0.982 Fit side-chains REVERT: A 85 ARG cc_start: 0.7844 (mtt90) cc_final: 0.7022 (mtm180) REVERT: A 92 LEU cc_start: 0.7563 (mm) cc_final: 0.7272 (mp) REVERT: A 122 ASP cc_start: 0.6307 (m-30) cc_final: 0.5938 (m-30) REVERT: A 216 LEU cc_start: 0.8705 (OUTLIER) cc_final: 0.8148 (tt) REVERT: A 251 LEU cc_start: 0.7473 (OUTLIER) cc_final: 0.7194 (mt) REVERT: A 263 ASN cc_start: 0.7736 (p0) cc_final: 0.7253 (p0) REVERT: A 400 GLU cc_start: 0.8018 (tp30) cc_final: 0.7373 (tt0) REVERT: A 808 ASN cc_start: 0.8273 (m-40) cc_final: 0.7318 (m110) REVERT: A 811 ASP cc_start: 0.7132 (t0) cc_final: 0.6784 (t70) REVERT: A 848 LEU cc_start: 0.7521 (OUTLIER) cc_final: 0.7157 (pp) REVERT: A 859 MET cc_start: 0.7046 (mmt) cc_final: 0.6173 (ptp) REVERT: A 1260 LEU cc_start: 0.8210 (OUTLIER) cc_final: 0.7943 (tt) REVERT: A 1353 MET cc_start: 0.8034 (tmm) cc_final: 0.7684 (tpp) REVERT: A 1387 LYS cc_start: 0.7996 (mtpp) cc_final: 0.7279 (mttt) REVERT: A 1389 ILE cc_start: 0.8370 (OUTLIER) cc_final: 0.7981 (pp) REVERT: A 1651 ARG cc_start: 0.6595 (tpp-160) cc_final: 0.5308 (tmm160) REVERT: A 1789 LEU cc_start: 0.8799 (OUTLIER) cc_final: 0.8589 (pp) outliers start: 35 outliers final: 21 residues processed: 176 average time/residue: 0.2283 time to fit residues: 54.1980 Evaluate side-chains 174 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 147 time to evaluate : 0.963 ------------------------------------------------------------------------------- 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 1260 LEU Chi-restraints excluded: chain A residue 1377 LEU Chi-restraints excluded: chain A residue 1385 SER Chi-restraints excluded: chain A residue 1389 ILE Chi-restraints excluded: chain A residue 1476 VAL Chi-restraints excluded: chain A residue 1501 VAL Chi-restraints excluded: chain A residue 1604 THR Chi-restraints excluded: chain A residue 1630 ILE Chi-restraints excluded: chain A residue 1668 THR Chi-restraints excluded: chain A residue 1687 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: 0.9990 chunk 57 optimal weight: 2.9990 chunk 82 optimal weight: 3.9990 chunk 83 optimal weight: 0.2980 chunk 62 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 24 optimal weight: 0.7980 chunk 90 optimal weight: 2.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1487 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.154316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.118973 restraints weight = 10447.626| |-----------------------------------------------------------------------------| r_work (start): 0.3167 rms_B_bonded: 1.74 r_work: 0.2979 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2847 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.3639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8743 Z= 0.130 Angle : 0.588 9.684 11826 Z= 0.282 Chirality : 0.042 0.264 1383 Planarity : 0.004 0.063 1414 Dihedral : 11.928 78.611 1589 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 3.33 % Allowed : 17.18 % 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: 0.73 (0.27), residues: 992 helix: 1.16 (0.19), residues: 731 sheet: -1.86 (1.55), residues: 12 loop : -1.34 (0.36), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1465 HIS 0.002 0.000 HIS A1609 PHE 0.020 0.001 PHE A 127 TYR 0.011 0.001 TYR A 374 ARG 0.005 0.000 ARG A 283 Details of bonding type rmsd link_NAG-ASN : bond 0.00448 ( 4) link_NAG-ASN : angle 2.04648 ( 12) hydrogen bonds : bond 0.04173 ( 485) hydrogen bonds : angle 4.06585 ( 1407) SS BOND : bond 0.00310 ( 4) SS BOND : angle 0.96070 ( 8) covalent geometry : bond 0.00305 ( 8735) covalent geometry : angle 0.58442 (11806) *********************** 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 182 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 152 time to evaluate : 0.983 Fit side-chains REVERT: A 85 ARG cc_start: 0.7730 (mtt90) cc_final: 0.6841 (mtm180) REVERT: A 92 LEU cc_start: 0.7370 (mm) cc_final: 0.7096 (mp) REVERT: A 122 ASP cc_start: 0.6133 (m-30) cc_final: 0.5734 (m-30) REVERT: A 216 LEU cc_start: 0.8658 (OUTLIER) cc_final: 0.8111 (tt) REVERT: A 251 LEU cc_start: 0.7409 (OUTLIER) cc_final: 0.7135 (mt) REVERT: A 263 ASN cc_start: 0.7650 (p0) cc_final: 0.7118 (p0) REVERT: A 400 GLU cc_start: 0.7924 (tp30) cc_final: 0.7264 (tt0) REVERT: A 808 ASN cc_start: 0.8160 (m-40) cc_final: 0.7348 (m110) REVERT: A 848 LEU cc_start: 0.7236 (OUTLIER) cc_final: 0.6940 (pp) REVERT: A 859 MET cc_start: 0.6795 (mmt) cc_final: 0.5828 (ptp) REVERT: A 1353 MET cc_start: 0.7628 (tmm) cc_final: 0.7291 (tpp) REVERT: A 1387 LYS cc_start: 0.7929 (mtpp) cc_final: 0.7204 (mttt) REVERT: A 1389 ILE cc_start: 0.8203 (OUTLIER) cc_final: 0.7855 (pp) REVERT: A 1651 ARG cc_start: 0.6334 (tpp-160) cc_final: 0.5068 (tmm160) REVERT: A 1789 LEU cc_start: 0.8653 (OUTLIER) cc_final: 0.8444 (pp) outliers start: 30 outliers final: 17 residues processed: 169 average time/residue: 0.2160 time to fit residues: 50.3782 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 : 1.018 ------------------------------------------------------------------------------- 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 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 1377 LEU 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 1700 LEU Chi-restraints excluded: chain A residue 1761 THR Chi-restraints excluded: chain A residue 1789 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 55 optimal weight: 0.9990 chunk 12 optimal weight: 0.9990 chunk 42 optimal weight: 0.5980 chunk 52 optimal weight: 2.9990 chunk 75 optimal weight: 0.5980 chunk 31 optimal weight: 0.0980 chunk 2 optimal weight: 0.0370 chunk 61 optimal weight: 2.9990 chunk 26 optimal weight: 0.7980 chunk 53 optimal weight: 0.7980 chunk 73 optimal weight: 4.9990 overall best weight: 0.4258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 918 GLN A1266 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.156910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.122090 restraints weight = 10594.917| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 1.73 r_work: 0.3027 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2896 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.3928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 8743 Z= 0.102 Angle : 0.550 10.211 11826 Z= 0.263 Chirality : 0.040 0.254 1383 Planarity : 0.004 0.061 1414 Dihedral : 10.986 78.086 1587 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.55 % Allowed : 17.96 % 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: 1.26 (0.27), residues: 992 helix: 1.58 (0.20), residues: 735 sheet: -1.78 (1.57), residues: 12 loop : -1.28 (0.37), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 925 HIS 0.001 0.000 HIS A1609 PHE 0.011 0.001 PHE A 128 TYR 0.009 0.001 TYR A 374 ARG 0.004 0.000 ARG A 834 Details of bonding type rmsd link_NAG-ASN : bond 0.00353 ( 4) link_NAG-ASN : angle 1.85766 ( 12) hydrogen bonds : bond 0.03533 ( 485) hydrogen bonds : angle 3.84036 ( 1407) SS BOND : bond 0.00202 ( 4) SS BOND : angle 0.74552 ( 8) covalent geometry : bond 0.00224 ( 8735) covalent geometry : angle 0.54708 (11806) *********************** 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 182 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 159 time to evaluate : 0.970 Fit side-chains REVERT: A 85 ARG cc_start: 0.7757 (mtt90) cc_final: 0.6894 (mtm180) REVERT: A 92 LEU cc_start: 0.7305 (mm) cc_final: 0.7087 (mp) REVERT: A 122 ASP cc_start: 0.6147 (m-30) cc_final: 0.5746 (m-30) REVERT: A 251 LEU cc_start: 0.7349 (OUTLIER) cc_final: 0.7014 (mt) REVERT: A 263 ASN cc_start: 0.7448 (p0) cc_final: 0.7023 (p0) REVERT: A 400 GLU cc_start: 0.7900 (tp30) cc_final: 0.7120 (mt-10) REVERT: A 808 ASN cc_start: 0.8083 (m-40) cc_final: 0.7218 (m110) REVERT: A 859 MET cc_start: 0.6716 (mmt) cc_final: 0.5762 (ptp) REVERT: A 1289 LEU cc_start: 0.8221 (OUTLIER) cc_final: 0.7997 (mt) REVERT: A 1353 MET cc_start: 0.7568 (tmm) cc_final: 0.7227 (tpp) REVERT: A 1387 LYS cc_start: 0.7854 (mtpp) cc_final: 0.7115 (mttt) REVERT: A 1389 ILE cc_start: 0.8134 (OUTLIER) cc_final: 0.7759 (pp) REVERT: A 1651 ARG cc_start: 0.6317 (tpp-160) cc_final: 0.5067 (tmm160) outliers start: 23 outliers final: 16 residues processed: 173 average time/residue: 0.2186 time to fit residues: 52.0861 Evaluate side-chains 167 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 148 time to evaluate : 0.915 ------------------------------------------------------------------------------- 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 357 VAL Chi-restraints excluded: chain A residue 792 LEU Chi-restraints excluded: chain A residue 867 THR 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 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 1700 LEU 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 46 optimal weight: 0.9990 chunk 76 optimal weight: 0.5980 chunk 18 optimal weight: 0.9990 chunk 1 optimal weight: 0.9990 chunk 38 optimal weight: 0.9990 chunk 29 optimal weight: 7.9990 chunk 93 optimal weight: 6.9990 chunk 24 optimal weight: 0.1980 chunk 43 optimal weight: 0.7980 chunk 8 optimal weight: 0.7980 chunk 25 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.3753 r_free = 0.3753 target = 0.157224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.121956 restraints weight = 10598.024| |-----------------------------------------------------------------------------| r_work (start): 0.3186 rms_B_bonded: 1.80 r_work: 0.2996 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2865 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.3932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8743 Z= 0.118 Angle : 0.572 9.616 11826 Z= 0.274 Chirality : 0.041 0.262 1383 Planarity : 0.004 0.060 1414 Dihedral : 10.922 78.170 1587 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.88 % Allowed : 18.29 % Favored : 78.82 % 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: 1.33 (0.27), residues: 992 helix: 1.63 (0.19), residues: 734 sheet: -1.55 (1.63), residues: 12 loop : -1.29 (0.37), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A1465 HIS 0.002 0.001 HIS A1609 PHE 0.020 0.001 PHE A 127 TYR 0.011 0.001 TYR A 374 ARG 0.008 0.000 ARG A 283 Details of bonding type rmsd link_NAG-ASN : bond 0.00337 ( 4) link_NAG-ASN : angle 1.80589 ( 12) hydrogen bonds : bond 0.03848 ( 485) hydrogen bonds : angle 3.90302 ( 1407) SS BOND : bond 0.00295 ( 4) SS BOND : angle 0.86047 ( 8) covalent geometry : bond 0.00272 ( 8735) covalent geometry : angle 0.56907 (11806) *********************** 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 173 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 147 time to evaluate : 0.960 Fit side-chains REVERT: A 85 ARG cc_start: 0.7733 (mtt90) cc_final: 0.6631 (mtm180) REVERT: A 92 LEU cc_start: 0.7374 (mm) cc_final: 0.7078 (mp) REVERT: A 121 ASP cc_start: 0.7402 (t70) cc_final: 0.7122 (t70) REVERT: A 122 ASP cc_start: 0.6164 (m-30) cc_final: 0.5686 (m-30) REVERT: A 216 LEU cc_start: 0.8680 (OUTLIER) cc_final: 0.8138 (tt) REVERT: A 251 LEU cc_start: 0.7411 (OUTLIER) cc_final: 0.7080 (mt) REVERT: A 263 ASN cc_start: 0.7735 (p0) cc_final: 0.7207 (p0) REVERT: A 400 GLU cc_start: 0.7905 (tp30) cc_final: 0.7088 (mt-10) REVERT: A 808 ASN cc_start: 0.8065 (m-40) cc_final: 0.7111 (m110) REVERT: A 859 MET cc_start: 0.6632 (mmt) cc_final: 0.5663 (ttt) REVERT: A 1289 LEU cc_start: 0.8261 (OUTLIER) cc_final: 0.7030 (tt) REVERT: A 1353 MET cc_start: 0.7570 (tmm) cc_final: 0.7241 (tpp) REVERT: A 1389 ILE cc_start: 0.8195 (OUTLIER) cc_final: 0.7797 (pp) REVERT: A 1651 ARG cc_start: 0.6396 (tpp-160) cc_final: 0.5108 (tmm160) outliers start: 26 outliers final: 21 residues processed: 161 average time/residue: 0.2091 time to fit residues: 46.3552 Evaluate side-chains 168 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 143 time to evaluate : 0.880 ------------------------------------------------------------------------------- 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 357 VAL Chi-restraints excluded: chain A residue 792 LEU 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 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 1667 ILE 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 31 optimal weight: 0.2980 chunk 35 optimal weight: 2.9990 chunk 32 optimal weight: 0.4980 chunk 65 optimal weight: 0.5980 chunk 98 optimal weight: 0.9990 chunk 67 optimal weight: 2.9990 chunk 11 optimal weight: 0.8980 chunk 84 optimal weight: 0.9980 chunk 30 optimal weight: 0.8980 chunk 71 optimal weight: 0.0870 chunk 55 optimal weight: 0.9990 overall best weight: 0.4758 ------------------------------------------------------------------------------- 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 = 0.3745 r_free = 0.3745 target = 0.156899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.121661 restraints weight = 10651.551| |-----------------------------------------------------------------------------| r_work (start): 0.3203 rms_B_bonded: 1.82 r_work: 0.3011 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2879 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.4086 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= 0.103 Angle : 0.543 9.581 11826 Z= 0.262 Chirality : 0.040 0.255 1383 Planarity : 0.004 0.061 1414 Dihedral : 10.669 77.633 1587 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.44 % Allowed : 18.51 % Favored : 79.05 % 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: 1.56 (0.27), residues: 992 helix: 1.81 (0.20), residues: 736 sheet: -1.56 (1.65), residues: 12 loop : -1.23 (0.37), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 925 HIS 0.001 0.000 HIS A1609 PHE 0.011 0.001 PHE A 128 TYR 0.009 0.001 TYR A 374 ARG 0.003 0.000 ARG A 834 Details of bonding type rmsd link_NAG-ASN : bond 0.00334 ( 4) link_NAG-ASN : angle 1.66935 ( 12) hydrogen bonds : bond 0.03553 ( 485) hydrogen bonds : angle 3.80225 ( 1407) SS BOND : bond 0.00220 ( 4) SS BOND : angle 0.71949 ( 8) covalent geometry : bond 0.00230 ( 8735) covalent geometry : angle 0.54055 (11806) *********************** 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 169 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 147 time to evaluate : 0.870 Fit side-chains REVERT: A 85 ARG cc_start: 0.7701 (mtt90) cc_final: 0.6608 (mtm180) REVERT: A 92 LEU cc_start: 0.7314 (mm) cc_final: 0.7061 (mp) REVERT: A 122 ASP cc_start: 0.6169 (m-30) cc_final: 0.5772 (m-30) REVERT: A 216 LEU cc_start: 0.8609 (OUTLIER) cc_final: 0.8044 (tt) REVERT: A 251 LEU cc_start: 0.7409 (OUTLIER) cc_final: 0.7057 (mt) REVERT: A 400 GLU cc_start: 0.7965 (tp30) cc_final: 0.7147 (mt-10) REVERT: A 859 MET cc_start: 0.6524 (mmt) cc_final: 0.5571 (ttt) REVERT: A 1353 MET cc_start: 0.7507 (tmm) cc_final: 0.7177 (tpp) REVERT: A 1389 ILE cc_start: 0.8145 (OUTLIER) cc_final: 0.7742 (pp) REVERT: A 1651 ARG cc_start: 0.6393 (tpp-160) cc_final: 0.5082 (tmm160) REVERT: A 1656 ASP cc_start: 0.7191 (t70) cc_final: 0.6885 (t70) outliers start: 22 outliers final: 17 residues processed: 160 average time/residue: 0.2000 time to fit residues: 44.4282 Evaluate side-chains 162 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 142 time to evaluate : 1.022 ------------------------------------------------------------------------------- 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 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 792 LEU 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 1761 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 82 optimal weight: 3.9990 chunk 24 optimal weight: 0.8980 chunk 70 optimal weight: 0.5980 chunk 77 optimal weight: 1.9990 chunk 54 optimal weight: 0.0170 chunk 21 optimal weight: 0.7980 chunk 18 optimal weight: 0.9990 chunk 96 optimal weight: 0.9980 chunk 79 optimal weight: 0.7980 chunk 50 optimal weight: 1.9990 chunk 48 optimal weight: 0.8980 overall best weight: 0.6218 ------------------------------------------------------------------------------- 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 = 0.3761 r_free = 0.3761 target = 0.158165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.122752 restraints weight = 10517.194| |-----------------------------------------------------------------------------| r_work (start): 0.3192 rms_B_bonded: 1.80 r_work: 0.3001 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2869 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.4049 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= 0.114 Angle : 0.567 9.611 11826 Z= 0.273 Chirality : 0.041 0.261 1383 Planarity : 0.004 0.060 1414 Dihedral : 10.672 77.719 1587 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.66 % Allowed : 18.40 % Favored : 78.94 % 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: 1.54 (0.27), residues: 992 helix: 1.79 (0.19), residues: 735 sheet: -1.61 (1.63), residues: 12 loop : -1.23 (0.38), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A1465 HIS 0.002 0.000 HIS A1609 PHE 0.022 0.001 PHE A 127 TYR 0.011 0.001 TYR A 374 ARG 0.004 0.000 ARG A 834 Details of bonding type rmsd link_NAG-ASN : bond 0.00339 ( 4) link_NAG-ASN : angle 1.61877 ( 12) hydrogen bonds : bond 0.03756 ( 485) hydrogen bonds : angle 3.86496 ( 1407) SS BOND : bond 0.00270 ( 4) SS BOND : angle 0.81585 ( 8) covalent geometry : bond 0.00263 ( 8735) covalent geometry : angle 0.56491 (11806) ********************** 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 166 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 142 time to evaluate : 0.881 Fit side-chains REVERT: A 85 ARG cc_start: 0.7490 (mtt90) cc_final: 0.6692 (mtm180) REVERT: A 92 LEU cc_start: 0.7327 (mm) cc_final: 0.7047 (mp) REVERT: A 121 ASP cc_start: 0.7352 (t70) cc_final: 0.7043 (t70) REVERT: A 122 ASP cc_start: 0.6195 (m-30) cc_final: 0.5720 (m-30) REVERT: A 216 LEU cc_start: 0.8631 (OUTLIER) cc_final: 0.8076 (tt) REVERT: A 251 LEU cc_start: 0.7337 (OUTLIER) cc_final: 0.6986 (mt) REVERT: A 400 GLU cc_start: 0.7979 (tp30) cc_final: 0.7156 (mt-10) REVERT: A 808 ASN cc_start: 0.8150 (m-40) cc_final: 0.7163 (m110) REVERT: A 859 MET cc_start: 0.6515 (mmt) cc_final: 0.5581 (ttt) REVERT: A 1289 LEU cc_start: 0.8330 (OUTLIER) cc_final: 0.7035 (tt) REVERT: A 1353 MET cc_start: 0.7449 (tmm) cc_final: 0.7117 (tpp) REVERT: A 1389 ILE cc_start: 0.8172 (OUTLIER) cc_final: 0.7771 (pp) REVERT: A 1651 ARG cc_start: 0.6427 (tpp-160) cc_final: 0.5137 (tmm160) REVERT: A 1669 LEU cc_start: 0.8008 (OUTLIER) cc_final: 0.7607 (tt) outliers start: 24 outliers final: 19 residues processed: 158 average time/residue: 0.1979 time to fit residues: 44.4470 Evaluate side-chains 165 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 141 time to evaluate : 0.924 ------------------------------------------------------------------------------- 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 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 792 LEU 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 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 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 1667 ILE Chi-restraints excluded: chain A residue 1669 LEU Chi-restraints excluded: chain A residue 1700 LEU 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 28 optimal weight: 3.9990 chunk 59 optimal weight: 1.9990 chunk 69 optimal weight: 0.9980 chunk 10 optimal weight: 0.5980 chunk 44 optimal weight: 0.0770 chunk 89 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 18 optimal weight: 0.8980 chunk 93 optimal weight: 8.9990 chunk 9 optimal weight: 0.8980 overall best weight: 0.6938 ------------------------------------------------------------------------------- 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 = 0.3753 r_free = 0.3753 target = 0.157342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.121963 restraints weight = 10634.671| |-----------------------------------------------------------------------------| r_work (start): 0.3182 rms_B_bonded: 1.77 r_work: 0.2995 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2866 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.4059 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= 0.119 Angle : 0.567 9.611 11826 Z= 0.274 Chirality : 0.041 0.262 1383 Planarity : 0.004 0.060 1414 Dihedral : 10.741 77.543 1587 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.66 % Allowed : 18.51 % Favored : 78.82 % 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: 1.57 (0.27), residues: 992 helix: 1.81 (0.19), residues: 734 sheet: -1.63 (1.61), residues: 12 loop : -1.20 (0.37), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 911 HIS 0.002 0.000 HIS A1609 PHE 0.012 0.001 PHE A 868 TYR 0.011 0.001 TYR A 374 ARG 0.003 0.000 ARG A 834 Details of bonding type rmsd link_NAG-ASN : bond 0.00357 ( 4) link_NAG-ASN : angle 1.61555 ( 12) hydrogen bonds : bond 0.03899 ( 485) hydrogen bonds : angle 3.88195 ( 1407) SS BOND : bond 0.00278 ( 4) SS BOND : angle 0.83259 ( 8) covalent geometry : bond 0.00277 ( 8735) covalent geometry : angle 0.56429 (11806) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6108.34 seconds wall clock time: 106 minutes 24.92 seconds (6384.92 seconds total)