Starting phenix.real_space_refine on Sat May 2 23:14:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dbn_46721/05_2026/9dbn_46721.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dbn_46721/05_2026/9dbn_46721.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.76 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9dbn_46721/05_2026/9dbn_46721.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dbn_46721/05_2026/9dbn_46721.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9dbn_46721/05_2026/9dbn_46721.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dbn_46721/05_2026/9dbn_46721.map" } resolution = 2.76 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.010 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: 5 Type Number sf(0) Gaussians P 10 5.49 5 S 64 5.16 5 C 6057 2.51 5 N 1373 2.21 5 O 1589 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9093 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 8163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1012, 8163 Classifications: {'peptide': 1012} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 982} Chain breaks: 2 Chain: "B" Number of atoms: 277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 277 Classifications: {'peptide': 35} Modifications used: {'COO': 1} Link IDs: {'TRANS': 34} Chain: "C" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 458 Unusual residues: {'CLR': 4, 'LPE': 5, 'PCW': 3} Classifications: {'peptide': 2, 'undetermined': 12} Link IDs: {'TRANS': 1, None: 12} Not linked: pdbres="CLR A2001 " pdbres="CLR A2002 " Not linked: pdbres="CLR A2002 " pdbres="CLR A2003 " Not linked: pdbres="CLR A2003 " pdbres="PCW A2004 " Not linked: pdbres="PCW A2004 " pdbres="LPE A2005 " Not linked: pdbres="LPE A2005 " pdbres="LPE A2006 " ... (remaining 7 not shown) Chain breaks: 1 Unresolved non-hydrogen bonds: 94 Unresolved non-hydrogen angles: 97 Unresolved non-hydrogen dihedrals: 94 Planarities with less than four sites: {'PCW:plan-2': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 2.27, per 1000 atoms: 0.25 Number of scatterers: 9093 At special positions: 0 Unit cell: (101.721, 105.856, 133.147, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 64 16.00 P 10 15.00 O 1589 8.00 N 1373 7.00 C 6057 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 276 " - pdb=" SG CYS A 319 " distance=2.03 Simple disulfide: pdb=" SG CYS A 310 " - pdb=" SG CYS A 325 " distance=2.03 Simple disulfide: pdb=" SG CYS A 857 " - pdb=" SG CYS A 866 " distance=2.03 Simple disulfide: pdb=" SG CYS A1310 " - pdb=" SG CYS A1332 " distance=2.04 Simple disulfide: pdb=" SG CYS A1678 " - pdb=" SG CYS A1692 " distance=2.03 Simple disulfide: pdb=" SG CYS B 2 " - pdb=" SG CYS B 16 " distance=2.03 Simple disulfide: pdb=" SG CYS B 9 " - pdb=" SG CYS B 21 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 28 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " NAG-ASN " NAG C 1 " - " ASN A 312 " " NAG D 1 " - " ASN A1312 " " NAG E 1 " - " ASN A1328 " " NAG F 1 " - " ASN A1336 " " NAG G 1 " - " ASN A 819 " Time building additional restraints: 1.11 Conformation dependent library (CDL) restraints added in 325.1 milliseconds 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1976 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 3 sheets defined 73.8% alpha, 2.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.48 Creating SS restraints... Processing helix chain 'A' and resid 232 through 246 removed outlier: 3.757A pdb=" N LEU A 246 " --> pdb=" O SER A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 268 Processing helix chain 'A' and resid 270 through 272 No H-bonds generated for 'chain 'A' and resid 270 through 272' Processing helix chain 'A' and resid 331 through 336 Processing helix chain 'A' and resid 341 through 355 Processing helix chain 'A' and resid 357 through 369 removed outlier: 3.974A pdb=" N LEU A 361 " --> pdb=" O SER A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 372 No H-bonds generated for 'chain 'A' and resid 370 through 372' Processing helix chain 'A' and resid 373 through 383 removed outlier: 3.930A pdb=" N PHE A 377 " --> pdb=" O TYR A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 407 Processing helix chain 'A' and resid 653 through 659 Processing helix chain 'A' and resid 666 through 683 removed outlier: 3.541A pdb=" N ILE A 671 " --> pdb=" O ALA A 667 " (cutoff:3.500A) Processing helix chain 'A' and resid 690 through 719 removed outlier: 3.504A pdb=" N ASN A 701 " --> pdb=" O LEU A 697 " (cutoff:3.500A) Processing helix chain 'A' and resid 720 through 726 removed outlier: 4.357A pdb=" N PHE A 725 " --> pdb=" O PRO A 721 " (cutoff:3.500A) Processing helix chain 'A' and resid 727 through 744 removed outlier: 4.185A pdb=" N ASP A 733 " --> pdb=" O TRP A 729 " (cutoff:3.500A) Processing helix chain 'A' and resid 752 through 757 removed outlier: 3.892A pdb=" N ARG A 756 " --> pdb=" O LEU A 752 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 768 removed outlier: 3.564A pdb=" N LYS A 768 " --> pdb=" O LYS A 765 " (cutoff:3.500A) Processing helix chain 'A' and resid 770 through 785 Processing helix chain 'A' and resid 787 through 816 removed outlier: 4.079A pdb=" N ILE A 793 " --> pdb=" O ASN A 789 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ALA A 795 " --> pdb=" O THR A 791 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N GLU A 811 " --> pdb=" O GLN A 807 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N ASN A 812 " --> pdb=" O LEU A 808 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 821 removed outlier: 3.911A pdb=" N ILE A 820 " --> pdb=" O ASN A 816 " (cutoff:3.500A) Processing helix chain 'A' and resid 835 through 848 Processing helix chain 'A' and resid 850 through 861 Processing helix chain 'A' and resid 862 through 892 Processing helix chain 'A' and resid 1137 through 1150 Processing helix chain 'A' and resid 1155 through 1170 removed outlier: 3.538A pdb=" N LEU A1169 " --> pdb=" O SER A1165 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ALA A1170 " --> pdb=" O SER A1166 " (cutoff:3.500A) Processing helix chain 'A' and resid 1173 through 1177 removed outlier: 3.528A pdb=" N ASP A1177 " --> pdb=" O TYR A1174 " (cutoff:3.500A) Processing helix chain 'A' and resid 1179 through 1208 removed outlier: 3.676A pdb=" N ALA A1184 " --> pdb=" O PRO A1180 " (cutoff:3.500A) Processing helix chain 'A' and resid 1209 through 1215 Processing helix chain 'A' and resid 1220 through 1238 Processing helix chain 'A' and resid 1243 through 1252 removed outlier: 3.662A pdb=" N LEU A1252 " --> pdb=" O ALA A1248 " (cutoff:3.500A) Processing helix chain 'A' and resid 1253 through 1257 Proline residue: A1257 - end of helix Processing helix chain 'A' and resid 1258 through 1264 removed outlier: 3.614A pdb=" N SER A1262 " --> pdb=" O LEU A1258 " (cutoff:3.500A) Processing helix chain 'A' and resid 1264 through 1276 Processing helix chain 'A' and resid 1277 through 1304 removed outlier: 4.094A pdb=" N PHE A1295 " --> pdb=" O PHE A1291 " (cutoff:3.500A) Processing helix chain 'A' and resid 1328 through 1335 Processing helix chain 'A' and resid 1352 through 1366 Processing helix chain 'A' and resid 1368 through 1379 removed outlier: 3.505A pdb=" N ILE A1372 " --> pdb=" O GLY A1368 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ALA A1375 " --> pdb=" O ASP A1371 " (cutoff:3.500A) Processing helix chain 'A' and resid 1393 through 1429 removed outlier: 3.875A pdb=" N TYR A1397 " --> pdb=" O TYR A1393 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N THR A1409 " --> pdb=" O GLY A1405 " (cutoff:3.500A) Processing helix chain 'A' and resid 1436 through 1451 Processing helix chain 'A' and resid 1463 through 1474 removed outlier: 4.253A pdb=" N PHE A1468 " --> pdb=" O LYS A1464 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N VAL A1469 " --> pdb=" O PHE A1465 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ASP A1471 " --> pdb=" O GLY A1467 " (cutoff:3.500A) Processing helix chain 'A' and resid 1475 through 1495 Processing helix chain 'A' and resid 1501 through 1530 Processing helix chain 'A' and resid 1532 through 1537 Processing helix chain 'A' and resid 1537 through 1562 removed outlier: 3.669A pdb=" N SER A1550 " --> pdb=" O VAL A1546 " (cutoff:3.500A) Processing helix chain 'A' and resid 1568 through 1577 Processing helix chain 'A' and resid 1580 through 1585 Processing helix chain 'A' and resid 1586 through 1588 No H-bonds generated for 'chain 'A' and resid 1586 through 1588' Processing helix chain 'A' and resid 1590 through 1629 Proline residue: A1605 - end of helix removed outlier: 3.792A pdb=" N SER A1627 " --> pdb=" O ILE A1623 " (cutoff:3.500A) Processing helix chain 'A' and resid 1646 through 1659 removed outlier: 4.077A pdb=" N THR A1659 " --> pdb=" O PHE A1655 " (cutoff:3.500A) Processing helix chain 'A' and resid 1662 through 1672 Proline residue: A1669 - end of helix Processing helix chain 'A' and resid 1694 through 1726 Processing sheet with id=AA1, first strand: chain 'A' and resid 274 through 278 Processing sheet with id=AA2, first strand: chain 'A' and resid 1318 through 1320 Processing sheet with id=AA3, first strand: chain 'B' and resid 19 through 21 removed outlier: 3.565A pdb=" N VAL B 20 " --> pdb=" O VAL B 29 " (cutoff:3.500A) 552 hydrogen bonds defined for protein. 1626 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.41 Time building geometry restraints manager: 1.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1415 1.32 - 1.45: 2558 1.45 - 1.57: 5213 1.57 - 1.70: 22 1.70 - 1.82: 102 Bond restraints: 9310 Sorted by residual: bond pdb=" C GLU A1502 " pdb=" N GLU A1503 " ideal model delta sigma weight residual 1.335 1.427 -0.092 1.31e-02 5.83e+03 4.94e+01 bond pdb=" C11 PCW A2004 " pdb=" O3 PCW A2004 " ideal model delta sigma weight residual 1.326 1.453 -0.127 2.00e-02 2.50e+03 4.05e+01 bond pdb=" C ASP A1419 " pdb=" N ASN A1420 " ideal model delta sigma weight residual 1.334 1.417 -0.083 1.33e-02 5.65e+03 3.91e+01 bond pdb=" C31 PCW A2008 " pdb=" O2 PCW A2008 " ideal model delta sigma weight residual 1.333 1.453 -0.120 2.00e-02 2.50e+03 3.61e+01 bond pdb=" C11 PCW A2008 " pdb=" O3 PCW A2008 " ideal model delta sigma weight residual 1.326 1.446 -0.120 2.00e-02 2.50e+03 3.61e+01 ... (remaining 9305 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.60: 11983 2.60 - 5.20: 481 5.20 - 7.80: 101 7.80 - 10.40: 18 10.40 - 13.00: 5 Bond angle restraints: 12588 Sorted by residual: angle pdb=" N PHE A1710 " pdb=" CA PHE A1710 " pdb=" C PHE A1710 " ideal model delta sigma weight residual 111.69 103.22 8.47 1.23e+00 6.61e-01 4.74e+01 angle pdb=" CA ASP A1639 " pdb=" CB ASP A1639 " pdb=" CG ASP A1639 " ideal model delta sigma weight residual 112.60 119.27 -6.67 1.00e+00 1.00e+00 4.44e+01 angle pdb=" N PHE A1223 " pdb=" CA PHE A1223 " pdb=" C PHE A1223 " ideal model delta sigma weight residual 111.36 104.64 6.72 1.09e+00 8.42e-01 3.80e+01 angle pdb=" N THR A 670 " pdb=" CA THR A 670 " pdb=" C THR A 670 " ideal model delta sigma weight residual 112.90 104.97 7.93 1.31e+00 5.83e-01 3.67e+01 angle pdb=" N MET A1394 " pdb=" CA MET A1394 " pdb=" C MET A1394 " ideal model delta sigma weight residual 113.18 106.00 7.18 1.21e+00 6.83e-01 3.52e+01 ... (remaining 12583 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.74: 5603 34.74 - 69.48: 322 69.48 - 104.22: 21 104.22 - 138.95: 12 138.95 - 173.69: 2 Dihedral angle restraints: 5960 sinusoidal: 2906 harmonic: 3054 Sorted by residual: dihedral pdb=" CB CYS A 857 " pdb=" SG CYS A 857 " pdb=" SG CYS A 866 " pdb=" CB CYS A 866 " ideal model delta sinusoidal sigma weight residual 93.00 153.64 -60.64 1 1.00e+01 1.00e-02 4.89e+01 dihedral pdb=" CB CYS B 2 " pdb=" SG CYS B 2 " pdb=" SG CYS B 16 " pdb=" CB CYS B 16 " ideal model delta sinusoidal sigma weight residual -86.00 -135.51 49.51 1 1.00e+01 1.00e-02 3.37e+01 dihedral pdb=" C40 P5S A2012 " pdb=" C38 P5S A2012 " pdb=" C39 P5S A2012 " pdb=" O47 P5S A2012 " ideal model delta sinusoidal sigma weight residual 326.44 152.75 173.69 1 3.00e+01 1.11e-03 2.13e+01 ... (remaining 5957 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 1201 0.062 - 0.124: 195 0.124 - 0.186: 49 0.186 - 0.248: 11 0.248 - 0.310: 2 Chirality restraints: 1458 Sorted by residual: chirality pdb=" C13 CLR A2014 " pdb=" C12 CLR A2014 " pdb=" C14 CLR A2014 " pdb=" C17 CLR A2014 " both_signs ideal model delta sigma weight residual False -2.93 -2.62 -0.31 2.00e-01 2.50e+01 2.41e+00 chirality pdb=" C5 NAG E 1 " pdb=" C4 NAG E 1 " pdb=" C6 NAG E 1 " pdb=" O5 NAG E 1 " both_signs ideal model delta sigma weight residual False -2.41 -2.14 -0.27 2.00e-01 2.50e+01 1.83e+00 chirality pdb=" C13 CLR A2003 " pdb=" C12 CLR A2003 " pdb=" C14 CLR A2003 " pdb=" C17 CLR A2003 " both_signs ideal model delta sigma weight residual False -2.93 -2.68 -0.25 2.00e-01 2.50e+01 1.54e+00 ... (remaining 1455 not shown) Planarity restraints: 1468 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C18 PCW A2007 " -0.100 2.00e-02 2.50e+03 2.28e-01 5.19e+02 pdb=" C19 PCW A2007 " 0.307 2.00e-02 2.50e+03 pdb=" C20 PCW A2007 " -0.306 2.00e-02 2.50e+03 pdb=" C21 PCW A2007 " 0.099 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A1399 " -0.018 2.00e-02 2.50e+03 3.50e-02 1.22e+01 pdb=" C VAL A1399 " 0.061 2.00e-02 2.50e+03 pdb=" O VAL A1399 " -0.022 2.00e-02 2.50e+03 pdb=" N ILE A1400 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A1419 " -0.016 2.00e-02 2.50e+03 3.28e-02 1.08e+01 pdb=" C ASP A1419 " 0.057 2.00e-02 2.50e+03 pdb=" O ASP A1419 " -0.022 2.00e-02 2.50e+03 pdb=" N ASN A1420 " -0.019 2.00e-02 2.50e+03 ... (remaining 1465 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.74: 896 2.74 - 3.28: 9609 3.28 - 3.82: 15898 3.82 - 4.36: 19005 4.36 - 4.90: 30951 Nonbonded interactions: 76359 Sorted by model distance: nonbonded pdb=" O ARG A 817 " pdb=" OG SER A 821 " model vdw 2.206 3.040 nonbonded pdb=" O ILE A 381 " pdb=" OG SER A 385 " model vdw 2.218 3.040 nonbonded pdb=" O LEU A 246 " pdb=" OG1 THR A 250 " model vdw 2.237 3.040 nonbonded pdb=" OG1 THR A1658 " pdb=" OH TYR A1705 " model vdw 2.240 3.040 nonbonded pdb=" OH TYR A 387 " pdb=" O LEU A1596 " model vdw 2.246 3.040 ... (remaining 76354 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 10.180 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6664 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 : 0.008 0.127 9333 Z= 0.481 Angle : 1.184 12.995 12649 Z= 0.668 Chirality : 0.053 0.310 1458 Planarity : 0.008 0.228 1463 Dihedral : 20.301 173.692 3960 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 12.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 1.72 % Allowed : 23.47 % Favored : 74.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.75 (0.26), residues: 1039 helix: 0.16 (0.20), residues: 700 sheet: None (None), residues: 0 loop : -1.78 (0.33), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 24 TYR 0.022 0.002 TYR A 362 PHE 0.025 0.002 PHE A 268 TRP 0.019 0.002 TRP A1308 HIS 0.007 0.001 HIS B 25 Details of bonding type rmsd covalent geometry : bond 0.00822 ( 9310) covalent geometry : angle 1.17777 (12588) SS BOND : bond 0.00500 ( 8) SS BOND : angle 2.19462 ( 16) hydrogen bonds : bond 0.15196 ( 552) hydrogen bonds : angle 7.23359 ( 1626) link_BETA1-4 : bond 0.00507 ( 10) link_BETA1-4 : angle 2.03638 ( 30) link_NAG-ASN : bond 0.00529 ( 5) link_NAG-ASN : angle 2.07814 ( 15) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 205 time to evaluate : 0.354 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 255 PHE cc_start: 0.7225 (t80) cc_final: 0.6842 (m-10) REVERT: A 834 ASP cc_start: 0.6539 (OUTLIER) cc_final: 0.6334 (m-30) REVERT: A 1381 GLU cc_start: 0.7727 (OUTLIER) cc_final: 0.7512 (mp0) REVERT: A 1601 MET cc_start: 0.7008 (tpt) cc_final: 0.6779 (tpt) REVERT: B 30 TRP cc_start: 0.6780 (m100) cc_final: 0.6347 (m100) REVERT: B 34 PHE cc_start: 0.5171 (p90) cc_final: 0.4887 (p90) outliers start: 16 outliers final: 5 residues processed: 216 average time/residue: 0.4349 time to fit residues: 102.2328 Evaluate side-chains 139 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 132 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 670 THR Chi-restraints excluded: chain A residue 746 VAL Chi-restraints excluded: chain A residue 834 ASP Chi-restraints excluded: chain A residue 1203 LEU Chi-restraints excluded: chain A residue 1381 GLU Chi-restraints excluded: chain A residue 1436 THR Chi-restraints excluded: chain B residue 29 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 49 optimal weight: 5.9990 chunk 97 optimal weight: 3.9990 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 0.7980 chunk 38 optimal weight: 0.6980 chunk 61 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 730 ASN A 891 ASN A1411 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4494 r_free = 0.4494 target = 0.144575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.116119 restraints weight = 16433.745| |-----------------------------------------------------------------------------| r_work (start): 0.4075 rms_B_bonded: 3.15 r_work: 0.3943 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.3943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6719 moved from start: 0.1962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 9333 Z= 0.164 Angle : 0.751 15.398 12649 Z= 0.364 Chirality : 0.044 0.287 1458 Planarity : 0.005 0.060 1463 Dihedral : 18.658 170.763 2023 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 13.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 5.27 % Allowed : 24.87 % Favored : 69.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.26), residues: 1039 helix: 0.61 (0.19), residues: 704 sheet: -2.40 (1.47), residues: 10 loop : -1.49 (0.35), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A1380 TYR 0.045 0.002 TYR A1146 PHE 0.016 0.002 PHE A1465 TRP 0.013 0.002 TRP A1369 HIS 0.004 0.001 HIS A 837 Details of bonding type rmsd covalent geometry : bond 0.00368 ( 9310) covalent geometry : angle 0.74346 (12588) SS BOND : bond 0.00288 ( 8) SS BOND : angle 0.99103 ( 16) hydrogen bonds : bond 0.04319 ( 552) hydrogen bonds : angle 5.23495 ( 1626) link_BETA1-4 : bond 0.00546 ( 10) link_BETA1-4 : angle 1.99393 ( 30) link_NAG-ASN : bond 0.00473 ( 5) link_NAG-ASN : angle 1.81891 ( 15) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 154 time to evaluate : 0.332 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 255 PHE cc_start: 0.6545 (t80) cc_final: 0.5991 (m-10) REVERT: A 680 ILE cc_start: 0.8287 (mt) cc_final: 0.8028 (mp) REVERT: A 684 MET cc_start: 0.7692 (mtp) cc_final: 0.7462 (mpp) REVERT: A 711 GLU cc_start: 0.8015 (tm-30) cc_final: 0.7419 (tp30) REVERT: A 770 TRP cc_start: 0.7411 (t60) cc_final: 0.7148 (t60) REVERT: A 893 PHE cc_start: 0.6897 (m-80) cc_final: 0.6383 (m-80) REVERT: A 1381 GLU cc_start: 0.8709 (OUTLIER) cc_final: 0.8435 (mm-30) REVERT: A 1387 LYS cc_start: 0.7705 (ttmt) cc_final: 0.7482 (ttmm) REVERT: A 1634 TRP cc_start: 0.7826 (m-10) cc_final: 0.6636 (m-10) REVERT: A 1716 MET cc_start: 0.7206 (mtp) cc_final: 0.6865 (ttt) REVERT: B 30 TRP cc_start: 0.6638 (m100) cc_final: 0.6038 (m100) REVERT: B 34 PHE cc_start: 0.5198 (p90) cc_final: 0.4904 (p90) outliers start: 49 outliers final: 13 residues processed: 185 average time/residue: 0.3442 time to fit residues: 70.9073 Evaluate side-chains 144 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 130 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 266 GLN Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 314 SER Chi-restraints excluded: chain A residue 705 THR Chi-restraints excluded: chain A residue 746 VAL Chi-restraints excluded: chain A residue 749 LYS Chi-restraints excluded: chain A residue 1158 ILE Chi-restraints excluded: chain A residue 1165 SER Chi-restraints excluded: chain A residue 1189 THR Chi-restraints excluded: chain A residue 1249 LEU Chi-restraints excluded: chain A residue 1380 ARG Chi-restraints excluded: chain A residue 1381 GLU Chi-restraints excluded: chain A residue 1553 SER Chi-restraints excluded: chain B residue 18 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 60 optimal weight: 5.9990 chunk 2 optimal weight: 0.7980 chunk 30 optimal weight: 0.8980 chunk 103 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 chunk 42 optimal weight: 3.9990 chunk 54 optimal weight: 0.8980 chunk 18 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 5 optimal weight: 5.9990 chunk 13 optimal weight: 1.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4486 r_free = 0.4486 target = 0.143754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.115615 restraints weight = 16451.474| |-----------------------------------------------------------------------------| r_work (start): 0.4063 rms_B_bonded: 3.10 r_work: 0.3933 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6750 moved from start: 0.2467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9333 Z= 0.152 Angle : 0.712 12.412 12649 Z= 0.341 Chirality : 0.043 0.310 1458 Planarity : 0.004 0.053 1463 Dihedral : 17.684 165.802 2016 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 12.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 5.81 % Allowed : 25.51 % Favored : 68.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.29 (0.26), residues: 1039 helix: 0.93 (0.20), residues: 701 sheet: -2.15 (1.48), residues: 10 loop : -1.28 (0.36), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A1380 TYR 0.027 0.002 TYR A1146 PHE 0.022 0.002 PHE A 707 TRP 0.013 0.001 TRP A1539 HIS 0.003 0.001 HIS A 837 Details of bonding type rmsd covalent geometry : bond 0.00340 ( 9310) covalent geometry : angle 0.70360 (12588) SS BOND : bond 0.00296 ( 8) SS BOND : angle 0.86964 ( 16) hydrogen bonds : bond 0.03934 ( 552) hydrogen bonds : angle 5.10716 ( 1626) link_BETA1-4 : bond 0.00510 ( 10) link_BETA1-4 : angle 1.85020 ( 30) link_NAG-ASN : bond 0.00377 ( 5) link_NAG-ASN : angle 1.99232 ( 15) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 141 time to evaluate : 0.277 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 255 PHE cc_start: 0.6575 (t80) cc_final: 0.5993 (m-10) REVERT: A 266 GLN cc_start: 0.7230 (OUTLIER) cc_final: 0.6898 (mp10) REVERT: A 323 TYR cc_start: 0.6086 (m-80) cc_final: 0.5726 (m-80) REVERT: A 680 ILE cc_start: 0.8302 (mt) cc_final: 0.8025 (mp) REVERT: A 684 MET cc_start: 0.7690 (mtp) cc_final: 0.7374 (mpp) REVERT: A 711 GLU cc_start: 0.7998 (tm-30) cc_final: 0.7450 (tp30) REVERT: A 770 TRP cc_start: 0.7437 (t60) cc_final: 0.7112 (t60) REVERT: A 893 PHE cc_start: 0.7170 (m-80) cc_final: 0.6683 (m-80) REVERT: A 1203 LEU cc_start: 0.6176 (OUTLIER) cc_final: 0.5266 (tt) REVERT: A 1333 LYS cc_start: 0.8661 (ttpp) cc_final: 0.7934 (tptp) REVERT: A 1381 GLU cc_start: 0.8694 (OUTLIER) cc_final: 0.8371 (mm-30) REVERT: A 1634 TRP cc_start: 0.7812 (m-10) cc_final: 0.6486 (m-10) REVERT: A 1716 MET cc_start: 0.7128 (OUTLIER) cc_final: 0.6908 (ttt) REVERT: B 30 TRP cc_start: 0.6576 (m100) cc_final: 0.5988 (m100) REVERT: B 34 PHE cc_start: 0.5152 (p90) cc_final: 0.4850 (p90) outliers start: 54 outliers final: 19 residues processed: 174 average time/residue: 0.3694 time to fit residues: 71.0407 Evaluate side-chains 147 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 124 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 266 GLN Chi-restraints excluded: chain A residue 268 PHE Chi-restraints excluded: chain A residue 314 SER Chi-restraints excluded: chain A residue 670 THR Chi-restraints excluded: chain A residue 705 THR Chi-restraints excluded: chain A residue 746 VAL Chi-restraints excluded: chain A residue 749 LYS Chi-restraints excluded: chain A residue 758 PHE Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 845 ILE Chi-restraints excluded: chain A residue 857 CYS Chi-restraints excluded: chain A residue 1158 ILE Chi-restraints excluded: chain A residue 1165 SER Chi-restraints excluded: chain A residue 1189 THR Chi-restraints excluded: chain A residue 1203 LEU Chi-restraints excluded: chain A residue 1249 LEU Chi-restraints excluded: chain A residue 1381 GLU Chi-restraints excluded: chain A residue 1416 VAL Chi-restraints excluded: chain A residue 1492 THR Chi-restraints excluded: chain A residue 1586 LEU Chi-restraints excluded: chain A residue 1716 MET Chi-restraints excluded: chain B residue 18 HIS Chi-restraints excluded: chain B residue 29 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 64 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 chunk 42 optimal weight: 0.8980 chunk 35 optimal weight: 0.5980 chunk 57 optimal weight: 0.2980 chunk 93 optimal weight: 1.9990 chunk 84 optimal weight: 3.9990 chunk 18 optimal weight: 10.0000 chunk 85 optimal weight: 0.0010 chunk 98 optimal weight: 0.9990 chunk 37 optimal weight: 2.9990 overall best weight: 0.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4497 r_free = 0.4497 target = 0.144606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.116681 restraints weight = 16551.108| |-----------------------------------------------------------------------------| r_work (start): 0.4101 rms_B_bonded: 3.12 r_work: 0.3979 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.3979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6700 moved from start: 0.2826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 9333 Z= 0.136 Angle : 0.691 11.402 12649 Z= 0.330 Chirality : 0.043 0.310 1458 Planarity : 0.004 0.046 1463 Dihedral : 16.927 175.542 2016 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 12.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 4.84 % Allowed : 27.13 % Favored : 68.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.26), residues: 1039 helix: 1.08 (0.20), residues: 699 sheet: -2.13 (1.46), residues: 10 loop : -1.18 (0.36), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1380 TYR 0.024 0.002 TYR A1240 PHE 0.025 0.002 PHE A1318 TRP 0.009 0.001 TRP A1663 HIS 0.004 0.001 HIS A 837 Details of bonding type rmsd covalent geometry : bond 0.00311 ( 9310) covalent geometry : angle 0.68318 (12588) SS BOND : bond 0.00267 ( 8) SS BOND : angle 0.74096 ( 16) hydrogen bonds : bond 0.03765 ( 552) hydrogen bonds : angle 5.02610 ( 1626) link_BETA1-4 : bond 0.00522 ( 10) link_BETA1-4 : angle 1.82732 ( 30) link_NAG-ASN : bond 0.00360 ( 5) link_NAG-ASN : angle 1.92860 ( 15) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 134 time to evaluate : 0.279 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 255 PHE cc_start: 0.6528 (t80) cc_final: 0.5959 (m-10) REVERT: A 266 GLN cc_start: 0.7238 (OUTLIER) cc_final: 0.6987 (mp10) REVERT: A 323 TYR cc_start: 0.6113 (m-80) cc_final: 0.5577 (m-80) REVERT: A 680 ILE cc_start: 0.8275 (mt) cc_final: 0.8027 (mp) REVERT: A 684 MET cc_start: 0.7663 (mtp) cc_final: 0.7331 (mpp) REVERT: A 749 LYS cc_start: 0.8653 (OUTLIER) cc_final: 0.8422 (ptpp) REVERT: A 770 TRP cc_start: 0.7365 (t60) cc_final: 0.7014 (t60) REVERT: A 893 PHE cc_start: 0.7344 (m-80) cc_final: 0.7012 (m-80) REVERT: A 1227 ASN cc_start: 0.8647 (m110) cc_final: 0.8395 (m110) REVERT: A 1313 TYR cc_start: 0.7169 (t80) cc_final: 0.6948 (t80) REVERT: A 1333 LYS cc_start: 0.8647 (ttpp) cc_final: 0.7973 (tptp) REVERT: A 1381 GLU cc_start: 0.8655 (OUTLIER) cc_final: 0.8343 (mm-30) REVERT: A 1435 MET cc_start: 0.6060 (ttm) cc_final: 0.5796 (ttp) REVERT: A 1633 ARG cc_start: 0.7349 (OUTLIER) cc_final: 0.6784 (tmt90) REVERT: B 30 TRP cc_start: 0.6576 (m100) cc_final: 0.6007 (m100) REVERT: B 34 PHE cc_start: 0.5138 (p90) cc_final: 0.4833 (p90) outliers start: 45 outliers final: 14 residues processed: 161 average time/residue: 0.3909 time to fit residues: 69.3974 Evaluate side-chains 144 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 126 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 266 GLN Chi-restraints excluded: chain A residue 314 SER Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 670 THR Chi-restraints excluded: chain A residue 749 LYS Chi-restraints excluded: chain A residue 758 PHE Chi-restraints excluded: chain A residue 845 ILE Chi-restraints excluded: chain A residue 857 CYS Chi-restraints excluded: chain A residue 1158 ILE Chi-restraints excluded: chain A residue 1165 SER Chi-restraints excluded: chain A residue 1189 THR Chi-restraints excluded: chain A residue 1249 LEU Chi-restraints excluded: chain A residue 1324 SER Chi-restraints excluded: chain A residue 1381 GLU Chi-restraints excluded: chain A residue 1492 THR Chi-restraints excluded: chain A residue 1553 SER Chi-restraints excluded: chain A residue 1633 ARG Chi-restraints excluded: chain B residue 29 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 32 optimal weight: 2.9990 chunk 18 optimal weight: 10.0000 chunk 58 optimal weight: 1.9990 chunk 47 optimal weight: 0.5980 chunk 83 optimal weight: 0.8980 chunk 74 optimal weight: 0.0050 chunk 85 optimal weight: 0.9980 chunk 86 optimal weight: 0.5980 chunk 38 optimal weight: 0.4980 chunk 14 optimal weight: 0.9990 chunk 35 optimal weight: 0.0770 overall best weight: 0.3552 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 ASN ** A 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1540 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4506 r_free = 0.4506 target = 0.145406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.117558 restraints weight = 16486.057| |-----------------------------------------------------------------------------| r_work (start): 0.4112 rms_B_bonded: 3.14 r_work: 0.3981 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.3981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6714 moved from start: 0.3070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9333 Z= 0.124 Angle : 0.669 10.633 12649 Z= 0.319 Chirality : 0.041 0.309 1458 Planarity : 0.004 0.042 1463 Dihedral : 16.431 178.585 2015 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 11.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 4.31 % Allowed : 28.96 % Favored : 66.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.66 (0.26), residues: 1039 helix: 1.21 (0.20), residues: 700 sheet: -2.05 (1.43), residues: 10 loop : -1.11 (0.35), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1380 TYR 0.024 0.002 TYR A1240 PHE 0.025 0.001 PHE A 707 TRP 0.017 0.001 TRP A1539 HIS 0.002 0.001 HIS A 837 Details of bonding type rmsd covalent geometry : bond 0.00271 ( 9310) covalent geometry : angle 0.65996 (12588) SS BOND : bond 0.00216 ( 8) SS BOND : angle 1.26102 ( 16) hydrogen bonds : bond 0.03662 ( 552) hydrogen bonds : angle 4.92431 ( 1626) link_BETA1-4 : bond 0.00499 ( 10) link_BETA1-4 : angle 1.83741 ( 30) link_NAG-ASN : bond 0.00339 ( 5) link_NAG-ASN : angle 1.82033 ( 15) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 136 time to evaluate : 0.299 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 255 PHE cc_start: 0.6606 (t80) cc_final: 0.6004 (m-10) REVERT: A 266 GLN cc_start: 0.7330 (OUTLIER) cc_final: 0.7071 (mp10) REVERT: A 323 TYR cc_start: 0.6333 (m-80) cc_final: 0.5762 (m-80) REVERT: A 680 ILE cc_start: 0.8304 (mt) cc_final: 0.8049 (mp) REVERT: A 684 MET cc_start: 0.7619 (mtp) cc_final: 0.7323 (mpp) REVERT: A 696 MET cc_start: 0.7103 (mmt) cc_final: 0.6732 (mmp) REVERT: A 770 TRP cc_start: 0.7361 (t60) cc_final: 0.6966 (t60) REVERT: A 844 ARG cc_start: 0.7681 (ttt180) cc_final: 0.7440 (ttt180) REVERT: A 1219 CYS cc_start: 0.7678 (OUTLIER) cc_final: 0.7373 (t) REVERT: A 1227 ASN cc_start: 0.8650 (m110) cc_final: 0.8377 (m110) REVERT: A 1313 TYR cc_start: 0.7193 (t80) cc_final: 0.6964 (t80) REVERT: A 1333 LYS cc_start: 0.8620 (ttpp) cc_final: 0.7984 (tptp) REVERT: A 1381 GLU cc_start: 0.8639 (OUTLIER) cc_final: 0.8326 (mm-30) REVERT: B 30 TRP cc_start: 0.6596 (m100) cc_final: 0.6138 (m100) REVERT: B 34 PHE cc_start: 0.5079 (p90) cc_final: 0.4791 (p90) outliers start: 40 outliers final: 14 residues processed: 163 average time/residue: 0.3645 time to fit residues: 65.8311 Evaluate side-chains 139 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 122 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 266 GLN Chi-restraints excluded: chain A residue 268 PHE Chi-restraints excluded: chain A residue 314 SER Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 670 THR Chi-restraints excluded: chain A residue 758 PHE Chi-restraints excluded: chain A residue 857 CYS Chi-restraints excluded: chain A residue 1158 ILE Chi-restraints excluded: chain A residue 1165 SER Chi-restraints excluded: chain A residue 1189 THR Chi-restraints excluded: chain A residue 1219 CYS Chi-restraints excluded: chain A residue 1249 LEU Chi-restraints excluded: chain A residue 1324 SER Chi-restraints excluded: chain A residue 1381 GLU Chi-restraints excluded: chain A residue 1416 VAL Chi-restraints excluded: chain A residue 1492 THR Chi-restraints excluded: chain A residue 1553 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 57 optimal weight: 0.5980 chunk 73 optimal weight: 4.9990 chunk 44 optimal weight: 0.9990 chunk 40 optimal weight: 0.6980 chunk 53 optimal weight: 0.7980 chunk 12 optimal weight: 1.9990 chunk 68 optimal weight: 0.7980 chunk 85 optimal weight: 2.9990 chunk 47 optimal weight: 0.9980 chunk 33 optimal weight: 0.9980 chunk 35 optimal weight: 4.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1423 GLN ** A1489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1540 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4493 r_free = 0.4493 target = 0.144225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.116556 restraints weight = 16622.727| |-----------------------------------------------------------------------------| r_work (start): 0.4085 rms_B_bonded: 3.13 r_work: 0.3955 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.3955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6752 moved from start: 0.3317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9333 Z= 0.138 Angle : 0.693 10.184 12649 Z= 0.332 Chirality : 0.042 0.314 1458 Planarity : 0.004 0.041 1463 Dihedral : 16.019 178.570 2015 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 13.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 4.20 % Allowed : 29.28 % Favored : 66.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.60 (0.26), residues: 1039 helix: 1.15 (0.19), residues: 701 sheet: -1.93 (1.45), residues: 10 loop : -1.10 (0.35), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1380 TYR 0.024 0.002 TYR A1240 PHE 0.028 0.001 PHE A 707 TRP 0.018 0.001 TRP A 850 HIS 0.002 0.001 HIS A 831 Details of bonding type rmsd covalent geometry : bond 0.00310 ( 9310) covalent geometry : angle 0.68384 (12588) SS BOND : bond 0.00210 ( 8) SS BOND : angle 1.15693 ( 16) hydrogen bonds : bond 0.03640 ( 552) hydrogen bonds : angle 4.97955 ( 1626) link_BETA1-4 : bond 0.00528 ( 10) link_BETA1-4 : angle 1.83062 ( 30) link_NAG-ASN : bond 0.00290 ( 5) link_NAG-ASN : angle 1.96244 ( 15) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 130 time to evaluate : 0.315 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 255 PHE cc_start: 0.6633 (t80) cc_final: 0.5984 (m-10) REVERT: A 266 GLN cc_start: 0.7356 (OUTLIER) cc_final: 0.7127 (mp10) REVERT: A 323 TYR cc_start: 0.6544 (m-80) cc_final: 0.5688 (m-80) REVERT: A 680 ILE cc_start: 0.8208 (mt) cc_final: 0.7932 (mm) REVERT: A 684 MET cc_start: 0.7674 (mtp) cc_final: 0.7345 (mpp) REVERT: A 696 MET cc_start: 0.7051 (mmt) cc_final: 0.6738 (mmp) REVERT: A 770 TRP cc_start: 0.7394 (t60) cc_final: 0.6972 (t60) REVERT: A 1219 CYS cc_start: 0.7752 (OUTLIER) cc_final: 0.7411 (t) REVERT: A 1227 ASN cc_start: 0.8670 (m110) cc_final: 0.8409 (m110) REVERT: A 1333 LYS cc_start: 0.8586 (ttpp) cc_final: 0.7949 (tptp) REVERT: A 1381 GLU cc_start: 0.8722 (OUTLIER) cc_final: 0.8398 (mm-30) REVERT: B 30 TRP cc_start: 0.6804 (m100) cc_final: 0.6124 (m100) REVERT: B 34 PHE cc_start: 0.5097 (p90) cc_final: 0.4775 (p90) outliers start: 39 outliers final: 19 residues processed: 154 average time/residue: 0.3538 time to fit residues: 60.4671 Evaluate side-chains 145 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 123 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 266 GLN Chi-restraints excluded: chain A residue 268 PHE Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 670 THR Chi-restraints excluded: chain A residue 705 THR Chi-restraints excluded: chain A residue 758 PHE Chi-restraints excluded: chain A residue 857 CYS Chi-restraints excluded: chain A residue 1158 ILE Chi-restraints excluded: chain A residue 1165 SER Chi-restraints excluded: chain A residue 1189 THR Chi-restraints excluded: chain A residue 1219 CYS Chi-restraints excluded: chain A residue 1249 LEU Chi-restraints excluded: chain A residue 1282 MET Chi-restraints excluded: chain A residue 1324 SER Chi-restraints excluded: chain A residue 1381 GLU Chi-restraints excluded: chain A residue 1416 VAL Chi-restraints excluded: chain A residue 1446 MET Chi-restraints excluded: chain A residue 1490 MET Chi-restraints excluded: chain A residue 1492 THR Chi-restraints excluded: chain A residue 1553 SER Chi-restraints excluded: chain A residue 1586 LEU Chi-restraints excluded: chain B residue 18 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 86 optimal weight: 0.8980 chunk 67 optimal weight: 3.9990 chunk 4 optimal weight: 2.9990 chunk 55 optimal weight: 0.6980 chunk 101 optimal weight: 20.0000 chunk 28 optimal weight: 0.9980 chunk 59 optimal weight: 1.9990 chunk 27 optimal weight: 5.9990 chunk 82 optimal weight: 2.9990 chunk 71 optimal weight: 0.0270 chunk 7 optimal weight: 1.9990 overall best weight: 0.9240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 686 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1227 ASN ** A1489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1540 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4484 r_free = 0.4484 target = 0.143326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.115512 restraints weight = 16720.400| |-----------------------------------------------------------------------------| r_work (start): 0.4081 rms_B_bonded: 3.13 r_work: 0.3949 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.3949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6797 moved from start: 0.3449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9333 Z= 0.147 Angle : 0.704 10.794 12649 Z= 0.337 Chirality : 0.043 0.315 1458 Planarity : 0.004 0.043 1463 Dihedral : 15.702 176.316 2015 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 12.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 4.63 % Allowed : 29.49 % Favored : 65.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.63 (0.26), residues: 1039 helix: 1.16 (0.20), residues: 701 sheet: -1.64 (1.49), residues: 10 loop : -1.08 (0.35), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1380 TYR 0.025 0.002 TYR A1240 PHE 0.027 0.002 PHE A 707 TRP 0.009 0.001 TRP A 850 HIS 0.003 0.001 HIS A 831 Details of bonding type rmsd covalent geometry : bond 0.00333 ( 9310) covalent geometry : angle 0.69598 (12588) SS BOND : bond 0.00360 ( 8) SS BOND : angle 1.01475 ( 16) hydrogen bonds : bond 0.03715 ( 552) hydrogen bonds : angle 4.94695 ( 1626) link_BETA1-4 : bond 0.00498 ( 10) link_BETA1-4 : angle 1.81127 ( 30) link_NAG-ASN : bond 0.00325 ( 5) link_NAG-ASN : angle 2.00988 ( 15) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 126 time to evaluate : 0.371 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 255 PHE cc_start: 0.6601 (t80) cc_final: 0.5962 (m-10) REVERT: A 266 GLN cc_start: 0.7415 (OUTLIER) cc_final: 0.7190 (mp10) REVERT: A 323 TYR cc_start: 0.6653 (m-80) cc_final: 0.5799 (m-80) REVERT: A 680 ILE cc_start: 0.8266 (mt) cc_final: 0.8044 (mm) REVERT: A 684 MET cc_start: 0.7694 (mtp) cc_final: 0.7442 (mpp) REVERT: A 696 MET cc_start: 0.7056 (mmt) cc_final: 0.6754 (mmp) REVERT: A 770 TRP cc_start: 0.7426 (t60) cc_final: 0.6986 (t60) REVERT: A 844 ARG cc_start: 0.7804 (ttt180) cc_final: 0.7362 (ttt180) REVERT: A 1203 LEU cc_start: 0.6224 (OUTLIER) cc_final: 0.5393 (tt) REVERT: A 1219 CYS cc_start: 0.7765 (OUTLIER) cc_final: 0.7433 (t) REVERT: A 1313 TYR cc_start: 0.7034 (t80) cc_final: 0.6806 (t80) REVERT: A 1333 LYS cc_start: 0.8597 (ttpp) cc_final: 0.7969 (tptp) REVERT: A 1381 GLU cc_start: 0.8738 (OUTLIER) cc_final: 0.8406 (mm-30) REVERT: B 30 TRP cc_start: 0.6745 (m100) cc_final: 0.6050 (m100) REVERT: B 34 PHE cc_start: 0.5124 (p90) cc_final: 0.4790 (p90) outliers start: 43 outliers final: 21 residues processed: 156 average time/residue: 0.3480 time to fit residues: 60.3344 Evaluate side-chains 146 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 121 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 266 GLN Chi-restraints excluded: chain A residue 268 PHE Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain A residue 670 THR Chi-restraints excluded: chain A residue 705 THR Chi-restraints excluded: chain A residue 758 PHE Chi-restraints excluded: chain A residue 857 CYS Chi-restraints excluded: chain A residue 1158 ILE Chi-restraints excluded: chain A residue 1165 SER Chi-restraints excluded: chain A residue 1189 THR Chi-restraints excluded: chain A residue 1203 LEU Chi-restraints excluded: chain A residue 1219 CYS Chi-restraints excluded: chain A residue 1249 LEU Chi-restraints excluded: chain A residue 1282 MET Chi-restraints excluded: chain A residue 1324 SER Chi-restraints excluded: chain A residue 1381 GLU Chi-restraints excluded: chain A residue 1416 VAL Chi-restraints excluded: chain A residue 1436 THR Chi-restraints excluded: chain A residue 1490 MET Chi-restraints excluded: chain A residue 1492 THR Chi-restraints excluded: chain A residue 1518 VAL Chi-restraints excluded: chain A residue 1553 SER Chi-restraints excluded: chain A residue 1586 LEU Chi-restraints excluded: chain B residue 29 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 82 optimal weight: 0.0970 chunk 85 optimal weight: 0.8980 chunk 52 optimal weight: 4.9990 chunk 29 optimal weight: 1.9990 chunk 63 optimal weight: 0.9980 chunk 62 optimal weight: 0.8980 chunk 9 optimal weight: 0.9980 chunk 64 optimal weight: 0.8980 chunk 23 optimal weight: 0.9990 chunk 77 optimal weight: 2.9990 chunk 54 optimal weight: 0.9990 overall best weight: 0.7578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1540 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4489 r_free = 0.4489 target = 0.143926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.115916 restraints weight = 16668.927| |-----------------------------------------------------------------------------| r_work (start): 0.4078 rms_B_bonded: 3.19 r_work: 0.3946 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.3946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6792 moved from start: 0.3591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9333 Z= 0.137 Angle : 0.705 10.640 12649 Z= 0.336 Chirality : 0.043 0.313 1458 Planarity : 0.004 0.043 1463 Dihedral : 15.427 173.883 2015 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 12.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 3.77 % Allowed : 30.68 % Favored : 65.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.67 (0.26), residues: 1039 helix: 1.18 (0.20), residues: 702 sheet: -1.64 (1.51), residues: 10 loop : -1.04 (0.36), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1380 TYR 0.025 0.002 TYR A1240 PHE 0.028 0.001 PHE A 707 TRP 0.010 0.001 TRP B 30 HIS 0.002 0.000 HIS A 837 Details of bonding type rmsd covalent geometry : bond 0.00307 ( 9310) covalent geometry : angle 0.69577 (12588) SS BOND : bond 0.00343 ( 8) SS BOND : angle 1.60721 ( 16) hydrogen bonds : bond 0.03651 ( 552) hydrogen bonds : angle 4.93199 ( 1626) link_BETA1-4 : bond 0.00510 ( 10) link_BETA1-4 : angle 1.81471 ( 30) link_NAG-ASN : bond 0.00283 ( 5) link_NAG-ASN : angle 1.98994 ( 15) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 127 time to evaluate : 0.290 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 255 PHE cc_start: 0.6574 (t80) cc_final: 0.5941 (m-10) REVERT: A 266 GLN cc_start: 0.7430 (OUTLIER) cc_final: 0.7167 (mp10) REVERT: A 323 TYR cc_start: 0.6633 (m-80) cc_final: 0.5762 (m-80) REVERT: A 680 ILE cc_start: 0.8268 (mt) cc_final: 0.8057 (mm) REVERT: A 684 MET cc_start: 0.7649 (mtp) cc_final: 0.7436 (mpp) REVERT: A 696 MET cc_start: 0.7056 (mmt) cc_final: 0.6747 (mmp) REVERT: A 770 TRP cc_start: 0.7387 (t60) cc_final: 0.6960 (t60) REVERT: A 844 ARG cc_start: 0.7815 (ttt180) cc_final: 0.7351 (ttt180) REVERT: A 1203 LEU cc_start: 0.6198 (OUTLIER) cc_final: 0.5383 (tt) REVERT: A 1219 CYS cc_start: 0.7875 (OUTLIER) cc_final: 0.7533 (t) REVERT: A 1333 LYS cc_start: 0.8589 (ttpp) cc_final: 0.7975 (tptp) REVERT: A 1381 GLU cc_start: 0.8721 (OUTLIER) cc_final: 0.8392 (mm-30) REVERT: A 1688 THR cc_start: 0.6026 (p) cc_final: 0.5741 (t) REVERT: B 30 TRP cc_start: 0.6824 (m100) cc_final: 0.6208 (m100) REVERT: B 34 PHE cc_start: 0.5148 (p90) cc_final: 0.4828 (p90) outliers start: 35 outliers final: 20 residues processed: 150 average time/residue: 0.3544 time to fit residues: 58.8778 Evaluate side-chains 150 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 126 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 266 GLN Chi-restraints excluded: chain A residue 268 PHE Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 670 THR Chi-restraints excluded: chain A residue 705 THR Chi-restraints excluded: chain A residue 758 PHE Chi-restraints excluded: chain A residue 1158 ILE Chi-restraints excluded: chain A residue 1165 SER Chi-restraints excluded: chain A residue 1189 THR Chi-restraints excluded: chain A residue 1203 LEU Chi-restraints excluded: chain A residue 1219 CYS Chi-restraints excluded: chain A residue 1249 LEU Chi-restraints excluded: chain A residue 1381 GLU Chi-restraints excluded: chain A residue 1416 VAL Chi-restraints excluded: chain A residue 1436 THR Chi-restraints excluded: chain A residue 1490 MET Chi-restraints excluded: chain A residue 1492 THR Chi-restraints excluded: chain A residue 1518 VAL Chi-restraints excluded: chain A residue 1553 SER Chi-restraints excluded: chain A residue 1586 LEU Chi-restraints excluded: chain A residue 1726 ASN Chi-restraints excluded: chain B residue 14 THR Chi-restraints excluded: chain B residue 18 HIS Chi-restraints excluded: chain B residue 29 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 70 optimal weight: 3.9990 chunk 25 optimal weight: 0.8980 chunk 35 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 56 optimal weight: 0.3980 chunk 42 optimal weight: 5.9990 chunk 17 optimal weight: 1.9990 chunk 59 optimal weight: 0.9990 chunk 92 optimal weight: 0.7980 chunk 95 optimal weight: 0.9980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4487 r_free = 0.4487 target = 0.143698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.115744 restraints weight = 16568.809| |-----------------------------------------------------------------------------| r_work (start): 0.4075 rms_B_bonded: 3.15 r_work: 0.3946 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.3946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6778 moved from start: 0.3721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9333 Z= 0.140 Angle : 0.712 10.458 12649 Z= 0.339 Chirality : 0.043 0.314 1458 Planarity : 0.004 0.043 1463 Dihedral : 15.161 170.634 2015 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 12.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 3.55 % Allowed : 30.68 % Favored : 65.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.68 (0.27), residues: 1039 helix: 1.17 (0.20), residues: 702 sheet: -1.43 (1.61), residues: 10 loop : -1.01 (0.36), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1380 TYR 0.025 0.002 TYR A1240 PHE 0.028 0.001 PHE A 707 TRP 0.009 0.001 TRP A 358 HIS 0.003 0.001 HIS A 831 Details of bonding type rmsd covalent geometry : bond 0.00317 ( 9310) covalent geometry : angle 0.70409 (12588) SS BOND : bond 0.00374 ( 8) SS BOND : angle 1.08764 ( 16) hydrogen bonds : bond 0.03704 ( 552) hydrogen bonds : angle 4.94095 ( 1626) link_BETA1-4 : bond 0.00509 ( 10) link_BETA1-4 : angle 1.80449 ( 30) link_NAG-ASN : bond 0.00294 ( 5) link_NAG-ASN : angle 1.97199 ( 15) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 130 time to evaluate : 0.347 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 255 PHE cc_start: 0.6531 (t80) cc_final: 0.5895 (m-10) REVERT: A 266 GLN cc_start: 0.7419 (OUTLIER) cc_final: 0.7148 (mp10) REVERT: A 323 TYR cc_start: 0.6675 (m-80) cc_final: 0.5773 (m-80) REVERT: A 680 ILE cc_start: 0.8256 (mt) cc_final: 0.8047 (mm) REVERT: A 684 MET cc_start: 0.7607 (mtp) cc_final: 0.7404 (mpp) REVERT: A 770 TRP cc_start: 0.7411 (t60) cc_final: 0.6972 (t60) REVERT: A 844 ARG cc_start: 0.7816 (ttt180) cc_final: 0.7374 (ttt180) REVERT: A 1203 LEU cc_start: 0.6181 (OUTLIER) cc_final: 0.5373 (tt) REVERT: A 1219 CYS cc_start: 0.7864 (OUTLIER) cc_final: 0.7518 (t) REVERT: A 1333 LYS cc_start: 0.8598 (ttpp) cc_final: 0.8008 (tptp) REVERT: A 1381 GLU cc_start: 0.8734 (OUTLIER) cc_final: 0.8486 (mm-30) REVERT: A 1597 LEU cc_start: 0.9078 (mm) cc_final: 0.8797 (mm) REVERT: B 30 TRP cc_start: 0.6854 (m100) cc_final: 0.6234 (m100) REVERT: B 34 PHE cc_start: 0.5105 (p90) cc_final: 0.4805 (p90) outliers start: 33 outliers final: 19 residues processed: 154 average time/residue: 0.3573 time to fit residues: 61.5085 Evaluate side-chains 149 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 126 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 266 GLN Chi-restraints excluded: chain A residue 268 PHE Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain A residue 670 THR Chi-restraints excluded: chain A residue 705 THR Chi-restraints excluded: chain A residue 706 ILE Chi-restraints excluded: chain A residue 758 PHE Chi-restraints excluded: chain A residue 1158 ILE Chi-restraints excluded: chain A residue 1165 SER Chi-restraints excluded: chain A residue 1189 THR Chi-restraints excluded: chain A residue 1203 LEU Chi-restraints excluded: chain A residue 1219 CYS Chi-restraints excluded: chain A residue 1249 LEU Chi-restraints excluded: chain A residue 1381 GLU Chi-restraints excluded: chain A residue 1416 VAL Chi-restraints excluded: chain A residue 1436 THR Chi-restraints excluded: chain A residue 1490 MET Chi-restraints excluded: chain A residue 1492 THR Chi-restraints excluded: chain A residue 1518 VAL Chi-restraints excluded: chain A residue 1553 SER Chi-restraints excluded: chain A residue 1586 LEU Chi-restraints excluded: chain B residue 29 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 82 optimal weight: 4.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 chunk 56 optimal weight: 5.9990 chunk 53 optimal weight: 2.9990 chunk 94 optimal weight: 2.9990 chunk 39 optimal weight: 0.7980 chunk 46 optimal weight: 10.0000 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4471 r_free = 0.4471 target = 0.142681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.114540 restraints weight = 16723.113| |-----------------------------------------------------------------------------| r_work (start): 0.4052 rms_B_bonded: 3.15 r_work: 0.3923 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.3923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6841 moved from start: 0.3846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 9333 Z= 0.160 Angle : 0.743 14.561 12649 Z= 0.355 Chirality : 0.044 0.317 1458 Planarity : 0.004 0.044 1463 Dihedral : 15.002 166.415 2015 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 13.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 2.58 % Allowed : 32.08 % Favored : 65.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.66 (0.27), residues: 1039 helix: 1.12 (0.20), residues: 699 sheet: -1.42 (1.63), residues: 10 loop : -0.90 (0.36), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1380 TYR 0.025 0.002 TYR A1240 PHE 0.028 0.002 PHE A 707 TRP 0.011 0.001 TRP A 358 HIS 0.003 0.001 HIS A 687 Details of bonding type rmsd covalent geometry : bond 0.00367 ( 9310) covalent geometry : angle 0.73508 (12588) SS BOND : bond 0.00400 ( 8) SS BOND : angle 1.06867 ( 16) hydrogen bonds : bond 0.03893 ( 552) hydrogen bonds : angle 4.96329 ( 1626) link_BETA1-4 : bond 0.00503 ( 10) link_BETA1-4 : angle 1.81774 ( 30) link_NAG-ASN : bond 0.00312 ( 5) link_NAG-ASN : angle 2.06812 ( 15) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 131 time to evaluate : 0.433 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 255 PHE cc_start: 0.6577 (t80) cc_final: 0.5909 (m-10) REVERT: A 266 GLN cc_start: 0.7422 (OUTLIER) cc_final: 0.7139 (mp10) REVERT: A 323 TYR cc_start: 0.6813 (m-80) cc_final: 0.5909 (m-80) REVERT: A 680 ILE cc_start: 0.8302 (mt) cc_final: 0.8087 (mp) REVERT: A 684 MET cc_start: 0.7591 (mtp) cc_final: 0.7384 (mpp) REVERT: A 770 TRP cc_start: 0.7508 (t60) cc_final: 0.7110 (t60) REVERT: A 844 ARG cc_start: 0.7852 (ttt180) cc_final: 0.7380 (ttt180) REVERT: A 1145 CYS cc_start: 0.8833 (m) cc_final: 0.7869 (p) REVERT: A 1203 LEU cc_start: 0.6170 (OUTLIER) cc_final: 0.5265 (tt) REVERT: A 1219 CYS cc_start: 0.8019 (OUTLIER) cc_final: 0.7705 (t) REVERT: A 1333 LYS cc_start: 0.8610 (ttpp) cc_final: 0.8021 (tptp) REVERT: A 1381 GLU cc_start: 0.8789 (OUTLIER) cc_final: 0.8532 (mm-30) REVERT: A 1597 LEU cc_start: 0.9113 (mm) cc_final: 0.8830 (mm) REVERT: B 30 TRP cc_start: 0.6853 (m100) cc_final: 0.6238 (m100) REVERT: B 34 PHE cc_start: 0.5181 (p90) cc_final: 0.4865 (p90) outliers start: 24 outliers final: 17 residues processed: 149 average time/residue: 0.3611 time to fit residues: 60.0112 Evaluate side-chains 149 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 128 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 266 GLN Chi-restraints excluded: chain A residue 268 PHE Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 670 THR Chi-restraints excluded: chain A residue 705 THR Chi-restraints excluded: chain A residue 706 ILE Chi-restraints excluded: chain A residue 758 PHE Chi-restraints excluded: chain A residue 1158 ILE Chi-restraints excluded: chain A residue 1165 SER Chi-restraints excluded: chain A residue 1189 THR Chi-restraints excluded: chain A residue 1203 LEU Chi-restraints excluded: chain A residue 1219 CYS Chi-restraints excluded: chain A residue 1249 LEU Chi-restraints excluded: chain A residue 1381 GLU Chi-restraints excluded: chain A residue 1416 VAL Chi-restraints excluded: chain A residue 1436 THR Chi-restraints excluded: chain A residue 1490 MET Chi-restraints excluded: chain A residue 1492 THR Chi-restraints excluded: chain A residue 1518 VAL Chi-restraints excluded: chain A residue 1553 SER Chi-restraints excluded: chain B residue 29 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 46 optimal weight: 10.0000 chunk 41 optimal weight: 0.6980 chunk 44 optimal weight: 3.9990 chunk 63 optimal weight: 0.5980 chunk 56 optimal weight: 0.9990 chunk 45 optimal weight: 4.9990 chunk 96 optimal weight: 0.0980 chunk 65 optimal weight: 0.8980 chunk 87 optimal weight: 3.9990 chunk 80 optimal weight: 0.9990 chunk 52 optimal weight: 0.0270 overall best weight: 0.4638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4504 r_free = 0.4504 target = 0.145325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.117410 restraints weight = 16413.195| |-----------------------------------------------------------------------------| r_work (start): 0.4110 rms_B_bonded: 3.20 r_work: 0.3983 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.3983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6734 moved from start: 0.4010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9333 Z= 0.131 Angle : 0.717 14.192 12649 Z= 0.342 Chirality : 0.043 0.309 1458 Planarity : 0.004 0.043 1463 Dihedral : 14.747 163.957 2015 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 12.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 2.15 % Allowed : 32.72 % Favored : 65.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.76 (0.27), residues: 1039 helix: 1.20 (0.20), residues: 697 sheet: -1.56 (1.62), residues: 10 loop : -0.85 (0.36), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1380 TYR 0.025 0.002 TYR A1240 PHE 0.028 0.001 PHE A 707 TRP 0.010 0.001 TRP A1663 HIS 0.001 0.000 HIS A 831 Details of bonding type rmsd covalent geometry : bond 0.00289 ( 9310) covalent geometry : angle 0.71000 (12588) SS BOND : bond 0.00267 ( 8) SS BOND : angle 0.98855 ( 16) hydrogen bonds : bond 0.03683 ( 552) hydrogen bonds : angle 4.91318 ( 1626) link_BETA1-4 : bond 0.00538 ( 10) link_BETA1-4 : angle 1.77609 ( 30) link_NAG-ASN : bond 0.00334 ( 5) link_NAG-ASN : angle 1.80293 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3564.74 seconds wall clock time: 61 minutes 35.62 seconds (3695.62 seconds total)