Starting phenix.real_space_refine on Sat May 2 21:49:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dbm_46720/05_2026/9dbm_46720.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dbm_46720/05_2026/9dbm_46720.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.22 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9dbm_46720/05_2026/9dbm_46720.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dbm_46720/05_2026/9dbm_46720.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9dbm_46720/05_2026/9dbm_46720.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dbm_46720/05_2026/9dbm_46720.map" } resolution = 3.22 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= 0.012 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 11 5.49 5 S 57 5.16 5 C 5862 2.51 5 N 1299 2.21 5 O 1526 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 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: 8755 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 8050 Number of conformers: 1 Conformer: "" Number of residues, atoms: 998, 8050 Classifications: {'peptide': 998} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 968} Chain breaks: 3 Chain: "B" 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: "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: "A" Number of atoms: 510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 510 Unusual residues: {'CLR': 5, 'LPE': 6, 'PCW': 3} Classifications: {'peptide': 2, 'undetermined': 14} Link IDs: {'TRANS': 1, None: 14} Not linked: pdbres="CLR A2001 " pdbres="CLR A2002 " Not linked: pdbres="CLR A2002 " pdbres="CLR A2003 " Not linked: pdbres="CLR A2003 " pdbres="CLR A2004 " Not linked: pdbres="CLR A2004 " pdbres="PCW A2005 " Not linked: pdbres="PCW A2005 " pdbres="LPE A2006 " ... (remaining 9 not shown) Chain breaks: 1 Unresolved non-hydrogen bonds: 104 Unresolved non-hydrogen angles: 107 Unresolved non-hydrogen dihedrals: 104 Planarities with less than four sites: {'PCW:plan-2': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 2.25, per 1000 atoms: 0.26 Number of scatterers: 8755 At special positions: 0 Unit cell: (92.29, 104.875, 130.884, 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 57 16.00 P 11 15.00 O 1526 8.00 N 1299 7.00 C 5862 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 276 " - pdb=" SG CYS A 319 " distance=2.04 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=2.04 Simple disulfide: pdb=" SG CYS A1310 " - pdb=" SG CYS A1332 " distance=2.03 Simple disulfide: pdb=" SG CYS A1678 " - pdb=" SG CYS A1692 " 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 B 1 " - " NAG B 2 " " NAG B 2 " - " BMA B 3 " " 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-ASN " NAG B 1 " - " ASN A 312 " " NAG C 1 " - " ASN A 819 " " NAG D 1 " - " ASN A1312 " " NAG E 1 " - " ASN A1328 " " NAG F 1 " - " ASN A1336 " Time building additional restraints: 1.18 Conformation dependent library (CDL) restraints added in 236.0 milliseconds 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1888 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 1 sheets defined 75.6% alpha, 0.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 Creating SS restraints... Processing helix chain 'A' and resid 232 through 241 Processing helix chain 'A' and resid 246 through 268 Processing helix chain 'A' and resid 341 through 354 removed outlier: 3.758A pdb=" N LEU A 347 " --> pdb=" O ALA A 343 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N SER A 348 " --> pdb=" O TRP A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 369 removed outlier: 3.984A pdb=" N LEU A 361 " --> pdb=" O SER A 357 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU A 366 " --> pdb=" O TYR A 362 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ARG A 367 " --> pdb=" O GLN A 363 " (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: 3.705A pdb=" N PHE A 377 " --> pdb=" O TYR A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 407 removed outlier: 3.888A pdb=" N THR A 407 " --> pdb=" O GLN A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 652 through 660 Processing helix chain 'A' and resid 664 through 683 removed outlier: 3.665A pdb=" N GLU A 668 " --> pdb=" O ASP A 664 " (cutoff:3.500A) Processing helix chain 'A' and resid 690 through 719 Processing helix chain 'A' and resid 727 through 743 removed outlier: 3.554A pdb=" N GLU A 743 " --> pdb=" O VAL A 739 " (cutoff:3.500A) Processing helix chain 'A' and resid 744 through 746 No H-bonds generated for 'chain 'A' and resid 744 through 746' Processing helix chain 'A' and resid 758 through 768 removed outlier: 3.958A 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: 3.856A pdb=" N THR A 791 " --> pdb=" O LEU A 787 " (cutoff:3.500A) removed outlier: 5.805A pdb=" N GLU A 811 " --> pdb=" O GLN A 807 " (cutoff:3.500A) removed outlier: 5.755A pdb=" N ASN A 812 " --> pdb=" O LEU A 808 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 821 removed outlier: 4.070A pdb=" N ILE A 820 " --> pdb=" O ASN A 816 " (cutoff:3.500A) Processing helix chain 'A' and resid 834 through 847 Processing helix chain 'A' and resid 850 through 859 removed outlier: 3.944A pdb=" N ALA A 856 " --> pdb=" O GLU A 852 " (cutoff:3.500A) Processing helix chain 'A' and resid 862 through 892 Processing helix chain 'A' and resid 1137 through 1150 removed outlier: 3.583A pdb=" N GLU A1150 " --> pdb=" O TYR A1146 " (cutoff:3.500A) Processing helix chain 'A' and resid 1151 through 1168 removed outlier: 3.895A pdb=" N PHE A1157 " --> pdb=" O TRP A1153 " (cutoff:3.500A) Processing helix chain 'A' and resid 1169 through 1172 Processing helix chain 'A' and resid 1173 through 1178 Processing helix chain 'A' and resid 1179 through 1209 Processing helix chain 'A' and resid 1209 through 1216 removed outlier: 3.929A pdb=" N ASN A1216 " --> pdb=" O LYS A1212 " (cutoff:3.500A) Processing helix chain 'A' and resid 1218 through 1238 removed outlier: 3.562A pdb=" N ILE A1225 " --> pdb=" O LEU A1221 " (cutoff:3.500A) Processing helix chain 'A' and resid 1243 through 1252 Processing helix chain 'A' and resid 1253 through 1261 Proline residue: A1257 - end of helix Processing helix chain 'A' and resid 1264 through 1276 Processing helix chain 'A' and resid 1277 through 1303 removed outlier: 4.067A pdb=" N ASN A1283 " --> pdb=" O PRO A1279 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N VAL A1284 " --> pdb=" O SER A1280 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N PHE A1295 " --> pdb=" O PHE A1291 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL A1300 " --> pdb=" O SER A1296 " (cutoff:3.500A) Processing helix chain 'A' and resid 1328 through 1335 Processing helix chain 'A' and resid 1336 through 1339 removed outlier: 3.642A pdb=" N GLY A1339 " --> pdb=" O ASN A1336 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1336 through 1339' Processing helix chain 'A' and resid 1352 through 1366 Processing helix chain 'A' and resid 1370 through 1379 removed outlier: 3.776A pdb=" N ALA A1375 " --> pdb=" O ASP A1371 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ALA A1376 " --> pdb=" O ILE A1372 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N VAL A1377 " --> pdb=" O MET A1373 " (cutoff:3.500A) Processing helix chain 'A' and resid 1391 through 1393 No H-bonds generated for 'chain 'A' and resid 1391 through 1393' Processing helix chain 'A' and resid 1394 through 1406 removed outlier: 4.040A pdb=" N PHE A1398 " --> pdb=" O MET A1394 " (cutoff:3.500A) Processing helix chain 'A' and resid 1409 through 1421 removed outlier: 3.586A pdb=" N PHE A1413 " --> pdb=" O THR A1409 " (cutoff:3.500A) Processing helix chain 'A' and resid 1421 through 1429 removed outlier: 5.835A pdb=" N LYS A1427 " --> pdb=" O GLN A1423 " (cutoff:3.500A) Processing helix chain 'A' and resid 1436 through 1453 removed outlier: 3.783A pdb=" N SER A1451 " --> pdb=" O LYS A1447 " (cutoff:3.500A) Processing helix chain 'A' and resid 1463 through 1474 removed outlier: 3.965A pdb=" N VAL A1469 " --> pdb=" O PHE A1465 " (cutoff:3.500A) Processing helix chain 'A' and resid 1477 through 1495 Processing helix chain 'A' and resid 1501 through 1512 Processing helix chain 'A' and resid 1513 through 1529 removed outlier: 3.653A pdb=" N VAL A1518 " --> pdb=" O PHE A1514 " (cutoff:3.500A) Processing helix chain 'A' and resid 1533 through 1536 removed outlier: 3.664A pdb=" N THR A1536 " --> pdb=" O TYR A1533 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1533 through 1536' Processing helix chain 'A' and resid 1537 through 1561 Processing helix chain 'A' and resid 1568 through 1576 removed outlier: 3.823A pdb=" N PHE A1572 " --> pdb=" O SER A1568 " (cutoff:3.500A) Processing helix chain 'A' and resid 1577 through 1584 removed outlier: 3.918A pdb=" N GLY A1581 " --> pdb=" O LEU A1577 " (cutoff:3.500A) Processing helix chain 'A' and resid 1585 through 1587 No H-bonds generated for 'chain 'A' and resid 1585 through 1587' Processing helix chain 'A' and resid 1592 through 1629 Proline residue: A1605 - end of helix Processing helix chain 'A' and resid 1646 through 1659 removed outlier: 4.262A 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 removed outlier: 3.517A pdb=" N ASN A1672 " --> pdb=" O SER A1668 " (cutoff:3.500A) Processing helix chain 'A' and resid 1694 through 1726 Processing sheet with id=AA1, first strand: chain 'A' and resid 1319 through 1320 515 hydrogen bonds defined for protein. 1497 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: 1.11 Time building geometry restraints manager: 1.44 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: 1305 1.32 - 1.45: 2444 1.45 - 1.57: 5097 1.57 - 1.69: 22 1.69 - 1.81: 94 Bond restraints: 8962 Sorted by residual: bond pdb=" C11 PCW A2009 " pdb=" O3 PCW A2009 " ideal model delta sigma weight residual 1.326 1.453 -0.127 2.00e-02 2.50e+03 4.05e+01 bond pdb=" C31 PCW A2009 " pdb=" O2 PCW A2009 " ideal model delta sigma weight residual 1.333 1.457 -0.124 2.00e-02 2.50e+03 3.85e+01 bond pdb=" CA ASP A 333 " pdb=" C ASP A 333 " ideal model delta sigma weight residual 1.526 1.481 0.045 1.22e-02 6.72e+03 1.33e+01 bond pdb=" N ASP A1315 " pdb=" CA ASP A1315 " ideal model delta sigma weight residual 1.456 1.504 -0.049 1.40e-02 5.10e+03 1.20e+01 bond pdb=" O33 LPE A2012 " pdb=" P LPE A2012 " ideal model delta sigma weight residual 1.673 1.604 0.069 2.00e-02 2.50e+03 1.18e+01 ... (remaining 8957 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.87: 11355 1.87 - 3.74: 584 3.74 - 5.61: 124 5.61 - 7.48: 50 7.48 - 9.35: 7 Bond angle restraints: 12120 Sorted by residual: angle pdb=" N MET A1161 " pdb=" CA MET A1161 " pdb=" C MET A1161 " ideal model delta sigma weight residual 113.28 105.85 7.43 1.22e+00 6.72e-01 3.71e+01 angle pdb=" N PHE A1421 " pdb=" CA PHE A1421 " pdb=" C PHE A1421 " ideal model delta sigma weight residual 113.41 106.52 6.89 1.22e+00 6.72e-01 3.19e+01 angle pdb=" N GLY A1368 " pdb=" CA GLY A1368 " pdb=" C GLY A1368 " ideal model delta sigma weight residual 115.30 107.57 7.73 1.39e+00 5.18e-01 3.09e+01 angle pdb=" N ASN A1312 " pdb=" CA ASN A1312 " pdb=" C ASN A1312 " ideal model delta sigma weight residual 108.90 99.91 8.99 1.63e+00 3.76e-01 3.04e+01 angle pdb=" N SER A 751 " pdb=" CA SER A 751 " pdb=" C SER A 751 " ideal model delta sigma weight residual 111.71 105.38 6.33 1.15e+00 7.56e-01 3.03e+01 ... (remaining 12115 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.72: 5346 27.72 - 55.45: 343 55.45 - 83.17: 71 83.17 - 110.90: 38 110.90 - 138.62: 16 Dihedral angle restraints: 5814 sinusoidal: 2899 harmonic: 2915 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 93.00 148.24 -55.24 1 1.00e+01 1.00e-02 4.13e+01 dihedral pdb=" CB CYS A 276 " pdb=" SG CYS A 276 " pdb=" SG CYS A 319 " pdb=" CB CYS A 319 " ideal model delta sinusoidal sigma weight residual 93.00 146.00 -53.00 1 1.00e+01 1.00e-02 3.82e+01 dihedral pdb=" CB CYS A 310 " pdb=" SG CYS A 310 " pdb=" SG CYS A 325 " pdb=" CB CYS A 325 " ideal model delta sinusoidal sigma weight residual -86.00 -136.26 50.26 1 1.00e+01 1.00e-02 3.46e+01 ... (remaining 5811 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.101: 1327 0.101 - 0.201: 69 0.201 - 0.302: 15 0.302 - 0.402: 2 0.402 - 0.503: 1 Chirality restraints: 1414 Sorted by residual: chirality pdb=" C1 NAG C 2 " pdb=" O4 NAG C 1 " pdb=" C2 NAG C 2 " pdb=" O5 NAG C 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.02 -0.38 2.00e-02 2.50e+03 3.56e+02 chirality pdb=" C1 BMA D 3 " pdb=" O4 NAG D 2 " pdb=" C2 BMA D 3 " pdb=" O5 BMA D 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.13 -0.27 2.00e-02 2.50e+03 1.77e+02 chirality pdb=" C1 NAG B 2 " pdb=" O4 NAG B 1 " pdb=" C2 NAG B 2 " pdb=" O5 NAG B 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.15 -0.25 2.00e-02 2.50e+03 1.62e+02 ... (remaining 1411 not shown) Planarity restraints: 1398 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 2 " -0.352 2.00e-02 2.50e+03 3.03e-01 1.15e+03 pdb=" C7 NAG D 2 " 0.082 2.00e-02 2.50e+03 pdb=" C8 NAG D 2 " -0.084 2.00e-02 2.50e+03 pdb=" N2 NAG D 2 " 0.538 2.00e-02 2.50e+03 pdb=" O7 NAG D 2 " -0.184 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG E 2 " -0.246 2.00e-02 2.50e+03 2.04e-01 5.22e+02 pdb=" C7 NAG E 2 " 0.067 2.00e-02 2.50e+03 pdb=" C8 NAG E 2 " -0.171 2.00e-02 2.50e+03 pdb=" N2 NAG E 2 " 0.338 2.00e-02 2.50e+03 pdb=" O7 NAG E 2 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG F 2 " 0.230 2.00e-02 2.50e+03 1.90e-01 4.53e+02 pdb=" C7 NAG F 2 " -0.061 2.00e-02 2.50e+03 pdb=" C8 NAG F 2 " 0.162 2.00e-02 2.50e+03 pdb=" N2 NAG F 2 " -0.313 2.00e-02 2.50e+03 pdb=" O7 NAG F 2 " -0.017 2.00e-02 2.50e+03 ... (remaining 1395 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1467 2.76 - 3.29: 9383 3.29 - 3.83: 14604 3.83 - 4.36: 17078 4.36 - 4.90: 28809 Nonbonded interactions: 71341 Sorted by model distance: nonbonded pdb=" OG SER A1568 " pdb=" OG1 THR A1570 " model vdw 2.220 3.040 nonbonded pdb=" O THR A 772 " pdb=" OG1 THR A 775 " model vdw 2.248 3.040 nonbonded pdb=" OD1 ASP A1543 " pdb=" N PHE A1544 " model vdw 2.285 3.120 nonbonded pdb=" O THR A1659 " pdb=" OG SER A1660 " model vdw 2.288 3.040 nonbonded pdb=" N GLY A 317 " pdb=" O ARG A 367 " model vdw 2.331 3.120 ... (remaining 71336 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 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } 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: 3.130 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: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.590 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6817 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 8982 Z= 0.454 Angle : 1.022 9.346 12175 Z= 0.573 Chirality : 0.055 0.503 1414 Planarity : 0.014 0.303 1393 Dihedral : 21.502 138.619 3911 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 0.68 % Allowed : 14.09 % Favored : 85.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 0.10 (0.28), residues: 990 helix: 0.63 (0.20), residues: 699 sheet: -3.67 (1.26), residues: 14 loop : -0.99 (0.39), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1689 TYR 0.014 0.001 TYR A1313 PHE 0.017 0.001 PHE A1303 TRP 0.012 0.001 TRP A1218 HIS 0.004 0.001 HIS A1631 Details of bonding type rmsd covalent geometry : bond 0.00783 ( 8962) covalent geometry : angle 1.01137 (12120) SS BOND : bond 0.00857 ( 5) SS BOND : angle 2.42799 ( 10) hydrogen bonds : bond 0.12822 ( 515) hydrogen bonds : angle 5.64167 ( 1497) link_BETA1-4 : bond 0.00241 ( 10) link_BETA1-4 : angle 1.63131 ( 30) link_NAG-ASN : bond 0.00529 ( 5) link_NAG-ASN : angle 3.53444 ( 15) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 175 time to evaluate : 0.312 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 245 LYS cc_start: 0.8223 (mttt) cc_final: 0.7893 (mtmt) REVERT: A 1483 MET cc_start: 0.5533 (mtp) cc_final: 0.4655 (ptt) REVERT: A 1527 MET cc_start: 0.7462 (tmm) cc_final: 0.6921 (tmm) REVERT: A 1689 ARG cc_start: 0.6789 (mtt180) cc_final: 0.5829 (ttp-110) outliers start: 6 outliers final: 3 residues processed: 179 average time/residue: 0.0786 time to fit residues: 21.0472 Evaluate side-chains 150 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 147 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 709 THR Chi-restraints excluded: chain A residue 779 ILE Chi-restraints excluded: chain A residue 1215 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 49 optimal weight: 0.9990 chunk 97 optimal weight: 0.7980 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 6.9990 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.9980 chunk 38 optimal weight: 0.9980 chunk 61 optimal weight: 0.6980 chunk 45 optimal weight: 6.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 390 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.105143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.088791 restraints weight = 30697.160| |-----------------------------------------------------------------------------| r_work (start): 0.3729 rms_B_bonded: 3.91 r_work (final): 0.3729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7481 moved from start: 0.1647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 8982 Z= 0.144 Angle : 0.711 9.504 12175 Z= 0.337 Chirality : 0.042 0.150 1414 Planarity : 0.004 0.045 1393 Dihedral : 18.636 130.807 2049 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 2.59 % Allowed : 16.57 % Favored : 80.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 0.61 (0.28), residues: 990 helix: 0.94 (0.20), residues: 704 sheet: -3.98 (1.24), residues: 14 loop : -0.56 (0.41), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 302 TYR 0.013 0.001 TYR A 400 PHE 0.024 0.002 PHE A 707 TRP 0.012 0.001 TRP A 830 HIS 0.003 0.001 HIS A1631 Details of bonding type rmsd covalent geometry : bond 0.00315 ( 8962) covalent geometry : angle 0.69517 (12120) SS BOND : bond 0.00320 ( 5) SS BOND : angle 0.59964 ( 10) hydrogen bonds : bond 0.03963 ( 515) hydrogen bonds : angle 4.36273 ( 1497) link_BETA1-4 : bond 0.00838 ( 10) link_BETA1-4 : angle 2.16572 ( 30) link_NAG-ASN : bond 0.00397 ( 5) link_NAG-ASN : angle 3.23306 ( 15) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 158 time to evaluate : 0.319 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 309 LEU cc_start: 0.7584 (mt) cc_final: 0.7322 (mp) REVERT: A 340 ASP cc_start: 0.8070 (p0) cc_final: 0.7870 (p0) REVERT: A 874 MET cc_start: 0.7263 (tpp) cc_final: 0.6597 (tpp) REVERT: A 1227 ASN cc_start: 0.9041 (m-40) cc_final: 0.8764 (m110) REVERT: A 1355 MET cc_start: 0.7991 (mmt) cc_final: 0.7778 (mmm) REVERT: A 1466 GLN cc_start: 0.5608 (mm-40) cc_final: 0.5178 (tp-100) REVERT: A 1483 MET cc_start: 0.5862 (mtp) cc_final: 0.4876 (ptt) REVERT: A 1527 MET cc_start: 0.7226 (OUTLIER) cc_final: 0.6789 (tmm) REVERT: A 1572 PHE cc_start: 0.8870 (OUTLIER) cc_final: 0.8616 (t80) REVERT: A 1601 MET cc_start: 0.8661 (tpp) cc_final: 0.8454 (tpp) REVERT: A 1604 LEU cc_start: 0.8924 (mt) cc_final: 0.8534 (tp) REVERT: A 1651 MET cc_start: 0.8811 (mmm) cc_final: 0.8522 (mmm) REVERT: A 1689 ARG cc_start: 0.6991 (mtt180) cc_final: 0.6098 (mtp85) REVERT: A 1722 LEU cc_start: 0.9097 (OUTLIER) cc_final: 0.8830 (mm) outliers start: 23 outliers final: 12 residues processed: 166 average time/residue: 0.0779 time to fit residues: 19.4106 Evaluate side-chains 151 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 136 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 684 MET Chi-restraints excluded: chain A residue 859 GLU Chi-restraints excluded: chain A residue 1189 THR Chi-restraints excluded: chain A residue 1198 VAL Chi-restraints excluded: chain A residue 1258 LEU Chi-restraints excluded: chain A residue 1412 LEU Chi-restraints excluded: chain A residue 1449 LEU Chi-restraints excluded: chain A residue 1468 PHE Chi-restraints excluded: chain A residue 1492 THR Chi-restraints excluded: chain A residue 1518 VAL Chi-restraints excluded: chain A residue 1527 MET Chi-restraints excluded: chain A residue 1572 PHE Chi-restraints excluded: chain A residue 1722 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 86 optimal weight: 6.9990 chunk 8 optimal weight: 6.9990 chunk 2 optimal weight: 0.9980 chunk 91 optimal weight: 0.9990 chunk 52 optimal weight: 4.9990 chunk 45 optimal weight: 6.9990 chunk 25 optimal weight: 5.9990 chunk 26 optimal weight: 6.9990 chunk 42 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 chunk 13 optimal weight: 0.7980 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1391 ASN A1476 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.101747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.085275 restraints weight = 30836.332| |-----------------------------------------------------------------------------| r_work (start): 0.3674 rms_B_bonded: 3.92 r_work (final): 0.3674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7568 moved from start: 0.2078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 8982 Z= 0.179 Angle : 0.688 8.550 12175 Z= 0.333 Chirality : 0.043 0.195 1414 Planarity : 0.004 0.040 1393 Dihedral : 16.401 150.929 2045 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 12.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 4.85 % Allowed : 16.23 % Favored : 78.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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 (0.28), residues: 990 helix: 1.02 (0.20), residues: 702 sheet: -3.26 (1.09), residues: 24 loop : -0.54 (0.41), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 844 TYR 0.019 0.002 TYR A 400 PHE 0.033 0.002 PHE A 707 TRP 0.011 0.001 TRP A1369 HIS 0.004 0.001 HIS A1631 Details of bonding type rmsd covalent geometry : bond 0.00403 ( 8962) covalent geometry : angle 0.67292 (12120) SS BOND : bond 0.00286 ( 5) SS BOND : angle 0.98821 ( 10) hydrogen bonds : bond 0.03980 ( 515) hydrogen bonds : angle 4.40568 ( 1497) link_BETA1-4 : bond 0.00934 ( 10) link_BETA1-4 : angle 2.19401 ( 30) link_NAG-ASN : bond 0.00531 ( 5) link_NAG-ASN : angle 2.82697 ( 15) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 147 time to evaluate : 0.332 Fit side-chains REVERT: A 245 LYS cc_start: 0.8451 (mtpt) cc_final: 0.8179 (mtpt) REVERT: A 398 MET cc_start: 0.9322 (ppp) cc_final: 0.9104 (ppp) REVERT: A 673 LEU cc_start: 0.8574 (tp) cc_final: 0.8353 (tt) REVERT: A 874 MET cc_start: 0.7399 (OUTLIER) cc_final: 0.6371 (tpp) REVERT: A 1227 ASN cc_start: 0.9094 (m-40) cc_final: 0.8824 (m110) REVERT: A 1303 PHE cc_start: 0.8713 (OUTLIER) cc_final: 0.8237 (p90) REVERT: A 1370 MET cc_start: 0.8838 (mmt) cc_final: 0.8563 (mmt) REVERT: A 1466 GLN cc_start: 0.5654 (mm-40) cc_final: 0.5209 (tp-100) REVERT: A 1483 MET cc_start: 0.5887 (mtp) cc_final: 0.4935 (ptt) REVERT: A 1527 MET cc_start: 0.7177 (tmm) cc_final: 0.6669 (tmm) REVERT: A 1572 PHE cc_start: 0.8883 (OUTLIER) cc_final: 0.8635 (t80) REVERT: A 1601 MET cc_start: 0.8739 (tpp) cc_final: 0.8470 (tpp) REVERT: A 1604 LEU cc_start: 0.8979 (mt) cc_final: 0.8568 (tp) REVERT: A 1689 ARG cc_start: 0.7135 (mtt180) cc_final: 0.6222 (mtp85) outliers start: 43 outliers final: 24 residues processed: 167 average time/residue: 0.0813 time to fit residues: 20.1461 Evaluate side-chains 161 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 134 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 684 MET Chi-restraints excluded: chain A residue 867 LEU Chi-restraints excluded: chain A residue 874 MET Chi-restraints excluded: chain A residue 881 VAL Chi-restraints excluded: chain A residue 1158 ILE Chi-restraints excluded: chain A residue 1189 THR Chi-restraints excluded: chain A residue 1198 VAL Chi-restraints excluded: chain A residue 1249 LEU Chi-restraints excluded: chain A residue 1251 THR Chi-restraints excluded: chain A residue 1258 LEU Chi-restraints excluded: chain A residue 1289 LEU Chi-restraints excluded: chain A residue 1297 ILE Chi-restraints excluded: chain A residue 1303 PHE Chi-restraints excluded: chain A residue 1357 TYR Chi-restraints excluded: chain A residue 1412 LEU Chi-restraints excluded: chain A residue 1449 LEU Chi-restraints excluded: chain A residue 1468 PHE Chi-restraints excluded: chain A residue 1481 THR Chi-restraints excluded: chain A residue 1488 LEU Chi-restraints excluded: chain A residue 1492 THR Chi-restraints excluded: chain A residue 1514 PHE Chi-restraints excluded: chain A residue 1572 PHE Chi-restraints excluded: chain A residue 1641 MET Chi-restraints excluded: chain A residue 1670 ILE Chi-restraints excluded: chain A residue 1715 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 91 optimal weight: 3.9990 chunk 73 optimal weight: 0.4980 chunk 1 optimal weight: 8.9990 chunk 85 optimal weight: 3.9990 chunk 88 optimal weight: 0.9990 chunk 82 optimal weight: 2.9990 chunk 80 optimal weight: 8.9990 chunk 13 optimal weight: 2.9990 chunk 28 optimal weight: 0.9990 chunk 6 optimal weight: 2.9990 chunk 2 optimal weight: 0.9980 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1349 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 = 0.4041 r_free = 0.4041 target = 0.102875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.086493 restraints weight = 30992.698| |-----------------------------------------------------------------------------| r_work (start): 0.3695 rms_B_bonded: 3.99 r_work (final): 0.3695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7549 moved from start: 0.2433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 8982 Z= 0.141 Angle : 0.662 8.906 12175 Z= 0.318 Chirality : 0.041 0.247 1414 Planarity : 0.004 0.039 1393 Dihedral : 15.396 168.634 2045 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 4.62 % Allowed : 19.39 % Favored : 75.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 0.79 (0.28), residues: 990 helix: 1.10 (0.20), residues: 701 sheet: -3.23 (1.06), residues: 24 loop : -0.48 (0.41), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 302 TYR 0.021 0.001 TYR A1717 PHE 0.021 0.001 PHE A1655 TRP 0.010 0.001 TRP A1369 HIS 0.003 0.001 HIS A1631 Details of bonding type rmsd covalent geometry : bond 0.00310 ( 8962) covalent geometry : angle 0.64886 (12120) SS BOND : bond 0.00216 ( 5) SS BOND : angle 0.80033 ( 10) hydrogen bonds : bond 0.03740 ( 515) hydrogen bonds : angle 4.36742 ( 1497) link_BETA1-4 : bond 0.00821 ( 10) link_BETA1-4 : angle 2.00137 ( 30) link_NAG-ASN : bond 0.00389 ( 5) link_NAG-ASN : angle 2.64987 ( 15) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 146 time to evaluate : 0.336 Fit side-chains REVERT: A 239 LEU cc_start: 0.9128 (tp) cc_final: 0.8849 (mt) REVERT: A 245 LYS cc_start: 0.8369 (mtpt) cc_final: 0.8164 (mtpt) REVERT: A 338 SER cc_start: 0.5228 (OUTLIER) cc_final: 0.4880 (m) REVERT: A 874 MET cc_start: 0.7232 (OUTLIER) cc_final: 0.6214 (tpp) REVERT: A 1154 PHE cc_start: 0.8602 (m-80) cc_final: 0.7842 (m-80) REVERT: A 1227 ASN cc_start: 0.9072 (m-40) cc_final: 0.8762 (m110) REVERT: A 1466 GLN cc_start: 0.5657 (mm-40) cc_final: 0.5238 (tp-100) REVERT: A 1483 MET cc_start: 0.5848 (mtp) cc_final: 0.4913 (ptt) REVERT: A 1527 MET cc_start: 0.7209 (tmm) cc_final: 0.6515 (tmm) REVERT: A 1534 TYR cc_start: 0.7249 (OUTLIER) cc_final: 0.6760 (p90) REVERT: A 1583 ILE cc_start: 0.7569 (mm) cc_final: 0.7087 (mm) REVERT: A 1601 MET cc_start: 0.8667 (tpp) cc_final: 0.8418 (tpp) REVERT: A 1602 MET cc_start: 0.8091 (mmm) cc_final: 0.7869 (mmp) REVERT: A 1622 SER cc_start: 0.8631 (m) cc_final: 0.8387 (m) REVERT: A 1682 LEU cc_start: 0.7439 (OUTLIER) cc_final: 0.7217 (tt) REVERT: A 1689 ARG cc_start: 0.7136 (mtt180) cc_final: 0.6200 (mtp85) REVERT: A 1717 TYR cc_start: 0.7729 (m-80) cc_final: 0.7487 (m-80) outliers start: 41 outliers final: 21 residues processed: 165 average time/residue: 0.0799 time to fit residues: 19.6228 Evaluate side-chains 165 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 140 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 338 SER Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 661 LEU Chi-restraints excluded: chain A residue 684 MET Chi-restraints excluded: chain A residue 867 LEU Chi-restraints excluded: chain A residue 874 MET Chi-restraints excluded: chain A residue 881 VAL Chi-restraints excluded: chain A residue 1189 THR Chi-restraints excluded: chain A residue 1215 THR Chi-restraints excluded: chain A residue 1249 LEU Chi-restraints excluded: chain A residue 1258 LEU Chi-restraints excluded: chain A residue 1297 ILE Chi-restraints excluded: chain A residue 1300 VAL Chi-restraints excluded: chain A residue 1357 TYR Chi-restraints excluded: chain A residue 1412 LEU Chi-restraints excluded: chain A residue 1449 LEU Chi-restraints excluded: chain A residue 1468 PHE Chi-restraints excluded: chain A residue 1473 VAL Chi-restraints excluded: chain A residue 1488 LEU Chi-restraints excluded: chain A residue 1492 THR Chi-restraints excluded: chain A residue 1514 PHE Chi-restraints excluded: chain A residue 1534 TYR Chi-restraints excluded: chain A residue 1641 MET Chi-restraints excluded: chain A residue 1682 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 90 optimal weight: 2.9990 chunk 49 optimal weight: 7.9990 chunk 52 optimal weight: 4.9990 chunk 57 optimal weight: 4.9990 chunk 66 optimal weight: 0.0070 chunk 54 optimal weight: 0.7980 chunk 95 optimal weight: 0.6980 chunk 87 optimal weight: 0.6980 chunk 39 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 77 optimal weight: 0.0870 overall best weight: 0.4576 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1349 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 = 0.4066 r_free = 0.4066 target = 0.104503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.088298 restraints weight = 30615.285| |-----------------------------------------------------------------------------| r_work (start): 0.3729 rms_B_bonded: 4.01 r_work (final): 0.3729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7497 moved from start: 0.2674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 8982 Z= 0.117 Angle : 0.659 11.195 12175 Z= 0.312 Chirality : 0.040 0.269 1414 Planarity : 0.004 0.043 1393 Dihedral : 14.678 172.291 2045 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 3.61 % Allowed : 21.20 % Favored : 75.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 0.95 (0.28), residues: 990 helix: 1.19 (0.20), residues: 699 sheet: -3.29 (0.98), residues: 24 loop : -0.27 (0.41), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 302 TYR 0.018 0.002 TYR A 362 PHE 0.029 0.001 PHE A1655 TRP 0.009 0.001 TRP A1539 HIS 0.003 0.001 HIS A1631 Details of bonding type rmsd covalent geometry : bond 0.00240 ( 8962) covalent geometry : angle 0.64881 (12120) SS BOND : bond 0.00152 ( 5) SS BOND : angle 0.72875 ( 10) hydrogen bonds : bond 0.03520 ( 515) hydrogen bonds : angle 4.29032 ( 1497) link_BETA1-4 : bond 0.00791 ( 10) link_BETA1-4 : angle 1.78691 ( 30) link_NAG-ASN : bond 0.00360 ( 5) link_NAG-ASN : angle 2.44335 ( 15) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 150 time to evaluate : 0.346 Fit side-chains REVERT: A 245 LYS cc_start: 0.8443 (mtpt) cc_final: 0.8210 (mtpt) REVERT: A 338 SER cc_start: 0.5401 (OUTLIER) cc_final: 0.5047 (m) REVERT: A 874 MET cc_start: 0.7091 (OUTLIER) cc_final: 0.6050 (tpp) REVERT: A 1154 PHE cc_start: 0.8583 (m-80) cc_final: 0.7880 (m-80) REVERT: A 1466 GLN cc_start: 0.5609 (mm-40) cc_final: 0.5238 (tp-100) REVERT: A 1483 MET cc_start: 0.5942 (mtp) cc_final: 0.5014 (ptt) REVERT: A 1527 MET cc_start: 0.7137 (tmm) cc_final: 0.6831 (tmm) REVERT: A 1601 MET cc_start: 0.8711 (tpp) cc_final: 0.8413 (tpp) REVERT: A 1603 SER cc_start: 0.8796 (t) cc_final: 0.8464 (p) REVERT: A 1604 LEU cc_start: 0.8957 (mt) cc_final: 0.8639 (tp) REVERT: A 1622 SER cc_start: 0.8663 (m) cc_final: 0.8332 (m) REVERT: A 1689 ARG cc_start: 0.7085 (mtt180) cc_final: 0.6132 (mtp180) outliers start: 32 outliers final: 18 residues processed: 167 average time/residue: 0.0737 time to fit residues: 18.7271 Evaluate side-chains 155 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 135 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 338 SER Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 684 MET Chi-restraints excluded: chain A residue 742 LEU Chi-restraints excluded: chain A residue 874 MET Chi-restraints excluded: chain A residue 881 VAL Chi-restraints excluded: chain A residue 1158 ILE Chi-restraints excluded: chain A residue 1189 THR Chi-restraints excluded: chain A residue 1258 LEU Chi-restraints excluded: chain A residue 1274 LEU Chi-restraints excluded: chain A residue 1300 VAL Chi-restraints excluded: chain A residue 1357 TYR Chi-restraints excluded: chain A residue 1412 LEU Chi-restraints excluded: chain A residue 1449 LEU Chi-restraints excluded: chain A residue 1468 PHE Chi-restraints excluded: chain A residue 1488 LEU Chi-restraints excluded: chain A residue 1492 THR Chi-restraints excluded: chain A residue 1514 PHE Chi-restraints excluded: chain A residue 1586 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 90 optimal weight: 5.9990 chunk 80 optimal weight: 10.0000 chunk 35 optimal weight: 0.3980 chunk 2 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 58 optimal weight: 4.9990 chunk 53 optimal weight: 0.9980 chunk 17 optimal weight: 10.0000 chunk 91 optimal weight: 0.9980 chunk 61 optimal weight: 0.9990 chunk 7 optimal weight: 5.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1227 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.103559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.087270 restraints weight = 31198.477| |-----------------------------------------------------------------------------| r_work (start): 0.3707 rms_B_bonded: 4.01 r_work (final): 0.3707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 moved from start: 0.2918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8982 Z= 0.133 Angle : 0.679 10.789 12175 Z= 0.323 Chirality : 0.042 0.234 1414 Planarity : 0.004 0.043 1393 Dihedral : 14.403 173.157 2045 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 3.61 % Allowed : 21.65 % Favored : 74.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 0.92 (0.28), residues: 990 helix: 1.15 (0.20), residues: 707 sheet: -3.18 (0.97), residues: 24 loop : -0.30 (0.42), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 302 TYR 0.023 0.002 TYR A1717 PHE 0.027 0.001 PHE A1655 TRP 0.009 0.001 TRP A1220 HIS 0.003 0.001 HIS A1631 Details of bonding type rmsd covalent geometry : bond 0.00289 ( 8962) covalent geometry : angle 0.66928 (12120) SS BOND : bond 0.00185 ( 5) SS BOND : angle 0.70232 ( 10) hydrogen bonds : bond 0.03608 ( 515) hydrogen bonds : angle 4.35280 ( 1497) link_BETA1-4 : bond 0.00761 ( 10) link_BETA1-4 : angle 1.74808 ( 30) link_NAG-ASN : bond 0.00395 ( 5) link_NAG-ASN : angle 2.45283 ( 15) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 145 time to evaluate : 0.309 Fit side-chains REVERT: A 239 LEU cc_start: 0.9053 (tp) cc_final: 0.8813 (pp) REVERT: A 338 SER cc_start: 0.5407 (OUTLIER) cc_final: 0.5048 (m) REVERT: A 874 MET cc_start: 0.7152 (OUTLIER) cc_final: 0.6072 (tpp) REVERT: A 1154 PHE cc_start: 0.8595 (m-80) cc_final: 0.7842 (m-80) REVERT: A 1466 GLN cc_start: 0.5608 (mm-40) cc_final: 0.5224 (tp-100) REVERT: A 1483 MET cc_start: 0.5798 (mtp) cc_final: 0.5020 (ptt) REVERT: A 1527 MET cc_start: 0.7108 (tmm) cc_final: 0.6636 (tmm) REVERT: A 1534 TYR cc_start: 0.7233 (OUTLIER) cc_final: 0.6727 (p90) REVERT: A 1601 MET cc_start: 0.8680 (tpp) cc_final: 0.8389 (tpp) REVERT: A 1603 SER cc_start: 0.8831 (t) cc_final: 0.8503 (p) REVERT: A 1604 LEU cc_start: 0.8969 (mt) cc_final: 0.8613 (tp) REVERT: A 1622 SER cc_start: 0.8594 (m) cc_final: 0.8390 (m) REVERT: A 1689 ARG cc_start: 0.7261 (mtt180) cc_final: 0.6323 (mtp180) REVERT: A 1717 TYR cc_start: 0.7741 (m-80) cc_final: 0.7492 (m-80) REVERT: A 1722 LEU cc_start: 0.9033 (mm) cc_final: 0.8759 (pp) outliers start: 32 outliers final: 20 residues processed: 158 average time/residue: 0.0738 time to fit residues: 17.6074 Evaluate side-chains 160 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 137 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 338 SER Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 661 LEU Chi-restraints excluded: chain A residue 684 MET Chi-restraints excluded: chain A residue 874 MET Chi-restraints excluded: chain A residue 881 VAL Chi-restraints excluded: chain A residue 1158 ILE Chi-restraints excluded: chain A residue 1189 THR Chi-restraints excluded: chain A residue 1215 THR Chi-restraints excluded: chain A residue 1258 LEU Chi-restraints excluded: chain A residue 1274 LEU Chi-restraints excluded: chain A residue 1357 TYR Chi-restraints excluded: chain A residue 1412 LEU Chi-restraints excluded: chain A residue 1449 LEU Chi-restraints excluded: chain A residue 1468 PHE Chi-restraints excluded: chain A residue 1488 LEU Chi-restraints excluded: chain A residue 1492 THR Chi-restraints excluded: chain A residue 1514 PHE Chi-restraints excluded: chain A residue 1534 TYR Chi-restraints excluded: chain A residue 1586 LEU Chi-restraints excluded: chain A residue 1715 ASN Chi-restraints excluded: chain A residue 1716 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 69 optimal weight: 3.9990 chunk 71 optimal weight: 4.9990 chunk 89 optimal weight: 0.6980 chunk 45 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 70 optimal weight: 3.9990 chunk 77 optimal weight: 7.9990 chunk 59 optimal weight: 0.3980 chunk 97 optimal weight: 0.9990 chunk 32 optimal weight: 4.9990 chunk 20 optimal weight: 3.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 363 GLN A 730 ASN ** A1349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.102027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.085745 restraints weight = 31515.256| |-----------------------------------------------------------------------------| r_work (start): 0.3681 rms_B_bonded: 4.01 r_work (final): 0.3681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.2978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8982 Z= 0.163 Angle : 0.692 13.152 12175 Z= 0.331 Chirality : 0.042 0.173 1414 Planarity : 0.004 0.042 1393 Dihedral : 14.305 171.901 2045 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 4.62 % Allowed : 21.42 % Favored : 73.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 0.81 (0.28), residues: 990 helix: 1.09 (0.20), residues: 713 sheet: -3.08 (0.99), residues: 24 loop : -0.46 (0.42), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 302 TYR 0.018 0.002 TYR A1705 PHE 0.043 0.002 PHE A1199 TRP 0.015 0.001 TRP A1539 HIS 0.003 0.001 HIS A 831 Details of bonding type rmsd covalent geometry : bond 0.00365 ( 8962) covalent geometry : angle 0.68245 (12120) SS BOND : bond 0.00204 ( 5) SS BOND : angle 0.74625 ( 10) hydrogen bonds : bond 0.03723 ( 515) hydrogen bonds : angle 4.41737 ( 1497) link_BETA1-4 : bond 0.00798 ( 10) link_BETA1-4 : angle 1.72774 ( 30) link_NAG-ASN : bond 0.00436 ( 5) link_NAG-ASN : angle 2.52209 ( 15) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 141 time to evaluate : 0.395 Fit side-chains REVERT: A 239 LEU cc_start: 0.9038 (tp) cc_final: 0.8793 (mt) REVERT: A 338 SER cc_start: 0.5219 (OUTLIER) cc_final: 0.4868 (m) REVERT: A 673 LEU cc_start: 0.8595 (tp) cc_final: 0.8354 (tt) REVERT: A 874 MET cc_start: 0.7200 (OUTLIER) cc_final: 0.6134 (tpp) REVERT: A 1154 PHE cc_start: 0.8648 (m-80) cc_final: 0.7875 (m-80) REVERT: A 1216 ASN cc_start: 0.8535 (m110) cc_final: 0.7971 (t0) REVERT: A 1227 ASN cc_start: 0.8957 (m-40) cc_final: 0.8609 (m110) REVERT: A 1303 PHE cc_start: 0.8643 (OUTLIER) cc_final: 0.7784 (p90) REVERT: A 1466 GLN cc_start: 0.5662 (mm-40) cc_final: 0.5253 (tp-100) REVERT: A 1483 MET cc_start: 0.5906 (mtp) cc_final: 0.5106 (ptt) REVERT: A 1494 MET cc_start: 0.6695 (OUTLIER) cc_final: 0.6474 (ppp) REVERT: A 1527 MET cc_start: 0.7116 (tmm) cc_final: 0.6625 (tmm) REVERT: A 1534 TYR cc_start: 0.7216 (OUTLIER) cc_final: 0.6688 (p90) REVERT: A 1601 MET cc_start: 0.8691 (tpp) cc_final: 0.8426 (tpp) REVERT: A 1689 ARG cc_start: 0.7331 (mtt180) cc_final: 0.6409 (mtp180) REVERT: A 1717 TYR cc_start: 0.7726 (m-80) cc_final: 0.7499 (m-80) REVERT: A 1722 LEU cc_start: 0.9033 (mm) cc_final: 0.8753 (pp) outliers start: 41 outliers final: 24 residues processed: 162 average time/residue: 0.0767 time to fit residues: 18.6983 Evaluate side-chains 166 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 137 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 338 SER Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 363 GLN Chi-restraints excluded: chain A residue 374 MET Chi-restraints excluded: chain A residue 661 LEU Chi-restraints excluded: chain A residue 684 MET Chi-restraints excluded: chain A residue 874 MET Chi-restraints excluded: chain A residue 881 VAL Chi-restraints excluded: chain A residue 1158 ILE Chi-restraints excluded: chain A residue 1189 THR Chi-restraints excluded: chain A residue 1205 TRP Chi-restraints excluded: chain A residue 1215 THR Chi-restraints excluded: chain A residue 1258 LEU Chi-restraints excluded: chain A residue 1289 LEU Chi-restraints excluded: chain A residue 1303 PHE Chi-restraints excluded: chain A residue 1357 TYR Chi-restraints excluded: chain A residue 1412 LEU Chi-restraints excluded: chain A residue 1449 LEU Chi-restraints excluded: chain A residue 1468 PHE Chi-restraints excluded: chain A residue 1473 VAL Chi-restraints excluded: chain A residue 1481 THR Chi-restraints excluded: chain A residue 1492 THR Chi-restraints excluded: chain A residue 1494 MET Chi-restraints excluded: chain A residue 1514 PHE Chi-restraints excluded: chain A residue 1534 TYR Chi-restraints excluded: chain A residue 1546 VAL Chi-restraints excluded: chain A residue 1586 LEU Chi-restraints excluded: chain A residue 1715 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 68 optimal weight: 0.9980 chunk 17 optimal weight: 8.9990 chunk 81 optimal weight: 0.8980 chunk 90 optimal weight: 3.9990 chunk 84 optimal weight: 4.9990 chunk 19 optimal weight: 5.9990 chunk 96 optimal weight: 1.9990 chunk 54 optimal weight: 0.9980 chunk 95 optimal weight: 0.7980 chunk 82 optimal weight: 3.9990 chunk 56 optimal weight: 0.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1349 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 = 0.4049 r_free = 0.4049 target = 0.103386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.087094 restraints weight = 30810.041| |-----------------------------------------------------------------------------| r_work (start): 0.3707 rms_B_bonded: 4.00 r_work (final): 0.3707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7528 moved from start: 0.3130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8982 Z= 0.130 Angle : 0.720 15.598 12175 Z= 0.338 Chirality : 0.042 0.303 1414 Planarity : 0.004 0.042 1393 Dihedral : 14.068 171.681 2045 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 3.27 % Allowed : 23.56 % Favored : 73.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 0.91 (0.28), residues: 990 helix: 1.17 (0.20), residues: 702 sheet: -2.97 (1.00), residues: 24 loop : -0.40 (0.41), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 302 TYR 0.017 0.002 TYR A1717 PHE 0.048 0.001 PHE A1199 TRP 0.013 0.001 TRP A1539 HIS 0.005 0.001 HIS A 833 Details of bonding type rmsd covalent geometry : bond 0.00281 ( 8962) covalent geometry : angle 0.71145 (12120) SS BOND : bond 0.00147 ( 5) SS BOND : angle 0.67425 ( 10) hydrogen bonds : bond 0.03674 ( 515) hydrogen bonds : angle 4.36500 ( 1497) link_BETA1-4 : bond 0.00793 ( 10) link_BETA1-4 : angle 1.65409 ( 30) link_NAG-ASN : bond 0.00340 ( 5) link_NAG-ASN : angle 2.42845 ( 15) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 140 time to evaluate : 0.259 Fit side-chains REVERT: A 239 LEU cc_start: 0.9103 (tp) cc_final: 0.8866 (mt) REVERT: A 338 SER cc_start: 0.5444 (OUTLIER) cc_final: 0.5072 (m) REVERT: A 874 MET cc_start: 0.7116 (OUTLIER) cc_final: 0.6036 (tpp) REVERT: A 1154 PHE cc_start: 0.8642 (m-80) cc_final: 0.7891 (m-80) REVERT: A 1216 ASN cc_start: 0.8522 (m110) cc_final: 0.7962 (t0) REVERT: A 1227 ASN cc_start: 0.9006 (m-40) cc_final: 0.8674 (m110) REVERT: A 1466 GLN cc_start: 0.5637 (mm-40) cc_final: 0.5258 (tp-100) REVERT: A 1483 MET cc_start: 0.5814 (mtp) cc_final: 0.5030 (ptt) REVERT: A 1527 MET cc_start: 0.7086 (tmm) cc_final: 0.6627 (tmm) REVERT: A 1534 TYR cc_start: 0.7161 (OUTLIER) cc_final: 0.6626 (p90) REVERT: A 1601 MET cc_start: 0.8708 (tpp) cc_final: 0.8435 (tpp) REVERT: A 1651 MET cc_start: 0.8842 (mmm) cc_final: 0.8603 (mmm) REVERT: A 1689 ARG cc_start: 0.7312 (mtt180) cc_final: 0.6412 (mtp180) REVERT: A 1722 LEU cc_start: 0.9041 (OUTLIER) cc_final: 0.8686 (pp) outliers start: 29 outliers final: 21 residues processed: 155 average time/residue: 0.0755 time to fit residues: 17.7408 Evaluate side-chains 160 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 135 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 338 SER Chi-restraints excluded: chain A residue 661 LEU Chi-restraints excluded: chain A residue 684 MET Chi-restraints excluded: chain A residue 874 MET Chi-restraints excluded: chain A residue 881 VAL Chi-restraints excluded: chain A residue 1158 ILE Chi-restraints excluded: chain A residue 1189 THR Chi-restraints excluded: chain A residue 1205 TRP Chi-restraints excluded: chain A residue 1215 THR Chi-restraints excluded: chain A residue 1258 LEU Chi-restraints excluded: chain A residue 1289 LEU Chi-restraints excluded: chain A residue 1357 TYR Chi-restraints excluded: chain A residue 1372 ILE Chi-restraints excluded: chain A residue 1412 LEU Chi-restraints excluded: chain A residue 1449 LEU Chi-restraints excluded: chain A residue 1468 PHE Chi-restraints excluded: chain A residue 1473 VAL Chi-restraints excluded: chain A residue 1492 THR Chi-restraints excluded: chain A residue 1514 PHE Chi-restraints excluded: chain A residue 1534 TYR Chi-restraints excluded: chain A residue 1586 LEU Chi-restraints excluded: chain A residue 1616 LEU Chi-restraints excluded: chain A residue 1721 ILE Chi-restraints excluded: chain A residue 1722 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 29 optimal weight: 8.9990 chunk 75 optimal weight: 2.9990 chunk 5 optimal weight: 7.9990 chunk 69 optimal weight: 2.9990 chunk 2 optimal weight: 0.9990 chunk 72 optimal weight: 2.9990 chunk 22 optimal weight: 0.6980 chunk 62 optimal weight: 0.9990 chunk 40 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 8 optimal weight: 4.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 853 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1349 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 = 0.4033 r_free = 0.4033 target = 0.102481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.086291 restraints weight = 31390.709| |-----------------------------------------------------------------------------| r_work (start): 0.3691 rms_B_bonded: 3.99 r_work (final): 0.3691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.3241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 8982 Z= 0.151 Angle : 0.721 15.179 12175 Z= 0.342 Chirality : 0.042 0.300 1414 Planarity : 0.004 0.041 1393 Dihedral : 13.929 169.786 2045 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 12.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 3.16 % Allowed : 23.22 % Favored : 73.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 0.83 (0.28), residues: 990 helix: 1.09 (0.20), residues: 711 sheet: -2.92 (0.99), residues: 24 loop : -0.43 (0.42), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 302 TYR 0.025 0.002 TYR A1717 PHE 0.048 0.002 PHE A1199 TRP 0.016 0.001 TRP A 850 HIS 0.003 0.001 HIS A1631 Details of bonding type rmsd covalent geometry : bond 0.00338 ( 8962) covalent geometry : angle 0.71220 (12120) SS BOND : bond 0.00190 ( 5) SS BOND : angle 0.73747 ( 10) hydrogen bonds : bond 0.03704 ( 515) hydrogen bonds : angle 4.41776 ( 1497) link_BETA1-4 : bond 0.00735 ( 10) link_BETA1-4 : angle 1.65577 ( 30) link_NAG-ASN : bond 0.00414 ( 5) link_NAG-ASN : angle 2.50982 ( 15) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 135 time to evaluate : 0.312 Fit side-chains REVERT: A 239 LEU cc_start: 0.9072 (tp) cc_final: 0.8851 (mt) REVERT: A 338 SER cc_start: 0.5217 (OUTLIER) cc_final: 0.4876 (m) REVERT: A 673 LEU cc_start: 0.8557 (tp) cc_final: 0.8314 (tt) REVERT: A 874 MET cc_start: 0.7206 (OUTLIER) cc_final: 0.5959 (tpp) REVERT: A 1216 ASN cc_start: 0.8534 (m110) cc_final: 0.8000 (t0) REVERT: A 1227 ASN cc_start: 0.9019 (m-40) cc_final: 0.8678 (m110) REVERT: A 1466 GLN cc_start: 0.5685 (mm-40) cc_final: 0.5331 (tp-100) REVERT: A 1483 MET cc_start: 0.5906 (mtp) cc_final: 0.5097 (ptt) REVERT: A 1527 MET cc_start: 0.7132 (tmm) cc_final: 0.6662 (tmm) REVERT: A 1534 TYR cc_start: 0.7263 (OUTLIER) cc_final: 0.6767 (p90) REVERT: A 1601 MET cc_start: 0.8602 (tpp) cc_final: 0.8347 (tpp) REVERT: A 1651 MET cc_start: 0.8786 (mmm) cc_final: 0.8552 (mmm) REVERT: A 1689 ARG cc_start: 0.7315 (mtt180) cc_final: 0.6422 (mtp180) REVERT: A 1722 LEU cc_start: 0.9047 (OUTLIER) cc_final: 0.8691 (pp) outliers start: 28 outliers final: 20 residues processed: 149 average time/residue: 0.0799 time to fit residues: 17.8169 Evaluate side-chains 159 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 135 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 338 SER Chi-restraints excluded: chain A residue 684 MET Chi-restraints excluded: chain A residue 874 MET Chi-restraints excluded: chain A residue 881 VAL Chi-restraints excluded: chain A residue 1158 ILE Chi-restraints excluded: chain A residue 1189 THR Chi-restraints excluded: chain A residue 1205 TRP Chi-restraints excluded: chain A residue 1215 THR Chi-restraints excluded: chain A residue 1258 LEU Chi-restraints excluded: chain A residue 1289 LEU Chi-restraints excluded: chain A residue 1357 TYR Chi-restraints excluded: chain A residue 1372 ILE Chi-restraints excluded: chain A residue 1412 LEU Chi-restraints excluded: chain A residue 1449 LEU Chi-restraints excluded: chain A residue 1468 PHE Chi-restraints excluded: chain A residue 1473 VAL Chi-restraints excluded: chain A residue 1492 THR Chi-restraints excluded: chain A residue 1514 PHE Chi-restraints excluded: chain A residue 1534 TYR Chi-restraints excluded: chain A residue 1546 VAL Chi-restraints excluded: chain A residue 1616 LEU Chi-restraints excluded: chain A residue 1715 ASN Chi-restraints excluded: chain A residue 1722 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 22 optimal weight: 0.9980 chunk 9 optimal weight: 4.9990 chunk 39 optimal weight: 0.9980 chunk 80 optimal weight: 0.6980 chunk 65 optimal weight: 6.9990 chunk 72 optimal weight: 8.9990 chunk 31 optimal weight: 1.9990 chunk 42 optimal weight: 0.2980 chunk 71 optimal weight: 2.9990 chunk 95 optimal weight: 3.9990 chunk 87 optimal weight: 0.0770 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1349 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 = 0.4075 r_free = 0.4075 target = 0.104903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.088768 restraints weight = 30867.255| |-----------------------------------------------------------------------------| r_work (start): 0.3738 rms_B_bonded: 4.03 r_work (final): 0.3738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7507 moved from start: 0.3450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 8982 Z= 0.118 Angle : 0.708 16.354 12175 Z= 0.331 Chirality : 0.042 0.298 1414 Planarity : 0.004 0.043 1393 Dihedral : 13.511 170.040 2045 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 2.93 % Allowed : 23.56 % Favored : 73.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 0.95 (0.28), residues: 990 helix: 1.18 (0.20), residues: 709 sheet: -2.88 (0.99), residues: 24 loop : -0.37 (0.41), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 302 TYR 0.018 0.001 TYR A1443 PHE 0.047 0.001 PHE A1199 TRP 0.014 0.001 TRP A1539 HIS 0.003 0.001 HIS A1631 Details of bonding type rmsd covalent geometry : bond 0.00248 ( 8962) covalent geometry : angle 0.70010 (12120) SS BOND : bond 0.00121 ( 5) SS BOND : angle 0.71899 ( 10) hydrogen bonds : bond 0.03540 ( 515) hydrogen bonds : angle 4.33195 ( 1497) link_BETA1-4 : bond 0.00778 ( 10) link_BETA1-4 : angle 1.54343 ( 30) link_NAG-ASN : bond 0.00327 ( 5) link_NAG-ASN : angle 2.34092 ( 15) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 145 time to evaluate : 0.321 Fit side-chains revert: symmetry clash REVERT: A 338 SER cc_start: 0.5405 (OUTLIER) cc_final: 0.5058 (m) REVERT: A 874 MET cc_start: 0.7005 (OUTLIER) cc_final: 0.5955 (tpp) REVERT: A 1161 MET cc_start: 0.7705 (tpp) cc_final: 0.7157 (tpp) REVERT: A 1227 ASN cc_start: 0.8996 (m-40) cc_final: 0.8660 (m110) REVERT: A 1370 MET cc_start: 0.8838 (mmt) cc_final: 0.7521 (mmt) REVERT: A 1466 GLN cc_start: 0.5838 (mm-40) cc_final: 0.5466 (tp-100) REVERT: A 1483 MET cc_start: 0.5902 (mtp) cc_final: 0.5102 (ptt) REVERT: A 1527 MET cc_start: 0.7094 (tmm) cc_final: 0.6667 (tmm) REVERT: A 1534 TYR cc_start: 0.7288 (OUTLIER) cc_final: 0.6838 (p90) REVERT: A 1604 LEU cc_start: 0.9028 (mt) cc_final: 0.8672 (tp) REVERT: A 1651 MET cc_start: 0.8781 (mmm) cc_final: 0.8549 (mmm) REVERT: A 1689 ARG cc_start: 0.7195 (mtt180) cc_final: 0.6324 (mtp180) REVERT: A 1722 LEU cc_start: 0.9033 (OUTLIER) cc_final: 0.8719 (pp) outliers start: 26 outliers final: 20 residues processed: 161 average time/residue: 0.0767 time to fit residues: 18.6325 Evaluate side-chains 157 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 133 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 338 SER Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 661 LEU Chi-restraints excluded: chain A residue 684 MET Chi-restraints excluded: chain A residue 874 MET Chi-restraints excluded: chain A residue 881 VAL Chi-restraints excluded: chain A residue 1158 ILE Chi-restraints excluded: chain A residue 1189 THR Chi-restraints excluded: chain A residue 1205 TRP Chi-restraints excluded: chain A residue 1215 THR Chi-restraints excluded: chain A residue 1258 LEU Chi-restraints excluded: chain A residue 1289 LEU Chi-restraints excluded: chain A residue 1357 TYR Chi-restraints excluded: chain A residue 1372 ILE Chi-restraints excluded: chain A residue 1412 LEU Chi-restraints excluded: chain A residue 1449 LEU Chi-restraints excluded: chain A residue 1468 PHE Chi-restraints excluded: chain A residue 1473 VAL Chi-restraints excluded: chain A residue 1481 THR Chi-restraints excluded: chain A residue 1492 THR Chi-restraints excluded: chain A residue 1514 PHE Chi-restraints excluded: chain A residue 1534 TYR Chi-restraints excluded: chain A residue 1722 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 0 optimal weight: 30.0000 chunk 68 optimal weight: 0.6980 chunk 26 optimal weight: 10.0000 chunk 3 optimal weight: 4.9990 chunk 65 optimal weight: 0.1980 chunk 52 optimal weight: 0.9990 chunk 88 optimal weight: 0.8980 chunk 22 optimal weight: 0.6980 chunk 93 optimal weight: 4.9990 chunk 83 optimal weight: 5.9990 chunk 43 optimal weight: 5.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1349 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 = 0.4071 r_free = 0.4071 target = 0.104359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.088146 restraints weight = 30960.057| |-----------------------------------------------------------------------------| r_work (start): 0.3734 rms_B_bonded: 4.06 r_work (final): 0.3734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7519 moved from start: 0.3518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8982 Z= 0.125 Angle : 0.724 15.623 12175 Z= 0.338 Chirality : 0.042 0.297 1414 Planarity : 0.004 0.043 1393 Dihedral : 13.345 169.037 2045 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 11.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 2.59 % Allowed : 24.13 % Favored : 73.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 0.87 (0.28), residues: 990 helix: 1.10 (0.20), residues: 710 sheet: -2.78 (0.99), residues: 24 loop : -0.34 (0.41), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 302 TYR 0.037 0.002 TYR A1717 PHE 0.051 0.001 PHE A1199 TRP 0.011 0.001 TRP A1539 HIS 0.003 0.001 HIS A1631 Details of bonding type rmsd covalent geometry : bond 0.00272 ( 8962) covalent geometry : angle 0.71685 (12120) SS BOND : bond 0.00142 ( 5) SS BOND : angle 0.71815 ( 10) hydrogen bonds : bond 0.03568 ( 515) hydrogen bonds : angle 4.33394 ( 1497) link_BETA1-4 : bond 0.00725 ( 10) link_BETA1-4 : angle 1.56335 ( 30) link_NAG-ASN : bond 0.00330 ( 5) link_NAG-ASN : angle 2.35528 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2101.07 seconds wall clock time: 37 minutes 2.49 seconds (2222.49 seconds total)