Starting phenix.real_space_refine on Sat May 2 22:01:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dbk_46718/05_2026/9dbk_46718.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dbk_46718/05_2026/9dbk_46718.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.12 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9dbk_46718/05_2026/9dbk_46718.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dbk_46718/05_2026/9dbk_46718.map" model { file = "/net/cci-nas-00/data/ceres_data/9dbk_46718/05_2026/9dbk_46718.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dbk_46718/05_2026/9dbk_46718.cif" } resolution = 3.12 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 12 5.49 5 S 57 5.16 5 C 5870 2.51 5 N 1300 2.21 5 O 1527 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 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: 8766 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 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: 532 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 532 Unusual residues: {'CLR': 5, 'LPE': 7, 'PCW': 3} Classifications: {'peptide': 2, 'undetermined': 15} Link IDs: {'TRANS': 1, None: 15} 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 10 not shown) Chain breaks: 1 Unresolved non-hydrogen bonds: 116 Unresolved non-hydrogen angles: 119 Unresolved non-hydrogen dihedrals: 116 Planarities with less than four sites: {'PCW:plan-2': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 2.35, per 1000 atoms: 0.27 Number of scatterers: 8766 At special positions: 0 Unit cell: (89.773, 104.875, 132.562, 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 12 15.00 O 1527 8.00 N 1300 7.00 C 5870 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=2.03 Simple disulfide: pdb=" SG CYS A 310 " - pdb=" SG CYS A 325 " distance=2.02 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=2.03 Simple disulfide: pdb=" SG CYS A1678 " - pdb=" SG CYS A1692 " distance=2.03 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 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: 1.14 Conformation dependent library (CDL) restraints added in 297.0 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: 50 helices and 2 sheets defined 78.0% alpha, 1.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.38 Creating SS restraints... Processing helix chain 'A' and resid 232 through 268 removed outlier: 4.677A pdb=" N ASP A 248 " --> pdb=" O LYS A 244 " (cutoff:3.500A) removed outlier: 5.202A pdb=" N VAL A 249 " --> pdb=" O LYS A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 336 removed outlier: 3.707A pdb=" N TYR A 336 " --> pdb=" O PRO A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 341 through 355 Processing helix chain 'A' and resid 357 through 369 removed outlier: 3.980A 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: 3.815A 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 652 through 660 Processing helix chain 'A' and resid 664 through 683 removed outlier: 3.973A pdb=" N GLU A 668 " --> pdb=" O ASP A 664 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU A 669 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing helix chain 'A' and resid 690 through 719 Processing helix chain 'A' and resid 727 through 746 Processing helix chain 'A' and resid 754 through 759 removed outlier: 4.219A pdb=" N ARG A 759 " --> pdb=" O LEU A 755 " (cutoff:3.500A) Processing helix chain 'A' and resid 760 through 768 removed outlier: 3.733A 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: 5.902A pdb=" N GLU A 811 " --> pdb=" O GLN A 807 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N ASN A 812 " --> pdb=" O LEU A 808 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 821 removed outlier: 4.221A pdb=" N ILE A 820 " --> pdb=" O ASN A 816 " (cutoff:3.500A) Processing helix chain 'A' and resid 834 through 848 Processing helix chain 'A' and resid 850 through 860 Processing helix chain 'A' and resid 862 through 894 removed outlier: 3.554A pdb=" N ILE A 868 " --> pdb=" O SER A 864 " (cutoff:3.500A) Processing helix chain 'A' and resid 1137 through 1151 Processing helix chain 'A' and resid 1151 through 1168 removed outlier: 3.503A pdb=" N GLY A1167 " --> pdb=" O LEU A1163 " (cutoff:3.500A) Processing helix chain 'A' and resid 1169 through 1172 removed outlier: 3.969A pdb=" N GLU A1172 " --> pdb=" O LEU A1169 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1169 through 1172' Processing helix chain 'A' and resid 1173 through 1178 removed outlier: 3.550A pdb=" N GLN A1178 " --> pdb=" O TYR A1175 " (cutoff:3.500A) Processing helix chain 'A' and resid 1179 through 1208 removed outlier: 3.989A pdb=" N LYS A1183 " --> pdb=" O LYS A1179 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N PHE A1195 " --> pdb=" O ARG A1191 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N MET A1201 " --> pdb=" O PHE A1197 " (cutoff:3.500A) Processing helix chain 'A' and resid 1209 through 1214 Processing helix chain 'A' and resid 1216 through 1238 removed outlier: 3.958A pdb=" N TRP A1220 " --> pdb=" O ASN A1216 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU A1221 " --> pdb=" O ALA A1217 " (cutoff:3.500A) Processing helix chain 'A' and resid 1243 through 1252 Processing helix chain 'A' and resid 1253 through 1258 Proline residue: A1257 - end of helix Processing helix chain 'A' and resid 1259 through 1264 removed outlier: 4.456A pdb=" N ARG A1263 " --> pdb=" O ARG A1259 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N PHE A1264 " --> pdb=" O ALA A1260 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1259 through 1264' Processing helix chain 'A' and resid 1264 through 1276 Processing helix chain 'A' and resid 1277 through 1303 removed outlier: 3.616A pdb=" N VAL A1287 " --> pdb=" O ASN A1283 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N PHE A1291 " --> pdb=" O VAL A1287 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N PHE A1295 " --> pdb=" O PHE A1291 " (cutoff:3.500A) Processing helix chain 'A' and resid 1328 through 1335 removed outlier: 3.730A pdb=" N LYS A1333 " --> pdb=" O LYS A1329 " (cutoff:3.500A) Processing helix chain 'A' and resid 1352 through 1365 Processing helix chain 'A' and resid 1368 through 1378 removed outlier: 3.758A pdb=" N ILE A1372 " --> pdb=" O GLY A1368 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VAL A1377 " --> pdb=" O MET A1373 " (cutoff:3.500A) Processing helix chain 'A' and resid 1394 through 1429 removed outlier: 4.126A pdb=" N PHE A1398 " --> pdb=" O MET A1394 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N PHE A1408 " --> pdb=" O PHE A1404 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N THR A1409 " --> pdb=" O GLY A1405 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N PHE A1413 " --> pdb=" O THR A1409 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LEU A1428 " --> pdb=" O GLN A1424 " (cutoff:3.500A) Processing helix chain 'A' and resid 1436 through 1451 Processing helix chain 'A' and resid 1463 through 1475 removed outlier: 4.427A pdb=" N VAL A1469 " --> pdb=" O PHE A1465 " (cutoff:3.500A) Processing helix chain 'A' and resid 1477 through 1496 removed outlier: 3.804A pdb=" N GLU A1496 " --> pdb=" O THR A1492 " (cutoff:3.500A) Processing helix chain 'A' and resid 1501 through 1531 Processing helix chain 'A' and resid 1532 through 1535 removed outlier: 3.935A pdb=" N PHE A1535 " --> pdb=" O GLN A1532 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1532 through 1535' Processing helix chain 'A' and resid 1539 through 1561 Processing helix chain 'A' and resid 1568 through 1576 Processing helix chain 'A' and resid 1577 through 1579 No H-bonds generated for 'chain 'A' and resid 1577 through 1579' Processing helix chain 'A' and resid 1580 through 1585 Processing helix chain 'A' and resid 1586 through 1590 Processing helix chain 'A' and resid 1592 through 1629 Proline residue: A1605 - end of helix Processing helix chain 'A' and resid 1639 through 1643 removed outlier: 4.198A pdb=" N ASN A1643 " --> pdb=" O ASP A1640 " (cutoff:3.500A) Processing helix chain 'A' and resid 1646 through 1659 removed outlier: 4.130A 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: 3.561A pdb=" N ASN A1672 " --> pdb=" O SER A1668 " (cutoff:3.500A) Processing helix chain 'A' and resid 1694 through 1726 removed outlier: 3.799A pdb=" N ILE A1700 " --> pdb=" O ALA A1696 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 275 through 278 Processing sheet with id=AA2, first strand: chain 'A' and resid 1309 through 1312 546 hydrogen bonds defined for protein. 1599 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: 1.45 Time building geometry restraints manager: 1.32 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: 1284 1.32 - 1.45: 2443 1.45 - 1.57: 5127 1.57 - 1.69: 24 1.69 - 1.81: 94 Bond restraints: 8972 Sorted by residual: 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 1.20e+01 bond pdb=" O33 LPE A2006 " pdb=" P LPE A2006 " ideal model delta sigma weight residual 1.673 1.604 0.069 2.00e-02 2.50e+03 1.19e+01 bond pdb=" O33 LPE A2007 " pdb=" P LPE A2007 " ideal model delta sigma weight residual 1.673 1.604 0.069 2.00e-02 2.50e+03 1.18e+01 bond pdb=" O33 LPE A2013 " pdb=" P LPE A2013 " ideal model delta sigma weight residual 1.673 1.605 0.068 2.00e-02 2.50e+03 1.14e+01 bond pdb=" O33 LPE A2014 " pdb=" P LPE A2014 " ideal model delta sigma weight residual 1.673 1.607 0.066 2.00e-02 2.50e+03 1.10e+01 ... (remaining 8967 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.88: 11505 1.88 - 3.75: 488 3.75 - 5.63: 95 5.63 - 7.50: 37 7.50 - 9.38: 7 Bond angle restraints: 12132 Sorted by residual: angle pdb=" N VAL A1198 " pdb=" CA VAL A1198 " pdb=" C VAL A1198 " ideal model delta sigma weight residual 111.58 104.11 7.47 1.06e+00 8.90e-01 4.97e+01 angle pdb=" CA PHE A1197 " pdb=" CB PHE A1197 " pdb=" CG PHE A1197 " ideal model delta sigma weight residual 113.80 107.34 6.46 1.00e+00 1.00e+00 4.18e+01 angle pdb=" N GLY A1368 " pdb=" CA GLY A1368 " pdb=" C GLY A1368 " ideal model delta sigma weight residual 115.32 107.21 8.11 1.38e+00 5.25e-01 3.45e+01 angle pdb=" N THR A1215 " pdb=" CA THR A1215 " pdb=" C THR A1215 " ideal model delta sigma weight residual 113.88 107.12 6.76 1.23e+00 6.61e-01 3.02e+01 angle pdb=" C LYS A 749 " pdb=" CA LYS A 749 " pdb=" CB LYS A 749 " ideal model delta sigma weight residual 116.63 111.31 5.32 1.16e+00 7.43e-01 2.10e+01 ... (remaining 12127 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.43: 5502 35.43 - 70.87: 246 70.87 - 106.30: 48 106.30 - 141.74: 17 141.74 - 177.17: 4 Dihedral angle restraints: 5817 sinusoidal: 2902 harmonic: 2915 Sorted by residual: dihedral pdb=" CB CYS A1310 " pdb=" SG CYS A1310 " pdb=" SG CYS A1332 " pdb=" CB CYS A1332 " ideal model delta sinusoidal sigma weight residual -86.00 -171.81 85.81 1 1.00e+01 1.00e-02 8.90e+01 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 93.00 176.19 -83.19 1 1.00e+01 1.00e-02 8.46e+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 93.00 171.44 -78.44 1 1.00e+01 1.00e-02 7.68e+01 ... (remaining 5814 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 1250 0.071 - 0.141: 133 0.141 - 0.212: 20 0.212 - 0.283: 6 0.283 - 0.354: 1 Chirality restraints: 1410 Sorted by residual: 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 -2.16 -0.24 2.00e-02 2.50e+03 1.48e+02 chirality pdb=" C1 NAG F 2 " pdb=" O4 NAG F 1 " pdb=" C2 NAG F 2 " pdb=" O5 NAG F 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.21 -0.19 2.00e-02 2.50e+03 9.42e+01 chirality pdb=" C1 BMA F 3 " pdb=" O4 NAG F 2 " pdb=" C2 BMA F 3 " pdb=" O5 BMA F 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.22 -0.18 2.00e-02 2.50e+03 8.39e+01 ... (remaining 1407 not shown) Planarity restraints: 1398 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 2 " 0.216 2.00e-02 2.50e+03 1.83e-01 4.17e+02 pdb=" C7 NAG D 2 " -0.050 2.00e-02 2.50e+03 pdb=" C8 NAG D 2 " 0.146 2.00e-02 2.50e+03 pdb=" N2 NAG D 2 " -0.310 2.00e-02 2.50e+03 pdb=" O7 NAG D 2 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C38 PCW A2008 " -0.194 2.00e-02 2.50e+03 1.95e-01 3.81e+02 pdb=" C39 PCW A2008 " 0.191 2.00e-02 2.50e+03 pdb=" C40 PCW A2008 " 0.200 2.00e-02 2.50e+03 pdb=" C41 PCW A2008 " -0.196 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG E 1 " -0.151 2.00e-02 2.50e+03 1.24e-01 1.93e+02 pdb=" C7 NAG E 1 " 0.046 2.00e-02 2.50e+03 pdb=" C8 NAG E 1 " -0.113 2.00e-02 2.50e+03 pdb=" N2 NAG E 1 " 0.197 2.00e-02 2.50e+03 pdb=" O7 NAG E 1 " 0.021 2.00e-02 2.50e+03 ... (remaining 1395 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.74: 973 2.74 - 3.28: 9312 3.28 - 3.82: 14602 3.82 - 4.36: 16859 4.36 - 4.90: 29093 Nonbonded interactions: 70839 Sorted by model distance: nonbonded pdb=" O ARG A 817 " pdb=" OG SER A 821 " model vdw 2.205 3.040 nonbonded pdb=" O ILE A 868 " pdb=" OG1 THR A 872 " model vdw 2.233 3.040 nonbonded pdb=" O ASN A 335 " pdb=" ND2 ASN A 335 " model vdw 2.239 3.120 nonbonded pdb=" O LYS A 727 " pdb=" OD1 ASN A 730 " model vdw 2.272 3.040 nonbonded pdb=" O MET A1618 " pdb=" OG SER A1622 " model vdw 2.273 3.040 ... (remaining 70834 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 '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: 4.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.830 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:1.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6500 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 : 0.007 0.069 8991 Z= 0.387 Angle : 0.967 13.238 12184 Z= 0.502 Chirality : 0.048 0.354 1410 Planarity : 0.010 0.195 1393 Dihedral : 21.327 177.171 3914 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 0.45 % Allowed : 13.19 % Favored : 86.36 % 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: 0.68 (0.27), residues: 990 helix: 1.07 (0.20), residues: 714 sheet: -2.48 (0.99), residues: 22 loop : -0.89 (0.41), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 756 TYR 0.014 0.001 TYR A1213 PHE 0.029 0.001 PHE A1197 TRP 0.014 0.001 TRP A 855 HIS 0.002 0.001 HIS A 831 Details of bonding type rmsd covalent geometry : bond 0.00701 ( 8972) covalent geometry : angle 0.91279 (12132) SS BOND : bond 0.00351 ( 5) SS BOND : angle 1.13466 ( 10) hydrogen bonds : bond 0.12811 ( 546) hydrogen bonds : angle 5.79492 ( 1599) link_BETA1-4 : bond 0.04568 ( 9) link_BETA1-4 : angle 6.41460 ( 27) link_NAG-ASN : bond 0.00421 ( 5) link_NAG-ASN : angle 3.29929 ( 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 168 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 164 time to evaluate : 0.310 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 299 ILE cc_start: 0.7624 (tp) cc_final: 0.7244 (tt) REVERT: A 395 VAL cc_start: 0.9092 (t) cc_final: 0.8875 (t) REVERT: A 674 CYS cc_start: 0.8524 (m) cc_final: 0.7918 (t) REVERT: A 1153 TRP cc_start: 0.7170 (m100) cc_final: 0.6776 (t60) REVERT: A 1160 PHE cc_start: 0.8306 (t80) cc_final: 0.8101 (t80) outliers start: 4 outliers final: 3 residues processed: 166 average time/residue: 0.0832 time to fit residues: 19.7497 Evaluate side-chains 129 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 126 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 1233 LEU Chi-restraints excluded: chain A residue 1494 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 49 optimal weight: 0.8980 chunk 97 optimal weight: 0.6980 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 6.9990 chunk 38 optimal weight: 0.8980 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 8.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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** A1178 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.108392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.089225 restraints weight = 26449.368| |-----------------------------------------------------------------------------| r_work (start): 0.3699 rms_B_bonded: 3.83 r_work: 0.3555 rms_B_bonded: 4.86 restraints_weight: 0.5000 r_work (final): 0.3555 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7505 moved from start: 0.1500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8991 Z= 0.138 Angle : 0.707 9.713 12184 Z= 0.328 Chirality : 0.045 0.475 1410 Planarity : 0.004 0.046 1393 Dihedral : 18.897 148.809 2055 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 3.16 % Allowed : 15.67 % Favored : 81.17 % 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: 0.92 (0.27), residues: 990 helix: 1.18 (0.19), residues: 732 sheet: -2.62 (0.95), residues: 22 loop : -0.68 (0.43), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1256 TYR 0.012 0.001 TYR A1443 PHE 0.021 0.001 PHE A 801 TRP 0.014 0.001 TRP A 855 HIS 0.002 0.001 HIS A 824 Details of bonding type rmsd covalent geometry : bond 0.00302 ( 8972) covalent geometry : angle 0.69259 (12132) SS BOND : bond 0.00158 ( 5) SS BOND : angle 0.87141 ( 10) hydrogen bonds : bond 0.03984 ( 546) hydrogen bonds : angle 4.35461 ( 1599) link_BETA1-4 : bond 0.00809 ( 9) link_BETA1-4 : angle 2.86063 ( 27) link_NAG-ASN : bond 0.00399 ( 5) link_NAG-ASN : angle 1.53435 ( 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 165 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 137 time to evaluate : 0.262 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 299 ILE cc_start: 0.7608 (tp) cc_final: 0.7203 (tt) REVERT: A 674 CYS cc_start: 0.8595 (m) cc_final: 0.8007 (t) REVERT: A 874 MET cc_start: 0.7663 (tmm) cc_final: 0.6672 (tmm) REVERT: A 1153 TRP cc_start: 0.7197 (m100) cc_final: 0.6721 (t60) REVERT: A 1525 MET cc_start: 0.5712 (tmm) cc_final: 0.5499 (tmm) REVERT: A 1527 MET cc_start: 0.6907 (tmm) cc_final: 0.6309 (ttt) REVERT: A 1556 PHE cc_start: 0.7945 (OUTLIER) cc_final: 0.7720 (m-80) REVERT: A 1624 PHE cc_start: 0.7942 (OUTLIER) cc_final: 0.7480 (t80) outliers start: 28 outliers final: 10 residues processed: 152 average time/residue: 0.0880 time to fit residues: 18.8748 Evaluate side-chains 134 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 122 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 696 MET Chi-restraints excluded: chain A residue 746 VAL Chi-restraints excluded: chain A residue 772 THR Chi-restraints excluded: chain A residue 867 LEU Chi-restraints excluded: chain A residue 1178 GLN Chi-restraints excluded: chain A residue 1249 LEU Chi-restraints excluded: chain A residue 1252 LEU Chi-restraints excluded: chain A residue 1412 LEU Chi-restraints excluded: chain A residue 1556 PHE Chi-restraints excluded: chain A residue 1624 PHE Chi-restraints excluded: chain A residue 1670 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 13 optimal weight: 0.1980 chunk 5 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 62 optimal weight: 0.6980 chunk 55 optimal weight: 0.3980 chunk 39 optimal weight: 0.7980 chunk 34 optimal weight: 0.9980 chunk 49 optimal weight: 3.9990 chunk 77 optimal weight: 4.9990 chunk 35 optimal weight: 0.6980 chunk 74 optimal weight: 2.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 355 GLN A 853 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.108977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.089817 restraints weight = 26303.860| |-----------------------------------------------------------------------------| r_work (start): 0.3716 rms_B_bonded: 3.85 r_work: 0.3574 rms_B_bonded: 4.88 restraints_weight: 0.5000 r_work (final): 0.3574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7486 moved from start: 0.1882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 8991 Z= 0.122 Angle : 0.656 9.699 12184 Z= 0.308 Chirality : 0.044 0.483 1410 Planarity : 0.004 0.041 1393 Dihedral : 16.319 137.355 2050 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 2.59 % Allowed : 17.47 % Favored : 79.93 % 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: 1.21 (0.28), residues: 990 helix: 1.39 (0.19), residues: 731 sheet: -2.41 (0.92), residues: 22 loop : -0.57 (0.44), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 844 TYR 0.015 0.001 TYR A 387 PHE 0.024 0.001 PHE A1160 TRP 0.016 0.001 TRP A1369 HIS 0.002 0.000 HIS A 824 Details of bonding type rmsd covalent geometry : bond 0.00270 ( 8972) covalent geometry : angle 0.64250 (12132) SS BOND : bond 0.00458 ( 5) SS BOND : angle 0.93014 ( 10) hydrogen bonds : bond 0.03700 ( 546) hydrogen bonds : angle 4.21414 ( 1599) link_BETA1-4 : bond 0.00690 ( 9) link_BETA1-4 : angle 2.70751 ( 27) link_NAG-ASN : bond 0.00160 ( 5) link_NAG-ASN : angle 1.20876 ( 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 158 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 135 time to evaluate : 0.349 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 299 ILE cc_start: 0.7561 (tp) cc_final: 0.7143 (tt) REVERT: A 674 CYS cc_start: 0.8571 (m) cc_final: 0.7974 (t) REVERT: A 697 LEU cc_start: 0.9177 (OUTLIER) cc_final: 0.8904 (mm) REVERT: A 874 MET cc_start: 0.7529 (tmm) cc_final: 0.6654 (tmm) REVERT: A 1153 TRP cc_start: 0.7208 (m100) cc_final: 0.6724 (t60) REVERT: A 1525 MET cc_start: 0.5828 (tmm) cc_final: 0.5549 (tmm) REVERT: A 1527 MET cc_start: 0.6923 (tmm) cc_final: 0.6370 (ttt) REVERT: A 1624 PHE cc_start: 0.7888 (OUTLIER) cc_final: 0.7438 (t80) outliers start: 23 outliers final: 13 residues processed: 145 average time/residue: 0.0832 time to fit residues: 17.4441 Evaluate side-chains 131 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 116 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 696 MET Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain A residue 867 LEU Chi-restraints excluded: chain A residue 1249 LEU Chi-restraints excluded: chain A residue 1252 LEU Chi-restraints excluded: chain A residue 1288 CYS Chi-restraints excluded: chain A residue 1357 TYR Chi-restraints excluded: chain A residue 1412 LEU Chi-restraints excluded: chain A residue 1488 LEU Chi-restraints excluded: chain A residue 1494 MET Chi-restraints excluded: chain A residue 1566 TYR Chi-restraints excluded: chain A residue 1596 LEU Chi-restraints excluded: chain A residue 1624 PHE Chi-restraints excluded: chain A residue 1711 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 93 optimal weight: 0.7980 chunk 17 optimal weight: 4.9990 chunk 42 optimal weight: 2.9990 chunk 38 optimal weight: 0.7980 chunk 28 optimal weight: 0.8980 chunk 56 optimal weight: 0.6980 chunk 0 optimal weight: 40.0000 chunk 1 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 74 optimal weight: 7.9990 chunk 32 optimal weight: 5.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 774 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.107228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.088442 restraints weight = 26729.362| |-----------------------------------------------------------------------------| r_work (start): 0.3693 rms_B_bonded: 3.77 r_work: 0.3548 rms_B_bonded: 4.80 restraints_weight: 0.5000 r_work (final): 0.3548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7517 moved from start: 0.2158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8991 Z= 0.133 Angle : 0.636 9.354 12184 Z= 0.302 Chirality : 0.044 0.490 1410 Planarity : 0.004 0.037 1393 Dihedral : 14.783 142.573 2048 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 3.61 % Allowed : 17.70 % Favored : 78.69 % 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: 1.44 (0.28), residues: 990 helix: 1.54 (0.19), residues: 719 sheet: -2.38 (0.89), residues: 22 loop : -0.31 (0.43), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1263 TYR 0.017 0.001 TYR A1443 PHE 0.022 0.001 PHE A1629 TRP 0.014 0.001 TRP A1369 HIS 0.002 0.000 HIS A 824 Details of bonding type rmsd covalent geometry : bond 0.00303 ( 8972) covalent geometry : angle 0.62473 (12132) SS BOND : bond 0.00188 ( 5) SS BOND : angle 1.15506 ( 10) hydrogen bonds : bond 0.03610 ( 546) hydrogen bonds : angle 4.18382 ( 1599) link_BETA1-4 : bond 0.00726 ( 9) link_BETA1-4 : angle 2.47406 ( 27) link_NAG-ASN : bond 0.00167 ( 5) link_NAG-ASN : angle 1.09886 ( 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 155 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 123 time to evaluate : 0.254 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 255 PHE cc_start: 0.8369 (t80) cc_final: 0.8124 (m-80) REVERT: A 299 ILE cc_start: 0.7631 (tp) cc_final: 0.7213 (tt) REVERT: A 674 CYS cc_start: 0.8638 (m) cc_final: 0.8039 (t) REVERT: A 697 LEU cc_start: 0.9180 (OUTLIER) cc_final: 0.8883 (mm) REVERT: A 760 LEU cc_start: 0.8854 (OUTLIER) cc_final: 0.8530 (mm) REVERT: A 874 MET cc_start: 0.7557 (tmm) cc_final: 0.6638 (tmm) REVERT: A 1153 TRP cc_start: 0.7247 (m100) cc_final: 0.6747 (t60) REVERT: A 1161 MET cc_start: 0.8760 (OUTLIER) cc_final: 0.8501 (mmm) REVERT: A 1222 ASP cc_start: 0.8820 (t0) cc_final: 0.8457 (t0) REVERT: A 1525 MET cc_start: 0.5885 (tmm) cc_final: 0.5601 (tmm) REVERT: A 1527 MET cc_start: 0.7096 (tmm) cc_final: 0.6589 (ttt) REVERT: A 1624 PHE cc_start: 0.7867 (OUTLIER) cc_final: 0.7421 (t80) outliers start: 32 outliers final: 15 residues processed: 139 average time/residue: 0.0826 time to fit residues: 16.4708 Evaluate side-chains 138 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 119 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 374 MET Chi-restraints excluded: chain A residue 696 MET Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain A residue 760 LEU Chi-restraints excluded: chain A residue 867 LEU Chi-restraints excluded: chain A residue 1161 MET Chi-restraints excluded: chain A residue 1249 LEU Chi-restraints excluded: chain A residue 1252 LEU Chi-restraints excluded: chain A residue 1288 CYS Chi-restraints excluded: chain A residue 1357 TYR Chi-restraints excluded: chain A residue 1412 LEU Chi-restraints excluded: chain A residue 1494 MET Chi-restraints excluded: chain A residue 1566 TYR Chi-restraints excluded: chain A residue 1596 LEU Chi-restraints excluded: chain A residue 1624 PHE Chi-restraints excluded: chain A residue 1660 SER Chi-restraints excluded: chain A residue 1697 VAL Chi-restraints excluded: chain A residue 1711 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 37 optimal weight: 0.7980 chunk 0 optimal weight: 40.0000 chunk 55 optimal weight: 0.8980 chunk 49 optimal weight: 2.9990 chunk 85 optimal weight: 6.9990 chunk 34 optimal weight: 0.9990 chunk 76 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 88 optimal weight: 0.7980 chunk 91 optimal weight: 1.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.107431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.088480 restraints weight = 26442.731| |-----------------------------------------------------------------------------| r_work (start): 0.3697 rms_B_bonded: 3.79 r_work: 0.3549 rms_B_bonded: 4.82 restraints_weight: 0.5000 r_work (final): 0.3549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7517 moved from start: 0.2376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8991 Z= 0.122 Angle : 0.620 10.116 12184 Z= 0.296 Chirality : 0.043 0.493 1410 Planarity : 0.004 0.035 1393 Dihedral : 14.092 150.404 2048 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.93 % Allowed : 19.73 % Favored : 77.34 % 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: 1.50 (0.28), residues: 990 helix: 1.61 (0.19), residues: 719 sheet: -2.92 (0.86), residues: 24 loop : -0.30 (0.44), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1263 TYR 0.019 0.001 TYR A 387 PHE 0.014 0.001 PHE A1629 TRP 0.025 0.001 TRP A1369 HIS 0.002 0.000 HIS A 824 Details of bonding type rmsd covalent geometry : bond 0.00274 ( 8972) covalent geometry : angle 0.61135 (12132) SS BOND : bond 0.00210 ( 5) SS BOND : angle 1.32856 ( 10) hydrogen bonds : bond 0.03512 ( 546) hydrogen bonds : angle 4.13631 ( 1599) link_BETA1-4 : bond 0.00625 ( 9) link_BETA1-4 : angle 2.10950 ( 27) link_NAG-ASN : bond 0.00121 ( 5) link_NAG-ASN : angle 1.10060 ( 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 149 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 123 time to evaluate : 0.330 Fit side-chains revert: symmetry clash REVERT: A 255 PHE cc_start: 0.8358 (t80) cc_final: 0.8132 (m-80) REVERT: A 299 ILE cc_start: 0.7644 (tp) cc_final: 0.7222 (tt) REVERT: A 674 CYS cc_start: 0.8643 (m) cc_final: 0.8038 (t) REVERT: A 697 LEU cc_start: 0.9184 (OUTLIER) cc_final: 0.8877 (mm) REVERT: A 756 ARG cc_start: 0.8804 (ttm110) cc_final: 0.8338 (mtt90) REVERT: A 760 LEU cc_start: 0.8844 (OUTLIER) cc_final: 0.8580 (mm) REVERT: A 874 MET cc_start: 0.7546 (tmm) cc_final: 0.6578 (tmm) REVERT: A 1153 TRP cc_start: 0.7229 (m100) cc_final: 0.6726 (t60) REVERT: A 1222 ASP cc_start: 0.8828 (t0) cc_final: 0.8470 (t0) REVERT: A 1427 LYS cc_start: 0.9165 (tptp) cc_final: 0.8855 (tmmt) REVERT: A 1525 MET cc_start: 0.5932 (tmm) cc_final: 0.5626 (tmm) REVERT: A 1624 PHE cc_start: 0.7882 (OUTLIER) cc_final: 0.7411 (t80) REVERT: A 1651 MET cc_start: 0.8964 (mmm) cc_final: 0.8648 (mmm) outliers start: 26 outliers final: 17 residues processed: 136 average time/residue: 0.0839 time to fit residues: 16.6363 Evaluate side-chains 134 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 114 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 696 MET Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain A residue 760 LEU Chi-restraints excluded: chain A residue 867 LEU Chi-restraints excluded: chain A residue 1161 MET Chi-restraints excluded: chain A residue 1197 PHE Chi-restraints excluded: chain A residue 1249 LEU Chi-restraints excluded: chain A residue 1252 LEU Chi-restraints excluded: chain A residue 1288 CYS Chi-restraints excluded: chain A residue 1357 TYR Chi-restraints excluded: chain A residue 1412 LEU Chi-restraints excluded: chain A residue 1416 VAL Chi-restraints excluded: chain A residue 1488 LEU Chi-restraints excluded: chain A residue 1494 MET Chi-restraints excluded: chain A residue 1566 TYR Chi-restraints excluded: chain A residue 1596 LEU Chi-restraints excluded: chain A residue 1624 PHE Chi-restraints excluded: chain A residue 1697 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 39 optimal weight: 0.8980 chunk 15 optimal weight: 0.6980 chunk 51 optimal weight: 0.5980 chunk 32 optimal weight: 4.9990 chunk 23 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 57 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 chunk 86 optimal weight: 0.9990 chunk 71 optimal weight: 5.9990 chunk 12 optimal weight: 4.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1352 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.107230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.088276 restraints weight = 26290.104| |-----------------------------------------------------------------------------| r_work (start): 0.3696 rms_B_bonded: 3.85 r_work: 0.3544 rms_B_bonded: 4.88 restraints_weight: 0.5000 r_work (final): 0.3544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 0.2543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8991 Z= 0.119 Angle : 0.608 10.077 12184 Z= 0.289 Chirality : 0.042 0.489 1410 Planarity : 0.004 0.034 1393 Dihedral : 13.382 160.443 2048 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 3.72 % Allowed : 19.50 % Favored : 76.78 % 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: 1.61 (0.28), residues: 990 helix: 1.69 (0.20), residues: 719 sheet: -2.88 (0.85), residues: 24 loop : -0.25 (0.44), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1263 TYR 0.019 0.001 TYR A 387 PHE 0.025 0.001 PHE A1160 TRP 0.019 0.001 TRP A1369 HIS 0.002 0.001 HIS A 833 Details of bonding type rmsd covalent geometry : bond 0.00265 ( 8972) covalent geometry : angle 0.60055 (12132) SS BOND : bond 0.00219 ( 5) SS BOND : angle 1.11524 ( 10) hydrogen bonds : bond 0.03408 ( 546) hydrogen bonds : angle 4.09552 ( 1599) link_BETA1-4 : bond 0.00618 ( 9) link_BETA1-4 : angle 1.90586 ( 27) link_NAG-ASN : bond 0.00127 ( 5) link_NAG-ASN : angle 1.09553 ( 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 153 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 120 time to evaluate : 0.319 Fit side-chains revert: symmetry clash REVERT: A 255 PHE cc_start: 0.8374 (t80) cc_final: 0.8164 (m-80) REVERT: A 299 ILE cc_start: 0.7687 (tp) cc_final: 0.7257 (tt) REVERT: A 697 LEU cc_start: 0.9197 (OUTLIER) cc_final: 0.8960 (mm) REVERT: A 756 ARG cc_start: 0.8819 (ttm110) cc_final: 0.8384 (mtt90) REVERT: A 760 LEU cc_start: 0.8871 (OUTLIER) cc_final: 0.8646 (mm) REVERT: A 874 MET cc_start: 0.7625 (tmm) cc_final: 0.6650 (tmm) REVERT: A 1153 TRP cc_start: 0.7256 (m100) cc_final: 0.6737 (t60) REVERT: A 1222 ASP cc_start: 0.8828 (t0) cc_final: 0.8530 (t70) REVERT: A 1427 LYS cc_start: 0.9166 (tptp) cc_final: 0.8851 (tmmt) REVERT: A 1525 MET cc_start: 0.6013 (tmm) cc_final: 0.5721 (tmm) REVERT: A 1527 MET cc_start: 0.6864 (tmm) cc_final: 0.6229 (ttt) REVERT: A 1624 PHE cc_start: 0.7874 (OUTLIER) cc_final: 0.7401 (t80) outliers start: 33 outliers final: 22 residues processed: 137 average time/residue: 0.0861 time to fit residues: 16.9646 Evaluate side-chains 138 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 113 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 696 MET Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain A residue 760 LEU Chi-restraints excluded: chain A residue 772 THR Chi-restraints excluded: chain A residue 867 LEU Chi-restraints excluded: chain A residue 882 LEU Chi-restraints excluded: chain A residue 1161 MET Chi-restraints excluded: chain A residue 1197 PHE Chi-restraints excluded: chain A residue 1249 LEU Chi-restraints excluded: chain A residue 1252 LEU Chi-restraints excluded: chain A residue 1288 CYS Chi-restraints excluded: chain A residue 1357 TYR Chi-restraints excluded: chain A residue 1370 MET Chi-restraints excluded: chain A residue 1412 LEU Chi-restraints excluded: chain A residue 1416 VAL Chi-restraints excluded: chain A residue 1488 LEU Chi-restraints excluded: chain A residue 1494 MET Chi-restraints excluded: chain A residue 1566 TYR Chi-restraints excluded: chain A residue 1596 LEU Chi-restraints excluded: chain A residue 1624 PHE Chi-restraints excluded: chain A residue 1670 ILE Chi-restraints excluded: chain A residue 1697 VAL Chi-restraints excluded: chain A residue 1711 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 90 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 chunk 8 optimal weight: 5.9990 chunk 74 optimal weight: 5.9990 chunk 23 optimal weight: 0.2980 chunk 64 optimal weight: 3.9990 chunk 79 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 34 optimal weight: 0.5980 chunk 56 optimal weight: 0.7980 chunk 92 optimal weight: 5.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 355 GLN A 390 ASN A1352 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.107508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.088534 restraints weight = 26330.987| |-----------------------------------------------------------------------------| r_work (start): 0.3701 rms_B_bonded: 3.83 r_work: 0.3552 rms_B_bonded: 4.83 restraints_weight: 0.5000 r_work (final): 0.3552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.2669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8991 Z= 0.116 Angle : 0.627 12.608 12184 Z= 0.294 Chirality : 0.043 0.481 1410 Planarity : 0.003 0.033 1393 Dihedral : 12.997 163.490 2048 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 3.38 % Allowed : 20.86 % Favored : 75.76 % 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: 1.46 (0.28), residues: 990 helix: 1.59 (0.19), residues: 734 sheet: -2.94 (0.83), residues: 24 loop : -0.47 (0.44), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 844 TYR 0.021 0.001 TYR A 387 PHE 0.014 0.001 PHE A1401 TRP 0.012 0.001 TRP A1369 HIS 0.001 0.000 HIS A 824 Details of bonding type rmsd covalent geometry : bond 0.00255 ( 8972) covalent geometry : angle 0.62054 (12132) SS BOND : bond 0.00189 ( 5) SS BOND : angle 0.96400 ( 10) hydrogen bonds : bond 0.03406 ( 546) hydrogen bonds : angle 4.12568 ( 1599) link_BETA1-4 : bond 0.00615 ( 9) link_BETA1-4 : angle 1.82737 ( 27) link_NAG-ASN : bond 0.00144 ( 5) link_NAG-ASN : angle 1.10164 ( 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 145 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 115 time to evaluate : 0.265 Fit side-chains revert: symmetry clash REVERT: A 299 ILE cc_start: 0.7715 (tp) cc_final: 0.7281 (tt) REVERT: A 400 TYR cc_start: 0.7397 (t80) cc_final: 0.7024 (t80) REVERT: A 756 ARG cc_start: 0.8833 (ttm110) cc_final: 0.8415 (mtt90) REVERT: A 760 LEU cc_start: 0.8880 (OUTLIER) cc_final: 0.8671 (mm) REVERT: A 874 MET cc_start: 0.7742 (tmm) cc_final: 0.6752 (tmm) REVERT: A 1153 TRP cc_start: 0.7302 (m100) cc_final: 0.6760 (t60) REVERT: A 1222 ASP cc_start: 0.8801 (t0) cc_final: 0.8450 (t0) REVERT: A 1427 LYS cc_start: 0.9170 (tptp) cc_final: 0.8856 (tmmt) REVERT: A 1527 MET cc_start: 0.6951 (tmm) cc_final: 0.6339 (ttt) REVERT: A 1624 PHE cc_start: 0.7886 (OUTLIER) cc_final: 0.7408 (t80) outliers start: 30 outliers final: 20 residues processed: 131 average time/residue: 0.0886 time to fit residues: 16.5341 Evaluate side-chains 134 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 112 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 696 MET Chi-restraints excluded: chain A residue 760 LEU Chi-restraints excluded: chain A residue 772 THR Chi-restraints excluded: chain A residue 867 LEU Chi-restraints excluded: chain A residue 882 LEU Chi-restraints excluded: chain A residue 1161 MET Chi-restraints excluded: chain A residue 1197 PHE Chi-restraints excluded: chain A residue 1249 LEU Chi-restraints excluded: chain A residue 1252 LEU Chi-restraints excluded: chain A residue 1357 TYR Chi-restraints excluded: chain A residue 1370 MET Chi-restraints excluded: chain A residue 1412 LEU Chi-restraints excluded: chain A residue 1416 VAL Chi-restraints excluded: chain A residue 1494 MET Chi-restraints excluded: chain A residue 1566 TYR Chi-restraints excluded: chain A residue 1596 LEU Chi-restraints excluded: chain A residue 1624 PHE Chi-restraints excluded: chain A residue 1635 GLU Chi-restraints excluded: chain A residue 1670 ILE Chi-restraints excluded: chain A residue 1697 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 72 optimal weight: 0.0470 chunk 85 optimal weight: 0.9980 chunk 51 optimal weight: 0.6980 chunk 93 optimal weight: 4.9990 chunk 67 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 90 optimal weight: 6.9990 chunk 55 optimal weight: 0.8980 chunk 58 optimal weight: 10.0000 chunk 96 optimal weight: 2.9990 chunk 57 optimal weight: 0.1980 overall best weight: 0.5678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.108091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.089232 restraints weight = 26196.068| |-----------------------------------------------------------------------------| r_work (start): 0.3718 rms_B_bonded: 3.82 r_work: 0.3569 rms_B_bonded: 4.84 restraints_weight: 0.5000 r_work (final): 0.3569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7517 moved from start: 0.2836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8991 Z= 0.113 Angle : 0.632 13.719 12184 Z= 0.294 Chirality : 0.043 0.466 1410 Planarity : 0.003 0.033 1393 Dihedral : 12.764 164.592 2048 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 2.71 % Allowed : 21.53 % Favored : 75.76 % 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: 1.53 (0.28), residues: 990 helix: 1.64 (0.20), residues: 734 sheet: -3.07 (0.82), residues: 24 loop : -0.45 (0.44), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1263 TYR 0.019 0.001 TYR A 387 PHE 0.015 0.001 PHE A1401 TRP 0.009 0.001 TRP A1369 HIS 0.001 0.000 HIS A 824 Details of bonding type rmsd covalent geometry : bond 0.00250 ( 8972) covalent geometry : angle 0.62602 (12132) SS BOND : bond 0.00169 ( 5) SS BOND : angle 0.84012 ( 10) hydrogen bonds : bond 0.03360 ( 546) hydrogen bonds : angle 4.11226 ( 1599) link_BETA1-4 : bond 0.00624 ( 9) link_BETA1-4 : angle 1.76614 ( 27) link_NAG-ASN : bond 0.00166 ( 5) link_NAG-ASN : angle 1.10469 ( 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 146 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 122 time to evaluate : 0.304 Fit side-chains revert: symmetry clash REVERT: A 299 ILE cc_start: 0.7606 (tp) cc_final: 0.7161 (tt) REVERT: A 302 ARG cc_start: 0.8958 (ttp80) cc_final: 0.8493 (tpp80) REVERT: A 400 TYR cc_start: 0.7544 (t80) cc_final: 0.7107 (t80) REVERT: A 697 LEU cc_start: 0.9194 (OUTLIER) cc_final: 0.8961 (mm) REVERT: A 756 ARG cc_start: 0.8863 (ttm110) cc_final: 0.8424 (mtt90) REVERT: A 874 MET cc_start: 0.7672 (tmm) cc_final: 0.6679 (tmm) REVERT: A 1153 TRP cc_start: 0.7277 (m100) cc_final: 0.6719 (t60) REVERT: A 1222 ASP cc_start: 0.8838 (t0) cc_final: 0.8487 (t0) REVERT: A 1427 LYS cc_start: 0.9173 (tptp) cc_final: 0.8847 (tmmt) REVERT: A 1527 MET cc_start: 0.6888 (tmm) cc_final: 0.6316 (ttt) REVERT: A 1624 PHE cc_start: 0.7881 (OUTLIER) cc_final: 0.7422 (t80) outliers start: 24 outliers final: 19 residues processed: 134 average time/residue: 0.0793 time to fit residues: 15.4530 Evaluate side-chains 136 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 115 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 696 MET Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain A residue 772 THR Chi-restraints excluded: chain A residue 867 LEU Chi-restraints excluded: chain A residue 1161 MET Chi-restraints excluded: chain A residue 1249 LEU Chi-restraints excluded: chain A residue 1252 LEU Chi-restraints excluded: chain A residue 1357 TYR Chi-restraints excluded: chain A residue 1370 MET Chi-restraints excluded: chain A residue 1412 LEU Chi-restraints excluded: chain A residue 1416 VAL Chi-restraints excluded: chain A residue 1488 LEU Chi-restraints excluded: chain A residue 1494 MET Chi-restraints excluded: chain A residue 1566 TYR Chi-restraints excluded: chain A residue 1596 LEU Chi-restraints excluded: chain A residue 1624 PHE Chi-restraints excluded: chain A residue 1635 GLU Chi-restraints excluded: chain A residue 1670 ILE Chi-restraints excluded: chain A residue 1697 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 83 optimal weight: 6.9990 chunk 33 optimal weight: 0.0060 chunk 43 optimal weight: 5.9990 chunk 76 optimal weight: 1.9990 chunk 0 optimal weight: 30.0000 chunk 90 optimal weight: 6.9990 chunk 71 optimal weight: 2.9990 chunk 54 optimal weight: 0.9990 chunk 14 optimal weight: 7.9990 chunk 86 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 overall best weight: 1.8004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1352 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.104949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.085899 restraints weight = 26689.194| |-----------------------------------------------------------------------------| r_work (start): 0.3657 rms_B_bonded: 3.82 r_work: 0.3507 rms_B_bonded: 4.81 restraints_weight: 0.5000 r_work (final): 0.3507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.2915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 8991 Z= 0.170 Angle : 0.666 11.265 12184 Z= 0.317 Chirality : 0.045 0.429 1410 Planarity : 0.004 0.033 1393 Dihedral : 12.825 165.105 2048 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 3.16 % Allowed : 21.08 % Favored : 75.76 % 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: 1.52 (0.27), residues: 990 helix: 1.57 (0.19), residues: 719 sheet: -2.51 (0.87), residues: 22 loop : -0.17 (0.44), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 360 TYR 0.019 0.002 TYR A1705 PHE 0.022 0.001 PHE A1701 TRP 0.012 0.001 TRP A 358 HIS 0.003 0.001 HIS A 831 Details of bonding type rmsd covalent geometry : bond 0.00393 ( 8972) covalent geometry : angle 0.65965 (12132) SS BOND : bond 0.00347 ( 5) SS BOND : angle 1.14795 ( 10) hydrogen bonds : bond 0.03776 ( 546) hydrogen bonds : angle 4.25320 ( 1599) link_BETA1-4 : bond 0.00588 ( 9) link_BETA1-4 : angle 1.76858 ( 27) link_NAG-ASN : bond 0.00289 ( 5) link_NAG-ASN : angle 1.32217 ( 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 139 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 111 time to evaluate : 0.322 Fit side-chains revert: symmetry clash REVERT: A 302 ARG cc_start: 0.8962 (ttp80) cc_final: 0.8560 (tpp80) REVERT: A 400 TYR cc_start: 0.7535 (t80) cc_final: 0.7083 (t80) REVERT: A 697 LEU cc_start: 0.9237 (OUTLIER) cc_final: 0.8975 (mm) REVERT: A 756 ARG cc_start: 0.8907 (ttm110) cc_final: 0.8477 (mtt90) REVERT: A 874 MET cc_start: 0.7731 (tmm) cc_final: 0.6735 (tmm) REVERT: A 1153 TRP cc_start: 0.7365 (m100) cc_final: 0.6795 (t60) REVERT: A 1222 ASP cc_start: 0.8880 (t0) cc_final: 0.8531 (t70) REVERT: A 1381 GLU cc_start: 0.8629 (tm-30) cc_final: 0.8350 (tm-30) REVERT: A 1427 LYS cc_start: 0.9184 (tptp) cc_final: 0.8876 (tmmt) REVERT: A 1490 MET cc_start: 0.8816 (ttt) cc_final: 0.8597 (ttt) REVERT: A 1527 MET cc_start: 0.6975 (tmm) cc_final: 0.6268 (ttt) REVERT: A 1624 PHE cc_start: 0.7915 (OUTLIER) cc_final: 0.7507 (t80) outliers start: 28 outliers final: 21 residues processed: 125 average time/residue: 0.0861 time to fit residues: 15.4343 Evaluate side-chains 129 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 106 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 696 MET Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain A residue 772 THR Chi-restraints excluded: chain A residue 867 LEU Chi-restraints excluded: chain A residue 1161 MET Chi-restraints excluded: chain A residue 1197 PHE Chi-restraints excluded: chain A residue 1249 LEU Chi-restraints excluded: chain A residue 1252 LEU Chi-restraints excluded: chain A residue 1357 TYR Chi-restraints excluded: chain A residue 1370 MET Chi-restraints excluded: chain A residue 1402 ILE Chi-restraints excluded: chain A residue 1412 LEU Chi-restraints excluded: chain A residue 1488 LEU Chi-restraints excluded: chain A residue 1494 MET Chi-restraints excluded: chain A residue 1566 TYR Chi-restraints excluded: chain A residue 1583 ILE Chi-restraints excluded: chain A residue 1596 LEU Chi-restraints excluded: chain A residue 1624 PHE Chi-restraints excluded: chain A residue 1670 ILE Chi-restraints excluded: chain A residue 1697 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 9 optimal weight: 0.9980 chunk 48 optimal weight: 3.9990 chunk 30 optimal weight: 0.9980 chunk 94 optimal weight: 1.9990 chunk 56 optimal weight: 0.7980 chunk 70 optimal weight: 0.0980 chunk 19 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 11 optimal weight: 4.9990 chunk 54 optimal weight: 0.8980 chunk 25 optimal weight: 8.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1352 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.106642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.087894 restraints weight = 26313.524| |-----------------------------------------------------------------------------| r_work (start): 0.3695 rms_B_bonded: 3.75 r_work: 0.3545 rms_B_bonded: 4.77 restraints_weight: 0.5000 r_work (final): 0.3545 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 moved from start: 0.3016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8991 Z= 0.120 Angle : 0.641 13.337 12184 Z= 0.300 Chirality : 0.043 0.380 1410 Planarity : 0.003 0.034 1393 Dihedral : 12.563 164.939 2048 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 2.25 % Allowed : 22.10 % Favored : 75.65 % 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: 1.57 (0.28), residues: 990 helix: 1.64 (0.19), residues: 719 sheet: -3.04 (0.83), residues: 24 loop : -0.18 (0.44), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1579 TYR 0.018 0.001 TYR A 387 PHE 0.016 0.001 PHE A1401 TRP 0.020 0.001 TRP A 770 HIS 0.001 0.000 HIS A 824 Details of bonding type rmsd covalent geometry : bond 0.00272 ( 8972) covalent geometry : angle 0.63611 (12132) SS BOND : bond 0.00189 ( 5) SS BOND : angle 0.94830 ( 10) hydrogen bonds : bond 0.03531 ( 546) hydrogen bonds : angle 4.15816 ( 1599) link_BETA1-4 : bond 0.00600 ( 9) link_BETA1-4 : angle 1.65427 ( 27) link_NAG-ASN : bond 0.00154 ( 5) link_NAG-ASN : angle 1.14170 ( 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 137 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 117 time to evaluate : 0.312 Fit side-chains revert: symmetry clash REVERT: A 299 ILE cc_start: 0.7701 (tp) cc_final: 0.7286 (tt) REVERT: A 302 ARG cc_start: 0.8972 (ttp80) cc_final: 0.8561 (tpp80) REVERT: A 697 LEU cc_start: 0.9211 (OUTLIER) cc_final: 0.8959 (mm) REVERT: A 756 ARG cc_start: 0.8911 (ttm110) cc_final: 0.8230 (mtm-85) REVERT: A 874 MET cc_start: 0.7673 (tmm) cc_final: 0.6667 (tmm) REVERT: A 1153 TRP cc_start: 0.7317 (m100) cc_final: 0.6750 (t60) REVERT: A 1222 ASP cc_start: 0.8894 (t0) cc_final: 0.8492 (t0) REVERT: A 1427 LYS cc_start: 0.9192 (tptp) cc_final: 0.8869 (tmmt) REVERT: A 1527 MET cc_start: 0.6810 (tmm) cc_final: 0.6197 (ttt) REVERT: A 1624 PHE cc_start: 0.7860 (OUTLIER) cc_final: 0.7420 (t80) outliers start: 20 outliers final: 17 residues processed: 124 average time/residue: 0.0845 time to fit residues: 14.9938 Evaluate side-chains 134 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 115 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 696 MET Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain A residue 744 LEU Chi-restraints excluded: chain A residue 772 THR Chi-restraints excluded: chain A residue 867 LEU Chi-restraints excluded: chain A residue 1161 MET Chi-restraints excluded: chain A residue 1197 PHE Chi-restraints excluded: chain A residue 1249 LEU Chi-restraints excluded: chain A residue 1252 LEU Chi-restraints excluded: chain A residue 1357 TYR Chi-restraints excluded: chain A residue 1370 MET Chi-restraints excluded: chain A residue 1488 LEU Chi-restraints excluded: chain A residue 1494 MET Chi-restraints excluded: chain A residue 1566 TYR Chi-restraints excluded: chain A residue 1596 LEU Chi-restraints excluded: chain A residue 1624 PHE Chi-restraints excluded: chain A residue 1670 ILE Chi-restraints excluded: chain A residue 1697 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 81 optimal weight: 6.9990 chunk 47 optimal weight: 3.9990 chunk 21 optimal weight: 0.7980 chunk 22 optimal weight: 5.9990 chunk 74 optimal weight: 7.9990 chunk 16 optimal weight: 9.9990 chunk 37 optimal weight: 0.7980 chunk 7 optimal weight: 9.9990 chunk 14 optimal weight: 0.7980 chunk 60 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.105475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.086666 restraints weight = 26656.194| |-----------------------------------------------------------------------------| r_work (start): 0.3678 rms_B_bonded: 3.74 r_work: 0.3529 rms_B_bonded: 4.77 restraints_weight: 0.5000 r_work (final): 0.3529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 moved from start: 0.3088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8991 Z= 0.141 Angle : 0.643 13.013 12184 Z= 0.305 Chirality : 0.043 0.388 1410 Planarity : 0.004 0.034 1393 Dihedral : 12.375 164.396 2048 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.59 % Allowed : 21.98 % Favored : 75.42 % 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: 1.51 (0.28), residues: 990 helix: 1.59 (0.19), residues: 719 sheet: -2.98 (0.84), residues: 24 loop : -0.19 (0.44), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1263 TYR 0.016 0.001 TYR A1443 PHE 0.018 0.001 PHE A1701 TRP 0.027 0.001 TRP A 770 HIS 0.002 0.001 HIS A 831 Details of bonding type rmsd covalent geometry : bond 0.00328 ( 8972) covalent geometry : angle 0.63754 (12132) SS BOND : bond 0.00251 ( 5) SS BOND : angle 1.03504 ( 10) hydrogen bonds : bond 0.03624 ( 546) hydrogen bonds : angle 4.21100 ( 1599) link_BETA1-4 : bond 0.00587 ( 9) link_BETA1-4 : angle 1.66110 ( 27) link_NAG-ASN : bond 0.00181 ( 5) link_NAG-ASN : angle 1.26623 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2487.33 seconds wall clock time: 43 minutes 20.49 seconds (2600.49 seconds total)