Starting phenix.real_space_refine on Sat May 2 21:57:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dbl_46719/05_2026/9dbl_46719.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dbl_46719/05_2026/9dbl_46719.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.24 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9dbl_46719/05_2026/9dbl_46719.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dbl_46719/05_2026/9dbl_46719.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9dbl_46719/05_2026/9dbl_46719.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dbl_46719/05_2026/9dbl_46719.map" } resolution = 3.24 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 4 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="CLR A2005 " Not linked: pdbres="CLR A2005 " pdbres="PCW 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: 2.25, per 1000 atoms: 0.26 Number of scatterers: 8766 At special positions: 0 Unit cell: (89.773, 103.197, 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=2.03 Simple disulfide: pdb=" SG CYS A 857 " - pdb=" SG CYS A 866 " distance=2.03 Simple disulfide: pdb=" SG CYS A1310 " - pdb=" SG CYS A1332 " distance=2.04 Simple disulfide: pdb=" SG CYS A1678 " - pdb=" SG CYS A1692 " distance=2.03 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: 1.10 Conformation dependent library (CDL) restraints added in 320.5 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: 48 helices and 2 sheets defined 76.0% alpha, 1.3% 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 268 removed outlier: 5.054A pdb=" N ASP A 248 " --> pdb=" O LYS A 244 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N VAL A 249 " --> pdb=" O LYS A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 341 through 355 Processing helix chain 'A' and resid 357 through 369 removed outlier: 4.003A 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: 3.913A pdb=" N PHE A 377 " --> pdb=" O TYR A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 407 Processing helix chain 'A' and resid 652 through 661 Processing helix chain 'A' and resid 664 through 683 removed outlier: 3.887A 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 720 through 724 Processing helix chain 'A' and resid 727 through 746 Processing helix chain 'A' and resid 752 through 759 removed outlier: 4.183A pdb=" N ARG A 759 " --> pdb=" O LEU A 755 " (cutoff:3.500A) Processing helix chain 'A' and resid 760 through 767 Processing helix chain 'A' and resid 770 through 785 removed outlier: 3.747A pdb=" N ASN A 774 " --> pdb=" O TRP A 770 " (cutoff:3.500A) Processing helix chain 'A' and resid 787 through 816 removed outlier: 3.717A pdb=" N THR A 791 " --> pdb=" O LEU A 787 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N GLU A 811 " --> pdb=" O GLN A 807 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N ASN A 812 " --> pdb=" O LEU A 808 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 821 removed outlier: 4.137A 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 861 Processing helix chain 'A' and resid 862 through 892 removed outlier: 3.566A pdb=" N LEU A 889 " --> pdb=" O PHE A 885 " (cutoff:3.500A) Processing helix chain 'A' and resid 1137 through 1150 removed outlier: 3.631A pdb=" N CYS A1145 " --> pdb=" O VAL A1141 " (cutoff:3.500A) Processing helix chain 'A' and resid 1151 through 1169 Processing helix chain 'A' and resid 1173 through 1178 removed outlier: 3.966A pdb=" N ASP A1177 " --> pdb=" O TYR A1174 " (cutoff:3.500A) Processing helix chain 'A' and resid 1179 through 1208 removed outlier: 3.531A pdb=" N LYS A1183 " --> pdb=" O LYS A1179 " (cutoff:3.500A) Processing helix chain 'A' and resid 1209 through 1215 Processing helix chain 'A' and resid 1216 through 1238 removed outlier: 3.574A pdb=" N ILE A1237 " --> pdb=" O LEU A1233 " (cutoff:3.500A) Processing helix chain 'A' and resid 1243 through 1252 Processing helix chain 'A' and resid 1253 through 1260 Proline residue: A1257 - end of helix removed outlier: 4.160A pdb=" N ALA A1260 " --> pdb=" O PRO A1257 " (cutoff:3.500A) Processing helix chain 'A' and resid 1264 through 1277 removed outlier: 3.703A pdb=" N ALA A1277 " --> pdb=" O ALA A1273 " (cutoff:3.500A) Processing helix chain 'A' and resid 1277 through 1304 removed outlier: 3.890A pdb=" N VAL A1284 " --> pdb=" O SER A1280 " (cutoff:3.500A) Processing helix chain 'A' and resid 1328 through 1335 Processing helix chain 'A' and resid 1352 through 1366 Processing helix chain 'A' and resid 1368 through 1379 removed outlier: 3.897A pdb=" N ILE A1372 " --> pdb=" O GLY A1368 " (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: 4.262A pdb=" N PHE A1398 " --> pdb=" O MET A1394 " (cutoff:3.500A) Processing helix chain 'A' and resid 1410 through 1428 removed outlier: 3.593A pdb=" N GLY A1415 " --> pdb=" O ASN A1411 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLN A1423 " --> pdb=" O ASP A1419 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LYS A1426 " --> pdb=" O ASN A1422 " (cutoff:3.500A) Processing helix chain 'A' and resid 1436 through 1450 removed outlier: 3.517A pdb=" N LYS A1441 " --> pdb=" O GLU A1437 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N TYR A1442 " --> pdb=" O GLU A1438 " (cutoff:3.500A) Processing helix chain 'A' and resid 1463 through 1475 removed outlier: 3.630A pdb=" N ILE A1472 " --> pdb=" O PHE A1468 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ARG A1475 " --> pdb=" O ASP A1471 " (cutoff:3.500A) Processing helix chain 'A' and resid 1477 through 1488 Processing helix chain 'A' and resid 1501 through 1530 removed outlier: 3.897A pdb=" N LYS A1526 " --> pdb=" O GLU A1522 " (cutoff:3.500A) Processing helix chain 'A' and resid 1534 through 1538 removed outlier: 4.200A pdb=" N GLY A1538 " --> pdb=" O PHE A1535 " (cutoff:3.500A) Processing helix chain 'A' and resid 1539 through 1563 removed outlier: 3.602A pdb=" N ASP A1543 " --> pdb=" O TRP A1539 " (cutoff:3.500A) Processing helix chain 'A' and resid 1569 through 1577 removed outlier: 3.931A pdb=" N ARG A1573 " --> pdb=" O PRO A1569 " (cutoff:3.500A) Processing helix chain 'A' and resid 1580 through 1585 Processing helix chain 'A' and resid 1586 through 1589 Processing helix chain 'A' and resid 1590 through 1629 Proline residue: A1605 - end of helix Processing helix chain 'A' and resid 1646 through 1659 removed outlier: 3.896A 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: 3.613A pdb=" N ASN A1672 " --> pdb=" O SER A1668 " (cutoff:3.500A) Processing helix chain 'A' and resid 1694 through 1726 removed outlier: 4.027A pdb=" N ILE A1700 " --> pdb=" O ALA A1696 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N PHE A1702 " --> pdb=" O GLY A1698 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N PHE A1710 " --> pdb=" O ILE A1706 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 277 through 278 Processing sheet with id=AA2, first strand: chain 'A' and resid 1318 through 1320 536 hydrogen bonds defined for protein. 1569 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: 1.33 Time building geometry restraints manager: 1.28 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: 1332 1.32 - 1.45: 2414 1.45 - 1.57: 5108 1.57 - 1.70: 24 1.70 - 1.82: 94 Bond restraints: 8972 Sorted by residual: bond pdb=" N ARG A1460 " pdb=" CA ARG A1460 " ideal model delta sigma weight residual 1.460 1.488 -0.028 7.10e-03 1.98e+04 1.56e+01 bond pdb=" CA TRP A1369 " pdb=" C TRP A1369 " ideal model delta sigma weight residual 1.523 1.475 0.048 1.35e-02 5.49e+03 1.26e+01 bond pdb=" O33 LPE A2015 " pdb=" P LPE A2015 " ideal model delta sigma weight residual 1.673 1.604 0.069 2.00e-02 2.50e+03 1.17e+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 1.15e+01 bond pdb=" O33 LPE A2014 " pdb=" P LPE A2014 " ideal model delta sigma weight residual 1.673 1.606 0.067 2.00e-02 2.50e+03 1.13e+01 ... (remaining 8967 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.11: 11585 2.11 - 4.23: 444 4.23 - 6.34: 80 6.34 - 8.46: 20 8.46 - 10.57: 3 Bond angle restraints: 12132 Sorted by residual: angle pdb=" N GLY A1368 " pdb=" CA GLY A1368 " pdb=" C GLY A1368 " ideal model delta sigma weight residual 115.32 104.75 10.57 1.38e+00 5.25e-01 5.87e+01 angle pdb=" N MET A1494 " pdb=" CA MET A1494 " pdb=" C MET A1494 " ideal model delta sigma weight residual 113.41 104.96 8.45 1.22e+00 6.72e-01 4.80e+01 angle pdb=" N MET A1370 " pdb=" CA MET A1370 " pdb=" C MET A1370 " ideal model delta sigma weight residual 111.14 117.53 -6.39 1.08e+00 8.57e-01 3.50e+01 angle pdb=" N ASN A1489 " pdb=" CA ASN A1489 " pdb=" C ASN A1489 " ideal model delta sigma weight residual 113.38 106.54 6.84 1.23e+00 6.61e-01 3.09e+01 angle pdb=" N LEU A1410 " pdb=" CA LEU A1410 " pdb=" C LEU A1410 " ideal model delta sigma weight residual 113.97 107.18 6.79 1.28e+00 6.10e-01 2.81e+01 ... (remaining 12127 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.62: 5381 29.62 - 59.23: 339 59.23 - 88.85: 54 88.85 - 118.47: 29 118.47 - 148.08: 14 Dihedral angle restraints: 5817 sinusoidal: 2902 harmonic: 2915 Sorted by residual: 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 93.00 168.19 -75.19 1 1.00e+01 1.00e-02 7.15e+01 dihedral pdb=" CB P5S A2016 " pdb=" OG P5S A2016 " pdb=" P12 P5S A2016 " pdb=" O13 P5S A2016 " ideal model delta sinusoidal sigma weight residual 47.21 -164.71 -148.08 1 3.00e+01 1.11e-03 1.97e+01 dihedral pdb=" N PCW A2010 " pdb=" C4 PCW A2010 " pdb=" C5 PCW A2010 " pdb=" O4P PCW A2010 " ideal model delta sinusoidal sigma weight residual -66.66 80.77 -147.43 1 3.00e+01 1.11e-03 1.97e+01 ... (remaining 5814 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.103: 1338 0.103 - 0.206: 61 0.206 - 0.309: 9 0.309 - 0.413: 0 0.413 - 0.516: 2 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 -1.88 -0.52 2.00e-02 2.50e+03 6.65e+02 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 -2.16 -0.24 2.00e-02 2.50e+03 1.48e+02 chirality pdb=" C1 BMA C 3 " pdb=" O4 NAG C 2 " pdb=" C2 BMA C 3 " pdb=" O5 BMA C 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.24 -0.16 2.00e-02 2.50e+03 6.44e+01 ... (remaining 1407 not shown) Planarity restraints: 1398 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C38 PCW A2006 " 0.211 2.00e-02 2.50e+03 2.10e-01 4.41e+02 pdb=" C39 PCW A2006 " -0.213 2.00e-02 2.50e+03 pdb=" C40 PCW A2006 " -0.207 2.00e-02 2.50e+03 pdb=" C41 PCW A2006 " 0.209 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C38 PCW A2009 " -0.090 2.00e-02 2.50e+03 1.84e-01 3.38e+02 pdb=" C39 PCW A2009 " 0.246 2.00e-02 2.50e+03 pdb=" C40 PCW A2009 " -0.243 2.00e-02 2.50e+03 pdb=" C41 PCW A2009 " 0.087 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG F 1 " -0.144 2.00e-02 2.50e+03 1.19e-01 1.77e+02 pdb=" C7 NAG F 1 " 0.037 2.00e-02 2.50e+03 pdb=" C8 NAG F 1 " -0.105 2.00e-02 2.50e+03 pdb=" N2 NAG F 1 " 0.193 2.00e-02 2.50e+03 pdb=" O7 NAG F 1 " 0.019 2.00e-02 2.50e+03 ... (remaining 1395 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1561 2.76 - 3.29: 9276 3.29 - 3.83: 14356 3.83 - 4.36: 17134 4.36 - 4.90: 28514 Nonbonded interactions: 70841 Sorted by model distance: nonbonded pdb=" O LYS A 301 " pdb=" OG1 THR A 304 " model vdw 2.221 3.040 nonbonded pdb=" OD1 ASP A1190 " pdb=" NH1 ARG A1256 " model vdw 2.228 3.120 nonbonded pdb=" OD1 ASP A1173 " pdb=" N TYR A1175 " model vdw 2.262 3.120 nonbonded pdb=" O ARG A1191 " pdb=" OG1 THR A1194 " model vdw 2.262 3.040 nonbonded pdb=" OG1 THR A 772 " pdb=" OD1 ASN A1283 " model vdw 2.283 3.040 ... (remaining 70836 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: 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: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 9.910 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 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:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6751 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 0.105 8991 Z= 0.437 Angle : 1.029 14.426 12184 Z= 0.552 Chirality : 0.053 0.516 1410 Planarity : 0.011 0.210 1393 Dihedral : 21.593 148.085 3914 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 0.79 % Allowed : 14.32 % Favored : 84.89 % 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: -0.49 (0.26), residues: 990 helix: 0.43 (0.19), residues: 715 sheet: -3.38 (1.29), residues: 12 loop : -2.15 (0.35), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 351 TYR 0.031 0.002 TYR A 724 PHE 0.021 0.002 PHE A1701 TRP 0.014 0.001 TRP A1369 HIS 0.005 0.001 HIS A 831 Details of bonding type rmsd covalent geometry : bond 0.00784 ( 8972) covalent geometry : angle 0.96677 (12132) SS BOND : bond 0.00328 ( 5) SS BOND : angle 1.30883 ( 10) hydrogen bonds : bond 0.13121 ( 536) hydrogen bonds : angle 5.60673 ( 1569) link_BETA1-4 : bond 0.04606 ( 9) link_BETA1-4 : angle 6.37923 ( 27) link_NAG-ASN : bond 0.04724 ( 5) link_NAG-ASN : angle 5.39220 ( 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 175 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 168 time to evaluate : 0.282 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 255 PHE cc_start: 0.8732 (t80) cc_final: 0.8176 (m-80) REVERT: A 874 MET cc_start: 0.7393 (tpp) cc_final: 0.7062 (tpt) REVERT: A 1370 MET cc_start: 0.8253 (mmm) cc_final: 0.7818 (mmm) REVERT: A 1479 ASP cc_start: 0.8575 (m-30) cc_final: 0.8211 (p0) REVERT: A 1527 MET cc_start: 0.6834 (ttm) cc_final: 0.5882 (tmm) REVERT: A 1601 MET cc_start: 0.7890 (tpt) cc_final: 0.7545 (tpp) REVERT: A 1622 SER cc_start: 0.8940 (m) cc_final: 0.8581 (m) outliers start: 7 outliers final: 6 residues processed: 171 average time/residue: 0.0769 time to fit residues: 19.7443 Evaluate side-chains 134 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 128 time to evaluate : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 274 ASN Chi-restraints excluded: chain A residue 1251 THR Chi-restraints excluded: chain A residue 1252 LEU Chi-restraints excluded: chain A residue 1409 THR Chi-restraints excluded: chain A residue 1650 SER Chi-restraints excluded: chain A residue 1670 ILE 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: 8.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 0.5980 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 5.9990 chunk 38 optimal weight: 0.9980 chunk 61 optimal weight: 0.7980 chunk 45 optimal weight: 8.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1227 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.102907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.086446 restraints weight = 29996.581| |-----------------------------------------------------------------------------| r_work (start): 0.3678 rms_B_bonded: 4.30 r_work (final): 0.3678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7355 moved from start: 0.1641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8991 Z= 0.147 Angle : 0.731 9.996 12184 Z= 0.351 Chirality : 0.045 0.314 1410 Planarity : 0.004 0.054 1393 Dihedral : 19.208 162.566 2057 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.48 % Allowed : 16.23 % Favored : 81.29 % 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: 0.33 (0.27), residues: 990 helix: 0.95 (0.19), residues: 716 sheet: -2.51 (1.49), residues: 10 loop : -1.60 (0.38), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 762 TYR 0.018 0.002 TYR A1213 PHE 0.015 0.001 PHE A1401 TRP 0.012 0.001 TRP A1369 HIS 0.001 0.001 HIS A1151 Details of bonding type rmsd covalent geometry : bond 0.00321 ( 8972) covalent geometry : angle 0.71726 (12132) SS BOND : bond 0.00345 ( 5) SS BOND : angle 1.60521 ( 10) hydrogen bonds : bond 0.04731 ( 536) hydrogen bonds : angle 4.34113 ( 1569) link_BETA1-4 : bond 0.00533 ( 9) link_BETA1-4 : angle 2.71509 ( 27) link_NAG-ASN : bond 0.00147 ( 5) link_NAG-ASN : angle 1.78953 ( 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 169 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 147 time to evaluate : 0.264 Fit side-chains revert: symmetry clash REVERT: A 255 PHE cc_start: 0.8417 (t80) cc_final: 0.7816 (m-80) REVERT: A 308 LEU cc_start: 0.5361 (OUTLIER) cc_final: 0.5000 (tt) REVERT: A 762 ARG cc_start: 0.8073 (mtt90) cc_final: 0.7746 (mpt180) REVERT: A 1233 LEU cc_start: 0.8956 (pp) cc_final: 0.8741 (pp) REVERT: A 1479 ASP cc_start: 0.8843 (m-30) cc_final: 0.8307 (p0) REVERT: A 1494 MET cc_start: 0.8087 (ptm) cc_final: 0.7304 (ppp) REVERT: A 1510 LYS cc_start: 0.8458 (mptt) cc_final: 0.7757 (tmtt) REVERT: A 1527 MET cc_start: 0.6594 (ttm) cc_final: 0.5802 (tmm) REVERT: A 1575 ILE cc_start: 0.8472 (mt) cc_final: 0.8182 (mp) REVERT: A 1601 MET cc_start: 0.8054 (tpt) cc_final: 0.7813 (tpp) REVERT: A 1602 MET cc_start: 0.7566 (mmm) cc_final: 0.7251 (mmm) REVERT: A 1622 SER cc_start: 0.8751 (m) cc_final: 0.8442 (m) REVERT: A 1624 PHE cc_start: 0.7956 (OUTLIER) cc_final: 0.7755 (t80) REVERT: A 1717 TYR cc_start: 0.8437 (m-10) cc_final: 0.7990 (m-80) outliers start: 22 outliers final: 11 residues processed: 158 average time/residue: 0.0680 time to fit residues: 16.6125 Evaluate side-chains 140 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 127 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 739 VAL Chi-restraints excluded: chain A residue 871 LEU Chi-restraints excluded: chain A residue 1252 LEU Chi-restraints excluded: chain A residue 1285 LEU Chi-restraints excluded: chain A residue 1357 TYR Chi-restraints excluded: chain A residue 1372 ILE Chi-restraints excluded: chain A residue 1392 VAL Chi-restraints excluded: chain A residue 1412 LEU Chi-restraints excluded: chain A residue 1492 THR Chi-restraints excluded: chain A residue 1518 VAL Chi-restraints excluded: chain A residue 1524 VAL Chi-restraints excluded: chain A residue 1624 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 13 optimal weight: 0.9990 chunk 5 optimal weight: 8.9990 chunk 92 optimal weight: 0.6980 chunk 62 optimal weight: 4.9990 chunk 55 optimal weight: 0.3980 chunk 39 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 chunk 77 optimal weight: 0.5980 chunk 35 optimal weight: 0.5980 chunk 74 optimal weight: 6.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- 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 = 0.4065 r_free = 0.4065 target = 0.103297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.086839 restraints weight = 29865.442| |-----------------------------------------------------------------------------| r_work (start): 0.3699 rms_B_bonded: 4.27 r_work (final): 0.3699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7366 moved from start: 0.2146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8991 Z= 0.127 Angle : 0.646 7.270 12184 Z= 0.311 Chirality : 0.043 0.292 1410 Planarity : 0.004 0.042 1393 Dihedral : 17.213 161.228 2050 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 2.59 % Allowed : 18.49 % 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: 0.48 (0.27), residues: 990 helix: 1.02 (0.19), residues: 714 sheet: -2.36 (1.75), residues: 12 loop : -1.41 (0.39), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 814 TYR 0.020 0.001 TYR A1213 PHE 0.021 0.001 PHE A 707 TRP 0.019 0.001 TRP A 827 HIS 0.002 0.001 HIS A 686 Details of bonding type rmsd covalent geometry : bond 0.00275 ( 8972) covalent geometry : angle 0.63182 (12132) SS BOND : bond 0.00383 ( 5) SS BOND : angle 1.76706 ( 10) hydrogen bonds : bond 0.04216 ( 536) hydrogen bonds : angle 4.14583 ( 1569) link_BETA1-4 : bond 0.00501 ( 9) link_BETA1-4 : angle 2.57110 ( 27) link_NAG-ASN : bond 0.00160 ( 5) link_NAG-ASN : angle 1.39683 ( 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 168 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 145 time to evaluate : 0.317 Fit side-chains revert: symmetry clash REVERT: A 255 PHE cc_start: 0.8416 (t80) cc_final: 0.7827 (m-80) REVERT: A 308 LEU cc_start: 0.5453 (OUTLIER) cc_final: 0.5164 (tt) REVERT: A 762 ARG cc_start: 0.7973 (mtt90) cc_final: 0.7772 (mpt180) REVERT: A 1233 LEU cc_start: 0.8963 (pp) cc_final: 0.8707 (pp) REVERT: A 1479 ASP cc_start: 0.8800 (m-30) cc_final: 0.8304 (p0) REVERT: A 1494 MET cc_start: 0.7868 (ptm) cc_final: 0.7208 (ppp) REVERT: A 1510 LYS cc_start: 0.8425 (mptt) cc_final: 0.7762 (tmtt) REVERT: A 1527 MET cc_start: 0.6587 (ttm) cc_final: 0.5760 (tmm) REVERT: A 1575 ILE cc_start: 0.8445 (OUTLIER) cc_final: 0.8140 (mp) REVERT: A 1601 MET cc_start: 0.8096 (tpt) cc_final: 0.7860 (tpp) REVERT: A 1670 ILE cc_start: 0.9217 (OUTLIER) cc_final: 0.8952 (tp) REVERT: A 1717 TYR cc_start: 0.8229 (m-10) cc_final: 0.7798 (m-80) outliers start: 23 outliers final: 12 residues processed: 154 average time/residue: 0.0719 time to fit residues: 16.9179 Evaluate side-chains 150 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 135 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 744 LEU Chi-restraints excluded: chain A residue 1169 LEU Chi-restraints excluded: chain A residue 1252 LEU Chi-restraints excluded: chain A residue 1357 TYR Chi-restraints excluded: chain A residue 1391 ASN Chi-restraints excluded: chain A residue 1392 VAL Chi-restraints excluded: chain A residue 1412 LEU Chi-restraints excluded: chain A residue 1481 THR Chi-restraints excluded: chain A residue 1483 MET Chi-restraints excluded: chain A residue 1492 THR Chi-restraints excluded: chain A residue 1524 VAL Chi-restraints excluded: chain A residue 1525 MET Chi-restraints excluded: chain A residue 1575 ILE Chi-restraints excluded: chain A residue 1670 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 93 optimal weight: 5.9990 chunk 17 optimal weight: 6.9990 chunk 42 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 56 optimal weight: 0.9980 chunk 0 optimal weight: 20.0000 chunk 1 optimal weight: 8.9990 chunk 72 optimal weight: 0.2980 chunk 74 optimal weight: 6.9990 chunk 32 optimal weight: 6.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.101959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.085383 restraints weight = 31079.380| |-----------------------------------------------------------------------------| r_work (start): 0.3677 rms_B_bonded: 4.36 r_work (final): 0.3677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7390 moved from start: 0.2404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8991 Z= 0.126 Angle : 0.609 7.863 12184 Z= 0.298 Chirality : 0.041 0.286 1410 Planarity : 0.003 0.041 1393 Dihedral : 16.278 171.183 2050 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 2.93 % Allowed : 20.07 % Favored : 77.00 % 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: 0.63 (0.27), residues: 990 helix: 1.11 (0.19), residues: 715 sheet: -2.04 (1.65), residues: 12 loop : -1.27 (0.40), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 814 TYR 0.013 0.001 TYR A 400 PHE 0.031 0.001 PHE A 707 TRP 0.018 0.001 TRP A 827 HIS 0.003 0.001 HIS A 837 Details of bonding type rmsd covalent geometry : bond 0.00278 ( 8972) covalent geometry : angle 0.59704 (12132) SS BOND : bond 0.00384 ( 5) SS BOND : angle 1.56645 ( 10) hydrogen bonds : bond 0.03998 ( 536) hydrogen bonds : angle 4.09130 ( 1569) link_BETA1-4 : bond 0.00425 ( 9) link_BETA1-4 : angle 2.28051 ( 27) link_NAG-ASN : bond 0.00186 ( 5) link_NAG-ASN : angle 1.31714 ( 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 167 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 141 time to evaluate : 0.263 Fit side-chains revert: symmetry clash REVERT: A 255 PHE cc_start: 0.8389 (t80) cc_final: 0.7807 (m-80) REVERT: A 308 LEU cc_start: 0.5379 (OUTLIER) cc_final: 0.5087 (tt) REVERT: A 799 PHE cc_start: 0.7577 (m-10) cc_final: 0.7249 (t80) REVERT: A 854 MET cc_start: 0.8133 (tpt) cc_final: 0.7866 (tpt) REVERT: A 1233 LEU cc_start: 0.9014 (pp) cc_final: 0.8750 (pp) REVERT: A 1479 ASP cc_start: 0.8879 (m-30) cc_final: 0.8357 (p0) REVERT: A 1494 MET cc_start: 0.7938 (ptm) cc_final: 0.7312 (ppp) REVERT: A 1510 LYS cc_start: 0.8423 (mptt) cc_final: 0.7716 (tmtt) REVERT: A 1527 MET cc_start: 0.6462 (ttm) cc_final: 0.5740 (tmm) REVERT: A 1575 ILE cc_start: 0.8474 (OUTLIER) cc_final: 0.8188 (mp) REVERT: A 1601 MET cc_start: 0.8170 (tpt) cc_final: 0.7926 (tpp) REVERT: A 1670 ILE cc_start: 0.9195 (OUTLIER) cc_final: 0.8959 (tp) REVERT: A 1717 TYR cc_start: 0.8238 (m-10) cc_final: 0.7920 (m-80) outliers start: 26 outliers final: 13 residues processed: 154 average time/residue: 0.0702 time to fit residues: 16.5354 Evaluate side-chains 150 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 134 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 739 VAL Chi-restraints excluded: chain A residue 744 LEU Chi-restraints excluded: chain A residue 1169 LEU Chi-restraints excluded: chain A residue 1252 LEU Chi-restraints excluded: chain A residue 1285 LEU Chi-restraints excluded: chain A residue 1357 TYR Chi-restraints excluded: chain A residue 1412 LEU Chi-restraints excluded: chain A residue 1481 THR Chi-restraints excluded: chain A residue 1492 THR Chi-restraints excluded: chain A residue 1512 ASN Chi-restraints excluded: chain A residue 1518 VAL Chi-restraints excluded: chain A residue 1524 VAL Chi-restraints excluded: chain A residue 1525 MET Chi-restraints excluded: chain A residue 1575 ILE Chi-restraints excluded: chain A residue 1670 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 37 optimal weight: 7.9990 chunk 0 optimal weight: 20.0000 chunk 55 optimal weight: 0.5980 chunk 49 optimal weight: 4.9990 chunk 85 optimal weight: 0.0970 chunk 34 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 53 optimal weight: 0.6980 chunk 88 optimal weight: 0.9990 chunk 91 optimal weight: 6.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- 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 = 0.4032 r_free = 0.4032 target = 0.101330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.084827 restraints weight = 30993.129| |-----------------------------------------------------------------------------| r_work (start): 0.3665 rms_B_bonded: 4.33 r_work (final): 0.3665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7455 moved from start: 0.2619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8991 Z= 0.125 Angle : 0.607 10.750 12184 Z= 0.297 Chirality : 0.041 0.336 1410 Planarity : 0.004 0.081 1393 Dihedral : 15.774 175.339 2050 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.71 % Allowed : 22.32 % Favored : 74.97 % 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 (0.27), residues: 990 helix: 1.11 (0.19), residues: 715 sheet: -1.65 (1.59), residues: 12 loop : -1.35 (0.40), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 762 TYR 0.011 0.001 TYR A1717 PHE 0.030 0.001 PHE A 707 TRP 0.009 0.001 TRP A 827 HIS 0.002 0.001 HIS A 686 Details of bonding type rmsd covalent geometry : bond 0.00276 ( 8972) covalent geometry : angle 0.59889 (12132) SS BOND : bond 0.00335 ( 5) SS BOND : angle 1.28324 ( 10) hydrogen bonds : bond 0.03900 ( 536) hydrogen bonds : angle 4.07726 ( 1569) link_BETA1-4 : bond 0.00435 ( 9) link_BETA1-4 : angle 1.90252 ( 27) link_NAG-ASN : bond 0.00196 ( 5) link_NAG-ASN : angle 1.28251 ( 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 158 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 134 time to evaluate : 0.386 Fit side-chains revert: symmetry clash REVERT: A 255 PHE cc_start: 0.8447 (t80) cc_final: 0.7888 (m-80) REVERT: A 308 LEU cc_start: 0.5577 (OUTLIER) cc_final: 0.5265 (tt) REVERT: A 799 PHE cc_start: 0.7638 (m-10) cc_final: 0.7320 (t80) REVERT: A 854 MET cc_start: 0.8189 (tpt) cc_final: 0.7849 (tpt) REVERT: A 1233 LEU cc_start: 0.8975 (pp) cc_final: 0.8694 (pp) REVERT: A 1291 PHE cc_start: 0.7994 (OUTLIER) cc_final: 0.7269 (t80) REVERT: A 1479 ASP cc_start: 0.8859 (m-30) cc_final: 0.8355 (p0) REVERT: A 1494 MET cc_start: 0.7904 (ptm) cc_final: 0.7319 (ppp) REVERT: A 1510 LYS cc_start: 0.8401 (mptt) cc_final: 0.7706 (tmtt) REVERT: A 1527 MET cc_start: 0.6503 (ttm) cc_final: 0.5767 (tmm) REVERT: A 1575 ILE cc_start: 0.8488 (OUTLIER) cc_final: 0.8198 (mp) REVERT: A 1601 MET cc_start: 0.8123 (tpt) cc_final: 0.7896 (tpp) REVERT: A 1670 ILE cc_start: 0.9201 (OUTLIER) cc_final: 0.8977 (tp) REVERT: A 1717 TYR cc_start: 0.8266 (m-10) cc_final: 0.7918 (m-80) outliers start: 24 outliers final: 14 residues processed: 148 average time/residue: 0.0655 time to fit residues: 15.1196 Evaluate side-chains 150 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 132 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 739 VAL Chi-restraints excluded: chain A residue 744 LEU Chi-restraints excluded: chain A residue 869 LEU Chi-restraints excluded: chain A residue 882 LEU Chi-restraints excluded: chain A residue 1169 LEU Chi-restraints excluded: chain A residue 1252 LEU Chi-restraints excluded: chain A residue 1291 PHE Chi-restraints excluded: chain A residue 1357 TYR Chi-restraints excluded: chain A residue 1392 VAL Chi-restraints excluded: chain A residue 1412 LEU Chi-restraints excluded: chain A residue 1481 THR Chi-restraints excluded: chain A residue 1492 THR Chi-restraints excluded: chain A residue 1518 VAL Chi-restraints excluded: chain A residue 1524 VAL Chi-restraints excluded: chain A residue 1525 MET Chi-restraints excluded: chain A residue 1575 ILE Chi-restraints excluded: chain A residue 1670 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 39 optimal weight: 0.9990 chunk 15 optimal weight: 5.9990 chunk 51 optimal weight: 2.9990 chunk 32 optimal weight: 7.9990 chunk 23 optimal weight: 0.3980 chunk 28 optimal weight: 0.5980 chunk 57 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 86 optimal weight: 6.9990 chunk 71 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- 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 = 0.4038 r_free = 0.4038 target = 0.101403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.084920 restraints weight = 31170.217| |-----------------------------------------------------------------------------| r_work (start): 0.3657 rms_B_bonded: 4.41 r_work (final): 0.3657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7459 moved from start: 0.2765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8991 Z= 0.129 Angle : 0.605 11.129 12184 Z= 0.297 Chirality : 0.041 0.323 1410 Planarity : 0.003 0.041 1393 Dihedral : 15.443 162.957 2050 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 3.04 % Allowed : 22.10 % Favored : 74.86 % 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: 0.62 (0.27), residues: 990 helix: 1.14 (0.20), residues: 712 sheet: -1.31 (1.56), residues: 12 loop : -1.43 (0.39), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 814 TYR 0.018 0.001 TYR A 400 PHE 0.027 0.001 PHE A 707 TRP 0.009 0.001 TRP A1369 HIS 0.002 0.001 HIS A 686 Details of bonding type rmsd covalent geometry : bond 0.00284 ( 8972) covalent geometry : angle 0.59805 (12132) SS BOND : bond 0.00361 ( 5) SS BOND : angle 1.30235 ( 10) hydrogen bonds : bond 0.03896 ( 536) hydrogen bonds : angle 4.08859 ( 1569) link_BETA1-4 : bond 0.00401 ( 9) link_BETA1-4 : angle 1.71448 ( 27) link_NAG-ASN : bond 0.00202 ( 5) link_NAG-ASN : angle 1.27854 ( 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 160 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 133 time to evaluate : 0.326 Fit side-chains revert: symmetry clash REVERT: A 255 PHE cc_start: 0.8440 (t80) cc_final: 0.7882 (m-80) REVERT: A 308 LEU cc_start: 0.5524 (OUTLIER) cc_final: 0.5196 (tt) REVERT: A 391 LEU cc_start: 0.9514 (OUTLIER) cc_final: 0.9300 (mm) REVERT: A 760 LEU cc_start: 0.8433 (OUTLIER) cc_final: 0.8110 (mm) REVERT: A 799 PHE cc_start: 0.7621 (m-10) cc_final: 0.7288 (t80) REVERT: A 1233 LEU cc_start: 0.8994 (pp) cc_final: 0.8704 (pp) REVERT: A 1291 PHE cc_start: 0.7967 (OUTLIER) cc_final: 0.7263 (t80) REVERT: A 1479 ASP cc_start: 0.8887 (m-30) cc_final: 0.8402 (p0) REVERT: A 1494 MET cc_start: 0.7917 (ptm) cc_final: 0.7272 (ppp) REVERT: A 1510 LYS cc_start: 0.8391 (mptt) cc_final: 0.7679 (tmtt) REVERT: A 1527 MET cc_start: 0.6517 (ttm) cc_final: 0.5791 (tmm) REVERT: A 1575 ILE cc_start: 0.8465 (OUTLIER) cc_final: 0.8181 (mp) REVERT: A 1601 MET cc_start: 0.8177 (tpt) cc_final: 0.7911 (tpp) REVERT: A 1717 TYR cc_start: 0.8333 (m-10) cc_final: 0.7959 (m-80) outliers start: 27 outliers final: 19 residues processed: 147 average time/residue: 0.0663 time to fit residues: 15.2553 Evaluate side-chains 151 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 127 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 739 VAL Chi-restraints excluded: chain A residue 744 LEU Chi-restraints excluded: chain A residue 760 LEU Chi-restraints excluded: chain A residue 869 LEU Chi-restraints excluded: chain A residue 882 LEU Chi-restraints excluded: chain A residue 1169 LEU Chi-restraints excluded: chain A residue 1201 MET Chi-restraints excluded: chain A residue 1252 LEU Chi-restraints excluded: chain A residue 1274 LEU Chi-restraints excluded: chain A residue 1291 PHE Chi-restraints excluded: chain A residue 1353 VAL Chi-restraints excluded: chain A residue 1357 TYR Chi-restraints excluded: chain A residue 1412 LEU Chi-restraints excluded: chain A residue 1481 THR Chi-restraints excluded: chain A residue 1483 MET Chi-restraints excluded: chain A residue 1492 THR Chi-restraints excluded: chain A residue 1505 THR Chi-restraints excluded: chain A residue 1518 VAL Chi-restraints excluded: chain A residue 1524 VAL Chi-restraints excluded: chain A residue 1525 MET Chi-restraints excluded: chain A residue 1575 ILE Chi-restraints excluded: chain A residue 1646 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 90 optimal weight: 0.9980 chunk 53 optimal weight: 3.9990 chunk 8 optimal weight: 5.9990 chunk 74 optimal weight: 5.9990 chunk 23 optimal weight: 0.6980 chunk 64 optimal weight: 1.9990 chunk 79 optimal weight: 5.9990 chunk 28 optimal weight: 0.6980 chunk 34 optimal weight: 2.9990 chunk 56 optimal weight: 0.9990 chunk 92 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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 = 0.4038 r_free = 0.4038 target = 0.101277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.084852 restraints weight = 31106.997| |-----------------------------------------------------------------------------| r_work (start): 0.3659 rms_B_bonded: 4.37 r_work (final): 0.3659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7476 moved from start: 0.2923 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= 0.124 Angle : 0.608 11.436 12184 Z= 0.297 Chirality : 0.042 0.375 1410 Planarity : 0.003 0.037 1393 Dihedral : 15.114 162.658 2050 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 3.04 % Allowed : 22.89 % Favored : 74.07 % 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 (0.27), residues: 990 helix: 1.11 (0.19), residues: 714 sheet: -1.25 (1.54), residues: 12 loop : -1.37 (0.40), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 814 TYR 0.014 0.001 TYR A 387 PHE 0.024 0.001 PHE A 707 TRP 0.009 0.001 TRP A1369 HIS 0.002 0.001 HIS A 686 Details of bonding type rmsd covalent geometry : bond 0.00273 ( 8972) covalent geometry : angle 0.60160 (12132) SS BOND : bond 0.00357 ( 5) SS BOND : angle 1.28098 ( 10) hydrogen bonds : bond 0.03870 ( 536) hydrogen bonds : angle 4.07778 ( 1569) link_BETA1-4 : bond 0.00421 ( 9) link_BETA1-4 : angle 1.60791 ( 27) link_NAG-ASN : bond 0.00173 ( 5) link_NAG-ASN : angle 1.27178 ( 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 160 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 133 time to evaluate : 0.317 Fit side-chains revert: symmetry clash REVERT: A 255 PHE cc_start: 0.8461 (t80) cc_final: 0.7899 (m-80) REVERT: A 308 LEU cc_start: 0.5609 (OUTLIER) cc_final: 0.5266 (tt) REVERT: A 799 PHE cc_start: 0.7600 (m-10) cc_final: 0.7275 (t80) REVERT: A 1233 LEU cc_start: 0.8997 (pp) cc_final: 0.8775 (pp) REVERT: A 1291 PHE cc_start: 0.7994 (OUTLIER) cc_final: 0.7286 (t80) REVERT: A 1479 ASP cc_start: 0.8896 (m-30) cc_final: 0.8415 (p0) REVERT: A 1494 MET cc_start: 0.7871 (ptm) cc_final: 0.7311 (ppp) REVERT: A 1510 LYS cc_start: 0.8360 (mptt) cc_final: 0.7664 (tmtt) REVERT: A 1527 MET cc_start: 0.6508 (ttm) cc_final: 0.5781 (tmm) REVERT: A 1575 ILE cc_start: 0.8452 (OUTLIER) cc_final: 0.8175 (mp) REVERT: A 1601 MET cc_start: 0.8115 (tpt) cc_final: 0.7873 (tpp) REVERT: A 1717 TYR cc_start: 0.8306 (m-10) cc_final: 0.7965 (m-80) outliers start: 27 outliers final: 18 residues processed: 150 average time/residue: 0.0671 time to fit residues: 15.7594 Evaluate side-chains 151 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 130 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 674 CYS Chi-restraints excluded: chain A residue 739 VAL Chi-restraints excluded: chain A residue 744 LEU Chi-restraints excluded: chain A residue 869 LEU Chi-restraints excluded: chain A residue 882 LEU Chi-restraints excluded: chain A residue 1169 LEU Chi-restraints excluded: chain A residue 1201 MET Chi-restraints excluded: chain A residue 1291 PHE Chi-restraints excluded: chain A residue 1357 TYR Chi-restraints excluded: chain A residue 1392 VAL Chi-restraints excluded: chain A residue 1412 LEU Chi-restraints excluded: chain A residue 1481 THR Chi-restraints excluded: chain A residue 1483 MET Chi-restraints excluded: chain A residue 1492 THR Chi-restraints excluded: chain A residue 1512 ASN Chi-restraints excluded: chain A residue 1518 VAL Chi-restraints excluded: chain A residue 1524 VAL Chi-restraints excluded: chain A residue 1525 MET Chi-restraints excluded: chain A residue 1575 ILE Chi-restraints excluded: chain A residue 1646 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 72 optimal weight: 20.0000 chunk 85 optimal weight: 0.8980 chunk 51 optimal weight: 3.9990 chunk 93 optimal weight: 0.9980 chunk 67 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 90 optimal weight: 0.4980 chunk 55 optimal weight: 0.1980 chunk 58 optimal weight: 3.9990 chunk 96 optimal weight: 4.9990 chunk 57 optimal weight: 3.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- 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 = 0.4032 r_free = 0.4032 target = 0.101022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.084559 restraints weight = 31033.557| |-----------------------------------------------------------------------------| r_work (start): 0.3653 rms_B_bonded: 4.36 r_work (final): 0.3653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7492 moved from start: 0.3019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8991 Z= 0.126 Angle : 0.646 14.731 12184 Z= 0.306 Chirality : 0.041 0.352 1410 Planarity : 0.003 0.037 1393 Dihedral : 14.811 162.669 2048 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 3.04 % Allowed : 23.45 % 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: 0.55 (0.27), residues: 990 helix: 1.05 (0.19), residues: 714 sheet: -1.07 (1.57), residues: 12 loop : -1.36 (0.40), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 814 TYR 0.021 0.001 TYR A 400 PHE 0.021 0.001 PHE A 707 TRP 0.009 0.001 TRP A1663 HIS 0.002 0.001 HIS A 686 Details of bonding type rmsd covalent geometry : bond 0.00278 ( 8972) covalent geometry : angle 0.64041 (12132) SS BOND : bond 0.00359 ( 5) SS BOND : angle 1.27496 ( 10) hydrogen bonds : bond 0.03887 ( 536) hydrogen bonds : angle 4.11153 ( 1569) link_BETA1-4 : bond 0.00379 ( 9) link_BETA1-4 : angle 1.54564 ( 27) link_NAG-ASN : bond 0.00190 ( 5) link_NAG-ASN : angle 1.28333 ( 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 159 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 132 time to evaluate : 0.421 Fit side-chains revert: symmetry clash REVERT: A 255 PHE cc_start: 0.8466 (t80) cc_final: 0.7851 (m-80) REVERT: A 308 LEU cc_start: 0.5610 (OUTLIER) cc_final: 0.5273 (tt) REVERT: A 799 PHE cc_start: 0.7572 (m-10) cc_final: 0.7246 (t80) REVERT: A 874 MET cc_start: 0.6521 (ttt) cc_final: 0.6225 (ttt) REVERT: A 1233 LEU cc_start: 0.9045 (pp) cc_final: 0.8772 (pp) REVERT: A 1291 PHE cc_start: 0.7980 (OUTLIER) cc_final: 0.7281 (t80) REVERT: A 1479 ASP cc_start: 0.8890 (m-30) cc_final: 0.8419 (p0) REVERT: A 1494 MET cc_start: 0.7898 (ptm) cc_final: 0.7303 (ppp) REVERT: A 1510 LYS cc_start: 0.8345 (mptt) cc_final: 0.7658 (tmtt) REVERT: A 1527 MET cc_start: 0.6581 (ttm) cc_final: 0.5837 (tmm) REVERT: A 1575 ILE cc_start: 0.8447 (OUTLIER) cc_final: 0.8169 (mp) REVERT: A 1601 MET cc_start: 0.8162 (tpt) cc_final: 0.7922 (tpp) REVERT: A 1717 TYR cc_start: 0.8277 (m-10) cc_final: 0.7948 (m-80) outliers start: 27 outliers final: 19 residues processed: 148 average time/residue: 0.0674 time to fit residues: 15.6180 Evaluate side-chains 150 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 128 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 674 CYS Chi-restraints excluded: chain A residue 739 VAL Chi-restraints excluded: chain A residue 744 LEU Chi-restraints excluded: chain A residue 882 LEU Chi-restraints excluded: chain A residue 1169 LEU Chi-restraints excluded: chain A residue 1201 MET Chi-restraints excluded: chain A residue 1252 LEU Chi-restraints excluded: chain A residue 1291 PHE Chi-restraints excluded: chain A residue 1357 TYR Chi-restraints excluded: chain A residue 1369 TRP Chi-restraints excluded: chain A residue 1412 LEU Chi-restraints excluded: chain A residue 1481 THR Chi-restraints excluded: chain A residue 1483 MET Chi-restraints excluded: chain A residue 1492 THR Chi-restraints excluded: chain A residue 1505 THR Chi-restraints excluded: chain A residue 1512 ASN Chi-restraints excluded: chain A residue 1518 VAL Chi-restraints excluded: chain A residue 1524 VAL Chi-restraints excluded: chain A residue 1525 MET Chi-restraints excluded: chain A residue 1575 ILE Chi-restraints excluded: chain A residue 1646 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 83 optimal weight: 8.9990 chunk 33 optimal weight: 0.6980 chunk 43 optimal weight: 7.9990 chunk 76 optimal weight: 0.0770 chunk 0 optimal weight: 20.0000 chunk 90 optimal weight: 1.9990 chunk 71 optimal weight: 0.9990 chunk 54 optimal weight: 2.9990 chunk 14 optimal weight: 0.9990 chunk 86 optimal weight: 3.9990 chunk 15 optimal weight: 4.9990 overall best weight: 0.9544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1656 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.101230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.084772 restraints weight = 30890.204| |-----------------------------------------------------------------------------| r_work (start): 0.3658 rms_B_bonded: 4.32 r_work (final): 0.3658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7486 moved from start: 0.3145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 8991 Z= 0.122 Angle : 0.634 12.787 12184 Z= 0.304 Chirality : 0.041 0.377 1410 Planarity : 0.003 0.036 1393 Dihedral : 14.541 162.684 2048 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 3.38 % Allowed : 23.45 % 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: 0.60 (0.27), residues: 990 helix: 1.08 (0.19), residues: 713 sheet: -1.08 (1.57), residues: 12 loop : -1.31 (0.40), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 814 TYR 0.017 0.001 TYR A1443 PHE 0.021 0.001 PHE A1598 TRP 0.007 0.001 TRP A1663 HIS 0.002 0.000 HIS A 686 Details of bonding type rmsd covalent geometry : bond 0.00272 ( 8972) covalent geometry : angle 0.62877 (12132) SS BOND : bond 0.00347 ( 5) SS BOND : angle 1.25187 ( 10) hydrogen bonds : bond 0.03820 ( 536) hydrogen bonds : angle 4.11958 ( 1569) link_BETA1-4 : bond 0.00390 ( 9) link_BETA1-4 : angle 1.49978 ( 27) link_NAG-ASN : bond 0.00169 ( 5) link_NAG-ASN : angle 1.27491 ( 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 161 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 131 time to evaluate : 0.271 Fit side-chains revert: symmetry clash REVERT: A 255 PHE cc_start: 0.8439 (t80) cc_final: 0.7842 (m-80) REVERT: A 308 LEU cc_start: 0.5642 (OUTLIER) cc_final: 0.5305 (tt) REVERT: A 799 PHE cc_start: 0.7557 (m-10) cc_final: 0.7182 (t80) REVERT: A 858 MET cc_start: 0.6242 (tmm) cc_final: 0.5806 (tmm) REVERT: A 874 MET cc_start: 0.6586 (ttt) cc_final: 0.6250 (ttt) REVERT: A 1233 LEU cc_start: 0.9065 (pp) cc_final: 0.8799 (pp) REVERT: A 1291 PHE cc_start: 0.7983 (OUTLIER) cc_final: 0.7240 (t80) REVERT: A 1479 ASP cc_start: 0.8889 (m-30) cc_final: 0.8420 (p0) REVERT: A 1494 MET cc_start: 0.7881 (ptm) cc_final: 0.7310 (ppp) REVERT: A 1510 LYS cc_start: 0.8325 (mptt) cc_final: 0.7648 (tmtt) REVERT: A 1527 MET cc_start: 0.6563 (ttm) cc_final: 0.5817 (tmm) REVERT: A 1575 ILE cc_start: 0.8439 (OUTLIER) cc_final: 0.8169 (mp) REVERT: A 1717 TYR cc_start: 0.8266 (m-10) cc_final: 0.7948 (m-80) outliers start: 30 outliers final: 21 residues processed: 148 average time/residue: 0.0660 time to fit residues: 15.2812 Evaluate side-chains 151 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 127 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 674 CYS Chi-restraints excluded: chain A residue 739 VAL Chi-restraints excluded: chain A residue 744 LEU Chi-restraints excluded: chain A residue 882 LEU Chi-restraints excluded: chain A residue 1169 LEU Chi-restraints excluded: chain A residue 1201 MET Chi-restraints excluded: chain A residue 1252 LEU Chi-restraints excluded: chain A residue 1274 LEU Chi-restraints excluded: chain A residue 1291 PHE Chi-restraints excluded: chain A residue 1346 VAL Chi-restraints excluded: chain A residue 1357 TYR Chi-restraints excluded: chain A residue 1369 TRP Chi-restraints excluded: chain A residue 1382 VAL Chi-restraints excluded: chain A residue 1412 LEU Chi-restraints excluded: chain A residue 1481 THR Chi-restraints excluded: chain A residue 1483 MET Chi-restraints excluded: chain A residue 1492 THR Chi-restraints excluded: chain A residue 1512 ASN Chi-restraints excluded: chain A residue 1518 VAL Chi-restraints excluded: chain A residue 1524 VAL Chi-restraints excluded: chain A residue 1525 MET Chi-restraints excluded: chain A residue 1575 ILE Chi-restraints excluded: chain A residue 1646 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 9 optimal weight: 0.9990 chunk 48 optimal weight: 7.9990 chunk 30 optimal weight: 2.9990 chunk 94 optimal weight: 0.1980 chunk 56 optimal weight: 0.6980 chunk 70 optimal weight: 5.9990 chunk 19 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 54 optimal weight: 0.6980 chunk 25 optimal weight: 20.0000 overall best weight: 0.6582 ------------------------------------------------------------------------------- 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** 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 = 0.101957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.085561 restraints weight = 30798.495| |-----------------------------------------------------------------------------| r_work (start): 0.3677 rms_B_bonded: 4.43 r_work (final): 0.3677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7442 moved from start: 0.3286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8991 Z= 0.116 Angle : 0.648 15.852 12184 Z= 0.308 Chirality : 0.041 0.353 1410 Planarity : 0.003 0.034 1393 Dihedral : 14.235 162.792 2048 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 2.14 % Allowed : 24.35 % 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: 0.59 (0.27), residues: 990 helix: 1.06 (0.19), residues: 711 sheet: -1.12 (1.57), residues: 12 loop : -1.26 (0.40), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 351 TYR 0.027 0.001 TYR A 400 PHE 0.015 0.001 PHE A1401 TRP 0.010 0.001 TRP A1663 HIS 0.002 0.000 HIS A 686 Details of bonding type rmsd covalent geometry : bond 0.00253 ( 8972) covalent geometry : angle 0.64363 (12132) SS BOND : bond 0.00374 ( 5) SS BOND : angle 1.25344 ( 10) hydrogen bonds : bond 0.03799 ( 536) hydrogen bonds : angle 4.11452 ( 1569) link_BETA1-4 : bond 0.00394 ( 9) link_BETA1-4 : angle 1.45162 ( 27) link_NAG-ASN : bond 0.00159 ( 5) link_NAG-ASN : angle 1.25886 ( 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 150 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 131 time to evaluate : 0.323 Fit side-chains revert: symmetry clash REVERT: A 255 PHE cc_start: 0.8411 (t80) cc_final: 0.7834 (m-10) REVERT: A 268 PHE cc_start: 0.6326 (m-80) cc_final: 0.6048 (m-80) REVERT: A 308 LEU cc_start: 0.5583 (OUTLIER) cc_final: 0.5245 (tt) REVERT: A 874 MET cc_start: 0.6682 (ttt) cc_final: 0.6434 (ttt) REVERT: A 1161 MET cc_start: 0.8800 (tpp) cc_final: 0.8578 (tpp) REVERT: A 1201 MET cc_start: 0.7986 (tpt) cc_final: 0.7713 (tpp) REVERT: A 1233 LEU cc_start: 0.9068 (pp) cc_final: 0.8800 (pp) REVERT: A 1479 ASP cc_start: 0.8858 (m-30) cc_final: 0.8386 (p0) REVERT: A 1494 MET cc_start: 0.7812 (ptm) cc_final: 0.7267 (ppp) REVERT: A 1510 LYS cc_start: 0.8293 (mptt) cc_final: 0.7603 (tmtt) REVERT: A 1527 MET cc_start: 0.6495 (ttm) cc_final: 0.5763 (tmm) REVERT: A 1717 TYR cc_start: 0.8247 (m-10) cc_final: 0.7925 (m-80) outliers start: 19 outliers final: 18 residues processed: 141 average time/residue: 0.0692 time to fit residues: 15.0876 Evaluate side-chains 148 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 129 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 674 CYS Chi-restraints excluded: chain A residue 739 VAL Chi-restraints excluded: chain A residue 871 LEU Chi-restraints excluded: chain A residue 882 LEU Chi-restraints excluded: chain A residue 1169 LEU Chi-restraints excluded: chain A residue 1252 LEU Chi-restraints excluded: chain A residue 1274 LEU Chi-restraints excluded: chain A residue 1346 VAL Chi-restraints excluded: chain A residue 1357 TYR Chi-restraints excluded: chain A residue 1369 TRP Chi-restraints excluded: chain A residue 1382 VAL Chi-restraints excluded: chain A residue 1412 LEU Chi-restraints excluded: chain A residue 1481 THR Chi-restraints excluded: chain A residue 1483 MET Chi-restraints excluded: chain A residue 1512 ASN Chi-restraints excluded: chain A residue 1518 VAL Chi-restraints excluded: chain A residue 1525 MET Chi-restraints excluded: chain A residue 1646 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 81 optimal weight: 4.9990 chunk 47 optimal weight: 0.0040 chunk 21 optimal weight: 2.9990 chunk 22 optimal weight: 0.7980 chunk 74 optimal weight: 4.9990 chunk 16 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 7 optimal weight: 8.9990 chunk 14 optimal weight: 0.9980 chunk 60 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 overall best weight: 0.9394 ------------------------------------------------------------------------------- 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 = 0.4047 r_free = 0.4047 target = 0.101739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.085317 restraints weight = 30612.410| |-----------------------------------------------------------------------------| r_work (start): 0.3672 rms_B_bonded: 4.39 r_work (final): 0.3672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7443 moved from start: 0.3345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 8991 Z= 0.126 Angle : 0.637 12.689 12184 Z= 0.309 Chirality : 0.042 0.394 1410 Planarity : 0.003 0.035 1393 Dihedral : 14.040 162.962 2048 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 2.37 % Allowed : 24.01 % 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: 0.57 (0.27), residues: 990 helix: 1.04 (0.19), residues: 712 sheet: -1.15 (1.54), residues: 12 loop : -1.27 (0.40), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 351 TYR 0.020 0.001 TYR A1443 PHE 0.041 0.001 PHE A1598 TRP 0.017 0.001 TRP A 850 HIS 0.002 0.000 HIS A 686 Details of bonding type rmsd covalent geometry : bond 0.00288 ( 8972) covalent geometry : angle 0.63258 (12132) SS BOND : bond 0.00339 ( 5) SS BOND : angle 1.23043 ( 10) hydrogen bonds : bond 0.03748 ( 536) hydrogen bonds : angle 4.09014 ( 1569) link_BETA1-4 : bond 0.00382 ( 9) link_BETA1-4 : angle 1.43477 ( 27) link_NAG-ASN : bond 0.00178 ( 5) link_NAG-ASN : angle 1.27071 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1970.39 seconds wall clock time: 34 minutes 40.16 seconds (2080.16 seconds total)