Starting phenix.real_space_refine on Fri Jul 3 01:39:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xmm_38482/07_2026/8xmm_38482.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xmm_38482/07_2026/8xmm_38482.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.89 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8xmm_38482/07_2026/8xmm_38482.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xmm_38482/07_2026/8xmm_38482.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8xmm_38482/07_2026/8xmm_38482.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xmm_38482/07_2026/8xmm_38482.map" } resolution = 2.89 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= 0.009 sd= 0.086 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 17 5.49 5 S 87 5.16 5 C 7567 2.51 5 N 1700 2.21 5 O 2018 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 135 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11389 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 9253 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1145, 9253 Classifications: {'peptide': 1145} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 1114} Chain breaks: 2 Chain: "B" Number of atoms: 1416 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1416 Classifications: {'peptide': 173} Link IDs: {'TRANS': 172} Chain: "C" 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: "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: "A" Number of atoms: 608 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 608 Unusual residues: {'1PW': 1, 'CLR': 1, 'LPE': 9, 'NAG': 2, 'PCW': 6} Classifications: {'peptide': 1, 'undetermined': 19} Link IDs: {None: 19} Unresolved non-hydrogen bonds: 162 Unresolved non-hydrogen angles: 169 Unresolved non-hydrogen dihedrals: 169 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'1PW:plan-1': 1, 'PCW:plan-4': 4} Unresolved non-hydrogen planarities: 12 Chain: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 2.29, per 1000 atoms: 0.20 Number of scatterers: 11389 At special positions: 0 Unit cell: (133.944, 126.259, 114.182, 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 87 16.00 P 17 15.00 O 2018 8.00 N 1700 7.00 C 7567 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS A 275 " - pdb=" SG CYS A 324 " distance=2.01 Simple disulfide: pdb=" SG CYS A 315 " - pdb=" SG CYS A 324 " distance=2.97 Simple disulfide: pdb=" SG CYS A 315 " - pdb=" SG CYS A 330 " distance=2.01 Simple disulfide: pdb=" SG CYS A 897 " - pdb=" SG CYS A 903 " distance=2.04 Simple disulfide: pdb=" SG CYS A 935 " - pdb=" SG CYS A 944 " distance=2.03 Simple disulfide: pdb=" SG CYS A1350 " - pdb=" SG CYS A1370 " distance=2.03 Simple disulfide: pdb=" SG CYS A1715 " - pdb=" SG CYS A1730 " distance=2.03 Simple disulfide: pdb=" SG CYS B 21 " - pdb=" SG CYS B 43 " distance=2.03 Simple disulfide: pdb=" SG CYS B 40 " - pdb=" SG CYS B 121 " 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 C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " NAG-ASN " NAG A2001 " - " ASN A1375 " " NAG A2002 " - " ASN A 283 " " NAG B 301 " - " ASN B 93 " " NAG B 302 " - " ASN B 110 " " NAG B 303 " - " ASN B 114 " " NAG B 304 " - " ASN B 135 " " NAG C 1 " - " ASN A1352 " " NAG D 1 " - " ASN A1366 " Time building additional restraints: 1.06 Conformation dependent library (CDL) restraints added in 537.0 milliseconds 2620 Ramachandran restraints generated. 1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2496 Finding SS restraints... Secondary structure from input PDB file: 59 helices and 4 sheets defined 72.2% alpha, 5.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing helix chain 'A' and resid 114 through 124 Processing helix chain 'A' and resid 126 through 143 removed outlier: 3.645A pdb=" N MET A 130 " --> pdb=" O SER A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 175 removed outlier: 3.994A pdb=" N VAL A 155 " --> pdb=" O TRP A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 205 Processing helix chain 'A' and resid 209 through 216 removed outlier: 3.775A pdb=" N PHE A 216 " --> pdb=" O ALA A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 222 Processing helix chain 'A' and resid 223 through 228 removed outlier: 4.002A pdb=" N VAL A 227 " --> pdb=" O LYS A 223 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ILE A 228 " --> pdb=" O THR A 224 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 223 through 228' Processing helix chain 'A' and resid 228 through 245 removed outlier: 4.162A pdb=" N LYS A 232 " --> pdb=" O ILE A 228 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N THR A 233 " --> pdb=" O PRO A 229 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LYS A 244 " --> pdb=" O GLN A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 267 Processing helix chain 'A' and resid 269 through 271 No H-bonds generated for 'chain 'A' and resid 269 through 271' Processing helix chain 'A' and resid 285 through 293 Processing helix chain 'A' and resid 295 through 303 removed outlier: 3.912A pdb=" N LYS A 301 " --> pdb=" O GLU A 297 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N TYR A 302 " --> pdb=" O ASP A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 341 Processing helix chain 'A' and resid 346 through 360 Processing helix chain 'A' and resid 362 through 374 removed outlier: 3.994A pdb=" N LEU A 366 " --> pdb=" O TYR A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 375 through 377 No H-bonds generated for 'chain 'A' and resid 375 through 377' Processing helix chain 'A' and resid 378 through 417 removed outlier: 3.919A pdb=" N PHE A 382 " --> pdb=" O TYR A 378 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N PHE A 391 " --> pdb=" O PHE A 387 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N TYR A 392 " --> pdb=" O LEU A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 727 through 742 Processing helix chain 'A' and resid 743 through 762 removed outlier: 4.191A pdb=" N ASP A 747 " --> pdb=" O ASP A 743 " (cutoff:3.500A) Processing helix chain 'A' and resid 769 through 797 removed outlier: 4.013A pdb=" N ALA A 797 " --> pdb=" O LEU A 793 " (cutoff:3.500A) Processing helix chain 'A' and resid 799 through 804 Processing helix chain 'A' and resid 806 through 825 removed outlier: 3.596A pdb=" N PHE A 811 " --> pdb=" O GLY A 807 " (cutoff:3.500A) Processing helix chain 'A' and resid 831 through 837 removed outlier: 4.075A pdb=" N ARG A 835 " --> pdb=" O LEU A 831 " (cutoff:3.500A) Processing helix chain 'A' and resid 838 through 848 removed outlier: 3.527A pdb=" N ARG A 841 " --> pdb=" O ARG A 838 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N PHE A 843 " --> pdb=" O LEU A 840 " (cutoff:3.500A) Processing helix chain 'A' and resid 849 through 862 removed outlier: 4.313A pdb=" N SER A 862 " --> pdb=" O ILE A 858 " (cutoff:3.500A) Processing helix chain 'A' and resid 862 through 889 removed outlier: 3.534A pdb=" N PHE A 866 " --> pdb=" O SER A 862 " (cutoff:3.500A) Processing helix chain 'A' and resid 890 through 895 Processing helix chain 'A' and resid 896 through 900 Processing helix chain 'A' and resid 912 through 925 Processing helix chain 'A' and resid 929 through 940 Processing helix chain 'A' and resid 940 through 955 removed outlier: 3.624A pdb=" N CYS A 944 " --> pdb=" O GLY A 940 " (cutoff:3.500A) Processing helix chain 'A' and resid 958 through 971 removed outlier: 3.835A pdb=" N LEU A 964 " --> pdb=" O LEU A 960 " (cutoff:3.500A) Processing helix chain 'A' and resid 1176 through 1191 Processing helix chain 'A' and resid 1191 through 1211 Processing helix chain 'A' and resid 1219 through 1249 removed outlier: 3.979A pdb=" N LYS A1231 " --> pdb=" O GLU A1227 " (cutoff:3.500A) Processing helix chain 'A' and resid 1249 through 1255 Processing helix chain 'A' and resid 1256 through 1278 Processing helix chain 'A' and resid 1283 through 1290 removed outlier: 3.758A pdb=" N SER A1288 " --> pdb=" O GLY A1284 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ARG A1290 " --> pdb=" O ILE A1286 " (cutoff:3.500A) Processing helix chain 'A' and resid 1291 through 1301 Proline residue: A1297 - end of helix Processing helix chain 'A' and resid 1304 through 1316 Processing helix chain 'A' and resid 1317 through 1344 removed outlier: 3.669A pdb=" N ASN A1323 " --> pdb=" O PRO A1319 " (cutoff:3.500A) Processing helix chain 'A' and resid 1366 through 1377 Processing helix chain 'A' and resid 1391 through 1405 removed outlier: 3.602A pdb=" N LEU A1397 " --> pdb=" O GLY A1393 " (cutoff:3.500A) Processing helix chain 'A' and resid 1407 through 1416 removed outlier: 3.699A pdb=" N ILE A1411 " --> pdb=" O GLY A1407 " (cutoff:3.500A) Processing helix chain 'A' and resid 1430 through 1432 No H-bonds generated for 'chain 'A' and resid 1430 through 1432' Processing helix chain 'A' and resid 1433 through 1467 removed outlier: 3.817A pdb=" N PHE A1437 " --> pdb=" O MET A1433 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N PHE A1446 " --> pdb=" O ILE A1442 " (cutoff:3.500A) Processing helix chain 'A' and resid 1475 through 1489 Processing helix chain 'A' and resid 1504 through 1514 Processing helix chain 'A' and resid 1514 through 1534 removed outlier: 3.775A pdb=" N ASP A1518 " --> pdb=" O ASN A1514 " (cutoff:3.500A) Processing helix chain 'A' and resid 1540 through 1570 Processing helix chain 'A' and resid 1576 through 1602 Processing helix chain 'A' and resid 1605 through 1614 Processing helix chain 'A' and resid 1616 through 1621 removed outlier: 4.081A pdb=" N ILE A1620 " --> pdb=" O ARG A1616 " (cutoff:3.500A) Processing helix chain 'A' and resid 1622 through 1626 removed outlier: 3.518A pdb=" N LYS A1625 " --> pdb=" O ARG A1622 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLY A1626 " --> pdb=" O LEU A1623 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1622 through 1626' Processing helix chain 'A' and resid 1627 through 1666 Proline residue: A1642 - end of helix Processing helix chain 'A' and resid 1683 through 1696 removed outlier: 4.087A pdb=" N THR A1696 " --> pdb=" O PHE A1692 " (cutoff:3.500A) Processing helix chain 'A' and resid 1699 through 1709 Proline residue: A1706 - end of helix removed outlier: 3.910A pdb=" N ASN A1709 " --> pdb=" O ALA A1705 " (cutoff:3.500A) Processing helix chain 'A' and resid 1732 through 1768 removed outlier: 4.037A pdb=" N ASN A1753 " --> pdb=" O LEU A1749 " (cutoff:3.500A) Processing helix chain 'B' and resid 153 through 192 removed outlier: 3.988A pdb=" N GLU B 190 " --> pdb=" O ALA B 186 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N THR B 191 " --> pdb=" O ALA B 187 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ALA B 192 " --> pdb=" O ALA B 188 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 273 through 276 Processing sheet with id=AA2, first strand: chain 'A' and resid 1357 through 1358 Processing sheet with id=AA3, first strand: chain 'B' and resid 29 through 31 removed outlier: 6.661A pdb=" N ALA B 30 " --> pdb=" O VAL B 147 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N ASN B 50 " --> pdb=" O PHE B 128 " (cutoff:3.500A) removed outlier: 9.209A pdb=" N THR B 53 " --> pdb=" O GLU B 74 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N GLU B 74 " --> pdb=" O THR B 53 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N THR B 55 " --> pdb=" O ARG B 72 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N ARG B 72 " --> pdb=" O THR B 55 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N TRP B 57 " --> pdb=" O ILE B 70 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 36 through 38 719 hydrogen bonds defined for protein. 2079 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: 1.85 Time building geometry restraints manager: 1.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.30: 1680 1.30 - 1.44: 3226 1.44 - 1.58: 6554 1.58 - 1.72: 33 1.72 - 1.86: 140 Bond restraints: 11633 Sorted by residual: bond pdb=" CA LYS A1187 " pdb=" C LYS A1187 " ideal model delta sigma weight residual 1.524 1.417 0.106 1.29e-02 6.01e+03 6.78e+01 bond pdb=" C PHE A 381 " pdb=" O PHE A 381 " ideal model delta sigma weight residual 1.236 1.154 0.083 1.15e-02 7.56e+03 5.18e+01 bond pdb=" CA TYR A1573 " pdb=" C TYR A1573 " ideal model delta sigma weight residual 1.524 1.435 0.090 1.29e-02 6.01e+03 4.82e+01 bond pdb=" C31 PCW A2012 " pdb=" O2 PCW A2012 " ideal model delta sigma weight residual 1.333 1.470 -0.137 2.00e-02 2.50e+03 4.67e+01 bond pdb=" CA PHE A 381 " pdb=" C PHE A 381 " ideal model delta sigma weight residual 1.524 1.439 0.085 1.27e-02 6.20e+03 4.49e+01 ... (remaining 11628 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.05: 15398 4.05 - 8.10: 251 8.10 - 12.15: 30 12.15 - 16.21: 3 16.21 - 20.26: 1 Bond angle restraints: 15683 Sorted by residual: angle pdb=" N TYR A1573 " pdb=" CA TYR A1573 " pdb=" C TYR A1573 " ideal model delta sigma weight residual 111.40 100.48 10.92 1.22e+00 6.72e-01 8.01e+01 angle pdb=" N SER A1568 " pdb=" CA SER A1568 " pdb=" C SER A1568 " ideal model delta sigma weight residual 111.36 119.79 -8.43 1.09e+00 8.42e-01 5.99e+01 angle pdb=" N PCW A2010 " pdb=" C5 PCW A2010 " pdb=" C4 PCW A2010 " ideal model delta sigma weight residual 116.95 96.69 20.26 3.00e+00 1.11e-01 4.56e+01 angle pdb=" N CYS A 897 " pdb=" CA CYS A 897 " pdb=" C CYS A 897 " ideal model delta sigma weight residual 111.36 118.21 -6.85 1.09e+00 8.42e-01 3.95e+01 angle pdb=" C HIS A 766 " pdb=" N PRO A 767 " pdb=" CA PRO A 767 " ideal model delta sigma weight residual 119.84 112.21 7.63 1.25e+00 6.40e-01 3.73e+01 ... (remaining 15678 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.96: 6735 33.96 - 67.91: 398 67.91 - 101.87: 49 101.87 - 135.82: 17 135.82 - 169.78: 2 Dihedral angle restraints: 7201 sinusoidal: 3335 harmonic: 3866 Sorted by residual: dihedral pdb=" CB CYS A1715 " pdb=" SG CYS A1715 " pdb=" SG CYS A1730 " pdb=" CB CYS A1730 " ideal model delta sinusoidal sigma weight residual 93.00 15.13 77.87 1 1.00e+01 1.00e-02 7.58e+01 dihedral pdb=" CB CYS A 315 " pdb=" SG CYS A 315 " pdb=" SG CYS A 330 " pdb=" CB CYS A 330 " ideal model delta sinusoidal sigma weight residual 93.00 145.16 -52.16 1 1.00e+01 1.00e-02 3.71e+01 dihedral pdb=" CA PHE B 54 " pdb=" C PHE B 54 " pdb=" N THR B 55 " pdb=" CA THR B 55 " ideal model delta harmonic sigma weight residual -180.00 -155.63 -24.37 0 5.00e+00 4.00e-02 2.37e+01 ... (remaining 7198 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.119: 1712 0.119 - 0.238: 50 0.238 - 0.357: 10 0.357 - 0.477: 2 0.477 - 0.596: 2 Chirality restraints: 1776 Sorted by residual: chirality pdb=" C1 NAG B 304 " pdb=" ND2 ASN B 135 " pdb=" C2 NAG B 304 " pdb=" O5 NAG B 304 " both_signs ideal model delta sigma weight residual False -2.40 -1.80 -0.60 2.00e-01 2.50e+01 8.87e+00 chirality pdb=" CA PHE A 391 " pdb=" N PHE A 391 " pdb=" C PHE A 391 " pdb=" CB PHE A 391 " both_signs ideal model delta sigma weight residual False 2.51 1.96 0.55 2.00e-01 2.50e+01 7.56e+00 chirality pdb=" C2 PCW A2011 " pdb=" C1 PCW A2011 " pdb=" C3 PCW A2011 " pdb=" O2 PCW A2011 " both_signs ideal model delta sigma weight residual False -2.32 -2.69 0.36 2.00e-01 2.50e+01 3.32e+00 ... (remaining 1773 not shown) Planarity restraints: 1850 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER A 390 " -0.021 2.00e-02 2.50e+03 4.08e-02 1.67e+01 pdb=" C SER A 390 " 0.071 2.00e-02 2.50e+03 pdb=" O SER A 390 " -0.026 2.00e-02 2.50e+03 pdb=" N PHE A 391 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 896 " -0.014 2.00e-02 2.50e+03 2.82e-02 7.96e+00 pdb=" C VAL A 896 " 0.049 2.00e-02 2.50e+03 pdb=" O VAL A 896 " -0.018 2.00e-02 2.50e+03 pdb=" N CYS A 897 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A1437 " 0.013 2.00e-02 2.50e+03 2.52e-02 6.35e+00 pdb=" C PHE A1437 " -0.044 2.00e-02 2.50e+03 pdb=" O PHE A1437 " 0.016 2.00e-02 2.50e+03 pdb=" N ILE A1438 " 0.015 2.00e-02 2.50e+03 ... (remaining 1847 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 147 2.64 - 3.21: 10540 3.21 - 3.77: 16816 3.77 - 4.34: 23918 4.34 - 4.90: 39876 Nonbonded interactions: 91297 Sorted by model distance: nonbonded pdb=" C4 PCW A2010 " pdb=" C7 PCW A2010 " model vdw 2.077 3.088 nonbonded pdb=" OE1 GLU B 23 " pdb=" NZ LYS B 140 " model vdw 2.295 3.120 nonbonded pdb=" N GLU B 82 " pdb=" OE1 GLU B 82 " model vdw 2.300 3.120 nonbonded pdb=" C31 LPE A2008 " pdb=" C3N LPE A2008 " model vdw 2.301 3.088 nonbonded pdb=" OD1 ASP A 192 " pdb=" NZ LYS A 223 " model vdw 2.306 3.120 ... (remaining 91292 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'D' } 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: 1.300 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: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.940 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.940 11652 Z= 0.696 Angle : 1.277 28.421 15731 Z= 0.626 Chirality : 0.059 0.596 1776 Planarity : 0.005 0.059 1842 Dihedral : 21.099 169.778 4678 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 0.34 % Allowed : 1.53 % Favored : 98.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 0.13 (0.23), residues: 1310 helix: 0.75 (0.17), residues: 862 sheet: -0.71 (0.64), residues: 67 loop : -1.13 (0.32), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 46 TYR 0.022 0.002 TYR A 392 PHE 0.022 0.002 PHE A1263 TRP 0.034 0.003 TRP A1408 HIS 0.006 0.002 HIS B 115 Details of bonding type rmsd/Z covalent geometry : bond 0.00988 / 0.54 (11633) covalent geometry : angle 1.19021 / 0.59 (15683) SS BOND : bond 0.31344 / 22.38 ( 9) SS BOND : angle 12.94608 / 7.30 ( 18) hydrogen bonds : bond 0.14964 / 10.06 ( 719) hydrogen bonds : angle 6.30830 / 4.71 ( 2079) link_BETA1-4 : bond 0.00487 / 0.34 ( 2) link_BETA1-4 : angle 2.45254 / 1.52 ( 6) link_NAG-ASN : bond 0.00311 / 0.18 ( 8) link_NAG-ASN : angle 3.99960 / 2.89 ( 24) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2620 Ramachandran restraints generated. 1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2620 Ramachandran restraints generated. 1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 158 time to evaluate : 0.407 Fit side-chains revert: symmetry clash REVERT: A 133 MET cc_start: 0.6523 (mmp) cc_final: 0.6283 (mmm) REVERT: A 184 LEU cc_start: 0.7629 (mm) cc_final: 0.6825 (tm) REVERT: A 278 ASN cc_start: 0.8839 (OUTLIER) cc_final: 0.8632 (t0) REVERT: A 742 MET cc_start: 0.7232 (mmm) cc_final: 0.6816 (tpp) REVERT: A 858 ILE cc_start: 0.8743 (mm) cc_final: 0.8147 (mp) REVERT: A 861 ASN cc_start: 0.7549 (m-40) cc_final: 0.7344 (p0) REVERT: A 1322 MET cc_start: 0.8281 (mmp) cc_final: 0.8036 (mmp) outliers start: 4 outliers final: 1 residues processed: 162 average time/residue: 0.4899 time to fit residues: 86.8202 Evaluate side-chains 132 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 130 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 278 ASN Chi-restraints excluded: chain A residue 324 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 0.9990 chunk 55 optimal weight: 0.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 240 GLN A 282 ASN A 360 GLN A 809 ASN A 853 ASN A 941 GLN A1463 GLN A1502 ASN A1505 GLN ** A1721 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.133934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.095476 restraints weight = 16306.282| |-----------------------------------------------------------------------------| r_work (start): 0.3141 rms_B_bonded: 2.03 r_work: 0.3013 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2887 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.1111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 11652 Z= 0.146 Angle : 0.620 9.370 15731 Z= 0.317 Chirality : 0.043 0.440 1776 Planarity : 0.004 0.060 1842 Dihedral : 18.830 177.094 2197 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 1.78 % Allowed : 10.85 % Favored : 87.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 1.08 (0.23), residues: 1310 helix: 1.52 (0.17), residues: 865 sheet: -0.41 (0.62), residues: 67 loop : -0.90 (0.32), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 117 TYR 0.021 0.002 TYR A 405 PHE 0.018 0.001 PHE A1263 TRP 0.021 0.001 TRP A 730 HIS 0.003 0.001 HIS A1721 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.15 (11633) covalent geometry : angle 0.60321 / 0.31 (15683) SS BOND : bond 0.00851 / 0.53 ( 9) SS BOND : angle 2.40267 / 1.20 ( 18) hydrogen bonds : bond 0.04923 / 3.24 ( 719) hydrogen bonds : angle 4.82765 / 3.55 ( 2079) link_BETA1-4 : bond 0.00385 / 0.26 ( 2) link_BETA1-4 : angle 1.17001 / 0.77 ( 6) link_NAG-ASN : bond 0.00288 / 0.13 ( 8) link_NAG-ASN : angle 3.02373 / 2.20 ( 24) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2620 Ramachandran restraints generated. 1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2620 Ramachandran restraints generated. 1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 139 time to evaluate : 0.399 Fit side-chains revert: symmetry clash REVERT: A 130 MET cc_start: 0.7235 (mmt) cc_final: 0.6869 (mmp) REVERT: A 147 ASN cc_start: 0.8915 (t0) cc_final: 0.8538 (p0) REVERT: A 184 LEU cc_start: 0.7483 (mm) cc_final: 0.6645 (tm) REVERT: A 220 ARG cc_start: 0.7236 (mtm180) cc_final: 0.6990 (mtm-85) REVERT: A 307 GLU cc_start: 0.8573 (OUTLIER) cc_final: 0.8336 (tt0) REVERT: A 742 MET cc_start: 0.6883 (mmm) cc_final: 0.6446 (tpp) REVERT: A 760 PHE cc_start: 0.8717 (OUTLIER) cc_final: 0.8000 (t80) REVERT: A 861 ASN cc_start: 0.7636 (m-40) cc_final: 0.7251 (m-40) REVERT: A 1639 MET cc_start: 0.7964 (mmm) cc_final: 0.7578 (mmm) outliers start: 21 outliers final: 5 residues processed: 149 average time/residue: 0.4581 time to fit residues: 74.6660 Evaluate side-chains 138 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 131 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 ARG Chi-restraints excluded: chain A residue 307 GLU Chi-restraints excluded: chain A residue 752 ILE Chi-restraints excluded: chain A residue 759 LEU Chi-restraints excluded: chain A residue 760 PHE Chi-restraints excluded: chain A residue 1330 ILE Chi-restraints excluded: chain B residue 49 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 29 optimal weight: 2.9990 chunk 106 optimal weight: 0.7980 chunk 115 optimal weight: 0.0040 chunk 91 optimal weight: 0.0170 chunk 77 optimal weight: 0.6980 chunk 121 optimal weight: 0.7980 chunk 26 optimal weight: 2.9990 chunk 113 optimal weight: 2.9990 chunk 109 optimal weight: 4.9990 chunk 28 optimal weight: 1.9990 chunk 111 optimal weight: 1.9990 overall best weight: 0.4630 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 240 GLN A 368 GLN A 809 ASN A1276 ASN ** A1721 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.135485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.095967 restraints weight = 16508.168| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 2.09 r_work: 0.3034 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2907 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.1602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.085 11652 Z= 0.115 Angle : 0.538 9.423 15731 Z= 0.276 Chirality : 0.040 0.353 1776 Planarity : 0.004 0.057 1842 Dihedral : 16.611 179.826 2194 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.86 % Allowed : 12.88 % Favored : 85.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 1.40 (0.23), residues: 1310 helix: 1.83 (0.17), residues: 870 sheet: -0.06 (0.60), residues: 67 loop : -1.04 (0.32), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 835 TYR 0.020 0.001 TYR B 180 PHE 0.017 0.001 PHE A 843 TRP 0.018 0.001 TRP A 730 HIS 0.002 0.001 HIS A 765 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.12 (11633) covalent geometry : angle 0.52661 / 0.27 (15683) SS BOND : bond 0.00308 / 0.18 ( 9) SS BOND : angle 1.41541 / 0.69 ( 18) hydrogen bonds : bond 0.04200 / 2.74 ( 719) hydrogen bonds : angle 4.45079 / 3.27 ( 2079) link_BETA1-4 : bond 0.00516 / 0.35 ( 2) link_BETA1-4 : angle 1.02124 / 0.64 ( 6) link_NAG-ASN : bond 0.00344 / 0.14 ( 8) link_NAG-ASN : angle 2.61217 / 1.82 ( 24) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2620 Ramachandran restraints generated. 1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2620 Ramachandran restraints generated. 1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 142 time to evaluate : 0.422 Fit side-chains revert: symmetry clash REVERT: A 147 ASN cc_start: 0.8882 (t0) cc_final: 0.8399 (p0) REVERT: A 184 LEU cc_start: 0.7427 (mm) cc_final: 0.6607 (tm) REVERT: A 216 PHE cc_start: 0.8814 (OUTLIER) cc_final: 0.8593 (t80) REVERT: A 307 GLU cc_start: 0.8557 (OUTLIER) cc_final: 0.8321 (tt0) REVERT: A 760 PHE cc_start: 0.8680 (OUTLIER) cc_final: 0.7905 (t80) REVERT: A 861 ASN cc_start: 0.7545 (m-40) cc_final: 0.7099 (m-40) REVERT: A 1201 MET cc_start: 0.8495 (mmp) cc_final: 0.8195 (mmp) REVERT: A 1639 MET cc_start: 0.8045 (mmm) cc_final: 0.7730 (mmm) REVERT: B 148 ASP cc_start: 0.8724 (t0) cc_final: 0.8420 (m-30) outliers start: 22 outliers final: 9 residues processed: 152 average time/residue: 0.4732 time to fit residues: 78.9805 Evaluate side-chains 145 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 133 time to evaluate : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 PHE Chi-restraints excluded: chain A residue 217 ARG Chi-restraints excluded: chain A residue 307 GLU Chi-restraints excluded: chain A residue 741 VAL Chi-restraints excluded: chain A residue 752 ILE Chi-restraints excluded: chain A residue 759 LEU Chi-restraints excluded: chain A residue 760 PHE Chi-restraints excluded: chain A residue 856 ILE Chi-restraints excluded: chain A residue 1270 LEU Chi-restraints excluded: chain A residue 1314 LEU Chi-restraints excluded: chain A residue 1330 ILE Chi-restraints excluded: chain B residue 49 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 1 optimal weight: 3.9990 chunk 7 optimal weight: 10.0000 chunk 118 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 120 optimal weight: 5.9990 chunk 73 optimal weight: 5.9990 chunk 67 optimal weight: 0.6980 chunk 33 optimal weight: 5.9990 chunk 82 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 chunk 14 optimal weight: 0.9980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 240 GLN A 412 ASN A 774 ASN A 809 ASN A1276 ASN ** A1721 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.133713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.095165 restraints weight = 16356.015| |-----------------------------------------------------------------------------| r_work (start): 0.3143 rms_B_bonded: 2.02 r_work: 0.3018 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2892 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.1725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 11652 Z= 0.140 Angle : 0.541 9.727 15731 Z= 0.278 Chirality : 0.041 0.374 1776 Planarity : 0.004 0.057 1842 Dihedral : 15.687 176.160 2194 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 1.78 % Allowed : 14.07 % Favored : 84.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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 (0.24), residues: 1310 helix: 1.90 (0.18), residues: 879 sheet: 0.03 (0.61), residues: 66 loop : -1.04 (0.32), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1218 TYR 0.017 0.001 TYR A 405 PHE 0.018 0.001 PHE A 843 TRP 0.017 0.001 TRP A 730 HIS 0.003 0.001 HIS A 765 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.14 (11633) covalent geometry : angle 0.52941 / 0.27 (15683) SS BOND : bond 0.00329 / 0.20 ( 9) SS BOND : angle 1.48674 / 0.70 ( 18) hydrogen bonds : bond 0.04247 / 2.76 ( 719) hydrogen bonds : angle 4.37347 / 3.21 ( 2079) link_BETA1-4 : bond 0.00396 / 0.28 ( 2) link_BETA1-4 : angle 1.23227 / 0.76 ( 6) link_NAG-ASN : bond 0.00270 / 0.14 ( 8) link_NAG-ASN : angle 2.61017 / 1.81 ( 24) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2620 Ramachandran restraints generated. 1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2620 Ramachandran restraints generated. 1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 141 time to evaluate : 0.493 Fit side-chains revert: symmetry clash REVERT: A 184 LEU cc_start: 0.7432 (mm) cc_final: 0.6620 (tm) REVERT: A 216 PHE cc_start: 0.8852 (OUTLIER) cc_final: 0.8591 (t80) REVERT: A 220 ARG cc_start: 0.7331 (mtm-85) cc_final: 0.7076 (mtm-85) REVERT: A 307 GLU cc_start: 0.8573 (OUTLIER) cc_final: 0.8329 (tt0) REVERT: A 760 PHE cc_start: 0.8667 (OUTLIER) cc_final: 0.7864 (t80) REVERT: A 861 ASN cc_start: 0.7489 (m-40) cc_final: 0.6971 (m-40) REVERT: A 1201 MET cc_start: 0.8450 (mmp) cc_final: 0.8112 (mmp) REVERT: A 1600 GLU cc_start: 0.8203 (tt0) cc_final: 0.7812 (tp30) REVERT: A 1639 MET cc_start: 0.8037 (mmm) cc_final: 0.7722 (mmm) REVERT: B 148 ASP cc_start: 0.8743 (t0) cc_final: 0.8432 (m-30) outliers start: 21 outliers final: 8 residues processed: 150 average time/residue: 0.4853 time to fit residues: 80.1233 Evaluate side-chains 145 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 134 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 PHE Chi-restraints excluded: chain A residue 217 ARG Chi-restraints excluded: chain A residue 307 GLU Chi-restraints excluded: chain A residue 741 VAL Chi-restraints excluded: chain A residue 752 ILE Chi-restraints excluded: chain A residue 759 LEU Chi-restraints excluded: chain A residue 760 PHE Chi-restraints excluded: chain A residue 839 LEU Chi-restraints excluded: chain A residue 1270 LEU Chi-restraints excluded: chain A residue 1314 LEU Chi-restraints excluded: chain B residue 49 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 115 optimal weight: 3.9990 chunk 23 optimal weight: 0.9990 chunk 93 optimal weight: 5.9990 chunk 84 optimal weight: 0.9990 chunk 109 optimal weight: 0.6980 chunk 53 optimal weight: 0.6980 chunk 51 optimal weight: 0.9990 chunk 48 optimal weight: 2.9990 chunk 87 optimal weight: 5.9990 chunk 68 optimal weight: 3.9990 chunk 50 optimal weight: 0.1980 overall best weight: 0.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 240 GLN A 412 ASN A 774 ASN A1276 ASN ** A1721 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.135382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.096644 restraints weight = 16274.182| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 2.02 r_work: 0.3040 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2914 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.1931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 11652 Z= 0.113 Angle : 0.512 9.783 15731 Z= 0.263 Chirality : 0.040 0.330 1776 Planarity : 0.004 0.055 1842 Dihedral : 14.919 172.515 2194 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.03 % Allowed : 15.76 % Favored : 82.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 1.69 (0.24), residues: 1310 helix: 2.03 (0.18), residues: 880 sheet: -0.01 (0.61), residues: 67 loop : -0.96 (0.33), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1218 TYR 0.021 0.001 TYR B 180 PHE 0.016 0.001 PHE A 843 TRP 0.016 0.001 TRP A 730 HIS 0.002 0.001 HIS A1721 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.11 (11633) covalent geometry : angle 0.50176 / 0.26 (15683) SS BOND : bond 0.00251 / 0.15 ( 9) SS BOND : angle 1.23097 / 0.59 ( 18) hydrogen bonds : bond 0.03944 / 2.56 ( 719) hydrogen bonds : angle 4.25409 / 3.12 ( 2079) link_BETA1-4 : bond 0.00333 / 0.24 ( 2) link_BETA1-4 : angle 1.20896 / 0.76 ( 6) link_NAG-ASN : bond 0.00318 / 0.15 ( 8) link_NAG-ASN : angle 2.40921 / 1.64 ( 24) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2620 Ramachandran restraints generated. 1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2620 Ramachandran restraints generated. 1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 141 time to evaluate : 0.470 Fit side-chains revert: symmetry clash REVERT: A 184 LEU cc_start: 0.7484 (mm) cc_final: 0.6669 (tm) REVERT: A 216 PHE cc_start: 0.8791 (OUTLIER) cc_final: 0.8515 (t80) REVERT: A 220 ARG cc_start: 0.7302 (mtm-85) cc_final: 0.7071 (mtm-85) REVERT: A 307 GLU cc_start: 0.8570 (OUTLIER) cc_final: 0.8318 (tt0) REVERT: A 760 PHE cc_start: 0.8670 (OUTLIER) cc_final: 0.7889 (t80) REVERT: A 791 MET cc_start: 0.7852 (tmm) cc_final: 0.7245 (tpp) REVERT: A 861 ASN cc_start: 0.7585 (m-40) cc_final: 0.7038 (m-40) REVERT: A 1201 MET cc_start: 0.8401 (mmp) cc_final: 0.8070 (mmp) REVERT: A 1600 GLU cc_start: 0.8188 (tt0) cc_final: 0.7844 (tp30) REVERT: A 1639 MET cc_start: 0.8027 (mmm) cc_final: 0.7709 (mmm) REVERT: B 148 ASP cc_start: 0.8732 (t0) cc_final: 0.8422 (m-30) outliers start: 24 outliers final: 8 residues processed: 155 average time/residue: 0.4766 time to fit residues: 81.5141 Evaluate side-chains 148 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 137 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 PHE Chi-restraints excluded: chain A residue 217 ARG Chi-restraints excluded: chain A residue 307 GLU Chi-restraints excluded: chain A residue 741 VAL Chi-restraints excluded: chain A residue 752 ILE Chi-restraints excluded: chain A residue 759 LEU Chi-restraints excluded: chain A residue 760 PHE Chi-restraints excluded: chain A residue 856 ILE Chi-restraints excluded: chain A residue 1270 LEU Chi-restraints excluded: chain A residue 1314 LEU Chi-restraints excluded: chain B residue 49 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 96 optimal weight: 1.9990 chunk 56 optimal weight: 4.9990 chunk 82 optimal weight: 1.9990 chunk 73 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 chunk 112 optimal weight: 1.9990 chunk 52 optimal weight: 0.6980 chunk 123 optimal weight: 4.9990 chunk 119 optimal weight: 0.7980 chunk 74 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 412 ASN A1276 ASN ** A1721 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.134899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.095108 restraints weight = 16585.639| |-----------------------------------------------------------------------------| r_work (start): 0.3152 rms_B_bonded: 2.09 r_work: 0.3027 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2900 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.2078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 11652 Z= 0.116 Angle : 0.513 10.148 15731 Z= 0.262 Chirality : 0.040 0.325 1776 Planarity : 0.003 0.054 1842 Dihedral : 14.392 169.588 2194 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 1.95 % Allowed : 16.53 % Favored : 81.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 1.74 (0.24), residues: 1310 helix: 2.08 (0.18), residues: 882 sheet: 0.01 (0.61), residues: 67 loop : -0.98 (0.33), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 838 TYR 0.017 0.001 TYR A 405 PHE 0.016 0.001 PHE A 843 TRP 0.014 0.001 TRP A 730 HIS 0.002 0.001 HIS A 915 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.12 (11633) covalent geometry : angle 0.50269 / 0.26 (15683) SS BOND : bond 0.00258 / 0.16 ( 9) SS BOND : angle 1.22513 / 0.58 ( 18) hydrogen bonds : bond 0.03929 / 2.55 ( 719) hydrogen bonds : angle 4.21509 / 3.09 ( 2079) link_BETA1-4 : bond 0.00548 / 0.39 ( 2) link_BETA1-4 : angle 1.24141 / 0.79 ( 6) link_NAG-ASN : bond 0.00300 / 0.15 ( 8) link_NAG-ASN : angle 2.39201 / 1.60 ( 24) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2620 Ramachandran restraints generated. 1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2620 Ramachandran restraints generated. 1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 138 time to evaluate : 0.331 Fit side-chains REVERT: A 220 ARG cc_start: 0.7314 (mtm-85) cc_final: 0.7068 (mtm-85) REVERT: A 307 GLU cc_start: 0.8577 (OUTLIER) cc_final: 0.8322 (tt0) REVERT: A 760 PHE cc_start: 0.8680 (OUTLIER) cc_final: 0.7797 (t80) REVERT: A 854 MET cc_start: 0.7886 (tmm) cc_final: 0.7566 (pp-130) REVERT: A 861 ASN cc_start: 0.7584 (m-40) cc_final: 0.7018 (m-40) REVERT: A 1201 MET cc_start: 0.8407 (mmp) cc_final: 0.8066 (mmp) REVERT: A 1600 GLU cc_start: 0.8184 (tt0) cc_final: 0.7883 (tp30) REVERT: A 1639 MET cc_start: 0.7950 (mmm) cc_final: 0.7730 (mmm) REVERT: A 1755 TYR cc_start: 0.8591 (OUTLIER) cc_final: 0.8094 (t80) REVERT: B 148 ASP cc_start: 0.8733 (t0) cc_final: 0.8411 (m-30) REVERT: B 152 ARG cc_start: 0.8702 (mtm-85) cc_final: 0.8454 (mtp85) REVERT: B 154 MET cc_start: 0.7096 (tpp) cc_final: 0.6628 (tpp) outliers start: 23 outliers final: 10 residues processed: 151 average time/residue: 0.4406 time to fit residues: 73.4475 Evaluate side-chains 148 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 135 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 MET Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 307 GLU Chi-restraints excluded: chain A residue 741 VAL Chi-restraints excluded: chain A residue 752 ILE Chi-restraints excluded: chain A residue 759 LEU Chi-restraints excluded: chain A residue 760 PHE Chi-restraints excluded: chain A residue 856 ILE Chi-restraints excluded: chain A residue 1270 LEU Chi-restraints excluded: chain A residue 1314 LEU Chi-restraints excluded: chain A residue 1751 VAL Chi-restraints excluded: chain A residue 1755 TYR Chi-restraints excluded: chain B residue 49 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 90 optimal weight: 3.9990 chunk 128 optimal weight: 5.9990 chunk 64 optimal weight: 0.6980 chunk 129 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 103 optimal weight: 0.9980 chunk 118 optimal weight: 0.8980 chunk 45 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 43 optimal weight: 8.9990 chunk 97 optimal weight: 7.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 240 GLN A 412 ASN A 809 ASN A1276 ASN A1721 HIS B 122 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.134371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.094461 restraints weight = 16429.465| |-----------------------------------------------------------------------------| r_work (start): 0.3139 rms_B_bonded: 2.08 r_work: 0.3012 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2886 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.2147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 11652 Z= 0.132 Angle : 0.530 10.419 15731 Z= 0.268 Chirality : 0.040 0.339 1776 Planarity : 0.004 0.054 1842 Dihedral : 14.006 167.008 2194 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 1.78 % Allowed : 17.29 % Favored : 80.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 1.75 (0.24), residues: 1310 helix: 2.09 (0.18), residues: 881 sheet: -0.04 (0.60), residues: 67 loop : -0.95 (0.32), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 838 TYR 0.022 0.001 TYR B 180 PHE 0.016 0.001 PHE A 843 TRP 0.018 0.001 TRP A 190 HIS 0.003 0.001 HIS A 765 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.13 (11633) covalent geometry : angle 0.52068 / 0.27 (15683) SS BOND : bond 0.00284 / 0.17 ( 9) SS BOND : angle 1.32417 / 0.63 ( 18) hydrogen bonds : bond 0.04023 / 2.61 ( 719) hydrogen bonds : angle 4.22141 / 3.10 ( 2079) link_BETA1-4 : bond 0.00330 / 0.23 ( 2) link_BETA1-4 : angle 1.19445 / 0.78 ( 6) link_NAG-ASN : bond 0.00235 / 0.13 ( 8) link_NAG-ASN : angle 2.31133 / 1.62 ( 24) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2620 Ramachandran restraints generated. 1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2620 Ramachandran restraints generated. 1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 137 time to evaluate : 0.289 Fit side-chains revert: symmetry clash REVERT: A 184 LEU cc_start: 0.7264 (mm) cc_final: 0.6330 (tm) REVERT: A 220 ARG cc_start: 0.7330 (mtm-85) cc_final: 0.7079 (mtm-85) REVERT: A 307 GLU cc_start: 0.8632 (OUTLIER) cc_final: 0.8397 (tt0) REVERT: A 760 PHE cc_start: 0.8588 (OUTLIER) cc_final: 0.7747 (t80) REVERT: A 768 MET cc_start: 0.8016 (OUTLIER) cc_final: 0.7738 (ttm) REVERT: A 791 MET cc_start: 0.7824 (tmm) cc_final: 0.7196 (tpp) REVERT: A 854 MET cc_start: 0.7924 (tmm) cc_final: 0.7602 (pp-130) REVERT: A 861 ASN cc_start: 0.7604 (m-40) cc_final: 0.7028 (m-40) REVERT: A 1201 MET cc_start: 0.8483 (mmp) cc_final: 0.8124 (mmp) REVERT: A 1600 GLU cc_start: 0.8182 (tt0) cc_final: 0.7843 (tp30) REVERT: A 1639 MET cc_start: 0.8021 (mmm) cc_final: 0.7791 (mmm) REVERT: A 1755 TYR cc_start: 0.8650 (OUTLIER) cc_final: 0.8162 (t80) REVERT: B 152 ARG cc_start: 0.8716 (mtm-85) cc_final: 0.8469 (mtp85) REVERT: B 154 MET cc_start: 0.7095 (tpp) cc_final: 0.6776 (tpp) outliers start: 21 outliers final: 10 residues processed: 149 average time/residue: 0.4659 time to fit residues: 76.2700 Evaluate side-chains 149 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 135 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 217 ARG Chi-restraints excluded: chain A residue 307 GLU Chi-restraints excluded: chain A residue 752 ILE Chi-restraints excluded: chain A residue 759 LEU Chi-restraints excluded: chain A residue 760 PHE Chi-restraints excluded: chain A residue 768 MET Chi-restraints excluded: chain A residue 856 ILE Chi-restraints excluded: chain A residue 1270 LEU Chi-restraints excluded: chain A residue 1314 LEU Chi-restraints excluded: chain A residue 1751 VAL Chi-restraints excluded: chain A residue 1755 TYR Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 172 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 86 optimal weight: 0.0570 chunk 69 optimal weight: 0.2980 chunk 43 optimal weight: 7.9990 chunk 116 optimal weight: 2.9990 chunk 7 optimal weight: 5.9990 chunk 81 optimal weight: 2.9990 chunk 32 optimal weight: 0.7980 chunk 109 optimal weight: 4.9990 chunk 35 optimal weight: 0.9990 chunk 12 optimal weight: 3.9990 chunk 88 optimal weight: 0.4980 overall best weight: 0.5300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 412 ASN A1276 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.135610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.096083 restraints weight = 16443.969| |-----------------------------------------------------------------------------| r_work (start): 0.3169 rms_B_bonded: 2.06 r_work: 0.3045 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2919 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.2317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.062 11652 Z= 0.105 Angle : 0.507 10.406 15731 Z= 0.257 Chirality : 0.039 0.300 1776 Planarity : 0.003 0.053 1842 Dihedral : 13.357 165.043 2194 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 1.53 % Allowed : 17.97 % Favored : 80.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 1.86 (0.24), residues: 1310 helix: 2.18 (0.18), residues: 882 sheet: 0.02 (0.60), residues: 67 loop : -0.94 (0.33), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 838 TYR 0.016 0.001 TYR A 405 PHE 0.019 0.001 PHE A 165 TRP 0.015 0.001 TRP A 190 HIS 0.002 0.000 HIS A 765 Details of bonding type rmsd/Z covalent geometry : bond 0.00226 / 0.10 (11633) covalent geometry : angle 0.49959 / 0.26 (15683) SS BOND : bond 0.00206 / 0.12 ( 9) SS BOND : angle 1.10128 / 0.53 ( 18) hydrogen bonds : bond 0.03749 / 2.43 ( 719) hydrogen bonds : angle 4.14023 / 3.04 ( 2079) link_BETA1-4 : bond 0.00347 / 0.24 ( 2) link_BETA1-4 : angle 1.09887 / 0.72 ( 6) link_NAG-ASN : bond 0.00303 / 0.14 ( 8) link_NAG-ASN : angle 2.07678 / 1.45 ( 24) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2620 Ramachandran restraints generated. 1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2620 Ramachandran restraints generated. 1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 140 time to evaluate : 0.408 Fit side-chains revert: symmetry clash REVERT: A 184 LEU cc_start: 0.7293 (mm) cc_final: 0.6340 (tm) REVERT: A 220 ARG cc_start: 0.7323 (mtm-85) cc_final: 0.7072 (mtm-85) REVERT: A 307 GLU cc_start: 0.8606 (OUTLIER) cc_final: 0.8359 (tt0) REVERT: A 760 PHE cc_start: 0.8582 (OUTLIER) cc_final: 0.8197 (t80) REVERT: A 768 MET cc_start: 0.7980 (OUTLIER) cc_final: 0.7693 (ttm) REVERT: A 791 MET cc_start: 0.7933 (tmm) cc_final: 0.7333 (tpp) REVERT: A 837 PHE cc_start: 0.8305 (m-10) cc_final: 0.7308 (m-80) REVERT: A 1201 MET cc_start: 0.8394 (mmp) cc_final: 0.8057 (mmp) REVERT: A 1600 GLU cc_start: 0.8143 (tt0) cc_final: 0.7834 (tp30) REVERT: A 1639 MET cc_start: 0.7887 (mmm) cc_final: 0.7647 (mmm) REVERT: A 1755 TYR cc_start: 0.8545 (OUTLIER) cc_final: 0.7981 (t80) REVERT: B 148 ASP cc_start: 0.8714 (t0) cc_final: 0.8383 (m-30) REVERT: B 152 ARG cc_start: 0.8703 (mtm-85) cc_final: 0.8479 (mtp85) REVERT: B 154 MET cc_start: 0.7154 (tpp) cc_final: 0.6872 (tpp) outliers start: 18 outliers final: 11 residues processed: 150 average time/residue: 0.4924 time to fit residues: 81.0387 Evaluate side-chains 154 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 139 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 MET Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 217 ARG Chi-restraints excluded: chain A residue 307 GLU Chi-restraints excluded: chain A residue 752 ILE Chi-restraints excluded: chain A residue 759 LEU Chi-restraints excluded: chain A residue 760 PHE Chi-restraints excluded: chain A residue 768 MET Chi-restraints excluded: chain A residue 856 ILE Chi-restraints excluded: chain A residue 919 ILE Chi-restraints excluded: chain A residue 1270 LEU Chi-restraints excluded: chain A residue 1314 LEU Chi-restraints excluded: chain A residue 1755 TYR Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 100 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 32 optimal weight: 0.8980 chunk 3 optimal weight: 0.0970 chunk 11 optimal weight: 0.8980 chunk 60 optimal weight: 0.8980 chunk 21 optimal weight: 0.8980 chunk 46 optimal weight: 0.7980 chunk 23 optimal weight: 0.7980 chunk 100 optimal weight: 3.9990 chunk 90 optimal weight: 2.9990 chunk 42 optimal weight: 0.5980 chunk 101 optimal weight: 0.6980 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 240 GLN A 412 ASN A1276 ASN A1378 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.135419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.095985 restraints weight = 16343.961| |-----------------------------------------------------------------------------| r_work (start): 0.3169 rms_B_bonded: 2.05 r_work: 0.3044 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2919 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.2365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.059 11652 Z= 0.106 Angle : 0.518 11.778 15731 Z= 0.260 Chirality : 0.039 0.299 1776 Planarity : 0.004 0.052 1842 Dihedral : 13.097 164.442 2194 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 1.53 % Allowed : 18.14 % Favored : 80.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 1.88 (0.24), residues: 1310 helix: 2.19 (0.18), residues: 884 sheet: 0.09 (0.60), residues: 67 loop : -0.94 (0.33), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 838 TYR 0.021 0.001 TYR B 180 PHE 0.014 0.001 PHE A 843 TRP 0.015 0.001 TRP A 190 HIS 0.002 0.000 HIS A 765 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.11 (11633) covalent geometry : angle 0.51065 / 0.26 (15683) SS BOND : bond 0.00224 / 0.14 ( 9) SS BOND : angle 1.10849 / 0.53 ( 18) hydrogen bonds : bond 0.03752 / 2.44 ( 719) hydrogen bonds : angle 4.12210 / 3.03 ( 2079) link_BETA1-4 : bond 0.00293 / 0.20 ( 2) link_BETA1-4 : angle 1.09241 / 0.72 ( 6) link_NAG-ASN : bond 0.00272 / 0.13 ( 8) link_NAG-ASN : angle 2.04945 / 1.43 ( 24) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2620 Ramachandran restraints generated. 1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2620 Ramachandran restraints generated. 1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 138 time to evaluate : 0.414 Fit side-chains revert: symmetry clash REVERT: A 184 LEU cc_start: 0.7297 (mm) cc_final: 0.6341 (tm) REVERT: A 220 ARG cc_start: 0.7279 (mtm-85) cc_final: 0.7031 (mtm-85) REVERT: A 307 GLU cc_start: 0.8596 (OUTLIER) cc_final: 0.8345 (tt0) REVERT: A 760 PHE cc_start: 0.8535 (OUTLIER) cc_final: 0.8187 (t80) REVERT: A 768 MET cc_start: 0.7958 (OUTLIER) cc_final: 0.7689 (ttm) REVERT: A 1201 MET cc_start: 0.8414 (mmp) cc_final: 0.8078 (mmp) REVERT: A 1600 GLU cc_start: 0.8129 (tt0) cc_final: 0.7835 (tp30) REVERT: A 1639 MET cc_start: 0.7950 (mmm) cc_final: 0.7737 (mmm) REVERT: A 1755 TYR cc_start: 0.8552 (OUTLIER) cc_final: 0.7990 (t80) REVERT: B 148 ASP cc_start: 0.8715 (t0) cc_final: 0.8381 (m-30) REVERT: B 152 ARG cc_start: 0.8711 (mtm-85) cc_final: 0.8494 (mtp85) REVERT: B 154 MET cc_start: 0.7132 (tpp) cc_final: 0.6869 (tpp) outliers start: 18 outliers final: 10 residues processed: 148 average time/residue: 0.4707 time to fit residues: 76.6671 Evaluate side-chains 151 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 137 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 217 ARG Chi-restraints excluded: chain A residue 307 GLU Chi-restraints excluded: chain A residue 752 ILE Chi-restraints excluded: chain A residue 759 LEU Chi-restraints excluded: chain A residue 760 PHE Chi-restraints excluded: chain A residue 768 MET Chi-restraints excluded: chain A residue 856 ILE Chi-restraints excluded: chain A residue 919 ILE Chi-restraints excluded: chain A residue 1270 LEU Chi-restraints excluded: chain A residue 1314 LEU Chi-restraints excluded: chain A residue 1751 VAL Chi-restraints excluded: chain A residue 1755 TYR Chi-restraints excluded: chain B residue 49 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 43 optimal weight: 7.9990 chunk 40 optimal weight: 0.0980 chunk 56 optimal weight: 3.9990 chunk 106 optimal weight: 0.7980 chunk 119 optimal weight: 5.9990 chunk 111 optimal weight: 0.7980 chunk 35 optimal weight: 0.9980 chunk 124 optimal weight: 0.8980 chunk 64 optimal weight: 4.9990 chunk 41 optimal weight: 0.6980 chunk 125 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 412 ASN A1276 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.135651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.096185 restraints weight = 16621.963| |-----------------------------------------------------------------------------| r_work (start): 0.3171 rms_B_bonded: 2.09 r_work: 0.3046 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2919 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.2448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.058 11652 Z= 0.107 Angle : 0.522 12.890 15731 Z= 0.262 Chirality : 0.039 0.292 1776 Planarity : 0.004 0.061 1842 Dihedral : 12.719 163.727 2194 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 1.44 % Allowed : 18.64 % Favored : 79.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 1.88 (0.24), residues: 1310 helix: 2.18 (0.18), residues: 884 sheet: 0.16 (0.61), residues: 67 loop : -0.94 (0.33), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 838 TYR 0.016 0.001 TYR A 405 PHE 0.024 0.001 PHE A 165 TRP 0.015 0.001 TRP A 730 HIS 0.002 0.000 HIS A 765 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.11 (11633) covalent geometry : angle 0.51515 / 0.26 (15683) SS BOND : bond 0.00229 / 0.14 ( 9) SS BOND : angle 1.10319 / 0.53 ( 18) hydrogen bonds : bond 0.03731 / 2.42 ( 719) hydrogen bonds : angle 4.12130 / 3.03 ( 2079) link_BETA1-4 : bond 0.00328 / 0.23 ( 2) link_BETA1-4 : angle 1.10162 / 0.73 ( 6) link_NAG-ASN : bond 0.00266 / 0.12 ( 8) link_NAG-ASN : angle 1.99717 / 1.38 ( 24) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2620 Ramachandran restraints generated. 1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2620 Ramachandran restraints generated. 1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 140 time to evaluate : 0.370 Fit side-chains revert: symmetry clash REVERT: A 184 LEU cc_start: 0.7303 (mm) cc_final: 0.6344 (tm) REVERT: A 220 ARG cc_start: 0.7268 (mtm-85) cc_final: 0.6931 (mtm-85) REVERT: A 307 GLU cc_start: 0.8596 (OUTLIER) cc_final: 0.8345 (tt0) REVERT: A 760 PHE cc_start: 0.8428 (OUTLIER) cc_final: 0.8087 (t80) REVERT: A 768 MET cc_start: 0.7960 (OUTLIER) cc_final: 0.7687 (ttm) REVERT: A 861 ASN cc_start: 0.7605 (m-40) cc_final: 0.7250 (m110) REVERT: A 1201 MET cc_start: 0.8410 (mmp) cc_final: 0.8069 (mmp) REVERT: A 1600 GLU cc_start: 0.8125 (tt0) cc_final: 0.7877 (tp30) REVERT: A 1639 MET cc_start: 0.8008 (mmm) cc_final: 0.7791 (mmm) REVERT: A 1755 TYR cc_start: 0.8557 (OUTLIER) cc_final: 0.7991 (t80) REVERT: B 148 ASP cc_start: 0.8741 (t0) cc_final: 0.8398 (m-30) REVERT: B 152 ARG cc_start: 0.8710 (mtm-85) cc_final: 0.8498 (mtp85) REVERT: B 154 MET cc_start: 0.7115 (tpp) cc_final: 0.6852 (tpp) outliers start: 17 outliers final: 9 residues processed: 149 average time/residue: 0.4810 time to fit residues: 78.8774 Evaluate side-chains 148 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 135 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 217 ARG Chi-restraints excluded: chain A residue 307 GLU Chi-restraints excluded: chain A residue 752 ILE Chi-restraints excluded: chain A residue 759 LEU Chi-restraints excluded: chain A residue 760 PHE Chi-restraints excluded: chain A residue 768 MET Chi-restraints excluded: chain A residue 919 ILE Chi-restraints excluded: chain A residue 1270 LEU Chi-restraints excluded: chain A residue 1314 LEU Chi-restraints excluded: chain A residue 1751 VAL Chi-restraints excluded: chain A residue 1755 TYR Chi-restraints excluded: chain B residue 49 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 128 optimal weight: 0.8980 chunk 100 optimal weight: 3.9990 chunk 42 optimal weight: 0.7980 chunk 117 optimal weight: 0.9990 chunk 47 optimal weight: 0.7980 chunk 26 optimal weight: 0.0670 chunk 125 optimal weight: 0.8980 chunk 38 optimal weight: 10.0000 chunk 114 optimal weight: 4.9990 chunk 55 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 overall best weight: 0.6918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 240 GLN A 412 ASN A1276 ASN A1378 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.135411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.095727 restraints weight = 16669.600| |-----------------------------------------------------------------------------| r_work (start): 0.3169 rms_B_bonded: 2.08 r_work: 0.3045 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2920 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.2466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.056 11652 Z= 0.111 Angle : 0.537 13.319 15731 Z= 0.266 Chirality : 0.039 0.293 1776 Planarity : 0.004 0.061 1842 Dihedral : 12.554 163.469 2194 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 1.36 % Allowed : 19.07 % Favored : 79.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 1.91 (0.24), residues: 1310 helix: 2.20 (0.18), residues: 883 sheet: 0.19 (0.61), residues: 67 loop : -0.93 (0.33), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 835 TYR 0.022 0.001 TYR B 180 PHE 0.015 0.001 PHE A1440 TRP 0.015 0.001 TRP A 730 HIS 0.002 0.000 HIS A 765 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.11 (11633) covalent geometry : angle 0.53011 / 0.26 (15683) SS BOND : bond 0.00239 / 0.15 ( 9) SS BOND : angle 1.16063 / 0.54 ( 18) hydrogen bonds : bond 0.03750 / 2.44 ( 719) hydrogen bonds : angle 4.11078 / 3.03 ( 2079) link_BETA1-4 : bond 0.00320 / 0.22 ( 2) link_BETA1-4 : angle 1.09327 / 0.72 ( 6) link_NAG-ASN : bond 0.00263 / 0.13 ( 8) link_NAG-ASN : angle 1.98482 / 1.37 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3783.22 seconds wall clock time: 65 minutes 12.83 seconds (3912.83 seconds total)