Starting phenix.real_space_refine on Fri Jul 3 01:22:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8tn9_41411/07_2026/8tn9_41411.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tn9_41411/07_2026/8tn9_41411.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.05 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8tn9_41411/07_2026/8tn9_41411.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tn9_41411/07_2026/8tn9_41411.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8tn9_41411/07_2026/8tn9_41411.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8tn9_41411/07_2026/8tn9_41411.cif" model { file = "/net/cci-nas-00/data/ceres_data/8tn9_41411/07_2026/8tn9_41411.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tn9_41411/07_2026/8tn9_41411.cif" } resolution = 3.05 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= 1.000 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: 4 Type Number sf(0) Gaussians S 54 5.16 5 C 7078 2.51 5 N 1891 2.21 5 O 2122 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 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: 11145 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 11089 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1368, 11089 Classifications: {'peptide': 1368} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 68, 'TRANS': 1299} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "A" 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 chiralities: 4 Time building chain proxies: 2.39, per 1000 atoms: 0.21 Number of scatterers: 11145 At special positions: 0 Unit cell: (115.5, 124.3, 93.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 54 16.00 O 2122 8.00 N 1891 7.00 C 7078 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 139 " - pdb=" SG CYS A 165 " distance=2.03 Simple disulfide: pdb=" SG CYS A 220 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 472 " - pdb=" SG CYS A 498 " distance=2.03 Simple disulfide: pdb=" SG CYS A 575 " - pdb=" SG CYS A 656 " distance=2.03 Simple disulfide: pdb=" SG CYS A1697 " - pdb=" SG CYS A1723 " distance=2.03 Simple disulfide: pdb=" SG CYS A1879 " - pdb=" SG CYS A2033 " distance=2.03 Simple disulfide: pdb=" SG CYS A2038 " - pdb=" SG CYS A2193 " 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 NAG-ASN " NAG A2201 " - " ASN A 269 " " NAG A2202 " - " ASN A1982 " " NAG A2203 " - " ASN A1675 " " NAG A2204 " - " ASN A 211 " Time building additional restraints: 0.70 Conformation dependent library (CDL) restraints added in 469.5 milliseconds 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2578 Finding SS restraints... Secondary structure from input PDB file: 16 helices and 21 sheets defined 7.0% alpha, 28.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... Processing helix chain 'A' and resid 105 through 109 Processing helix chain 'A' and resid 149 through 156 removed outlier: 3.855A pdb=" N PHE A 154 " --> pdb=" O LEU A 150 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ASN A 155 " --> pdb=" O ILE A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 195 removed outlier: 3.530A pdb=" N LYS A 194 " --> pdb=" O ASP A 191 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N SER A 195 " --> pdb=" O GLU A 192 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 191 through 195' Processing helix chain 'A' and resid 284 through 290 removed outlier: 3.761A pdb=" N ALA A 290 " --> pdb=" O LYS A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 305 removed outlier: 3.880A pdb=" N THR A 305 " --> pdb=" O PRO A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 482 through 488 Processing helix chain 'A' and resid 524 through 528 Processing helix chain 'A' and resid 530 through 536 removed outlier: 3.710A pdb=" N ASN A 536 " --> pdb=" O GLU A 532 " (cutoff:3.500A) Processing helix chain 'A' and resid 551 through 556 Processing helix chain 'A' and resid 565 through 569 removed outlier: 3.566A pdb=" N ILE A 569 " --> pdb=" O PRO A 566 " (cutoff:3.500A) Processing helix chain 'A' and resid 1535 through 1544 removed outlier: 3.892A pdb=" N TRP A1542 " --> pdb=" O ASN A1538 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N TYR A1543 " --> pdb=" O ILE A1539 " (cutoff:3.500A) Processing helix chain 'A' and resid 1685 through 1689 Processing helix chain 'A' and resid 1707 through 1712 Processing helix chain 'A' and resid 1860 through 1865 Processing helix chain 'A' and resid 1891 through 1893 No H-bonds generated for 'chain 'A' and resid 1891 through 1893' Processing helix chain 'A' and resid 1905 through 1910 removed outlier: 3.654A pdb=" N ARG A1910 " --> pdb=" O ARG A1907 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 36 through 40 removed outlier: 3.604A pdb=" N ILE A 70 " --> pdb=" O TRP A 124 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 64 through 65 removed outlier: 6.864A pdb=" N ALA A 64 " --> pdb=" O CYS A 165 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 209 through 210 Processing sheet with id=AA4, first strand: chain 'A' and resid 214 through 219 removed outlier: 7.769A pdb=" N ASP A 297 " --> pdb=" O PRO A 215 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N ILE A 217 " --> pdb=" O ASP A 297 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 248 through 250 Processing sheet with id=AA6, first strand: chain 'A' and resid 323 through 325 Processing sheet with id=AA7, first strand: chain 'A' and resid 328 through 330 removed outlier: 3.640A pdb=" N MET A 367 " --> pdb=" O GLU A 329 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 396 through 397 Processing sheet with id=AA9, first strand: chain 'A' and resid 558 through 561 removed outlier: 7.191A pdb=" N ASP A 513 " --> pdb=" O GLN A 581 " (cutoff:3.500A) removed outlier: 8.740A pdb=" N HIS A 583 " --> pdb=" O ASP A 513 " (cutoff:3.500A) removed outlier: 8.740A pdb=" N GLU A 515 " --> pdb=" O HIS A 583 " (cutoff:3.500A) removed outlier: 9.672A pdb=" N CYS A 585 " --> pdb=" O GLU A 515 " (cutoff:3.500A) removed outlier: 10.007A pdb=" N GLN A 517 " --> pdb=" O CYS A 585 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 612 through 615 Processing sheet with id=AB2, first strand: chain 'A' and resid 1588 through 1595 removed outlier: 4.129A pdb=" N TYR A1555 " --> pdb=" O TYR A1595 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N ARG A1552 " --> pdb=" O GLN A1629 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N ARG A1631 " --> pdb=" O ARG A1552 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N TYR A1554 " --> pdb=" O ARG A1631 " (cutoff:3.500A) removed outlier: 7.761A pdb=" N LYS A1633 " --> pdb=" O TYR A1554 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N ILE A1556 " --> pdb=" O LYS A1633 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N SER A1676 " --> pdb=" O ASN A1634 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 1620 through 1623 removed outlier: 6.249A pdb=" N ILE A1620 " --> pdb=" O LEU A1721 " (cutoff:3.500A) removed outlier: 7.950A pdb=" N CYS A1723 " --> pdb=" O ILE A1620 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N ALA A1622 " --> pdb=" O CYS A1723 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 1739 through 1744 removed outlier: 6.224A pdb=" N ARG A1739 " --> pdb=" O ARG A1799 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N HIS A1801 " --> pdb=" O ARG A1739 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N PHE A1741 " --> pdb=" O HIS A1801 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N LEU A1803 " --> pdb=" O PHE A1741 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N LEU A1743 " --> pdb=" O LEU A1803 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1746 through 1747 removed outlier: 3.714A pdb=" N MET A1746 " --> pdb=" O ALA A1779 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ALA A1779 " --> pdb=" O MET A1746 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'A' and resid 1791 through 1793 removed outlier: 6.847A pdb=" N MET A1792 " --> pdb=" O MET A1875 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1881 through 1882 removed outlier: 6.859A pdb=" N GLN A2031 " --> pdb=" O THR A1946 " (cutoff:3.500A) removed outlier: 10.179A pdb=" N ILE A1944 " --> pdb=" O PRO A2006 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N THR A1946 " --> pdb=" O PHE A2004 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1895 through 1897 removed outlier: 6.361A pdb=" N GLU A1964 " --> pdb=" O THR A2018 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N ALA A2020 " --> pdb=" O THR A1962 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N THR A1962 " --> pdb=" O ALA A2020 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 1920 through 1921 Processing sheet with id=AC1, first strand: chain 'A' and resid 2055 through 2056 removed outlier: 12.417A pdb=" N LEU A2095 " --> pdb=" O LYS A2178 " (cutoff:3.500A) removed outlier: 11.032A pdb=" N LYS A2178 " --> pdb=" O LEU A2095 " (cutoff:3.500A) removed outlier: 12.529A pdb=" N ILE A2097 " --> pdb=" O ILE A2176 " (cutoff:3.500A) removed outlier: 11.721A pdb=" N ILE A2176 " --> pdb=" O ILE A2097 " (cutoff:3.500A) removed outlier: 12.044A pdb=" N LEU A2099 " --> pdb=" O ARG A2174 " (cutoff:3.500A) removed outlier: 11.258A pdb=" N ARG A2174 " --> pdb=" O LEU A2099 " (cutoff:3.500A) removed outlier: 10.331A pdb=" N LYS A2101 " --> pdb=" O PHE A2172 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N PHE A2172 " --> pdb=" O LYS A2101 " (cutoff:3.500A) removed outlier: 7.837A pdb=" N ALA A2107 " --> pdb=" O PRO A2166 " (cutoff:3.500A) removed outlier: 11.901A pdb=" N ILE A2109 " --> pdb=" O PHE A2164 " (cutoff:3.500A) removed outlier: 11.940A pdb=" N PHE A2164 " --> pdb=" O ILE A2109 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N SER A2124 " --> pdb=" O LYS A2178 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N TRP A2180 " --> pdb=" O VAL A2122 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N VAL A2122 " --> pdb=" O TRP A2180 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N TYR A2125 " --> pdb=" O PHE A2150 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 2137 through 2138 removed outlier: 7.256A pdb=" N VAL A2122 " --> pdb=" O TRP A2180 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N TRP A2180 " --> pdb=" O VAL A2122 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N SER A2124 " --> pdb=" O LYS A2178 " (cutoff:3.500A) removed outlier: 11.940A pdb=" N PHE A2164 " --> pdb=" O ILE A2109 " (cutoff:3.500A) removed outlier: 11.901A pdb=" N ILE A2109 " --> pdb=" O PHE A2164 " (cutoff:3.500A) removed outlier: 7.837A pdb=" N ALA A2107 " --> pdb=" O PRO A2166 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N PHE A2172 " --> pdb=" O LYS A2101 " (cutoff:3.500A) removed outlier: 10.331A pdb=" N LYS A2101 " --> pdb=" O PHE A2172 " (cutoff:3.500A) removed outlier: 11.258A pdb=" N ARG A2174 " --> pdb=" O LEU A2099 " (cutoff:3.500A) removed outlier: 12.044A pdb=" N LEU A2099 " --> pdb=" O ARG A2174 " (cutoff:3.500A) removed outlier: 11.721A pdb=" N ILE A2176 " --> pdb=" O ILE A2097 " (cutoff:3.500A) removed outlier: 12.529A pdb=" N ILE A2097 " --> pdb=" O ILE A2176 " (cutoff:3.500A) removed outlier: 11.032A pdb=" N LYS A2178 " --> pdb=" O LEU A2095 " (cutoff:3.500A) removed outlier: 12.417A pdb=" N LEU A2095 " --> pdb=" O LYS A2178 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N PHE A2191 " --> pdb=" O THR A2106 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N ILE A2108 " --> pdb=" O GLU A2189 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N GLU A2189 " --> pdb=" O ILE A2108 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 2061 through 2062 223 hydrogen bonds defined for protein. 546 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: 2.16 Time building geometry restraints manager: 1.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3579 1.34 - 1.46: 2531 1.46 - 1.58: 5240 1.58 - 1.70: 0 1.70 - 1.82: 90 Bond restraints: 11440 Sorted by residual: bond pdb=" N MET A1736 " pdb=" CA MET A1736 " ideal model delta sigma weight residual 1.456 1.490 -0.034 1.32e-02 5.74e+03 6.55e+00 bond pdb=" N PHE A 668 " pdb=" CA PHE A 668 " ideal model delta sigma weight residual 1.457 1.490 -0.032 1.29e-02 6.01e+03 6.29e+00 bond pdb=" N ASP A1737 " pdb=" CA ASP A1737 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.24e-02 6.50e+03 5.99e+00 bond pdb=" N SER A1732 " pdb=" CA SER A1732 " ideal model delta sigma weight residual 1.458 1.486 -0.028 1.19e-02 7.06e+03 5.53e+00 bond pdb=" N MET A1734 " pdb=" CA MET A1734 " ideal model delta sigma weight residual 1.451 1.488 -0.037 1.70e-02 3.46e+03 4.73e+00 ... (remaining 11435 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.00: 15181 2.00 - 3.99: 283 3.99 - 5.99: 28 5.99 - 7.99: 7 7.99 - 9.99: 5 Bond angle restraints: 15504 Sorted by residual: angle pdb=" N ASP A 549 " pdb=" CA ASP A 549 " pdb=" C ASP A 549 " ideal model delta sigma weight residual 109.15 119.14 -9.99 1.67e+00 3.59e-01 3.58e+01 angle pdb=" C ASP A 548 " pdb=" N ASP A 549 " pdb=" CA ASP A 549 " ideal model delta sigma weight residual 122.28 113.15 9.13 1.77e+00 3.19e-01 2.66e+01 angle pdb=" C LYS A 386 " pdb=" N GLU A 387 " pdb=" CA GLU A 387 " ideal model delta sigma weight residual 121.54 129.79 -8.25 1.91e+00 2.74e-01 1.86e+01 angle pdb=" N PHE A 668 " pdb=" CA PHE A 668 " pdb=" C PHE A 668 " ideal model delta sigma weight residual 110.80 102.24 8.56 2.13e+00 2.20e-01 1.61e+01 angle pdb=" CA ASN A1733 " pdb=" C ASN A1733 " pdb=" O ASN A1733 " ideal model delta sigma weight residual 122.64 118.01 4.63 1.25e+00 6.40e-01 1.37e+01 ... (remaining 15499 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.87: 6121 17.87 - 35.75: 567 35.75 - 53.62: 108 53.62 - 71.49: 17 71.49 - 89.36: 9 Dihedral angle restraints: 6822 sinusoidal: 2808 harmonic: 4014 Sorted by residual: dihedral pdb=" CB CYS A 575 " pdb=" SG CYS A 575 " pdb=" SG CYS A 656 " pdb=" CB CYS A 656 " ideal model delta sinusoidal sigma weight residual 93.00 36.89 56.11 1 1.00e+01 1.00e-02 4.25e+01 dihedral pdb=" CA ASP A1514 " pdb=" C ASP A1514 " pdb=" N TYR A1515 " pdb=" CA TYR A1515 " ideal model delta harmonic sigma weight residual 180.00 152.87 27.13 0 5.00e+00 4.00e-02 2.94e+01 dihedral pdb=" CA GLU A 669 " pdb=" C GLU A 669 " pdb=" N PRO A 670 " pdb=" CA PRO A 670 " ideal model delta harmonic sigma weight residual 180.00 153.74 26.26 0 5.00e+00 4.00e-02 2.76e+01 ... (remaining 6819 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 1202 0.045 - 0.091: 306 0.091 - 0.136: 123 0.136 - 0.182: 11 0.182 - 0.227: 2 Chirality restraints: 1644 Sorted by residual: chirality pdb=" CB ILE A 514 " pdb=" CA ILE A 514 " pdb=" CG1 ILE A 514 " pdb=" CG2 ILE A 514 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.23 2.00e-01 2.50e+01 1.29e+00 chirality pdb=" CA PHE A 668 " pdb=" N PHE A 668 " pdb=" C PHE A 668 " pdb=" CB PHE A 668 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 1.00e+00 chirality pdb=" CA MET A1734 " pdb=" N MET A1734 " pdb=" C MET A1734 " pdb=" CB MET A1734 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 6.89e-01 ... (remaining 1641 not shown) Planarity restraints: 1997 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU A2069 " -0.053 5.00e-02 4.00e+02 8.05e-02 1.04e+01 pdb=" N PRO A2070 " 0.139 5.00e-02 4.00e+02 pdb=" CA PRO A2070 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO A2070 " -0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 269 " -0.025 2.00e-02 2.50e+03 2.29e-02 6.53e+00 pdb=" CG ASN A 269 " 0.028 2.00e-02 2.50e+03 pdb=" OD1 ASN A 269 " -0.002 2.00e-02 2.50e+03 pdb=" ND2 ASN A 269 " 0.024 2.00e-02 2.50e+03 pdb=" C1 NAG A2201 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 548 " 0.012 2.00e-02 2.50e+03 2.44e-02 5.97e+00 pdb=" C ASP A 548 " -0.042 2.00e-02 2.50e+03 pdb=" O ASP A 548 " 0.016 2.00e-02 2.50e+03 pdb=" N ASP A 549 " 0.014 2.00e-02 2.50e+03 ... (remaining 1994 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 124 2.60 - 3.17: 9556 3.17 - 3.75: 16204 3.75 - 4.32: 23600 4.32 - 4.90: 39171 Nonbonded interactions: 88655 Sorted by model distance: nonbonded pdb=" O THR A 31 " pdb=" OG SER A 201 " model vdw 2.022 3.040 nonbonded pdb=" OG SER A1970 " pdb=" O ASN A1972 " model vdw 2.119 3.040 nonbonded pdb=" OH TYR A 453 " pdb=" OH TYR A 455 " model vdw 2.161 3.040 nonbonded pdb=" OE2 GLU A1559 " pdb=" OH TYR A1595 " model vdw 2.166 3.040 nonbonded pdb=" O VAL A 261 " pdb=" OG1 THR A 264 " model vdw 2.192 3.040 ... (remaining 88650 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 1.120 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: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 11.360 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 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 : 0.003 0.037 11451 Z= 0.171 Angle : 0.674 9.986 15530 Z= 0.364 Chirality : 0.047 0.227 1644 Planarity : 0.005 0.080 1993 Dihedral : 14.280 89.364 4223 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.04 % Favored : 89.96 % Rotamer: Outliers : 0.25 % Allowed : 0.74 % Favored : 99.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.35 (0.22), residues: 1364 helix: -2.67 (0.60), residues: 56 sheet: -0.44 (0.29), residues: 361 loop : -2.10 (0.19), residues: 947 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 39 TYR 0.032 0.001 TYR A1510 PHE 0.016 0.001 PHE A 462 TRP 0.012 0.001 TRP A1754 HIS 0.007 0.001 HIS A2128 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.17 (11440) covalent geometry : angle 0.66798 / 0.36 (15504) SS BOND : bond 0.00141 / 0.10 ( 7) SS BOND : angle 0.98673 / 0.62 ( 14) hydrogen bonds : bond 0.25407 / 16.72 ( 212) hydrogen bonds : angle 10.47978 / 7.16 ( 546) link_NAG-ASN : bond 0.00389 / 0.19 ( 4) link_NAG-ASN : angle 3.11637 / 2.06 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 166 time to evaluate : 0.385 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 203 MET cc_start: 0.6404 (pmm) cc_final: 0.5854 (ptp) REVERT: A 279 ILE cc_start: 0.8823 (tt) cc_final: 0.8368 (tt) REVERT: A 288 LEU cc_start: 0.8146 (tp) cc_final: 0.7940 (tp) REVERT: A 577 ASP cc_start: 0.7509 (t70) cc_final: 0.7127 (t0) REVERT: A 1734 MET cc_start: 0.8512 (OUTLIER) cc_final: 0.8211 (mtt) outliers start: 3 outliers final: 1 residues processed: 167 average time/residue: 0.1025 time to fit residues: 24.6315 Evaluate side-chains 136 residues out of total 1223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 134 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1733 ASN Chi-restraints excluded: chain A residue 1734 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 0.0570 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 0.9990 chunk 55 optimal weight: 6.9990 overall best weight: 1.6104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 5 GLN A 73 HIS ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 351 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 379 HIS A 526 ASN ** A 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1817 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1940 GLN A1951 GLN ** A2111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.155780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.123704 restraints weight = 16514.889| |-----------------------------------------------------------------------------| r_work (start): 0.3709 rms_B_bonded: 2.78 r_work: 0.3543 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3543 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.1286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 11451 Z= 0.230 Angle : 0.710 10.606 15530 Z= 0.370 Chirality : 0.049 0.302 1644 Planarity : 0.005 0.057 1993 Dihedral : 6.123 56.574 1505 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.90 % Favored : 90.10 % Rotamer: Outliers : 1.80 % Allowed : 8.67 % Favored : 89.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.49 (0.21), residues: 1364 helix: -2.67 (0.64), residues: 48 sheet: -0.87 (0.26), residues: 396 loop : -2.08 (0.19), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 39 TYR 0.028 0.002 TYR A1510 PHE 0.019 0.002 PHE A1872 TRP 0.016 0.001 TRP A1754 HIS 0.008 0.001 HIS A2128 Details of bonding type rmsd/Z covalent geometry : bond 0.00520 / 0.23 (11440) covalent geometry : angle 0.70630 / 0.37 (15504) SS BOND : bond 0.00342 / 0.24 ( 7) SS BOND : angle 0.88160 / 0.51 ( 14) hydrogen bonds : bond 0.04871 / 3.23 ( 212) hydrogen bonds : angle 7.54479 / 5.16 ( 546) link_NAG-ASN : bond 0.00640 / 0.31 ( 4) link_NAG-ASN : angle 2.77667 / 1.78 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 147 time to evaluate : 0.431 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 TYR cc_start: 0.5886 (OUTLIER) cc_final: 0.5172 (p90) REVERT: A 279 ILE cc_start: 0.8658 (tt) cc_final: 0.8445 (tt) REVERT: A 517 GLN cc_start: 0.6385 (mt0) cc_final: 0.6106 (mm-40) REVERT: A 529 TRP cc_start: 0.5807 (t-100) cc_final: 0.5093 (t-100) REVERT: A 577 ASP cc_start: 0.7793 (t70) cc_final: 0.7366 (t0) outliers start: 22 outliers final: 14 residues processed: 157 average time/residue: 0.0886 time to fit residues: 20.6469 Evaluate side-chains 144 residues out of total 1223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 129 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 TYR Chi-restraints excluded: chain A residue 222 HIS Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 487 ILE Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain A residue 605 TYR Chi-restraints excluded: chain A residue 1548 ASN Chi-restraints excluded: chain A residue 1648 SER Chi-restraints excluded: chain A residue 1733 ASN Chi-restraints excluded: chain A residue 1831 LEU Chi-restraints excluded: chain A residue 1940 GLN Chi-restraints excluded: chain A residue 1986 ASN Chi-restraints excluded: chain A residue 2015 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 74 optimal weight: 0.3980 chunk 80 optimal weight: 2.9990 chunk 29 optimal weight: 0.9980 chunk 61 optimal weight: 0.9990 chunk 48 optimal weight: 0.9990 chunk 103 optimal weight: 3.9990 chunk 104 optimal weight: 0.9980 chunk 36 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 chunk 57 optimal weight: 2.9990 chunk 111 optimal weight: 0.8980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 351 HIS A 526 ASN ** A 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1817 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1940 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.157287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.126351 restraints weight = 16593.133| |-----------------------------------------------------------------------------| r_work (start): 0.3754 rms_B_bonded: 2.71 r_work: 0.3578 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.1488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11451 Z= 0.150 Angle : 0.650 15.822 15530 Z= 0.333 Chirality : 0.047 0.292 1644 Planarity : 0.004 0.045 1993 Dihedral : 5.732 29.475 1502 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.31 % Favored : 90.69 % Rotamer: Outliers : 2.29 % Allowed : 12.44 % Favored : 85.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.50 (0.21), residues: 1364 helix: -2.79 (0.60), residues: 54 sheet: -0.93 (0.26), residues: 391 loop : -2.04 (0.19), residues: 919 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 39 TYR 0.020 0.001 TYR A1510 PHE 0.014 0.002 PHE A 538 TRP 0.017 0.001 TRP A1665 HIS 0.005 0.001 HIS A2128 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.15 (11440) covalent geometry : angle 0.64664 / 0.33 (15504) SS BOND : bond 0.00366 / 0.20 ( 7) SS BOND : angle 0.69714 / 0.42 ( 14) hydrogen bonds : bond 0.04026 / 2.69 ( 212) hydrogen bonds : angle 7.05711 / 4.83 ( 546) link_NAG-ASN : bond 0.00183 / 0.09 ( 4) link_NAG-ASN : angle 2.37191 / 1.54 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 139 time to evaluate : 0.391 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 TYR cc_start: 0.5829 (OUTLIER) cc_final: 0.5151 (p90) REVERT: A 335 TYR cc_start: 0.7588 (m-80) cc_final: 0.7196 (m-80) REVERT: A 405 ILE cc_start: 0.7890 (mm) cc_final: 0.7622 (mm) REVERT: A 517 GLN cc_start: 0.6517 (mm110) cc_final: 0.6277 (mm-40) REVERT: A 577 ASP cc_start: 0.7744 (t70) cc_final: 0.7304 (t0) REVERT: A 649 LEU cc_start: 0.8062 (tp) cc_final: 0.7635 (tt) REVERT: A 1679 THR cc_start: 0.7454 (OUTLIER) cc_final: 0.6990 (m) REVERT: A 1881 MET cc_start: 0.8143 (mtp) cc_final: 0.7774 (mtp) REVERT: A 1932 LYS cc_start: 0.8337 (tptm) cc_final: 0.8060 (tptp) outliers start: 28 outliers final: 18 residues processed: 156 average time/residue: 0.0849 time to fit residues: 19.8847 Evaluate side-chains 151 residues out of total 1223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 131 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 38 TYR Chi-restraints excluded: chain A residue 135 ASP Chi-restraints excluded: chain A residue 222 HIS Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 487 ILE Chi-restraints excluded: chain A residue 522 VAL Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain A residue 1548 ASN Chi-restraints excluded: chain A residue 1648 SER Chi-restraints excluded: chain A residue 1679 THR Chi-restraints excluded: chain A residue 1831 LEU Chi-restraints excluded: chain A residue 1865 ARG Chi-restraints excluded: chain A residue 1940 GLN Chi-restraints excluded: chain A residue 2005 ASP Chi-restraints excluded: chain A residue 2015 ILE Chi-restraints excluded: chain A residue 2028 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 60 optimal weight: 3.9990 chunk 122 optimal weight: 1.9990 chunk 37 optimal weight: 5.9990 chunk 18 optimal weight: 3.9990 chunk 64 optimal weight: 4.9990 chunk 131 optimal weight: 0.0980 chunk 31 optimal weight: 10.0000 chunk 46 optimal weight: 2.9990 chunk 8 optimal weight: 0.6980 chunk 55 optimal weight: 0.3980 chunk 110 optimal weight: 0.7980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 246 GLN A 526 ASN ** A 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1729 HIS ** A1817 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1940 GLN A2036 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.157900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.127097 restraints weight = 16629.911| |-----------------------------------------------------------------------------| r_work (start): 0.3761 rms_B_bonded: 2.67 r_work: 0.3588 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.1687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 11451 Z= 0.142 Angle : 0.634 18.312 15530 Z= 0.323 Chirality : 0.046 0.286 1644 Planarity : 0.004 0.037 1993 Dihedral : 5.536 26.710 1500 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.60 % Favored : 90.40 % Rotamer: Outliers : 2.86 % Allowed : 14.32 % Favored : 82.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.46 (0.21), residues: 1364 helix: -2.70 (0.61), residues: 54 sheet: -0.99 (0.25), residues: 393 loop : -1.97 (0.19), residues: 917 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 39 TYR 0.020 0.001 TYR A1515 PHE 0.014 0.001 PHE A1872 TRP 0.012 0.001 TRP A1754 HIS 0.005 0.001 HIS A2128 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.14 (11440) covalent geometry : angle 0.63108 / 0.32 (15504) SS BOND : bond 0.00187 / 0.14 ( 7) SS BOND : angle 0.64910 / 0.38 ( 14) hydrogen bonds : bond 0.03548 / 2.36 ( 212) hydrogen bonds : angle 6.73480 / 4.59 ( 546) link_NAG-ASN : bond 0.00196 / 0.10 ( 4) link_NAG-ASN : angle 2.38671 / 1.53 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 143 time to evaluate : 0.409 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 TYR cc_start: 0.5811 (OUTLIER) cc_final: 0.5101 (p90) REVERT: A 335 TYR cc_start: 0.7548 (m-80) cc_final: 0.7128 (m-80) REVERT: A 405 ILE cc_start: 0.7788 (mm) cc_final: 0.7508 (mm) REVERT: A 517 GLN cc_start: 0.6539 (mm110) cc_final: 0.6321 (mm-40) REVERT: A 577 ASP cc_start: 0.7756 (t70) cc_final: 0.7320 (t0) REVERT: A 649 LEU cc_start: 0.8099 (tp) cc_final: 0.7666 (tt) REVERT: A 1679 THR cc_start: 0.7486 (OUTLIER) cc_final: 0.7039 (m) REVERT: A 2061 LYS cc_start: 0.8229 (tptp) cc_final: 0.7973 (tptp) outliers start: 35 outliers final: 20 residues processed: 167 average time/residue: 0.0838 time to fit residues: 21.0569 Evaluate side-chains 153 residues out of total 1223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 131 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 38 TYR Chi-restraints excluded: chain A residue 84 ILE Chi-restraints excluded: chain A residue 222 HIS Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 487 ILE Chi-restraints excluded: chain A residue 522 VAL Chi-restraints excluded: chain A residue 575 CYS Chi-restraints excluded: chain A residue 605 TYR Chi-restraints excluded: chain A residue 635 LEU Chi-restraints excluded: chain A residue 1648 SER Chi-restraints excluded: chain A residue 1679 THR Chi-restraints excluded: chain A residue 1733 ASN Chi-restraints excluded: chain A residue 1831 LEU Chi-restraints excluded: chain A residue 1865 ARG Chi-restraints excluded: chain A residue 1940 GLN Chi-restraints excluded: chain A residue 2005 ASP Chi-restraints excluded: chain A residue 2008 ILE Chi-restraints excluded: chain A residue 2028 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 7 optimal weight: 2.9990 chunk 65 optimal weight: 0.7980 chunk 80 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 127 optimal weight: 2.9990 chunk 53 optimal weight: 10.0000 chunk 135 optimal weight: 6.9990 chunk 44 optimal weight: 9.9990 chunk 124 optimal weight: 5.9990 chunk 18 optimal weight: 3.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1729 HIS A1940 GLN A1951 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.152844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.121767 restraints weight = 16701.791| |-----------------------------------------------------------------------------| r_work (start): 0.3684 rms_B_bonded: 2.69 r_work: 0.3500 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3500 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.2032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.063 11451 Z= 0.288 Angle : 0.766 20.986 15530 Z= 0.389 Chirality : 0.050 0.311 1644 Planarity : 0.005 0.064 1993 Dihedral : 5.953 27.083 1500 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.56 % Favored : 89.44 % Rotamer: Outliers : 3.27 % Allowed : 15.63 % Favored : 81.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.66 (0.21), residues: 1364 helix: -2.78 (0.63), residues: 48 sheet: -1.20 (0.25), residues: 407 loop : -2.09 (0.19), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1799 TYR 0.029 0.002 TYR A1515 PHE 0.022 0.002 PHE A 462 TRP 0.019 0.002 TRP A1754 HIS 0.008 0.002 HIS A2128 Details of bonding type rmsd/Z covalent geometry : bond 0.00661 / 0.29 (11440) covalent geometry : angle 0.76008 / 0.39 (15504) SS BOND : bond 0.00569 / 0.31 ( 7) SS BOND : angle 1.39992 / 0.67 ( 14) hydrogen bonds : bond 0.03937 / 2.58 ( 212) hydrogen bonds : angle 6.97451 / 4.76 ( 546) link_NAG-ASN : bond 0.00685 / 0.34 ( 4) link_NAG-ASN : angle 3.25222 / 2.10 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 132 time to evaluate : 0.290 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 ILE cc_start: 0.8596 (OUTLIER) cc_final: 0.8384 (mt) REVERT: A 335 TYR cc_start: 0.7852 (m-80) cc_final: 0.7624 (m-80) REVERT: A 385 MET cc_start: 0.6968 (ptm) cc_final: 0.6626 (ptm) REVERT: A 407 PHE cc_start: 0.7868 (OUTLIER) cc_final: 0.7607 (t80) REVERT: A 577 ASP cc_start: 0.7770 (t70) cc_final: 0.7356 (t0) REVERT: A 603 PHE cc_start: 0.8545 (OUTLIER) cc_final: 0.8109 (m-80) REVERT: A 649 LEU cc_start: 0.8296 (tp) cc_final: 0.7847 (tt) REVERT: A 1881 MET cc_start: 0.8234 (mtp) cc_final: 0.7905 (mtp) REVERT: A 2061 LYS cc_start: 0.8261 (tptp) cc_final: 0.7963 (tptp) outliers start: 40 outliers final: 30 residues processed: 163 average time/residue: 0.0858 time to fit residues: 21.1182 Evaluate side-chains 159 residues out of total 1223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 126 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 38 TYR Chi-restraints excluded: chain A residue 84 ILE Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 407 PHE Chi-restraints excluded: chain A residue 487 ILE Chi-restraints excluded: chain A residue 522 VAL Chi-restraints excluded: chain A residue 575 CYS Chi-restraints excluded: chain A residue 603 PHE Chi-restraints excluded: chain A residue 605 TYR Chi-restraints excluded: chain A residue 635 LEU Chi-restraints excluded: chain A residue 1548 ASN Chi-restraints excluded: chain A residue 1630 VAL Chi-restraints excluded: chain A residue 1648 SER Chi-restraints excluded: chain A residue 1679 THR Chi-restraints excluded: chain A residue 1733 ASN Chi-restraints excluded: chain A residue 1736 MET Chi-restraints excluded: chain A residue 1831 LEU Chi-restraints excluded: chain A residue 1837 LEU Chi-restraints excluded: chain A residue 1843 THR Chi-restraints excluded: chain A residue 1865 ARG Chi-restraints excluded: chain A residue 1940 GLN Chi-restraints excluded: chain A residue 1955 HIS Chi-restraints excluded: chain A residue 1986 ASN Chi-restraints excluded: chain A residue 2008 ILE Chi-restraints excluded: chain A residue 2015 ILE Chi-restraints excluded: chain A residue 2028 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 45 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 chunk 40 optimal weight: 0.6980 chunk 22 optimal weight: 1.9990 chunk 83 optimal weight: 0.9980 chunk 102 optimal weight: 0.7980 chunk 13 optimal weight: 0.8980 chunk 44 optimal weight: 6.9990 chunk 92 optimal weight: 2.9990 chunk 130 optimal weight: 0.9980 chunk 84 optimal weight: 1.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1729 HIS A1940 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.155243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.123839 restraints weight = 16769.446| |-----------------------------------------------------------------------------| r_work (start): 0.3724 rms_B_bonded: 2.78 r_work: 0.3550 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.2072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 11451 Z= 0.152 Angle : 0.696 25.046 15530 Z= 0.345 Chirality : 0.047 0.291 1644 Planarity : 0.004 0.050 1993 Dihedral : 5.687 25.933 1500 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.38 % Favored : 90.62 % Rotamer: Outliers : 2.70 % Allowed : 17.51 % Favored : 79.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.63 (0.21), residues: 1364 helix: -2.94 (0.58), residues: 54 sheet: -1.16 (0.25), residues: 404 loop : -2.05 (0.19), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 608 TYR 0.021 0.001 TYR A1515 PHE 0.014 0.001 PHE A1872 TRP 0.013 0.001 TRP A1754 HIS 0.005 0.001 HIS A2128 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.15 (11440) covalent geometry : angle 0.68635 / 0.34 (15504) SS BOND : bond 0.01003 / 0.34 ( 7) SS BOND : angle 3.15368 / 1.51 ( 14) hydrogen bonds : bond 0.03231 / 2.09 ( 212) hydrogen bonds : angle 6.68692 / 4.57 ( 546) link_NAG-ASN : bond 0.00193 / 0.10 ( 4) link_NAG-ASN : angle 2.55997 / 1.67 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 131 time to evaluate : 0.487 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 TYR cc_start: 0.6331 (OUTLIER) cc_final: 0.5182 (p90) REVERT: A 89 ILE cc_start: 0.8561 (OUTLIER) cc_final: 0.8352 (mt) REVERT: A 335 TYR cc_start: 0.7766 (m-80) cc_final: 0.7414 (m-80) REVERT: A 385 MET cc_start: 0.6765 (ptm) cc_final: 0.6397 (ptm) REVERT: A 517 GLN cc_start: 0.6881 (mm-40) cc_final: 0.6276 (mm110) REVERT: A 577 ASP cc_start: 0.7724 (t70) cc_final: 0.7284 (t0) REVERT: A 603 PHE cc_start: 0.8387 (OUTLIER) cc_final: 0.7985 (m-10) REVERT: A 649 LEU cc_start: 0.8150 (tp) cc_final: 0.7713 (tt) REVERT: A 1679 THR cc_start: 0.7647 (OUTLIER) cc_final: 0.7241 (m) REVERT: A 1881 MET cc_start: 0.8172 (mtp) cc_final: 0.7823 (mtp) REVERT: A 2069 GLU cc_start: 0.8003 (mm-30) cc_final: 0.7702 (mm-30) REVERT: A 2174 ARG cc_start: 0.6994 (ttm170) cc_final: 0.6714 (ttm170) outliers start: 33 outliers final: 23 residues processed: 155 average time/residue: 0.0904 time to fit residues: 21.0691 Evaluate side-chains 156 residues out of total 1223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 129 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 38 TYR Chi-restraints excluded: chain A residue 84 ILE Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 487 ILE Chi-restraints excluded: chain A residue 522 VAL Chi-restraints excluded: chain A residue 575 CYS Chi-restraints excluded: chain A residue 603 PHE Chi-restraints excluded: chain A residue 605 TYR Chi-restraints excluded: chain A residue 635 LEU Chi-restraints excluded: chain A residue 1648 SER Chi-restraints excluded: chain A residue 1679 THR Chi-restraints excluded: chain A residue 1733 ASN Chi-restraints excluded: chain A residue 1831 LEU Chi-restraints excluded: chain A residue 1841 PHE Chi-restraints excluded: chain A residue 1843 THR Chi-restraints excluded: chain A residue 1865 ARG Chi-restraints excluded: chain A residue 1955 HIS Chi-restraints excluded: chain A residue 2008 ILE Chi-restraints excluded: chain A residue 2015 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 121 optimal weight: 0.3980 chunk 80 optimal weight: 2.9990 chunk 36 optimal weight: 5.9990 chunk 104 optimal weight: 1.9990 chunk 130 optimal weight: 0.9990 chunk 59 optimal weight: 3.9990 chunk 132 optimal weight: 0.0770 chunk 93 optimal weight: 0.0470 chunk 91 optimal weight: 1.9990 chunk 111 optimal weight: 2.9990 chunk 72 optimal weight: 0.9990 overall best weight: 0.5040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 471 GLN ** A 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 591 ASN A1729 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.157738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.126305 restraints weight = 16498.817| |-----------------------------------------------------------------------------| r_work (start): 0.3758 rms_B_bonded: 2.71 r_work: 0.3589 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.2184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 11451 Z= 0.122 Angle : 0.655 25.360 15530 Z= 0.322 Chirality : 0.046 0.211 1644 Planarity : 0.004 0.049 1993 Dihedral : 5.365 24.945 1500 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.38 % Favored : 90.62 % Rotamer: Outliers : 2.86 % Allowed : 18.41 % Favored : 78.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.52 (0.21), residues: 1364 helix: -2.72 (0.61), residues: 54 sheet: -1.01 (0.25), residues: 405 loop : -2.03 (0.19), residues: 905 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 39 TYR 0.015 0.001 TYR A1515 PHE 0.013 0.001 PHE A1872 TRP 0.012 0.001 TRP A1754 HIS 0.004 0.001 HIS A 362 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.12 (11440) covalent geometry : angle 0.64754 / 0.32 (15504) SS BOND : bond 0.00883 / 0.29 ( 7) SS BOND : angle 2.46789 / 1.20 ( 14) hydrogen bonds : bond 0.02920 / 1.89 ( 212) hydrogen bonds : angle 6.33869 / 4.31 ( 546) link_NAG-ASN : bond 0.00382 / 0.18 ( 4) link_NAG-ASN : angle 2.36433 / 1.55 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 136 time to evaluate : 0.446 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 TYR cc_start: 0.6018 (OUTLIER) cc_final: 0.5224 (p90) REVERT: A 329 GLU cc_start: 0.7833 (tt0) cc_final: 0.7496 (tt0) REVERT: A 335 TYR cc_start: 0.7737 (m-80) cc_final: 0.7470 (m-80) REVERT: A 577 ASP cc_start: 0.7658 (t70) cc_final: 0.7257 (t0) REVERT: A 649 LEU cc_start: 0.8106 (tp) cc_final: 0.7708 (tt) REVERT: A 1679 THR cc_start: 0.7732 (OUTLIER) cc_final: 0.7345 (m) REVERT: A 1691 GLU cc_start: 0.7059 (mp0) cc_final: 0.6839 (mp0) REVERT: A 1709 GLU cc_start: 0.8118 (mm-30) cc_final: 0.7864 (mm-30) REVERT: A 2061 LYS cc_start: 0.8884 (tmtt) cc_final: 0.8573 (tppt) REVERT: A 2069 GLU cc_start: 0.7911 (mm-30) cc_final: 0.7653 (mm-30) REVERT: A 2174 ARG cc_start: 0.6960 (ttm170) cc_final: 0.6720 (ttm170) outliers start: 35 outliers final: 21 residues processed: 162 average time/residue: 0.0939 time to fit residues: 22.7801 Evaluate side-chains 150 residues out of total 1223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 127 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 38 TYR Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain A residue 487 ILE Chi-restraints excluded: chain A residue 522 VAL Chi-restraints excluded: chain A residue 575 CYS Chi-restraints excluded: chain A residue 605 TYR Chi-restraints excluded: chain A residue 1630 VAL Chi-restraints excluded: chain A residue 1648 SER Chi-restraints excluded: chain A residue 1679 THR Chi-restraints excluded: chain A residue 1733 ASN Chi-restraints excluded: chain A residue 1831 LEU Chi-restraints excluded: chain A residue 1841 PHE Chi-restraints excluded: chain A residue 1843 THR Chi-restraints excluded: chain A residue 1865 ARG Chi-restraints excluded: chain A residue 1955 HIS Chi-restraints excluded: chain A residue 2008 ILE Chi-restraints excluded: chain A residue 2015 ILE Chi-restraints excluded: chain A residue 2028 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 0 optimal weight: 2.9990 chunk 111 optimal weight: 3.9990 chunk 64 optimal weight: 5.9990 chunk 56 optimal weight: 0.0170 chunk 8 optimal weight: 0.3980 chunk 32 optimal weight: 3.9990 chunk 65 optimal weight: 0.6980 chunk 26 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 133 optimal weight: 0.5980 chunk 22 optimal weight: 0.9980 overall best weight: 0.5418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1729 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.158089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.127803 restraints weight = 16534.977| |-----------------------------------------------------------------------------| r_work (start): 0.3774 rms_B_bonded: 2.70 r_work: 0.3604 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.2269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 11451 Z= 0.121 Angle : 0.640 22.157 15530 Z= 0.318 Chirality : 0.046 0.253 1644 Planarity : 0.004 0.050 1993 Dihedral : 5.262 24.817 1500 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.09 % Favored : 90.91 % Rotamer: Outliers : 2.21 % Allowed : 19.07 % Favored : 78.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.46 (0.21), residues: 1364 helix: -2.73 (0.62), residues: 54 sheet: -0.94 (0.25), residues: 401 loop : -2.00 (0.19), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 608 TYR 0.015 0.001 TYR A1515 PHE 0.013 0.001 PHE A1872 TRP 0.012 0.001 TRP A1754 HIS 0.004 0.001 HIS A2128 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 (11440) covalent geometry : angle 0.63360 / 0.32 (15504) SS BOND : bond 0.00856 / 0.29 ( 7) SS BOND : angle 2.28819 / 1.13 ( 14) hydrogen bonds : bond 0.02870 / 1.85 ( 212) hydrogen bonds : angle 6.24198 / 4.23 ( 546) link_NAG-ASN : bond 0.00113 / 0.05 ( 4) link_NAG-ASN : angle 2.25114 / 1.47 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 136 time to evaluate : 0.416 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 SER cc_start: 0.7232 (t) cc_final: 0.6995 (t) REVERT: A 38 TYR cc_start: 0.5906 (OUTLIER) cc_final: 0.5193 (p90) REVERT: A 329 GLU cc_start: 0.7788 (tt0) cc_final: 0.7439 (tt0) REVERT: A 335 TYR cc_start: 0.7730 (m-80) cc_final: 0.7479 (m-80) REVERT: A 407 PHE cc_start: 0.8114 (t80) cc_final: 0.7867 (t80) REVERT: A 577 ASP cc_start: 0.7653 (t70) cc_final: 0.7247 (t0) REVERT: A 649 LEU cc_start: 0.8033 (tp) cc_final: 0.7620 (tt) REVERT: A 1679 THR cc_start: 0.7752 (OUTLIER) cc_final: 0.7352 (m) REVERT: A 1932 LYS cc_start: 0.8327 (tptm) cc_final: 0.8050 (tptp) REVERT: A 2061 LYS cc_start: 0.8880 (tmtt) cc_final: 0.8558 (tppt) REVERT: A 2069 GLU cc_start: 0.7891 (mm-30) cc_final: 0.7532 (mm-30) REVERT: A 2174 ARG cc_start: 0.6887 (ttm170) cc_final: 0.6640 (ttm170) outliers start: 27 outliers final: 25 residues processed: 159 average time/residue: 0.0921 time to fit residues: 22.3281 Evaluate side-chains 160 residues out of total 1223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 133 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 38 TYR Chi-restraints excluded: chain A residue 84 ILE Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 296 ILE Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain A residue 459 ILE Chi-restraints excluded: chain A residue 522 VAL Chi-restraints excluded: chain A residue 575 CYS Chi-restraints excluded: chain A residue 605 TYR Chi-restraints excluded: chain A residue 635 LEU Chi-restraints excluded: chain A residue 1630 VAL Chi-restraints excluded: chain A residue 1648 SER Chi-restraints excluded: chain A residue 1679 THR Chi-restraints excluded: chain A residue 1733 ASN Chi-restraints excluded: chain A residue 1831 LEU Chi-restraints excluded: chain A residue 1841 PHE Chi-restraints excluded: chain A residue 1843 THR Chi-restraints excluded: chain A residue 1865 ARG Chi-restraints excluded: chain A residue 1955 HIS Chi-restraints excluded: chain A residue 2008 ILE Chi-restraints excluded: chain A residue 2015 ILE Chi-restraints excluded: chain A residue 2028 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 31 optimal weight: 9.9990 chunk 74 optimal weight: 1.9990 chunk 66 optimal weight: 20.0000 chunk 2 optimal weight: 7.9990 chunk 37 optimal weight: 4.9990 chunk 65 optimal weight: 1.9990 chunk 105 optimal weight: 2.9990 chunk 69 optimal weight: 3.9990 chunk 54 optimal weight: 9.9990 chunk 126 optimal weight: 5.9990 chunk 115 optimal weight: 1.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 398 GLN ** A 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1729 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.150908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.120130 restraints weight = 16748.846| |-----------------------------------------------------------------------------| r_work (start): 0.3661 rms_B_bonded: 2.79 r_work: 0.3465 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.2501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.066 11451 Z= 0.331 Angle : 0.801 21.704 15530 Z= 0.406 Chirality : 0.051 0.347 1644 Planarity : 0.005 0.072 1993 Dihedral : 5.985 26.344 1500 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.78 % Favored : 89.22 % Rotamer: Outliers : 2.54 % Allowed : 19.07 % Favored : 78.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.73 (0.21), residues: 1364 helix: -2.89 (0.63), residues: 48 sheet: -1.25 (0.25), residues: 406 loop : -2.13 (0.19), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A1593 TYR 0.034 0.002 TYR A1515 PHE 0.025 0.002 PHE A 462 TRP 0.016 0.002 TRP A1754 HIS 0.008 0.002 HIS A2128 Details of bonding type rmsd/Z covalent geometry : bond 0.00758 / 0.33 (11440) covalent geometry : angle 0.79243 / 0.40 (15504) SS BOND : bond 0.00852 / 0.33 ( 7) SS BOND : angle 2.47539 / 1.18 ( 14) hydrogen bonds : bond 0.03889 / 2.51 ( 212) hydrogen bonds : angle 6.92575 / 4.72 ( 546) link_NAG-ASN : bond 0.00739 / 0.36 ( 4) link_NAG-ASN : angle 3.39777 / 2.19 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 123 time to evaluate : 0.426 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 335 TYR cc_start: 0.8145 (m-80) cc_final: 0.7842 (m-80) REVERT: A 492 ILE cc_start: 0.8347 (tp) cc_final: 0.8000 (tt) REVERT: A 517 GLN cc_start: 0.7080 (mm-40) cc_final: 0.6616 (mm110) REVERT: A 577 ASP cc_start: 0.7823 (t70) cc_final: 0.7350 (t0) REVERT: A 649 LEU cc_start: 0.8272 (tp) cc_final: 0.7821 (tt) REVERT: A 1932 LYS cc_start: 0.8470 (tptm) cc_final: 0.8225 (tptp) REVERT: A 2061 LYS cc_start: 0.8863 (tmtt) cc_final: 0.8551 (tppt) REVERT: A 2174 ARG cc_start: 0.7086 (ttm170) cc_final: 0.6850 (ttm170) outliers start: 31 outliers final: 26 residues processed: 149 average time/residue: 0.0920 time to fit residues: 20.7676 Evaluate side-chains 147 residues out of total 1223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 121 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 38 TYR Chi-restraints excluded: chain A residue 84 ILE Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 296 ILE Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain A residue 459 ILE Chi-restraints excluded: chain A residue 487 ILE Chi-restraints excluded: chain A residue 522 VAL Chi-restraints excluded: chain A residue 575 CYS Chi-restraints excluded: chain A residue 605 TYR Chi-restraints excluded: chain A residue 1630 VAL Chi-restraints excluded: chain A residue 1648 SER Chi-restraints excluded: chain A residue 1679 THR Chi-restraints excluded: chain A residue 1733 ASN Chi-restraints excluded: chain A residue 1831 LEU Chi-restraints excluded: chain A residue 1841 PHE Chi-restraints excluded: chain A residue 1843 THR Chi-restraints excluded: chain A residue 1955 HIS Chi-restraints excluded: chain A residue 1986 ASN Chi-restraints excluded: chain A residue 2008 ILE Chi-restraints excluded: chain A residue 2015 ILE Chi-restraints excluded: chain A residue 2028 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 14 optimal weight: 0.8980 chunk 45 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 70 optimal weight: 6.9990 chunk 85 optimal weight: 0.9980 chunk 130 optimal weight: 2.9990 chunk 18 optimal weight: 0.8980 chunk 5 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 102 optimal weight: 0.8980 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 534 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 = 0.4103 r_free = 0.4103 target = 0.154718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.124153 restraints weight = 16758.051| |-----------------------------------------------------------------------------| r_work (start): 0.3727 rms_B_bonded: 2.73 r_work: 0.3546 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.2480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 11451 Z= 0.156 Angle : 0.698 24.658 15530 Z= 0.346 Chirality : 0.047 0.261 1644 Planarity : 0.004 0.050 1993 Dihedral : 5.642 25.497 1500 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.09 % Favored : 90.91 % Rotamer: Outliers : 2.37 % Allowed : 19.39 % Favored : 78.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.74 (0.21), residues: 1364 helix: -3.08 (0.57), residues: 54 sheet: -1.22 (0.25), residues: 409 loop : -2.14 (0.19), residues: 901 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 39 TYR 0.022 0.001 TYR A1515 PHE 0.016 0.002 PHE A1872 TRP 0.012 0.001 TRP A1754 HIS 0.007 0.001 HIS A1775 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.16 (11440) covalent geometry : angle 0.68998 / 0.34 (15504) SS BOND : bond 0.00857 / 0.30 ( 7) SS BOND : angle 2.34515 / 1.16 ( 14) hydrogen bonds : bond 0.03110 / 2.01 ( 212) hydrogen bonds : angle 6.61776 / 4.50 ( 546) link_NAG-ASN : bond 0.00385 / 0.19 ( 4) link_NAG-ASN : angle 2.94890 / 1.92 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 127 time to evaluate : 0.392 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 SER cc_start: 0.7243 (t) cc_final: 0.7013 (t) REVERT: A 38 TYR cc_start: 0.6324 (OUTLIER) cc_final: 0.5004 (p90) REVERT: A 335 TYR cc_start: 0.7899 (m-80) cc_final: 0.7652 (m-80) REVERT: A 407 PHE cc_start: 0.8285 (t80) cc_final: 0.7973 (t80) REVERT: A 492 ILE cc_start: 0.8346 (tp) cc_final: 0.8059 (tt) REVERT: A 577 ASP cc_start: 0.7798 (t70) cc_final: 0.7319 (t0) REVERT: A 649 LEU cc_start: 0.8102 (tp) cc_final: 0.7681 (tt) REVERT: A 1679 THR cc_start: 0.7933 (OUTLIER) cc_final: 0.7528 (m) REVERT: A 1932 LYS cc_start: 0.8405 (tptm) cc_final: 0.8137 (tptp) REVERT: A 2061 LYS cc_start: 0.8870 (tmtt) cc_final: 0.8530 (tppt) REVERT: A 2174 ARG cc_start: 0.6966 (ttm170) cc_final: 0.6707 (ttm170) outliers start: 29 outliers final: 26 residues processed: 152 average time/residue: 0.0796 time to fit residues: 18.4782 Evaluate side-chains 153 residues out of total 1223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 125 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 38 TYR Chi-restraints excluded: chain A residue 84 ILE Chi-restraints excluded: chain A residue 91 TYR Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 296 ILE Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain A residue 459 ILE Chi-restraints excluded: chain A residue 487 ILE Chi-restraints excluded: chain A residue 522 VAL Chi-restraints excluded: chain A residue 575 CYS Chi-restraints excluded: chain A residue 605 TYR Chi-restraints excluded: chain A residue 1630 VAL Chi-restraints excluded: chain A residue 1648 SER Chi-restraints excluded: chain A residue 1679 THR Chi-restraints excluded: chain A residue 1733 ASN Chi-restraints excluded: chain A residue 1831 LEU Chi-restraints excluded: chain A residue 1841 PHE Chi-restraints excluded: chain A residue 1843 THR Chi-restraints excluded: chain A residue 1955 HIS Chi-restraints excluded: chain A residue 2008 ILE Chi-restraints excluded: chain A residue 2015 ILE Chi-restraints excluded: chain A residue 2028 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 105 optimal weight: 0.8980 chunk 70 optimal weight: 7.9990 chunk 21 optimal weight: 0.0970 chunk 135 optimal weight: 3.9990 chunk 56 optimal weight: 3.9990 chunk 35 optimal weight: 0.0060 chunk 79 optimal weight: 0.8980 chunk 110 optimal weight: 0.9990 chunk 115 optimal weight: 4.9990 chunk 34 optimal weight: 40.0000 chunk 25 optimal weight: 2.9990 overall best weight: 0.5796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1729 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.156828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.124925 restraints weight = 16625.054| |-----------------------------------------------------------------------------| r_work (start): 0.3728 rms_B_bonded: 2.88 r_work: 0.3569 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.2524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 11451 Z= 0.128 Angle : 0.661 23.421 15530 Z= 0.327 Chirality : 0.047 0.264 1644 Planarity : 0.004 0.048 1993 Dihedral : 5.311 25.948 1500 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.12 % Favored : 89.88 % Rotamer: Outliers : 2.45 % Allowed : 19.31 % Favored : 78.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.54 (0.21), residues: 1364 helix: -2.76 (0.65), residues: 48 sheet: -1.07 (0.25), residues: 406 loop : -2.03 (0.19), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 39 TYR 0.014 0.001 TYR A1515 PHE 0.014 0.001 PHE A1872 TRP 0.013 0.001 TRP A1754 HIS 0.004 0.001 HIS A2128 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 (11440) covalent geometry : angle 0.65458 / 0.33 (15504) SS BOND : bond 0.00727 / 0.24 ( 7) SS BOND : angle 2.20707 / 1.09 ( 14) hydrogen bonds : bond 0.02862 / 1.85 ( 212) hydrogen bonds : angle 6.31840 / 4.28 ( 546) link_NAG-ASN : bond 0.00274 / 0.13 ( 4) link_NAG-ASN : angle 2.36219 / 1.55 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2489.25 seconds wall clock time: 43 minutes 34.34 seconds (2614.34 seconds total)