Starting phenix.real_space_refine on Wed Feb 4 16:08:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9hn5_52307/02_2026/9hn5_52307.cif Found real_map, /net/cci-nas-00/data/ceres_data/9hn5_52307/02_2026/9hn5_52307.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.96 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9hn5_52307/02_2026/9hn5_52307.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9hn5_52307/02_2026/9hn5_52307.map" model { file = "/net/cci-nas-00/data/ceres_data/9hn5_52307/02_2026/9hn5_52307.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9hn5_52307/02_2026/9hn5_52307.cif" } resolution = 2.96 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= -0.019 sd= 0.354 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: 6 Type Number sf(0) Gaussians Zn 1 6.06 5 P 2 5.49 5 S 57 5.16 5 C 7172 2.51 5 N 1972 2.21 5 O 2110 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11314 Number of models: 1 Model: "" Number of chains: 3 Chain: "B" Number of atoms: 283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 283 Classifications: {'peptide': 38} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'TRANS': 37} Chain breaks: 2 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'ASP:plan': 3, 'GLN:plan1': 1, 'HIS:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 26 Chain: "A" Number of atoms: 11030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1480, 11030 Classifications: {'peptide': 1480} Incomplete info: {'truncation_to_alanine': 144} Link IDs: {'PCIS': 2, 'PTRANS': 69, 'TRANS': 1408} Chain breaks: 6 Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 503 Unresolved non-hydrogen angles: 636 Unresolved non-hydrogen dihedrals: 416 Unresolved non-hydrogen chiralities: 46 Planarities with less than four sites: {'GLN:plan1': 15, 'ARG:plan': 11, 'GLU:plan': 9, 'HIS:plan': 4, 'PHE:plan': 5, 'TRP:plan': 1, 'ASP:plan': 6, 'TYR:plan': 5, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 269 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 6098 SG CYS A1146 62.224 80.050 74.912 1.00 30.00 S ATOM 6112 SG CYS A1148 58.656 78.662 74.800 1.00 73.07 S ATOM 6132 SG CYS A1151 61.487 76.767 73.096 1.00 81.59 S Time building chain proxies: 2.64, per 1000 atoms: 0.23 Number of scatterers: 11314 At special positions: 0 Unit cell: (91.1424, 93.8496, 175.968, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 1 29.99 S 57 16.00 P 2 15.00 O 2110 8.00 N 1972 7.00 C 7172 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 637 " - pdb=" SG CYS A 687 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.02 Conformation dependent library (CDL) restraints added in 602.1 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A2201 " pdb="ZN ZN A2201 " - pdb=" ND1 HIS A1142 " pdb="ZN ZN A2201 " - pdb=" SG CYS A1146 " pdb="ZN ZN A2201 " - pdb=" SG CYS A1151 " pdb="ZN ZN A2201 " - pdb=" SG CYS A1148 " Number of angles added : 3 2986 Ramachandran restraints generated. 1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2870 Finding SS restraints... Secondary structure from input PDB file: 71 helices and 2 sheets defined 74.8% alpha, 3.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.45 Creating SS restraints... Processing helix chain 'A' and resid 246 through 263 Processing helix chain 'A' and resid 267 through 282 removed outlier: 3.725A pdb=" N ALA A 271 " --> pdb=" O HIS A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 304 Processing helix chain 'A' and resid 307 through 328 removed outlier: 3.821A pdb=" N VAL A 311 " --> pdb=" O GLY A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 351 removed outlier: 3.738A pdb=" N LEU A 336 " --> pdb=" O PRO A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 380 Processing helix chain 'A' and resid 380 through 386 removed outlier: 3.948A pdb=" N GLY A 384 " --> pdb=" O ASP A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 414 Processing helix chain 'A' and resid 420 through 442 removed outlier: 3.669A pdb=" N THR A 424 " --> pdb=" O LEU A 420 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N ASP A 428 " --> pdb=" O THR A 424 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N SER A 429 " --> pdb=" O GLN A 425 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLU A 442 " --> pdb=" O LEU A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 446 through 470 Processing helix chain 'A' and resid 472 through 490 Proline residue: A 482 - end of helix Processing helix chain 'A' and resid 499 through 517 removed outlier: 3.814A pdb=" N CYS A 506 " --> pdb=" O LYS A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 534 Processing helix chain 'A' and resid 538 through 559 removed outlier: 3.949A pdb=" N MET A 542 " --> pdb=" O SER A 538 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N GLU A 544 " --> pdb=" O GLU A 540 " (cutoff:3.500A) Proline residue: A 545 - end of helix Processing helix chain 'A' and resid 562 through 567 removed outlier: 3.689A pdb=" N LYS A 567 " --> pdb=" O GLU A 563 " (cutoff:3.500A) Processing helix chain 'A' and resid 577 through 595 removed outlier: 3.561A pdb=" N VAL A 595 " --> pdb=" O ALA A 591 " (cutoff:3.500A) Processing helix chain 'A' and resid 599 through 614 Processing helix chain 'A' and resid 618 through 639 Processing helix chain 'A' and resid 641 through 646 Processing helix chain 'A' and resid 648 through 662 removed outlier: 3.574A pdb=" N SER A 662 " --> pdb=" O GLN A 658 " (cutoff:3.500A) Processing helix chain 'A' and resid 669 through 703 Processing helix chain 'A' and resid 729 through 734 removed outlier: 3.712A pdb=" N ILE A 733 " --> pdb=" O LEU A 729 " (cutoff:3.500A) Processing helix chain 'A' and resid 736 through 760 removed outlier: 3.918A pdb=" N LEU A 747 " --> pdb=" O GLN A 743 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N LYS A 760 " --> pdb=" O GLU A 756 " (cutoff:3.500A) Processing helix chain 'A' and resid 768 through 786 removed outlier: 3.505A pdb=" N THR A 772 " --> pdb=" O CYS A 768 " (cutoff:3.500A) Processing helix chain 'A' and resid 788 through 807 removed outlier: 3.502A pdb=" N ALA A 792 " --> pdb=" O LYS A 788 " (cutoff:3.500A) Processing helix chain 'A' and resid 808 through 827 Processing helix chain 'A' and resid 828 through 844 removed outlier: 3.572A pdb=" N ALA A 832 " --> pdb=" O CYS A 828 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LYS A 844 " --> pdb=" O ALA A 840 " (cutoff:3.500A) Processing helix chain 'A' and resid 850 through 871 Processing helix chain 'A' and resid 873 through 887 Processing helix chain 'A' and resid 888 through 892 removed outlier: 3.605A pdb=" N GLN A 891 " --> pdb=" O PRO A 888 " (cutoff:3.500A) Processing helix chain 'A' and resid 894 through 913 Processing helix chain 'A' and resid 915 through 919 removed outlier: 3.531A pdb=" N LEU A 919 " --> pdb=" O SER A 916 " (cutoff:3.500A) Processing helix chain 'A' and resid 920 through 929 Processing helix chain 'A' and resid 934 through 954 Processing helix chain 'A' and resid 955 through 959 removed outlier: 4.062A pdb=" N ILE A 958 " --> pdb=" O GLY A 955 " (cutoff:3.500A) Processing helix chain 'A' and resid 974 through 1002 removed outlier: 3.776A pdb=" N TRP A 981 " --> pdb=" O LEU A 977 " (cutoff:3.500A) Processing helix chain 'A' and resid 1003 through 1022 Processing helix chain 'A' and resid 1023 through 1041 Processing helix chain 'A' and resid 1043 through 1062 Processing helix chain 'A' and resid 1138 through 1142 removed outlier: 3.666A pdb=" N HIS A1142 " --> pdb=" O PHE A1139 " (cutoff:3.500A) Processing helix chain 'A' and resid 1148 through 1153 Processing helix chain 'A' and resid 1153 through 1174 Processing helix chain 'A' and resid 1176 through 1207 Proline residue: A1192 - end of helix Processing helix chain 'A' and resid 1219 through 1237 Processing helix chain 'A' and resid 1242 through 1257 removed outlier: 3.883A pdb=" N GLN A1248 " --> pdb=" O GLN A1244 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ARG A1257 " --> pdb=" O PHE A1253 " (cutoff:3.500A) Processing helix chain 'A' and resid 1261 through 1278 Processing helix chain 'A' and resid 1286 through 1292 removed outlier: 3.737A pdb=" N SER A1290 " --> pdb=" O LEU A1287 " (cutoff:3.500A) Processing helix chain 'A' and resid 1572 through 1589 Processing helix chain 'A' and resid 1593 through 1609 Processing helix chain 'A' and resid 1612 through 1623 removed outlier: 3.514A pdb=" N SER A1623 " --> pdb=" O LEU A1619 " (cutoff:3.500A) Processing helix chain 'A' and resid 1625 through 1646 Processing helix chain 'A' and resid 1668 through 1678 Processing helix chain 'A' and resid 1688 through 1700 Processing helix chain 'A' and resid 1749 through 1768 removed outlier: 3.507A pdb=" N SER A1768 " --> pdb=" O GLN A1764 " (cutoff:3.500A) Processing helix chain 'A' and resid 1772 through 1798 Processing helix chain 'A' and resid 1799 through 1807 removed outlier: 3.538A pdb=" N TRP A1802 " --> pdb=" O LEU A1799 " (cutoff:3.500A) Processing helix chain 'A' and resid 1813 through 1830 removed outlier: 4.267A pdb=" N GLU A1824 " --> pdb=" O SER A1820 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N LEU A1825 " --> pdb=" O ARG A1821 " (cutoff:3.500A) Processing helix chain 'A' and resid 1835 through 1845 removed outlier: 3.765A pdb=" N GLY A1845 " --> pdb=" O ILE A1841 " (cutoff:3.500A) Processing helix chain 'A' and resid 1846 through 1849 Processing helix chain 'A' and resid 1850 through 1862 Processing helix chain 'A' and resid 1865 through 1880 removed outlier: 3.607A pdb=" N ALA A1869 " --> pdb=" O GLN A1865 " (cutoff:3.500A) Processing helix chain 'A' and resid 1903 through 1911 Proline residue: A1908 - end of helix removed outlier: 3.694A pdb=" N GLN A1911 " --> pdb=" O PRO A1908 " (cutoff:3.500A) Processing helix chain 'A' and resid 1920 through 1933 removed outlier: 3.637A pdb=" N LEU A1924 " --> pdb=" O SER A1920 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N TYR A1933 " --> pdb=" O ILE A1929 " (cutoff:3.500A) Processing helix chain 'A' and resid 1936 through 1941 Processing helix chain 'A' and resid 1958 through 1971 removed outlier: 4.781A pdb=" N ALA A1967 " --> pdb=" O GLU A1963 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N ASN A1968 " --> pdb=" O GLN A1964 " (cutoff:3.500A) Processing helix chain 'A' and resid 1984 through 1995 Processing helix chain 'A' and resid 2011 through 2017 Processing helix chain 'A' and resid 2044 through 2052 removed outlier: 3.829A pdb=" N LYS A2048 " --> pdb=" O GLY A2044 " (cutoff:3.500A) Processing helix chain 'A' and resid 2065 through 2084 removed outlier: 4.219A pdb=" N GLY A2084 " --> pdb=" O TRP A2080 " (cutoff:3.500A) Processing helix chain 'A' and resid 2088 through 2096 removed outlier: 3.890A pdb=" N TYR A2092 " --> pdb=" O PRO A2088 " (cutoff:3.500A) Processing helix chain 'A' and resid 2097 through 2099 No H-bonds generated for 'chain 'A' and resid 2097 through 2099' Processing sheet with id=AA1, first strand: chain 'A' and resid 1737 through 1742 removed outlier: 4.237A pdb=" N THR A1724 " --> pdb=" O ALA A1714 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 1975 through 1979 removed outlier: 6.372A pdb=" N PHE A1949 " --> pdb=" O ILE A1999 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N ALA A2001 " --> pdb=" O PHE A1949 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N VAL A1951 " --> pdb=" O ALA A2001 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N TYR A1998 " --> pdb=" O LEU A2025 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N ALA A2024 " --> pdb=" O LEU A2058 " (cutoff:3.500A) removed outlier: 8.473A pdb=" N ASN A2060 " --> pdb=" O ALA A2024 " (cutoff:3.500A) removed outlier: 9.315A pdb=" N LEU A2026 " --> pdb=" O ASN A2060 " (cutoff:3.500A) 832 hydrogen bonds defined for protein. 2448 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: 2.19 Time building geometry restraints manager: 1.29 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: 3768 1.34 - 1.46: 1839 1.46 - 1.58: 5838 1.58 - 1.69: 2 1.69 - 1.81: 75 Bond restraints: 11522 Sorted by residual: bond pdb=" O3P SEP B 175 " pdb=" P SEP B 175 " ideal model delta sigma weight residual 1.610 1.515 0.095 2.00e-02 2.50e+03 2.26e+01 bond pdb=" O1P SEP B 175 " pdb=" P SEP B 175 " ideal model delta sigma weight residual 1.610 1.515 0.095 2.00e-02 2.50e+03 2.24e+01 bond pdb=" O2P SEP B 175 " pdb=" P SEP B 175 " ideal model delta sigma weight residual 1.610 1.516 0.094 2.00e-02 2.50e+03 2.23e+01 bond pdb=" O2P SEP B 185 " pdb=" P SEP B 185 " ideal model delta sigma weight residual 1.610 1.517 0.093 2.00e-02 2.50e+03 2.17e+01 bond pdb=" O3P SEP B 185 " pdb=" P SEP B 185 " ideal model delta sigma weight residual 1.610 1.517 0.093 2.00e-02 2.50e+03 2.16e+01 ... (remaining 11517 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.70: 14648 1.70 - 3.41: 903 3.41 - 5.11: 124 5.11 - 6.81: 12 6.81 - 8.51: 3 Bond angle restraints: 15690 Sorted by residual: angle pdb=" CA ASP A 851 " pdb=" CB ASP A 851 " pdb=" CG ASP A 851 " ideal model delta sigma weight residual 112.60 117.18 -4.58 1.00e+00 1.00e+00 2.10e+01 angle pdb=" CA ASP A 577 " pdb=" CB ASP A 577 " pdb=" CG ASP A 577 " ideal model delta sigma weight residual 112.60 117.08 -4.48 1.00e+00 1.00e+00 2.00e+01 angle pdb=" N LEU A 769 " pdb=" CA LEU A 769 " pdb=" C LEU A 769 " ideal model delta sigma weight residual 112.89 107.52 5.37 1.24e+00 6.50e-01 1.87e+01 angle pdb=" N PRO A1863 " pdb=" CA PRO A1863 " pdb=" CB PRO A1863 " ideal model delta sigma weight residual 101.88 97.69 4.19 1.01e+00 9.80e-01 1.72e+01 angle pdb=" N PRO A1866 " pdb=" CA PRO A1866 " pdb=" C PRO A1866 " ideal model delta sigma weight residual 113.57 118.82 -5.25 1.31e+00 5.83e-01 1.60e+01 ... (remaining 15685 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.48: 6129 14.48 - 28.97: 533 28.97 - 43.45: 193 43.45 - 57.94: 80 57.94 - 72.42: 27 Dihedral angle restraints: 6962 sinusoidal: 2548 harmonic: 4414 Sorted by residual: dihedral pdb=" CB CYS A 637 " pdb=" SG CYS A 637 " pdb=" SG CYS A 687 " pdb=" CB CYS A 687 " ideal model delta sinusoidal sigma weight residual -86.00 -146.22 60.22 1 1.00e+01 1.00e-02 4.83e+01 dihedral pdb=" CA PRO A1592 " pdb=" C PRO A1592 " pdb=" N PRO A1593 " pdb=" CA PRO A1593 " ideal model delta harmonic sigma weight residual 180.00 162.62 17.38 0 5.00e+00 4.00e-02 1.21e+01 dihedral pdb=" CB MET A1907 " pdb=" CG MET A1907 " pdb=" SD MET A1907 " pdb=" CE MET A1907 " ideal model delta sinusoidal sigma weight residual 60.00 1.71 58.29 3 1.50e+01 4.44e-03 9.46e+00 ... (remaining 6959 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 1369 0.043 - 0.087: 319 0.087 - 0.130: 122 0.130 - 0.173: 33 0.173 - 0.217: 14 Chirality restraints: 1857 Sorted by residual: chirality pdb=" CA CYS A 477 " pdb=" N CYS A 477 " pdb=" C CYS A 477 " pdb=" CB CYS A 477 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.17e+00 chirality pdb=" CA VAL A 552 " pdb=" N VAL A 552 " pdb=" C VAL A 552 " pdb=" CB VAL A 552 " both_signs ideal model delta sigma weight residual False 2.44 2.65 -0.21 2.00e-01 2.50e+01 1.09e+00 chirality pdb=" CA VAL A 435 " pdb=" N VAL A 435 " pdb=" C VAL A 435 " pdb=" CB VAL A 435 " both_signs ideal model delta sigma weight residual False 2.44 2.64 -0.20 2.00e-01 2.50e+01 1.03e+00 ... (remaining 1854 not shown) Planarity restraints: 2010 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A2008 " -0.264 9.50e-02 1.11e+02 1.18e-01 8.63e+00 pdb=" NE ARG A2008 " 0.017 2.00e-02 2.50e+03 pdb=" CZ ARG A2008 " -0.000 2.00e-02 2.50e+03 pdb=" NH1 ARG A2008 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG A2008 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 800 " 0.264 9.50e-02 1.11e+02 1.18e-01 8.59e+00 pdb=" NE ARG A 800 " -0.016 2.00e-02 2.50e+03 pdb=" CZ ARG A 800 " -0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG A 800 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A 800 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A1136 " -0.047 5.00e-02 4.00e+02 7.13e-02 8.14e+00 pdb=" N PRO A1137 " 0.123 5.00e-02 4.00e+02 pdb=" CA PRO A1137 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO A1137 " -0.039 5.00e-02 4.00e+02 ... (remaining 2007 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 283 2.71 - 3.26: 11508 3.26 - 3.81: 18558 3.81 - 4.35: 23141 4.35 - 4.90: 38724 Nonbonded interactions: 92214 Sorted by model distance: nonbonded pdb=" O MET A 455 " pdb=" OG SER A 458 " model vdw 2.167 3.040 nonbonded pdb=" O GLU A 448 " pdb=" ND1 HIS A 452 " model vdw 2.170 3.120 nonbonded pdb=" OH TYR A1927 " pdb=" O CYS A2054 " model vdw 2.304 3.040 nonbonded pdb=" OE1 GLU A1795 " pdb=" OG SER A1909 " model vdw 2.308 3.040 nonbonded pdb=" NH1 ARG A 947 " pdb=" OE2 GLU A1013 " model vdw 2.346 3.120 ... (remaining 92209 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 ========== 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: 5.750 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: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 13.650 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.095 11527 Z= 0.432 Angle : 0.848 8.513 15695 Z= 0.581 Chirality : 0.049 0.217 1857 Planarity : 0.008 0.118 2010 Dihedral : 14.626 72.422 4089 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.32 % Allowed : 15.44 % Favored : 83.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % 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: 1.90 (0.21), residues: 1493 helix: 1.98 (0.16), residues: 1035 sheet: 1.80 (0.76), residues: 48 loop : -0.66 (0.30), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 168 TYR 0.039 0.002 TYR A 459 PHE 0.023 0.002 PHE A1921 TRP 0.029 0.002 TRP A1777 HIS 0.007 0.001 HIS A1635 Details of bonding type rmsd covalent geometry : bond 0.00651 (11522) covalent geometry : angle 0.84800 (15690) SS BOND : bond 0.00732 ( 1) SS BOND : angle 0.55151 ( 2) hydrogen bonds : bond 0.14156 ( 832) hydrogen bonds : angle 5.16096 ( 2448) metal coordination : bond 0.00456 ( 4) metal coordination : angle 1.08828 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2986 Ramachandran restraints generated. 1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2986 Ramachandran restraints generated. 1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1291 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 148 time to evaluate : 0.456 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1976 ARG cc_start: 0.8344 (ttp-110) cc_final: 0.8117 (mtp85) outliers start: 15 outliers final: 10 residues processed: 162 average time/residue: 0.7957 time to fit residues: 136.9443 Evaluate side-chains 140 residues out of total 1291 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 130 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 442 GLU Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 978 VAL Chi-restraints excluded: chain A residue 1284 THR Chi-restraints excluded: chain A residue 1290 SER Chi-restraints excluded: chain A residue 1885 VAL Chi-restraints excluded: chain A residue 1982 VAL Chi-restraints excluded: chain A residue 2031 SER Chi-restraints excluded: chain A residue 2046 VAL Chi-restraints excluded: chain A residue 2117 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 30.0000 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 0.0770 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 0.9990 chunk 149 optimal weight: 0.8980 overall best weight: 0.7738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 402 HIS A 470 HIS A 504 HIS A 510 GLN A 704 GLN A 732 ASN A 918 ASN A 943 HIS A1138 ASN A1208 HIS A1599 HIS A1745 GLN A1764 GLN A1955 HIS A1957 ASN A1995 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.067085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.2399 r_free = 0.2399 target = 0.043708 restraints weight = 25827.227| |-----------------------------------------------------------------------------| r_work (start): 0.2391 rms_B_bonded: 1.62 r_work: 0.2293 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.2185 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.2185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8917 moved from start: 0.1283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 11527 Z= 0.194 Angle : 0.611 7.336 15695 Z= 0.319 Chirality : 0.039 0.143 1857 Planarity : 0.005 0.059 2010 Dihedral : 6.254 174.399 1626 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 3.33 % Allowed : 17.19 % Favored : 79.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % 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: 2.36 (0.21), residues: 1493 helix: 2.29 (0.16), residues: 1044 sheet: 2.02 (0.75), residues: 48 loop : -0.49 (0.30), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 767 TYR 0.016 0.002 TYR A2092 PHE 0.024 0.002 PHE A1921 TRP 0.042 0.002 TRP A 436 HIS 0.008 0.002 HIS A1635 Details of bonding type rmsd covalent geometry : bond 0.00447 (11522) covalent geometry : angle 0.61137 (15690) SS BOND : bond 0.00790 ( 1) SS BOND : angle 0.33753 ( 2) hydrogen bonds : bond 0.05904 ( 832) hydrogen bonds : angle 4.21364 ( 2448) metal coordination : bond 0.00870 ( 4) metal coordination : angle 0.67283 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2986 Ramachandran restraints generated. 1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2986 Ramachandran restraints generated. 1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1291 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 133 time to evaluate : 0.438 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 172 ARG cc_start: 0.9153 (OUTLIER) cc_final: 0.8932 (mtt180) REVERT: A 397 TYR cc_start: 0.6861 (t80) cc_final: 0.6640 (t80) REVERT: A 436 TRP cc_start: 0.8212 (m-10) cc_final: 0.7800 (m-90) REVERT: A 455 MET cc_start: 0.8814 (ppp) cc_final: 0.8312 (ppp) REVERT: A 465 TYR cc_start: 0.8824 (t80) cc_final: 0.8594 (t80) REVERT: A 473 TYR cc_start: 0.8320 (m-80) cc_final: 0.8023 (m-80) REVERT: A 509 LEU cc_start: 0.7956 (OUTLIER) cc_final: 0.7748 (mt) REVERT: A 514 LEU cc_start: 0.8204 (OUTLIER) cc_final: 0.7969 (mp) REVERT: A 519 LYS cc_start: 0.7234 (pptt) cc_final: 0.6063 (pptt) REVERT: A 954 MET cc_start: 0.9234 (OUTLIER) cc_final: 0.8894 (ptp) REVERT: A 1022 GLN cc_start: 0.9080 (OUTLIER) cc_final: 0.8740 (mp10) outliers start: 38 outliers final: 14 residues processed: 153 average time/residue: 0.7341 time to fit residues: 119.8462 Evaluate side-chains 144 residues out of total 1291 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 125 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 172 ARG Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain A residue 402 HIS Chi-restraints excluded: chain A residue 504 HIS Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 729 LEU Chi-restraints excluded: chain A residue 737 LEU Chi-restraints excluded: chain A residue 757 LEU Chi-restraints excluded: chain A residue 954 MET Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 978 VAL Chi-restraints excluded: chain A residue 1022 GLN Chi-restraints excluded: chain A residue 1140 LEU Chi-restraints excluded: chain A residue 1219 LEU Chi-restraints excluded: chain A residue 1881 GLN Chi-restraints excluded: chain A residue 1981 GLU Chi-restraints excluded: chain A residue 2031 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 30 optimal weight: 0.9980 chunk 16 optimal weight: 20.0000 chunk 136 optimal weight: 0.5980 chunk 62 optimal weight: 0.5980 chunk 14 optimal weight: 7.9990 chunk 33 optimal weight: 0.5980 chunk 143 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 24 optimal weight: 0.6980 chunk 19 optimal weight: 7.9990 chunk 35 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 402 HIS A 504 HIS A 943 HIS A1745 GLN A1957 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.066843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.2393 r_free = 0.2393 target = 0.043434 restraints weight = 25863.313| |-----------------------------------------------------------------------------| r_work (start): 0.2386 rms_B_bonded: 1.62 r_work: 0.2287 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2179 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.2179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8922 moved from start: 0.1471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 11527 Z= 0.177 Angle : 0.586 9.938 15695 Z= 0.305 Chirality : 0.038 0.139 1857 Planarity : 0.005 0.052 2010 Dihedral : 4.203 34.960 1616 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 2.98 % Allowed : 17.19 % Favored : 79.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % 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: 1493 helix: 2.42 (0.15), residues: 1044 sheet: 2.07 (0.74), residues: 48 loop : -0.52 (0.30), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 168 TYR 0.017 0.002 TYR A2092 PHE 0.022 0.002 PHE A1921 TRP 0.028 0.002 TRP A 436 HIS 0.015 0.002 HIS A 402 Details of bonding type rmsd covalent geometry : bond 0.00410 (11522) covalent geometry : angle 0.58634 (15690) SS BOND : bond 0.00675 ( 1) SS BOND : angle 0.48076 ( 2) hydrogen bonds : bond 0.05549 ( 832) hydrogen bonds : angle 4.06848 ( 2448) metal coordination : bond 0.00771 ( 4) metal coordination : angle 0.75662 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2986 Ramachandran restraints generated. 1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2986 Ramachandran restraints generated. 1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1291 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 126 time to evaluate : 0.464 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 172 ARG cc_start: 0.9136 (OUTLIER) cc_final: 0.8908 (mtt180) REVERT: A 436 TRP cc_start: 0.8136 (m-10) cc_final: 0.7863 (m-90) REVERT: A 452 HIS cc_start: 0.8535 (m-70) cc_final: 0.8288 (m-70) REVERT: A 455 MET cc_start: 0.8904 (ppp) cc_final: 0.8280 (ppp) REVERT: A 465 TYR cc_start: 0.8924 (t80) cc_final: 0.8672 (t80) REVERT: A 473 TYR cc_start: 0.8334 (m-80) cc_final: 0.7945 (m-80) REVERT: A 1022 GLN cc_start: 0.9103 (OUTLIER) cc_final: 0.8865 (mp10) outliers start: 34 outliers final: 18 residues processed: 149 average time/residue: 0.7498 time to fit residues: 119.3365 Evaluate side-chains 143 residues out of total 1291 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 123 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 172 ARG Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain A residue 402 HIS Chi-restraints excluded: chain A residue 504 HIS Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 729 LEU Chi-restraints excluded: chain A residue 737 LEU Chi-restraints excluded: chain A residue 757 LEU Chi-restraints excluded: chain A residue 816 SER Chi-restraints excluded: chain A residue 952 LEU Chi-restraints excluded: chain A residue 954 MET Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 978 VAL Chi-restraints excluded: chain A residue 1022 GLN Chi-restraints excluded: chain A residue 1140 LEU Chi-restraints excluded: chain A residue 1219 LEU Chi-restraints excluded: chain A residue 1715 THR Chi-restraints excluded: chain A residue 1746 ASN Chi-restraints excluded: chain A residue 1881 GLN Chi-restraints excluded: chain A residue 1981 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 40 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 chunk 125 optimal weight: 0.6980 chunk 24 optimal weight: 5.9990 chunk 29 optimal weight: 0.7980 chunk 65 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 136 optimal weight: 0.9990 chunk 150 optimal weight: 0.9980 chunk 72 optimal weight: 0.7980 chunk 133 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 402 HIS A 504 HIS A 943 HIS A1745 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.066215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.2374 r_free = 0.2374 target = 0.042743 restraints weight = 26059.710| |-----------------------------------------------------------------------------| r_work (start): 0.2366 rms_B_bonded: 1.63 r_work: 0.2267 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.2159 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.2159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8933 moved from start: 0.1609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 11527 Z= 0.197 Angle : 0.596 5.966 15695 Z= 0.310 Chirality : 0.038 0.139 1857 Planarity : 0.005 0.055 2010 Dihedral : 4.177 33.531 1615 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 3.86 % Allowed : 17.02 % Favored : 79.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % 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: 2.47 (0.21), residues: 1493 helix: 2.38 (0.15), residues: 1047 sheet: 2.03 (0.74), residues: 48 loop : -0.49 (0.30), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 168 TYR 0.017 0.002 TYR A2092 PHE 0.023 0.002 PHE A1921 TRP 0.020 0.002 TRP A 436 HIS 0.007 0.001 HIS A1635 Details of bonding type rmsd covalent geometry : bond 0.00463 (11522) covalent geometry : angle 0.59483 (15690) SS BOND : bond 0.01260 ( 1) SS BOND : angle 3.08212 ( 2) hydrogen bonds : bond 0.05664 ( 832) hydrogen bonds : angle 4.04929 ( 2448) metal coordination : bond 0.00957 ( 4) metal coordination : angle 0.95183 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2986 Ramachandran restraints generated. 1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2986 Ramachandran restraints generated. 1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1291 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 123 time to evaluate : 0.470 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 436 TRP cc_start: 0.8216 (m-10) cc_final: 0.7792 (m-90) REVERT: A 465 TYR cc_start: 0.8954 (t80) cc_final: 0.8731 (OUTLIER) REVERT: A 783 TYR cc_start: 0.9168 (OUTLIER) cc_final: 0.7964 (m-80) REVERT: A 951 LEU cc_start: 0.9247 (OUTLIER) cc_final: 0.8958 (mp) REVERT: A 1022 GLN cc_start: 0.9128 (OUTLIER) cc_final: 0.8780 (mp10) REVERT: A 1774 ARG cc_start: 0.9037 (OUTLIER) cc_final: 0.8704 (ttm110) outliers start: 44 outliers final: 29 residues processed: 154 average time/residue: 0.7222 time to fit residues: 119.0541 Evaluate side-chains 153 residues out of total 1291 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 121 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 167 ASP Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain A residue 402 HIS Chi-restraints excluded: chain A residue 504 HIS Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 729 LEU Chi-restraints excluded: chain A residue 745 LYS Chi-restraints excluded: chain A residue 757 LEU Chi-restraints excluded: chain A residue 783 TYR Chi-restraints excluded: chain A residue 810 SER Chi-restraints excluded: chain A residue 816 SER Chi-restraints excluded: chain A residue 951 LEU Chi-restraints excluded: chain A residue 952 LEU Chi-restraints excluded: chain A residue 954 MET Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 978 VAL Chi-restraints excluded: chain A residue 1011 CYS Chi-restraints excluded: chain A residue 1022 GLN Chi-restraints excluded: chain A residue 1027 CYS Chi-restraints excluded: chain A residue 1140 LEU Chi-restraints excluded: chain A residue 1715 THR Chi-restraints excluded: chain A residue 1717 GLN Chi-restraints excluded: chain A residue 1746 ASN Chi-restraints excluded: chain A residue 1774 ARG Chi-restraints excluded: chain A residue 1881 GLN Chi-restraints excluded: chain A residue 1885 VAL Chi-restraints excluded: chain A residue 1896 ASP Chi-restraints excluded: chain A residue 1981 GLU Chi-restraints excluded: chain A residue 2031 SER Chi-restraints excluded: chain A residue 2046 VAL Chi-restraints excluded: chain A residue 2117 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 25 optimal weight: 2.9990 chunk 62 optimal weight: 0.5980 chunk 81 optimal weight: 0.6980 chunk 21 optimal weight: 3.9990 chunk 101 optimal weight: 0.9980 chunk 134 optimal weight: 0.9990 chunk 39 optimal weight: 0.9990 chunk 1 optimal weight: 5.9990 chunk 73 optimal weight: 0.9990 chunk 80 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 402 HIS A 452 HIS A 504 HIS A 643 GLN A1745 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.065803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.2367 r_free = 0.2367 target = 0.042460 restraints weight = 25939.809| |-----------------------------------------------------------------------------| r_work (start): 0.2358 rms_B_bonded: 1.62 r_work: 0.2260 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2153 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.2153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8938 moved from start: 0.1723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 11527 Z= 0.199 Angle : 0.599 8.495 15695 Z= 0.312 Chirality : 0.038 0.138 1857 Planarity : 0.005 0.059 2010 Dihedral : 4.193 32.165 1615 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 3.95 % Allowed : 17.72 % Favored : 78.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % 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: 2.40 (0.21), residues: 1493 helix: 2.36 (0.15), residues: 1051 sheet: 2.02 (0.73), residues: 48 loop : -0.66 (0.30), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 168 TYR 0.044 0.002 TYR A 459 PHE 0.023 0.002 PHE A1921 TRP 0.024 0.002 TRP A 436 HIS 0.017 0.002 HIS A 452 Details of bonding type rmsd covalent geometry : bond 0.00470 (11522) covalent geometry : angle 0.59866 (15690) SS BOND : bond 0.01020 ( 1) SS BOND : angle 1.35992 ( 2) hydrogen bonds : bond 0.05651 ( 832) hydrogen bonds : angle 4.03290 ( 2448) metal coordination : bond 0.00945 ( 4) metal coordination : angle 1.01806 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2986 Ramachandran restraints generated. 1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2986 Ramachandran restraints generated. 1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1291 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 122 time to evaluate : 0.431 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 465 TYR cc_start: 0.8961 (t80) cc_final: 0.8669 (t80) REVERT: A 535 GLN cc_start: 0.7473 (tp40) cc_final: 0.7257 (tp-100) REVERT: A 783 TYR cc_start: 0.9161 (OUTLIER) cc_final: 0.7893 (m-80) REVERT: A 951 LEU cc_start: 0.9254 (OUTLIER) cc_final: 0.8972 (mp) REVERT: A 1022 GLN cc_start: 0.9148 (OUTLIER) cc_final: 0.8795 (mp10) REVERT: A 1774 ARG cc_start: 0.9045 (OUTLIER) cc_final: 0.8714 (ttm110) outliers start: 45 outliers final: 28 residues processed: 154 average time/residue: 0.6880 time to fit residues: 113.5717 Evaluate side-chains 153 residues out of total 1291 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 121 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 167 ASP Chi-restraints excluded: chain B residue 186 THR Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain A residue 402 HIS Chi-restraints excluded: chain A residue 504 HIS Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 729 LEU Chi-restraints excluded: chain A residue 745 LYS Chi-restraints excluded: chain A residue 757 LEU Chi-restraints excluded: chain A residue 783 TYR Chi-restraints excluded: chain A residue 810 SER Chi-restraints excluded: chain A residue 816 SER Chi-restraints excluded: chain A residue 951 LEU Chi-restraints excluded: chain A residue 952 LEU Chi-restraints excluded: chain A residue 954 MET Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 978 VAL Chi-restraints excluded: chain A residue 1011 CYS Chi-restraints excluded: chain A residue 1022 GLN Chi-restraints excluded: chain A residue 1027 CYS Chi-restraints excluded: chain A residue 1140 LEU Chi-restraints excluded: chain A residue 1715 THR Chi-restraints excluded: chain A residue 1717 GLN Chi-restraints excluded: chain A residue 1746 ASN Chi-restraints excluded: chain A residue 1774 ARG Chi-restraints excluded: chain A residue 1881 GLN Chi-restraints excluded: chain A residue 1885 VAL Chi-restraints excluded: chain A residue 1981 GLU Chi-restraints excluded: chain A residue 2031 SER Chi-restraints excluded: chain A residue 2046 VAL Chi-restraints excluded: chain A residue 2117 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 120 optimal weight: 0.5980 chunk 18 optimal weight: 5.9990 chunk 1 optimal weight: 2.9990 chunk 34 optimal weight: 0.7980 chunk 49 optimal weight: 0.3980 chunk 103 optimal weight: 0.9980 chunk 86 optimal weight: 0.0070 chunk 61 optimal weight: 0.8980 chunk 74 optimal weight: 1.9990 chunk 45 optimal weight: 0.5980 chunk 82 optimal weight: 0.8980 overall best weight: 0.4798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 402 HIS ** A 452 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 470 HIS A 504 HIS A 643 GLN A1240 ASN A1745 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.066848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.2399 r_free = 0.2399 target = 0.043540 restraints weight = 26030.844| |-----------------------------------------------------------------------------| r_work (start): 0.2390 rms_B_bonded: 1.64 r_work: 0.2295 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.2187 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.2187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8919 moved from start: 0.1812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11527 Z= 0.147 Angle : 0.565 9.313 15695 Z= 0.292 Chirality : 0.036 0.139 1857 Planarity : 0.005 0.058 2010 Dihedral : 4.053 26.815 1615 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 3.25 % Allowed : 19.21 % Favored : 77.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % 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: 2.68 (0.22), residues: 1493 helix: 2.57 (0.15), residues: 1045 sheet: 1.97 (0.73), residues: 48 loop : -0.48 (0.31), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 168 TYR 0.017 0.002 TYR A2092 PHE 0.020 0.002 PHE A1921 TRP 0.022 0.002 TRP A 436 HIS 0.019 0.001 HIS A 402 Details of bonding type rmsd covalent geometry : bond 0.00328 (11522) covalent geometry : angle 0.56475 (15690) SS BOND : bond 0.00600 ( 1) SS BOND : angle 0.79905 ( 2) hydrogen bonds : bond 0.04976 ( 832) hydrogen bonds : angle 3.92415 ( 2448) metal coordination : bond 0.00471 ( 4) metal coordination : angle 0.68220 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2986 Ramachandran restraints generated. 1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2986 Ramachandran restraints generated. 1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1291 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 128 time to evaluate : 0.434 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 465 TYR cc_start: 0.9011 (t80) cc_final: 0.8698 (t80) REVERT: A 472 LEU cc_start: 0.8779 (mm) cc_final: 0.8504 (mm) REVERT: A 502 LYS cc_start: 0.8430 (mtmt) cc_final: 0.8216 (mmmt) REVERT: A 783 TYR cc_start: 0.9161 (OUTLIER) cc_final: 0.7876 (m-80) REVERT: A 951 LEU cc_start: 0.9232 (OUTLIER) cc_final: 0.8929 (mp) REVERT: A 1022 GLN cc_start: 0.9111 (OUTLIER) cc_final: 0.8755 (mp10) outliers start: 37 outliers final: 22 residues processed: 152 average time/residue: 0.7502 time to fit residues: 121.7095 Evaluate side-chains 148 residues out of total 1291 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 123 time to evaluate : 0.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 167 ASP Chi-restraints excluded: chain B residue 186 THR Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain A residue 402 HIS Chi-restraints excluded: chain A residue 504 HIS Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 729 LEU Chi-restraints excluded: chain A residue 745 LYS Chi-restraints excluded: chain A residue 757 LEU Chi-restraints excluded: chain A residue 783 TYR Chi-restraints excluded: chain A residue 816 SER Chi-restraints excluded: chain A residue 951 LEU Chi-restraints excluded: chain A residue 954 MET Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 1022 GLN Chi-restraints excluded: chain A residue 1140 LEU Chi-restraints excluded: chain A residue 1219 LEU Chi-restraints excluded: chain A residue 1746 ASN Chi-restraints excluded: chain A residue 1881 GLN Chi-restraints excluded: chain A residue 1885 VAL Chi-restraints excluded: chain A residue 1981 GLU Chi-restraints excluded: chain A residue 2031 SER Chi-restraints excluded: chain A residue 2046 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 34 optimal weight: 0.9980 chunk 113 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 116 optimal weight: 0.8980 chunk 31 optimal weight: 0.5980 chunk 57 optimal weight: 0.6980 chunk 38 optimal weight: 0.5980 chunk 51 optimal weight: 0.6980 chunk 35 optimal weight: 0.9980 chunk 29 optimal weight: 0.9990 chunk 13 optimal weight: 9.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 402 HIS ** A 452 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 504 HIS A 643 GLN A1745 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.066300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2383 r_free = 0.2383 target = 0.043002 restraints weight = 26198.253| |-----------------------------------------------------------------------------| r_work (start): 0.2374 rms_B_bonded: 1.64 r_work: 0.2276 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.2169 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.2169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8929 moved from start: 0.1866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 11527 Z= 0.175 Angle : 0.602 10.761 15695 Z= 0.309 Chirality : 0.038 0.138 1857 Planarity : 0.005 0.062 2010 Dihedral : 4.030 17.118 1614 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 3.33 % Allowed : 19.74 % Favored : 76.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % 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: 2.65 (0.22), residues: 1493 helix: 2.56 (0.15), residues: 1044 sheet: 1.96 (0.73), residues: 48 loop : -0.50 (0.31), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 168 TYR 0.017 0.002 TYR A2092 PHE 0.021 0.002 PHE A1921 TRP 0.020 0.002 TRP A 436 HIS 0.014 0.001 HIS A 452 Details of bonding type rmsd covalent geometry : bond 0.00409 (11522) covalent geometry : angle 0.60158 (15690) SS BOND : bond 0.00800 ( 1) SS BOND : angle 0.42580 ( 2) hydrogen bonds : bond 0.05256 ( 832) hydrogen bonds : angle 3.93861 ( 2448) metal coordination : bond 0.00718 ( 4) metal coordination : angle 0.91767 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2986 Ramachandran restraints generated. 1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2986 Ramachandran restraints generated. 1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1291 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 124 time to evaluate : 0.409 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 465 TYR cc_start: 0.9004 (t80) cc_final: 0.8721 (OUTLIER) REVERT: A 472 LEU cc_start: 0.8753 (mm) cc_final: 0.8470 (mm) REVERT: A 509 LEU cc_start: 0.7925 (OUTLIER) cc_final: 0.7567 (tm) REVERT: A 522 GLN cc_start: 0.8570 (tm-30) cc_final: 0.8214 (tm-30) REVERT: A 783 TYR cc_start: 0.9163 (OUTLIER) cc_final: 0.7893 (m-80) REVERT: A 951 LEU cc_start: 0.9242 (OUTLIER) cc_final: 0.8929 (mp) REVERT: A 1022 GLN cc_start: 0.9135 (OUTLIER) cc_final: 0.8880 (mp10) outliers start: 38 outliers final: 26 residues processed: 150 average time/residue: 0.7503 time to fit residues: 120.2782 Evaluate side-chains 152 residues out of total 1291 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 123 time to evaluate : 0.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 167 ASP Chi-restraints excluded: chain B residue 186 THR Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain A residue 402 HIS Chi-restraints excluded: chain A residue 504 HIS Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 729 LEU Chi-restraints excluded: chain A residue 745 LYS Chi-restraints excluded: chain A residue 757 LEU Chi-restraints excluded: chain A residue 783 TYR Chi-restraints excluded: chain A residue 810 SER Chi-restraints excluded: chain A residue 816 SER Chi-restraints excluded: chain A residue 873 LYS Chi-restraints excluded: chain A residue 951 LEU Chi-restraints excluded: chain A residue 954 MET Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 1022 GLN Chi-restraints excluded: chain A residue 1027 CYS Chi-restraints excluded: chain A residue 1140 LEU Chi-restraints excluded: chain A residue 1219 LEU Chi-restraints excluded: chain A residue 1746 ASN Chi-restraints excluded: chain A residue 1881 GLN Chi-restraints excluded: chain A residue 1885 VAL Chi-restraints excluded: chain A residue 1981 GLU Chi-restraints excluded: chain A residue 2031 SER Chi-restraints excluded: chain A residue 2046 VAL Chi-restraints excluded: chain A residue 2117 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 120 optimal weight: 0.5980 chunk 7 optimal weight: 0.9990 chunk 101 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 108 optimal weight: 0.7980 chunk 5 optimal weight: 8.9990 chunk 143 optimal weight: 0.8980 chunk 31 optimal weight: 0.9980 chunk 1 optimal weight: 0.2980 chunk 61 optimal weight: 0.9980 chunk 125 optimal weight: 0.0040 overall best weight: 0.5192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 402 HIS ** A 452 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 504 HIS A 643 GLN A1745 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.066805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.2401 r_free = 0.2401 target = 0.043572 restraints weight = 26016.561| |-----------------------------------------------------------------------------| r_work (start): 0.2392 rms_B_bonded: 1.64 r_work: 0.2295 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.2188 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.2188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8919 moved from start: 0.1922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11527 Z= 0.152 Angle : 0.602 12.317 15695 Z= 0.307 Chirality : 0.037 0.154 1857 Planarity : 0.005 0.065 2010 Dihedral : 3.972 16.626 1614 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 3.33 % Allowed : 20.26 % Favored : 76.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % 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 (0.22), residues: 1493 helix: 2.62 (0.15), residues: 1046 sheet: 1.88 (0.73), residues: 48 loop : -0.46 (0.31), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 558 TYR 0.043 0.002 TYR A 459 PHE 0.020 0.002 PHE A1921 TRP 0.022 0.002 TRP A 436 HIS 0.023 0.002 HIS A 452 Details of bonding type rmsd covalent geometry : bond 0.00349 (11522) covalent geometry : angle 0.60183 (15690) SS BOND : bond 0.00627 ( 1) SS BOND : angle 0.43174 ( 2) hydrogen bonds : bond 0.04938 ( 832) hydrogen bonds : angle 3.88606 ( 2448) metal coordination : bond 0.00468 ( 4) metal coordination : angle 0.76395 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2986 Ramachandran restraints generated. 1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2986 Ramachandran restraints generated. 1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1291 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 125 time to evaluate : 0.465 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 465 TYR cc_start: 0.8968 (t80) cc_final: 0.8692 (OUTLIER) REVERT: A 472 LEU cc_start: 0.8718 (mm) cc_final: 0.8423 (mm) REVERT: A 509 LEU cc_start: 0.7799 (OUTLIER) cc_final: 0.7449 (tm) REVERT: A 522 GLN cc_start: 0.8590 (tm-30) cc_final: 0.8232 (tm-30) REVERT: A 783 TYR cc_start: 0.9163 (OUTLIER) cc_final: 0.7877 (m-80) REVERT: A 951 LEU cc_start: 0.9227 (OUTLIER) cc_final: 0.8917 (mp) REVERT: A 1022 GLN cc_start: 0.9120 (OUTLIER) cc_final: 0.8863 (mp10) outliers start: 38 outliers final: 25 residues processed: 152 average time/residue: 0.6960 time to fit residues: 113.2097 Evaluate side-chains 150 residues out of total 1291 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 122 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 167 ASP Chi-restraints excluded: chain B residue 186 THR Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain A residue 402 HIS Chi-restraints excluded: chain A residue 504 HIS Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 729 LEU Chi-restraints excluded: chain A residue 783 TYR Chi-restraints excluded: chain A residue 816 SER Chi-restraints excluded: chain A residue 873 LYS Chi-restraints excluded: chain A residue 951 LEU Chi-restraints excluded: chain A residue 954 MET Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 1011 CYS Chi-restraints excluded: chain A residue 1022 GLN Chi-restraints excluded: chain A residue 1027 CYS Chi-restraints excluded: chain A residue 1140 LEU Chi-restraints excluded: chain A residue 1219 LEU Chi-restraints excluded: chain A residue 1746 ASN Chi-restraints excluded: chain A residue 1881 GLN Chi-restraints excluded: chain A residue 1885 VAL Chi-restraints excluded: chain A residue 1926 SER Chi-restraints excluded: chain A residue 1981 GLU Chi-restraints excluded: chain A residue 2031 SER Chi-restraints excluded: chain A residue 2046 VAL Chi-restraints excluded: chain A residue 2117 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 51 optimal weight: 0.9990 chunk 99 optimal weight: 0.7980 chunk 26 optimal weight: 0.0970 chunk 54 optimal weight: 0.7980 chunk 102 optimal weight: 0.8980 chunk 112 optimal weight: 0.0670 chunk 90 optimal weight: 0.0670 chunk 115 optimal weight: 1.9990 chunk 119 optimal weight: 0.7980 chunk 65 optimal weight: 0.9980 chunk 124 optimal weight: 0.8980 overall best weight: 0.3654 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 402 HIS A 504 HIS A 643 GLN A1745 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.067276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.2408 r_free = 0.2408 target = 0.043922 restraints weight = 25962.946| |-----------------------------------------------------------------------------| r_work (start): 0.2400 rms_B_bonded: 1.65 r_work: 0.2303 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2198 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.2198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8906 moved from start: 0.2007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11527 Z= 0.136 Angle : 0.598 10.166 15695 Z= 0.306 Chirality : 0.037 0.218 1857 Planarity : 0.005 0.068 2010 Dihedral : 3.937 18.874 1614 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 2.89 % Allowed : 21.05 % Favored : 76.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % 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: 2.81 (0.22), residues: 1493 helix: 2.67 (0.16), residues: 1051 sheet: 1.88 (0.73), residues: 48 loop : -0.47 (0.31), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 558 TYR 0.016 0.001 TYR A2092 PHE 0.018 0.001 PHE A1921 TRP 0.021 0.001 TRP A 436 HIS 0.005 0.001 HIS A 504 Details of bonding type rmsd covalent geometry : bond 0.00305 (11522) covalent geometry : angle 0.59806 (15690) SS BOND : bond 0.00484 ( 1) SS BOND : angle 0.55648 ( 2) hydrogen bonds : bond 0.04598 ( 832) hydrogen bonds : angle 3.84370 ( 2448) metal coordination : bond 0.00320 ( 4) metal coordination : angle 0.65407 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2986 Ramachandran restraints generated. 1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2986 Ramachandran restraints generated. 1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1291 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 126 time to evaluate : 0.314 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 438 LEU cc_start: 0.8317 (OUTLIER) cc_final: 0.7970 (tt) REVERT: A 472 LEU cc_start: 0.8716 (mm) cc_final: 0.8392 (mm) REVERT: A 783 TYR cc_start: 0.9159 (OUTLIER) cc_final: 0.7854 (m-80) REVERT: A 951 LEU cc_start: 0.9214 (OUTLIER) cc_final: 0.8927 (mp) REVERT: A 1022 GLN cc_start: 0.9076 (OUTLIER) cc_final: 0.8815 (mp10) outliers start: 33 outliers final: 21 residues processed: 147 average time/residue: 0.7114 time to fit residues: 111.7802 Evaluate side-chains 149 residues out of total 1291 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 124 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 167 ASP Chi-restraints excluded: chain B residue 186 THR Chi-restraints excluded: chain A residue 402 HIS Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 455 MET Chi-restraints excluded: chain A residue 504 HIS Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain A residue 729 LEU Chi-restraints excluded: chain A residue 783 TYR Chi-restraints excluded: chain A residue 810 SER Chi-restraints excluded: chain A residue 816 SER Chi-restraints excluded: chain A residue 873 LYS Chi-restraints excluded: chain A residue 951 LEU Chi-restraints excluded: chain A residue 954 MET Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 1022 GLN Chi-restraints excluded: chain A residue 1140 LEU Chi-restraints excluded: chain A residue 1219 LEU Chi-restraints excluded: chain A residue 1746 ASN Chi-restraints excluded: chain A residue 1885 VAL Chi-restraints excluded: chain A residue 1981 GLU Chi-restraints excluded: chain A residue 2031 SER Chi-restraints excluded: chain A residue 2046 VAL Chi-restraints excluded: chain A residue 2117 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 35 optimal weight: 0.9990 chunk 100 optimal weight: 0.9980 chunk 10 optimal weight: 30.0000 chunk 24 optimal weight: 1.9990 chunk 61 optimal weight: 0.8980 chunk 93 optimal weight: 0.9980 chunk 116 optimal weight: 0.9980 chunk 115 optimal weight: 0.9980 chunk 99 optimal weight: 0.0570 chunk 64 optimal weight: 0.5980 chunk 2 optimal weight: 2.9990 overall best weight: 0.7098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 402 HIS ** A 452 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 504 HIS A 643 GLN A1745 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.066219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2374 r_free = 0.2374 target = 0.042793 restraints weight = 26082.152| |-----------------------------------------------------------------------------| r_work (start): 0.2366 rms_B_bonded: 1.65 r_work: 0.2267 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2163 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.2163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8928 moved from start: 0.2016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 11527 Z= 0.179 Angle : 0.645 12.244 15695 Z= 0.332 Chirality : 0.039 0.220 1857 Planarity : 0.006 0.071 2010 Dihedral : 4.008 19.415 1614 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.63 % Allowed : 21.49 % Favored : 75.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % 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: 2.68 (0.22), residues: 1493 helix: 2.57 (0.15), residues: 1052 sheet: 1.94 (0.73), residues: 48 loop : -0.52 (0.31), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG B 168 TYR 0.045 0.002 TYR A 459 PHE 0.021 0.002 PHE A1921 TRP 0.023 0.002 TRP A 436 HIS 0.023 0.002 HIS A 452 Details of bonding type rmsd covalent geometry : bond 0.00421 (11522) covalent geometry : angle 0.64483 (15690) SS BOND : bond 0.00812 ( 1) SS BOND : angle 0.24218 ( 2) hydrogen bonds : bond 0.05175 ( 832) hydrogen bonds : angle 3.90659 ( 2448) metal coordination : bond 0.00745 ( 4) metal coordination : angle 1.04653 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2986 Ramachandran restraints generated. 1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2986 Ramachandran restraints generated. 1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1291 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 123 time to evaluate : 0.411 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 438 LEU cc_start: 0.8314 (OUTLIER) cc_final: 0.7994 (tt) REVERT: A 502 LYS cc_start: 0.8432 (ttmt) cc_final: 0.8192 (mmmt) REVERT: A 783 TYR cc_start: 0.9165 (OUTLIER) cc_final: 0.7898 (m-80) REVERT: A 951 LEU cc_start: 0.9234 (OUTLIER) cc_final: 0.8924 (mp) REVERT: A 1022 GLN cc_start: 0.9131 (OUTLIER) cc_final: 0.8870 (mp10) outliers start: 30 outliers final: 21 residues processed: 143 average time/residue: 0.7295 time to fit residues: 111.5020 Evaluate side-chains 146 residues out of total 1291 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 121 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 167 ASP Chi-restraints excluded: chain B residue 186 THR Chi-restraints excluded: chain A residue 402 HIS Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 455 MET Chi-restraints excluded: chain A residue 504 HIS Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 729 LEU Chi-restraints excluded: chain A residue 783 TYR Chi-restraints excluded: chain A residue 810 SER Chi-restraints excluded: chain A residue 816 SER Chi-restraints excluded: chain A residue 873 LYS Chi-restraints excluded: chain A residue 951 LEU Chi-restraints excluded: chain A residue 954 MET Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 1022 GLN Chi-restraints excluded: chain A residue 1140 LEU Chi-restraints excluded: chain A residue 1715 THR Chi-restraints excluded: chain A residue 1746 ASN Chi-restraints excluded: chain A residue 1885 VAL Chi-restraints excluded: chain A residue 1926 SER Chi-restraints excluded: chain A residue 1981 GLU Chi-restraints excluded: chain A residue 2031 SER Chi-restraints excluded: chain A residue 2046 VAL Chi-restraints excluded: chain A residue 2117 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 35 optimal weight: 0.4980 chunk 75 optimal weight: 0.3980 chunk 125 optimal weight: 0.5980 chunk 128 optimal weight: 0.0870 chunk 135 optimal weight: 0.8980 chunk 12 optimal weight: 1.9990 chunk 79 optimal weight: 0.5980 chunk 71 optimal weight: 0.4980 chunk 31 optimal weight: 0.3980 chunk 76 optimal weight: 0.5980 chunk 134 optimal weight: 0.0030 overall best weight: 0.2768 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 402 HIS A 504 HIS A 643 GLN A1745 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.067630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2420 r_free = 0.2420 target = 0.044350 restraints weight = 26230.067| |-----------------------------------------------------------------------------| r_work (start): 0.2413 rms_B_bonded: 1.65 r_work: 0.2316 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2211 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.2211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8898 moved from start: 0.2109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 11527 Z= 0.132 Angle : 0.609 11.792 15695 Z= 0.311 Chirality : 0.036 0.150 1857 Planarity : 0.005 0.068 2010 Dihedral : 3.904 20.108 1614 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 2.11 % Allowed : 22.02 % Favored : 75.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % 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: 2.89 (0.22), residues: 1493 helix: 2.74 (0.15), residues: 1051 sheet: 1.90 (0.73), residues: 48 loop : -0.44 (0.31), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 168 TYR 0.016 0.002 TYR A2092 PHE 0.016 0.001 PHE A1921 TRP 0.023 0.001 TRP A 436 HIS 0.006 0.001 HIS A 452 Details of bonding type rmsd covalent geometry : bond 0.00290 (11522) covalent geometry : angle 0.60857 (15690) SS BOND : bond 0.00422 ( 1) SS BOND : angle 0.61866 ( 2) hydrogen bonds : bond 0.04439 ( 832) hydrogen bonds : angle 3.79960 ( 2448) metal coordination : bond 0.00208 ( 4) metal coordination : angle 0.58246 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4254.55 seconds wall clock time: 73 minutes 27.12 seconds (4407.12 seconds total)