Starting phenix.real_space_refine on Fri Jul 3 23:05:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8dg5_27416/07_2026/8dg5_27416.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dg5_27416/07_2026/8dg5_27416.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.26 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/8dg5_27416/07_2026/8dg5_27416.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8dg5_27416/07_2026/8dg5_27416.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8dg5_27416/07_2026/8dg5_27416.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dg5_27416/07_2026/8dg5_27416.map" model { file = "/net/cci-nas-00/data/ceres_data/8dg5_27416/07_2026/8dg5_27416.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dg5_27416/07_2026/8dg5_27416.cif" } resolution = 3.26 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.039 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 P 51 5.49 5 Mg 11 5.21 5 S 88 5.16 5 C 10124 2.51 5 N 2859 2.21 5 O 3136 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 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: 16269 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 13175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1635, 13175 Classifications: {'peptide': 1635} Link IDs: {'PTRANS': 98, 'TRANS': 1536} Chain breaks: 14 Chain: "E" Number of atoms: 1057 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 1057 Classifications: {'RNA': 50} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 23, 'rna3p_pyr': 26} Link IDs: {'rna2p': 1, 'rna3p': 48} Chain breaks: 1 Chain: "K" Number of atoms: 2005 Number of conformers: 1 Conformer: "" Number of residues, atoms: 252, 2005 Classifications: {'peptide': 252} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 240} Chain breaks: 3 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 29 Unusual residues: {' MG': 8, 'U5P%rna2p': 1} Classifications: {'RNA_mixed': 1, 'undetermined': 8} Modifications used: {'rna2p': 1} Link IDs: {None: 8} Time building chain proxies: 2.57, per 1000 atoms: 0.16 Number of scatterers: 16269 At special positions: 0 Unit cell: (156.04, 128.65, 146.08, 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) S 88 16.00 P 51 15.00 Mg 11 11.99 O 3136 8.00 N 2859 7.00 C 10124 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.13 Conformation dependent library (CDL) restraints added in 505.2 milliseconds 3698 Ramachandran restraints generated. 1849 Oldfield, 0 Emsley, 1849 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3602 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 15 sheets defined 47.9% alpha, 9.2% beta 17 base pairs and 32 stacking pairs defined. Time for finding SS restraints: 1.42 Creating SS restraints... Processing helix chain 'A' and resid 19 through 31 Processing helix chain 'A' and resid 39 through 59 Processing helix chain 'A' and resid 79 through 88 removed outlier: 3.879A pdb=" N THR A 83 " --> pdb=" O CYS A 79 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N MET A 84 " --> pdb=" O SER A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 127 Processing helix chain 'A' and resid 145 through 157 Proline residue: A 154 - end of helix Processing helix chain 'A' and resid 187 through 199 Processing helix chain 'A' and resid 232 through 251 removed outlier: 3.763A pdb=" N SER A 247 " --> pdb=" O ASN A 243 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N PHE A 248 " --> pdb=" O THR A 244 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LEU A 249 " --> pdb=" O HIS A 245 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N ASP A 251 " --> pdb=" O SER A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 285 Processing helix chain 'A' and resid 286 through 293 Processing helix chain 'A' and resid 294 through 311 removed outlier: 4.340A pdb=" N HIS A 304 " --> pdb=" O ARG A 300 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N PHE A 305 " --> pdb=" O ALA A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 346 removed outlier: 3.656A pdb=" N ARG A 345 " --> pdb=" O HIS A 341 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N HIS A 346 " --> pdb=" O ALA A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 360 Processing helix chain 'A' and resid 362 through 374 removed outlier: 3.673A pdb=" N ARG A 366 " --> pdb=" O SER A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 503 through 519 Processing helix chain 'A' and resid 520 through 523 removed outlier: 3.659A pdb=" N LYS A 523 " --> pdb=" O PRO A 520 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 520 through 523' Processing helix chain 'A' and resid 540 through 560 removed outlier: 3.740A pdb=" N ALA A 544 " --> pdb=" O GLU A 540 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ARG A 550 " --> pdb=" O LEU A 546 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N GLU A 553 " --> pdb=" O ARG A 549 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N MET A 560 " --> pdb=" O LYS A 556 " (cutoff:3.500A) Processing helix chain 'A' and resid 569 through 573 removed outlier: 3.711A pdb=" N GLU A 573 " --> pdb=" O SER A 570 " (cutoff:3.500A) Processing helix chain 'A' and resid 592 through 601 Processing helix chain 'A' and resid 629 through 639 Processing helix chain 'A' and resid 760 through 784 Processing helix chain 'A' and resid 791 through 802 removed outlier: 3.715A pdb=" N GLN A 795 " --> pdb=" O PRO A 791 " (cutoff:3.500A) Processing helix chain 'A' and resid 821 through 833 removed outlier: 3.610A pdb=" N ALA A 825 " --> pdb=" O ASP A 821 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ILE A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N ASN A 830 " --> pdb=" O ILE A 826 " (cutoff:3.500A) Processing helix chain 'A' and resid 884 through 904 removed outlier: 3.804A pdb=" N ALA A 888 " --> pdb=" O THR A 884 " (cutoff:3.500A) Processing helix chain 'A' and resid 931 through 941 removed outlier: 4.016A pdb=" N ILE A 937 " --> pdb=" O GLU A 933 " (cutoff:3.500A) Processing helix chain 'A' and resid 960 through 964 removed outlier: 3.746A pdb=" N CYS A 964 " --> pdb=" O SER A 961 " (cutoff:3.500A) Processing helix chain 'A' and resid 1047 through 1062 removed outlier: 3.537A pdb=" N CYS A1051 " --> pdb=" O GLU A1047 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ASN A1057 " --> pdb=" O ASN A1053 " (cutoff:3.500A) Processing helix chain 'A' and resid 1098 through 1108 removed outlier: 3.885A pdb=" N ASN A1108 " --> pdb=" O LEU A1104 " (cutoff:3.500A) Processing helix chain 'A' and resid 1117 through 1124 removed outlier: 4.650A pdb=" N ARG A1121 " --> pdb=" O PRO A1117 " (cutoff:3.500A) Processing helix chain 'A' and resid 1171 through 1179 Processing helix chain 'A' and resid 1220 through 1230 Processing helix chain 'A' and resid 1248 through 1282 Proline residue: A1259 - end of helix Processing helix chain 'A' and resid 1526 through 1533 Processing helix chain 'A' and resid 1535 through 1548 removed outlier: 3.740A pdb=" N ARG A1540 " --> pdb=" O ASN A1536 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLN A1541 " --> pdb=" O ALA A1537 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLN A1543 " --> pdb=" O GLU A1539 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N GLN A1544 " --> pdb=" O ARG A1540 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LYS A1546 " --> pdb=" O TYR A1542 " (cutoff:3.500A) Processing helix chain 'A' and resid 1567 through 1581 Processing helix chain 'A' and resid 1607 through 1616 Processing helix chain 'A' and resid 1624 through 1629 Processing helix chain 'A' and resid 1635 through 1650 Processing helix chain 'A' and resid 1722 through 1731 Processing helix chain 'A' and resid 1732 through 1736 removed outlier: 3.675A pdb=" N ASN A1736 " --> pdb=" O SER A1733 " (cutoff:3.500A) Processing helix chain 'A' and resid 1741 through 1764 removed outlier: 3.780A pdb=" N THR A1746 " --> pdb=" O GLU A1742 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N ILE A1747 " --> pdb=" O ARG A1743 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N TYR A1764 " --> pdb=" O LEU A1760 " (cutoff:3.500A) Processing helix chain 'A' and resid 1768 through 1780 removed outlier: 3.915A pdb=" N LEU A1772 " --> pdb=" O HIS A1768 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N HIS A1774 " --> pdb=" O GLY A1770 " (cutoff:3.500A) Processing helix chain 'A' and resid 1781 through 1792 Processing helix chain 'A' and resid 1794 through 1798 removed outlier: 4.024A pdb=" N MET A1798 " --> pdb=" O GLY A1795 " (cutoff:3.500A) Processing helix chain 'A' and resid 1819 through 1824 Processing helix chain 'A' and resid 1836 through 1846 Processing helix chain 'A' and resid 1847 through 1854 removed outlier: 3.626A pdb=" N CYS A1851 " --> pdb=" O SER A1847 " (cutoff:3.500A) Processing helix chain 'A' and resid 1900 through 1931 Proline residue: A1920 - end of helix Processing helix chain 'A' and resid 1981 through 1990 Processing helix chain 'A' and resid 1993 through 2001 Processing helix chain 'A' and resid 2006 through 2015 removed outlier: 4.038A pdb=" N LEU A2010 " --> pdb=" O ASP A2006 " (cutoff:3.500A) Processing helix chain 'A' and resid 2028 through 2049 removed outlier: 3.715A pdb=" N LEU A2034 " --> pdb=" O ARG A2030 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N ALA A2037 " --> pdb=" O PHE A2033 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLU A2049 " --> pdb=" O ARG A2045 " (cutoff:3.500A) Processing helix chain 'A' and resid 2055 through 2065 removed outlier: 3.923A pdb=" N ARG A2063 " --> pdb=" O LEU A2059 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA A2065 " --> pdb=" O ASP A2061 " (cutoff:3.500A) Processing helix chain 'A' and resid 2068 through 2079 Processing helix chain 'A' and resid 2089 through 2107 Processing helix chain 'A' and resid 2131 through 2149 removed outlier: 3.829A pdb=" N ALA A2142 " --> pdb=" O PHE A2138 " (cutoff:3.500A) Processing helix chain 'A' and resid 2153 through 2174 removed outlier: 4.147A pdb=" N ASN A2162 " --> pdb=" O HIS A2158 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N MET A2163 " --> pdb=" O VAL A2159 " (cutoff:3.500A) Proline residue: A2166 - end of helix Processing helix chain 'A' and resid 2178 through 2187 Processing helix chain 'A' and resid 2223 through 2240 removed outlier: 3.825A pdb=" N ALA A2227 " --> pdb=" O ASN A2223 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N LYS A2240 " --> pdb=" O LEU A2236 " (cutoff:3.500A) Processing helix chain 'K' and resid 135 through 145 Processing helix chain 'K' and resid 188 through 205 Processing helix chain 'K' and resid 252 through 262 removed outlier: 3.838A pdb=" N GLN K 256 " --> pdb=" O ILE K 252 " (cutoff:3.500A) Processing helix chain 'K' and resid 300 through 319 removed outlier: 3.821A pdb=" N THR K 319 " --> pdb=" O ARG K 315 " (cutoff:3.500A) Processing helix chain 'K' and resid 359 through 374 Processing helix chain 'K' and resid 376 through 385 removed outlier: 4.080A pdb=" N LEU K 380 " --> pdb=" O GLY K 376 " (cutoff:3.500A) Processing helix chain 'K' and resid 393 through 405 removed outlier: 3.737A pdb=" N LEU K 397 " --> pdb=" O ASP K 393 " (cutoff:3.500A) Processing helix chain 'K' and resid 443 through 464 Processing sheet with id=AA1, first strand: chain 'A' and resid 64 through 66 removed outlier: 7.780A pdb=" N VAL A 64 " --> pdb=" O GLU A 136 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ILE A 138 " --> pdb=" O VAL A 64 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N VAL A 66 " --> pdb=" O ILE A 138 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 583 through 586 removed outlier: 6.124A pdb=" N VAL A 584 " --> pdb=" O VAL A 611 " (cutoff:3.500A) removed outlier: 7.549A pdb=" N LEU A 613 " --> pdb=" O VAL A 584 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N ARG A 586 " --> pdb=" O LEU A 613 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N HIS A 220 " --> pdb=" O HIS A 610 " (cutoff:3.500A) removed outlier: 8.197A pdb=" N ILE A 612 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N TYR A 222 " --> pdb=" O ILE A 612 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N VAL A 614 " --> pdb=" O TYR A 222 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N VAL A 224 " --> pdb=" O VAL A 614 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL A1585 " --> pdb=" O ILE A 223 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLN A 225 " --> pdb=" O VAL A1585 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 852 through 855 Processing sheet with id=AA4, first strand: chain 'A' and resid 952 through 956 Processing sheet with id=AA5, first strand: chain 'A' and resid 1023 through 1026 removed outlier: 6.707A pdb=" N GLU A1030 " --> pdb=" O GLN A 984 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1023 through 1026 removed outlier: 6.707A pdb=" N GLU A1030 " --> pdb=" O GLN A 984 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N PHE A1008 " --> pdb=" O ILE A 979 " (cutoff:3.500A) removed outlier: 9.273A pdb=" N LEU A 981 " --> pdb=" O GLN A1006 " (cutoff:3.500A) removed outlier: 10.646A pdb=" N GLN A1006 " --> pdb=" O LEU A 981 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1072 through 1073 removed outlier: 3.974A pdb=" N LEU A1072 " --> pdb=" O TYR A1815 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1136 through 1138 removed outlier: 3.683A pdb=" N MET A1137 " --> pdb=" O THR A1243 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1153 through 1155 Processing sheet with id=AB1, first strand: chain 'A' and resid 1937 through 1941 removed outlier: 3.717A pdb=" N VAL A1964 " --> pdb=" O THR A1938 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 2125 through 2126 removed outlier: 3.581A pdb=" N ILE A2220 " --> pdb=" O ALA A2125 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 2192 through 2193 Processing sheet with id=AB4, first strand: chain 'K' and resid 152 through 159 removed outlier: 3.611A pdb=" N GLY K 152 " --> pdb=" O SER K 172 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N ARG K 168 " --> pdb=" O VAL K 156 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N ILE K 158 " --> pdb=" O THR K 166 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N THR K 166 " --> pdb=" O ILE K 158 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'K' and resid 268 through 273 removed outlier: 4.034A pdb=" N SER K 268 " --> pdb=" O SER K 288 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N THR K 284 " --> pdb=" O GLU K 272 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'K' and resid 409 through 413 673 hydrogen bonds defined for protein. 1965 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 40 hydrogen bonds 76 hydrogen bond angles 0 basepair planarities 17 basepair parallelities 32 stacking parallelities Total time for adding SS restraints: 3.50 Time building geometry restraints manager: 1.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.09 - 1.33: 3529 1.33 - 1.57: 12958 1.57 - 1.80: 200 1.80 - 2.04: 27 2.04 - 2.28: 1 Bond restraints: 16715 Sorted by residual: bond pdb=" CB PRO A2188 " pdb=" CG PRO A2188 " ideal model delta sigma weight residual 1.492 2.280 -0.788 5.00e-02 4.00e+02 2.49e+02 bond pdb=" CG PRO A2188 " pdb=" CD PRO A2188 " ideal model delta sigma weight residual 1.503 1.091 0.412 3.40e-02 8.65e+02 1.47e+02 bond pdb=" CG PRO K 251 " pdb=" CD PRO K 251 " ideal model delta sigma weight residual 1.503 1.094 0.409 3.40e-02 8.65e+02 1.45e+02 bond pdb=" CG PRO K 165 " pdb=" CD PRO K 165 " ideal model delta sigma weight residual 1.503 1.125 0.378 3.40e-02 8.65e+02 1.24e+02 bond pdb=" O5' U5P E 101 " pdb=" P U5P E 101 " ideal model delta sigma weight residual 1.711 1.588 0.123 2.00e-02 2.50e+03 3.78e+01 ... (remaining 16710 not shown) Histogram of bond angle deviations from ideal: 0.00 - 16.15: 22866 16.15 - 32.30: 9 32.30 - 48.46: 0 48.46 - 64.61: 0 64.61 - 80.76: 2 Bond angle restraints: 22877 Sorted by residual: angle pdb=" CB PRO A2188 " pdb=" CG PRO A2188 " pdb=" CD PRO A2188 " ideal model delta sigma weight residual 106.10 25.34 80.76 3.20e+00 9.77e-02 6.37e+02 angle pdb=" CB PRO K 251 " pdb=" CG PRO K 251 " pdb=" CD PRO K 251 " ideal model delta sigma weight residual 106.10 179.94 -73.84 3.20e+00 9.77e-02 5.32e+02 angle pdb=" CA PRO A2188 " pdb=" N PRO A2188 " pdb=" CD PRO A2188 " ideal model delta sigma weight residual 112.00 83.27 28.73 1.40e+00 5.10e-01 4.21e+02 angle pdb=" N PRO K 251 " pdb=" CD PRO K 251 " pdb=" CG PRO K 251 " ideal model delta sigma weight residual 103.20 72.61 30.59 1.50e+00 4.44e-01 4.16e+02 angle pdb=" N PRO K 165 " pdb=" CD PRO K 165 " pdb=" CG PRO K 165 " ideal model delta sigma weight residual 103.20 77.96 25.24 1.50e+00 4.44e-01 2.83e+02 ... (remaining 22872 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.56: 9546 27.56 - 55.12: 477 55.12 - 82.67: 25 82.67 - 110.23: 7 110.23 - 137.79: 1 Dihedral angle restraints: 10056 sinusoidal: 4515 harmonic: 5541 Sorted by residual: dihedral pdb=" CA ALA A 606 " pdb=" C ALA A 606 " pdb=" N PRO A 607 " pdb=" CA PRO A 607 " ideal model delta harmonic sigma weight residual 180.00 125.49 54.51 0 5.00e+00 4.00e-02 1.19e+02 dihedral pdb=" CA GLN A 862 " pdb=" C GLN A 862 " pdb=" N TYR A 863 " pdb=" CA TYR A 863 " ideal model delta harmonic sigma weight residual 180.00 130.97 49.03 0 5.00e+00 4.00e-02 9.62e+01 dihedral pdb=" N PRO A2188 " pdb=" CG PRO A2188 " pdb=" CD PRO A2188 " pdb=" CB PRO A2188 " ideal model delta sinusoidal sigma weight residual -30.00 -167.79 137.79 1 1.50e+01 4.44e-03 7.43e+01 ... (remaining 10053 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.098: 2364 0.098 - 0.195: 202 0.195 - 0.293: 15 0.293 - 0.390: 13 0.390 - 0.488: 1 Chirality restraints: 2595 Sorted by residual: chirality pdb=" CG LEU A 50 " pdb=" CB LEU A 50 " pdb=" CD1 LEU A 50 " pdb=" CD2 LEU A 50 " both_signs ideal model delta sigma weight residual False -2.59 -2.10 -0.49 2.00e-01 2.50e+01 5.95e+00 chirality pdb=" CB VAL A 14 " pdb=" CA VAL A 14 " pdb=" CG1 VAL A 14 " pdb=" CG2 VAL A 14 " both_signs ideal model delta sigma weight residual False -2.63 -2.25 -0.38 2.00e-01 2.50e+01 3.67e+00 chirality pdb=" CB VAL A 22 " pdb=" CA VAL A 22 " pdb=" CG1 VAL A 22 " pdb=" CG2 VAL A 22 " both_signs ideal model delta sigma weight residual False -2.63 -2.25 -0.38 2.00e-01 2.50e+01 3.59e+00 ... (remaining 2592 not shown) Planarity restraints: 2767 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN K 250 " 0.113 5.00e-02 4.00e+02 1.70e-01 4.63e+01 pdb=" N PRO K 251 " -0.294 5.00e-02 4.00e+02 pdb=" CA PRO K 251 " 0.102 5.00e-02 4.00e+02 pdb=" CD PRO K 251 " 0.079 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 863 " 0.034 2.00e-02 2.50e+03 2.90e-02 1.68e+01 pdb=" CG TYR A 863 " -0.070 2.00e-02 2.50e+03 pdb=" CD1 TYR A 863 " 0.020 2.00e-02 2.50e+03 pdb=" CD2 TYR A 863 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR A 863 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR A 863 " 0.017 2.00e-02 2.50e+03 pdb=" CZ TYR A 863 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR A 863 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER A2165 " 0.065 5.00e-02 4.00e+02 9.51e-02 1.45e+01 pdb=" N PRO A2166 " -0.164 5.00e-02 4.00e+02 pdb=" CA PRO A2166 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO A2166 " 0.056 5.00e-02 4.00e+02 ... (remaining 2764 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 185 2.59 - 3.17: 12802 3.17 - 3.75: 26738 3.75 - 4.32: 35343 4.32 - 4.90: 57531 Nonbonded interactions: 132599 Sorted by model distance: nonbonded pdb=" OD1 ASP A1749 " pdb="MG MG A2301 " model vdw 2.013 2.170 nonbonded pdb=" OP1 C E 39 " pdb="MG MG E 102 " model vdw 2.045 2.170 nonbonded pdb=" OP2 C E 39 " pdb="MG MG E 108 " model vdw 2.050 2.170 nonbonded pdb=" OP2 A E 10 " pdb="MG MG E 105 " model vdw 2.057 2.170 nonbonded pdb=" O ILE A 357 " pdb=" OG SER A 361 " model vdw 2.215 3.040 ... (remaining 132594 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: 7.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 14.760 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 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:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6938 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 : 0.011 0.788 16716 Z= 0.374 Angle : 1.416 80.760 22877 Z= 0.665 Chirality : 0.062 0.488 2595 Planarity : 0.009 0.170 2767 Dihedral : 14.986 137.790 6454 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.32 % Allowed : 7.95 % Favored : 91.73 % Rotamer: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.92 % Cis-general : 0.00 % Twisted Proline : 1.83 % Twisted General : 0.06 % 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 (0.18), residues: 1849 helix: -1.41 (0.16), residues: 810 sheet: -1.94 (0.34), residues: 202 loop : -2.09 (0.21), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 518 TYR 0.070 0.003 TYR A 863 PHE 0.056 0.003 PHE K 173 TRP 0.032 0.002 TRP A 848 HIS 0.024 0.002 HIS A1896 Details of bonding type rmsd/Z covalent geometry : bond 0.01105 / 0.37 (16715) covalent geometry : angle 1.41635 / 0.66 (22877) hydrogen bonds : bond 0.13857 / 9.27 ( 702) hydrogen bonds : angle 7.17939 / 5.00 ( 2041) Misc. bond : bond 0.03985 / 2.10 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3698 Ramachandran restraints generated. 1849 Oldfield, 0 Emsley, 1849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3698 Ramachandran restraints generated. 1849 Oldfield, 0 Emsley, 1849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 183 time to evaluate : 0.565 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 529 TYR cc_start: 0.6776 (p90) cc_final: 0.6014 (p90) REVERT: A 1769 GLU cc_start: 0.6633 (pp20) cc_final: 0.6277 (pp20) REVERT: A 2166 PRO cc_start: 0.7639 (Cg_endo) cc_final: 0.7432 (Cg_exo) REVERT: K 314 MET cc_start: 0.5185 (pmm) cc_final: 0.4533 (pmm) outliers start: 0 outliers final: 0 residues processed: 183 average time/residue: 0.1070 time to fit residues: 29.9927 Evaluate side-chains 143 residues out of total 1673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 143 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 98 optimal weight: 0.6980 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 0.3980 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 0.6980 chunk 91 optimal weight: 0.0370 chunk 149 optimal weight: 0.9990 overall best weight: 0.5258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 150 GLN A 502 ASN ** A 830 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1124 GLN A1235 GLN ** A1544 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4570 r_free = 0.4570 target = 0.185383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.151869 restraints weight = 26986.175| |-----------------------------------------------------------------------------| r_work (start): 0.4177 rms_B_bonded: 2.89 r_work: 0.3987 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6999 moved from start: 0.1251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.122 16716 Z= 0.131 Angle : 0.669 14.465 22877 Z= 0.332 Chirality : 0.040 0.227 2595 Planarity : 0.007 0.144 2767 Dihedral : 8.834 102.703 2665 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.71 % Favored : 93.08 % Rotamer: Outliers : 1.14 % Allowed : 8.19 % Favored : 90.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.92 % Cis-general : 0.00 % Twisted Proline : 0.92 % Twisted General : 0.06 % 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: -1.70 (0.19), residues: 1849 helix: -0.24 (0.17), residues: 844 sheet: -2.18 (0.34), residues: 217 loop : -1.71 (0.22), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1065 TYR 0.039 0.001 TYR A 863 PHE 0.035 0.002 PHE A2171 TRP 0.009 0.001 TRP A 848 HIS 0.006 0.001 HIS A 303 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.13 (16715) covalent geometry : angle 0.66860 / 0.33 (22877) hydrogen bonds : bond 0.04152 / 2.81 ( 702) hydrogen bonds : angle 4.99603 / 3.47 ( 2041) Misc. bond : bond 0.00033 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3698 Ramachandran restraints generated. 1849 Oldfield, 0 Emsley, 1849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3698 Ramachandran restraints generated. 1849 Oldfield, 0 Emsley, 1849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 165 time to evaluate : 0.491 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 307 GLN cc_start: 0.6810 (mm110) cc_final: 0.6137 (mm-40) REVERT: A 863 TYR cc_start: 0.6920 (OUTLIER) cc_final: 0.6567 (m-80) REVERT: A 1208 TYR cc_start: 0.5387 (p90) cc_final: 0.4960 (p90) REVERT: A 1769 GLU cc_start: 0.6587 (pp20) cc_final: 0.6104 (pp20) REVERT: K 258 MET cc_start: 0.3920 (OUTLIER) cc_final: 0.1407 (mmp) outliers start: 19 outliers final: 9 residues processed: 176 average time/residue: 0.1271 time to fit residues: 33.9375 Evaluate side-chains 153 residues out of total 1673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 142 time to evaluate : 0.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 84 MET Chi-restraints excluded: chain A residue 863 TYR Chi-restraints excluded: chain A residue 1154 ILE Chi-restraints excluded: chain A residue 1616 LEU Chi-restraints excluded: chain A residue 1950 ILE Chi-restraints excluded: chain A residue 2205 VAL Chi-restraints excluded: chain K residue 140 LEU Chi-restraints excluded: chain K residue 258 MET Chi-restraints excluded: chain K residue 380 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 117 optimal weight: 0.6980 chunk 153 optimal weight: 0.9980 chunk 83 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 184 optimal weight: 1.9990 chunk 72 optimal weight: 5.9990 chunk 134 optimal weight: 1.9990 chunk 48 optimal weight: 9.9990 chunk 62 optimal weight: 0.5980 chunk 158 optimal weight: 1.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 303 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 344 HIS A1124 GLN A1287 GLN ** A1544 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4525 r_free = 0.4525 target = 0.181301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.147451 restraints weight = 27273.446| |-----------------------------------------------------------------------------| r_work (start): 0.4127 rms_B_bonded: 2.80 r_work: 0.3924 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7091 moved from start: 0.1515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 16716 Z= 0.175 Angle : 0.668 13.951 22877 Z= 0.329 Chirality : 0.042 0.252 2595 Planarity : 0.006 0.129 2767 Dihedral : 8.639 101.653 2665 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.46 % Favored : 92.32 % Rotamer: Outliers : 2.21 % Allowed : 11.95 % Favored : 85.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.92 % Cis-general : 0.00 % Twisted Proline : 0.92 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.44 (0.19), residues: 1849 helix: 0.06 (0.18), residues: 849 sheet: -2.07 (0.35), residues: 215 loop : -1.70 (0.22), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1141 TYR 0.039 0.002 TYR A 863 PHE 0.026 0.002 PHE A2171 TRP 0.012 0.001 TRP A 848 HIS 0.006 0.001 HIS A1896 Details of bonding type rmsd/Z covalent geometry : bond 0.00405 / 0.17 (16715) covalent geometry : angle 0.66789 / 0.33 (22877) hydrogen bonds : bond 0.04452 / 2.95 ( 702) hydrogen bonds : angle 4.87921 / 3.40 ( 2041) Misc. bond : bond 0.00078 / 0.04 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3698 Ramachandran restraints generated. 1849 Oldfield, 0 Emsley, 1849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3698 Ramachandran restraints generated. 1849 Oldfield, 0 Emsley, 1849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 139 time to evaluate : 0.584 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 37 LEU cc_start: 0.5976 (OUTLIER) cc_final: 0.5701 (tt) REVERT: A 231 MET cc_start: 0.5404 (mmt) cc_final: 0.4813 (tpp) REVERT: A 567 ILE cc_start: 0.7571 (OUTLIER) cc_final: 0.7284 (pt) REVERT: A 863 TYR cc_start: 0.6937 (OUTLIER) cc_final: 0.6519 (m-80) REVERT: A 1208 TYR cc_start: 0.5521 (p90) cc_final: 0.5039 (p90) REVERT: A 1769 GLU cc_start: 0.6648 (pp20) cc_final: 0.6148 (pp20) REVERT: K 423 PHE cc_start: 0.8595 (m-80) cc_final: 0.8033 (m-80) outliers start: 37 outliers final: 20 residues processed: 165 average time/residue: 0.1221 time to fit residues: 30.8223 Evaluate side-chains 161 residues out of total 1673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 138 time to evaluate : 0.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 53 GLU Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 84 MET Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 567 ILE Chi-restraints excluded: chain A residue 863 TYR Chi-restraints excluded: chain A residue 999 TYR Chi-restraints excluded: chain A residue 1243 THR Chi-restraints excluded: chain A residue 1289 ILE Chi-restraints excluded: chain A residue 1616 LEU Chi-restraints excluded: chain A residue 1930 LEU Chi-restraints excluded: chain A residue 1950 ILE Chi-restraints excluded: chain A residue 2062 LEU Chi-restraints excluded: chain A residue 2168 ILE Chi-restraints excluded: chain A residue 2205 VAL Chi-restraints excluded: chain K residue 202 ASP Chi-restraints excluded: chain K residue 375 THR Chi-restraints excluded: chain K residue 380 LEU Chi-restraints excluded: chain K residue 394 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 65 optimal weight: 0.1980 chunk 22 optimal weight: 0.9990 chunk 69 optimal weight: 1.9990 chunk 129 optimal weight: 5.9990 chunk 19 optimal weight: 0.8980 chunk 7 optimal weight: 0.9990 chunk 97 optimal weight: 0.8980 chunk 118 optimal weight: 0.6980 chunk 49 optimal weight: 1.9990 chunk 91 optimal weight: 3.9990 chunk 188 optimal weight: 4.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 303 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1062 ASN A1124 GLN A1287 GLN A1544 GLN K 448 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4552 r_free = 0.4552 target = 0.184039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.150465 restraints weight = 27171.418| |-----------------------------------------------------------------------------| r_work (start): 0.4159 rms_B_bonded: 2.80 r_work: 0.3973 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7014 moved from start: 0.1744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 16716 Z= 0.131 Angle : 0.619 11.092 22877 Z= 0.302 Chirality : 0.040 0.262 2595 Planarity : 0.005 0.112 2767 Dihedral : 8.471 102.322 2665 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.76 % Favored : 93.08 % Rotamer: Outliers : 2.39 % Allowed : 14.11 % Favored : 83.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.92 % Cis-general : 0.00 % Twisted Proline : 0.92 % 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: -1.11 (0.20), residues: 1849 helix: 0.41 (0.18), residues: 847 sheet: -1.93 (0.36), residues: 205 loop : -1.64 (0.22), residues: 797 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG K 306 TYR 0.037 0.001 TYR A 863 PHE 0.040 0.002 PHE A2171 TRP 0.012 0.001 TRP A 848 HIS 0.006 0.001 HIS A1896 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.13 (16715) covalent geometry : angle 0.61906 / 0.30 (22877) hydrogen bonds : bond 0.03830 / 2.56 ( 702) hydrogen bonds : angle 4.59074 / 3.18 ( 2041) Misc. bond : bond 0.00073 / 0.04 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3698 Ramachandran restraints generated. 1849 Oldfield, 0 Emsley, 1849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3698 Ramachandran restraints generated. 1849 Oldfield, 0 Emsley, 1849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 153 time to evaluate : 0.542 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 37 LEU cc_start: 0.5871 (OUTLIER) cc_final: 0.5537 (tt) REVERT: A 284 ASN cc_start: 0.6513 (t0) cc_final: 0.6112 (p0) REVERT: A 512 LEU cc_start: 0.6023 (mt) cc_final: 0.5821 (mt) REVERT: A 518 ARG cc_start: 0.7238 (mmp80) cc_final: 0.6975 (mmp80) REVERT: A 567 ILE cc_start: 0.7347 (OUTLIER) cc_final: 0.6971 (pt) REVERT: A 1070 LEU cc_start: 0.6628 (OUTLIER) cc_final: 0.6302 (pp) REVERT: A 1208 TYR cc_start: 0.5521 (p90) cc_final: 0.5035 (p90) REVERT: A 1769 GLU cc_start: 0.6562 (pp20) cc_final: 0.6114 (pp20) REVERT: A 1850 ILE cc_start: 0.6499 (OUTLIER) cc_final: 0.6060 (tp) REVERT: K 295 MET cc_start: 0.1419 (OUTLIER) cc_final: 0.1214 (mmp) REVERT: K 423 PHE cc_start: 0.8540 (m-80) cc_final: 0.7962 (m-80) outliers start: 40 outliers final: 22 residues processed: 182 average time/residue: 0.1210 time to fit residues: 33.8731 Evaluate side-chains 167 residues out of total 1673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 140 time to evaluate : 0.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 53 GLU Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 84 MET Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 567 ILE Chi-restraints excluded: chain A residue 1070 LEU Chi-restraints excluded: chain A residue 1154 ILE Chi-restraints excluded: chain A residue 1243 THR Chi-restraints excluded: chain A residue 1289 ILE Chi-restraints excluded: chain A residue 1850 ILE Chi-restraints excluded: chain A residue 1930 LEU Chi-restraints excluded: chain A residue 1950 ILE Chi-restraints excluded: chain A residue 2062 LEU Chi-restraints excluded: chain A residue 2168 ILE Chi-restraints excluded: chain A residue 2205 VAL Chi-restraints excluded: chain K residue 140 LEU Chi-restraints excluded: chain K residue 202 ASP Chi-restraints excluded: chain K residue 255 LEU Chi-restraints excluded: chain K residue 295 MET Chi-restraints excluded: chain K residue 375 THR Chi-restraints excluded: chain K residue 380 LEU Chi-restraints excluded: chain K residue 394 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 41 optimal weight: 2.9990 chunk 107 optimal weight: 0.9980 chunk 128 optimal weight: 1.9990 chunk 106 optimal weight: 0.9990 chunk 81 optimal weight: 1.9990 chunk 97 optimal weight: 4.9990 chunk 135 optimal weight: 7.9990 chunk 63 optimal weight: 0.0670 chunk 58 optimal weight: 4.9990 chunk 42 optimal weight: 0.5980 chunk 23 optimal weight: 3.9990 overall best weight: 0.9322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 303 HIS ** A 633 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1174 HIS ** K 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4533 r_free = 0.4533 target = 0.182503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.149132 restraints weight = 27137.315| |-----------------------------------------------------------------------------| r_work (start): 0.4143 rms_B_bonded: 2.96 r_work: 0.3945 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7042 moved from start: 0.1929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 16716 Z= 0.144 Angle : 0.619 13.964 22877 Z= 0.304 Chirality : 0.041 0.251 2595 Planarity : 0.005 0.102 2767 Dihedral : 8.347 103.219 2665 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.68 % Favored : 92.16 % Rotamer: Outliers : 2.81 % Allowed : 15.12 % Favored : 82.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.92 % Cis-general : 0.00 % Twisted Proline : 0.92 % 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: -1.00 (0.20), residues: 1849 helix: 0.57 (0.18), residues: 844 sheet: -1.94 (0.35), residues: 210 loop : -1.63 (0.22), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG K 311 TYR 0.012 0.001 TYR A 254 PHE 0.033 0.002 PHE A2171 TRP 0.013 0.001 TRP A 848 HIS 0.006 0.001 HIS A1174 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.14 (16715) covalent geometry : angle 0.61861 / 0.30 (22877) hydrogen bonds : bond 0.03890 / 2.57 ( 702) hydrogen bonds : angle 4.52730 / 3.14 ( 2041) Misc. bond : bond 0.00088 / 0.05 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3698 Ramachandran restraints generated. 1849 Oldfield, 0 Emsley, 1849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3698 Ramachandran restraints generated. 1849 Oldfield, 0 Emsley, 1849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 149 time to evaluate : 0.603 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 37 LEU cc_start: 0.6015 (OUTLIER) cc_final: 0.5678 (tt) REVERT: A 84 MET cc_start: 0.7545 (OUTLIER) cc_final: 0.7344 (mmm) REVERT: A 284 ASN cc_start: 0.6528 (t0) cc_final: 0.6145 (p0) REVERT: A 567 ILE cc_start: 0.7448 (OUTLIER) cc_final: 0.7066 (pt) REVERT: A 1070 LEU cc_start: 0.6695 (OUTLIER) cc_final: 0.6367 (pp) REVERT: A 1208 TYR cc_start: 0.5604 (p90) cc_final: 0.5134 (p90) REVERT: A 1769 GLU cc_start: 0.6664 (pp20) cc_final: 0.6198 (pp20) REVERT: A 1850 ILE cc_start: 0.6493 (OUTLIER) cc_final: 0.6040 (tp) REVERT: K 423 PHE cc_start: 0.8629 (m-80) cc_final: 0.8036 (m-80) outliers start: 47 outliers final: 31 residues processed: 180 average time/residue: 0.1138 time to fit residues: 31.7961 Evaluate side-chains 173 residues out of total 1673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 137 time to evaluate : 0.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 53 GLU Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 84 MET Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 567 ILE Chi-restraints excluded: chain A residue 966 CYS Chi-restraints excluded: chain A residue 1031 VAL Chi-restraints excluded: chain A residue 1070 LEU Chi-restraints excluded: chain A residue 1154 ILE Chi-restraints excluded: chain A residue 1174 HIS Chi-restraints excluded: chain A residue 1243 THR Chi-restraints excluded: chain A residue 1247 PHE Chi-restraints excluded: chain A residue 1289 ILE Chi-restraints excluded: chain A residue 1587 HIS Chi-restraints excluded: chain A residue 1616 LEU Chi-restraints excluded: chain A residue 1650 HIS Chi-restraints excluded: chain A residue 1850 ILE Chi-restraints excluded: chain A residue 1930 LEU Chi-restraints excluded: chain A residue 1950 ILE Chi-restraints excluded: chain A residue 2062 LEU Chi-restraints excluded: chain A residue 2094 ASP Chi-restraints excluded: chain A residue 2168 ILE Chi-restraints excluded: chain A residue 2205 VAL Chi-restraints excluded: chain K residue 140 LEU Chi-restraints excluded: chain K residue 202 ASP Chi-restraints excluded: chain K residue 255 LEU Chi-restraints excluded: chain K residue 375 THR Chi-restraints excluded: chain K residue 380 LEU Chi-restraints excluded: chain K residue 394 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 166 optimal weight: 4.9990 chunk 152 optimal weight: 4.9990 chunk 83 optimal weight: 0.5980 chunk 113 optimal weight: 1.9990 chunk 94 optimal weight: 2.9990 chunk 136 optimal weight: 4.9990 chunk 71 optimal weight: 0.5980 chunk 108 optimal weight: 6.9990 chunk 60 optimal weight: 0.7980 chunk 160 optimal weight: 0.8980 chunk 30 optimal weight: 1.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 830 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1174 HIS K 448 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4537 r_free = 0.4537 target = 0.182645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.149593 restraints weight = 27334.555| |-----------------------------------------------------------------------------| r_work (start): 0.4148 rms_B_bonded: 2.96 r_work: 0.3945 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7054 moved from start: 0.2019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 16716 Z= 0.147 Angle : 0.623 15.459 22877 Z= 0.305 Chirality : 0.041 0.244 2595 Planarity : 0.005 0.094 2767 Dihedral : 8.307 103.891 2665 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.36 % Favored : 92.48 % Rotamer: Outliers : 2.81 % Allowed : 16.68 % Favored : 80.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.92 % Cis-general : 0.00 % Twisted Proline : 0.92 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.95 (0.20), residues: 1849 helix: 0.57 (0.18), residues: 849 sheet: -1.94 (0.35), residues: 210 loop : -1.55 (0.23), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG K 311 TYR 0.018 0.001 TYR A 529 PHE 0.027 0.002 PHE A2171 TRP 0.020 0.001 TRP K 313 HIS 0.012 0.001 HIS K 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.15 (16715) covalent geometry : angle 0.62288 / 0.31 (22877) hydrogen bonds : bond 0.03864 / 2.56 ( 702) hydrogen bonds : angle 4.51197 / 3.13 ( 2041) Misc. bond : bond 0.00095 / 0.05 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3698 Ramachandran restraints generated. 1849 Oldfield, 0 Emsley, 1849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3698 Ramachandran restraints generated. 1849 Oldfield, 0 Emsley, 1849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 134 time to evaluate : 0.644 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 37 LEU cc_start: 0.5936 (OUTLIER) cc_final: 0.5582 (tt) REVERT: A 231 MET cc_start: 0.5310 (mmt) cc_final: 0.4754 (tpp) REVERT: A 284 ASN cc_start: 0.6451 (t0) cc_final: 0.6082 (p0) REVERT: A 1070 LEU cc_start: 0.6768 (OUTLIER) cc_final: 0.6461 (pp) REVERT: A 1208 TYR cc_start: 0.5648 (p90) cc_final: 0.5176 (p90) REVERT: A 1769 GLU cc_start: 0.6660 (pp20) cc_final: 0.6217 (pp20) REVERT: A 1850 ILE cc_start: 0.6499 (OUTLIER) cc_final: 0.5934 (tp) REVERT: K 423 PHE cc_start: 0.8634 (m-80) cc_final: 0.8027 (m-80) outliers start: 47 outliers final: 33 residues processed: 169 average time/residue: 0.1180 time to fit residues: 30.7267 Evaluate side-chains 166 residues out of total 1673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 130 time to evaluate : 0.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 53 GLU Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 514 GLU Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 966 CYS Chi-restraints excluded: chain A residue 999 TYR Chi-restraints excluded: chain A residue 1031 VAL Chi-restraints excluded: chain A residue 1070 LEU Chi-restraints excluded: chain A residue 1154 ILE Chi-restraints excluded: chain A residue 1174 HIS Chi-restraints excluded: chain A residue 1243 THR Chi-restraints excluded: chain A residue 1289 ILE Chi-restraints excluded: chain A residue 1547 ASN Chi-restraints excluded: chain A residue 1587 HIS Chi-restraints excluded: chain A residue 1616 LEU Chi-restraints excluded: chain A residue 1850 ILE Chi-restraints excluded: chain A residue 1930 LEU Chi-restraints excluded: chain A residue 1950 ILE Chi-restraints excluded: chain A residue 2062 LEU Chi-restraints excluded: chain A residue 2094 ASP Chi-restraints excluded: chain A residue 2205 VAL Chi-restraints excluded: chain K residue 140 LEU Chi-restraints excluded: chain K residue 171 VAL Chi-restraints excluded: chain K residue 202 ASP Chi-restraints excluded: chain K residue 255 LEU Chi-restraints excluded: chain K residue 375 THR Chi-restraints excluded: chain K residue 380 LEU Chi-restraints excluded: chain K residue 394 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 115 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 100 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 41 optimal weight: 0.8980 chunk 50 optimal weight: 0.9980 chunk 108 optimal weight: 5.9990 chunk 88 optimal weight: 3.9990 chunk 34 optimal weight: 0.7980 chunk 167 optimal weight: 5.9990 chunk 139 optimal weight: 2.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 159 HIS A1174 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4518 r_free = 0.4518 target = 0.180906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.147608 restraints weight = 27239.873| |-----------------------------------------------------------------------------| r_work (start): 0.4121 rms_B_bonded: 2.93 r_work: 0.3915 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7102 moved from start: 0.2119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 16716 Z= 0.178 Angle : 0.656 16.679 22877 Z= 0.321 Chirality : 0.042 0.244 2595 Planarity : 0.005 0.086 2767 Dihedral : 8.328 105.280 2665 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.16 % Allowed : 8.06 % Favored : 91.78 % Rotamer: Outliers : 2.93 % Allowed : 17.75 % Favored : 79.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.92 % Cis-general : 0.00 % Twisted Proline : 0.92 % 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: -1.07 (0.20), residues: 1849 helix: 0.47 (0.18), residues: 848 sheet: -2.00 (0.35), residues: 210 loop : -1.61 (0.23), residues: 791 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 967 TYR 0.024 0.002 TYR A 529 PHE 0.026 0.002 PHE A2171 TRP 0.017 0.002 TRP K 313 HIS 0.008 0.001 HIS K 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00417 / 0.18 (16715) covalent geometry : angle 0.65587 / 0.32 (22877) hydrogen bonds : bond 0.04112 / 2.72 ( 702) hydrogen bonds : angle 4.60197 / 3.20 ( 2041) Misc. bond : bond 0.00119 / 0.06 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3698 Ramachandran restraints generated. 1849 Oldfield, 0 Emsley, 1849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3698 Ramachandran restraints generated. 1849 Oldfield, 0 Emsley, 1849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 137 time to evaluate : 0.563 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 37 LEU cc_start: 0.5961 (OUTLIER) cc_final: 0.5633 (tt) REVERT: A 231 MET cc_start: 0.5190 (mmt) cc_final: 0.4643 (tpp) REVERT: A 284 ASN cc_start: 0.6439 (t0) cc_final: 0.6062 (p0) REVERT: A 1070 LEU cc_start: 0.6705 (OUTLIER) cc_final: 0.6399 (pp) REVERT: A 1208 TYR cc_start: 0.5631 (p90) cc_final: 0.5188 (p90) REVERT: A 1769 GLU cc_start: 0.6715 (pp20) cc_final: 0.6217 (pp20) REVERT: A 1850 ILE cc_start: 0.6472 (OUTLIER) cc_final: 0.6108 (tp) REVERT: A 2189 GLU cc_start: 0.6155 (OUTLIER) cc_final: 0.5761 (tt0) REVERT: K 423 PHE cc_start: 0.8618 (m-80) cc_final: 0.7998 (m-80) outliers start: 49 outliers final: 35 residues processed: 172 average time/residue: 0.1102 time to fit residues: 29.3622 Evaluate side-chains 170 residues out of total 1673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 131 time to evaluate : 0.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 53 GLU Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 514 GLU Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 966 CYS Chi-restraints excluded: chain A residue 1013 THR Chi-restraints excluded: chain A residue 1031 VAL Chi-restraints excluded: chain A residue 1070 LEU Chi-restraints excluded: chain A residue 1084 ILE Chi-restraints excluded: chain A residue 1154 ILE Chi-restraints excluded: chain A residue 1174 HIS Chi-restraints excluded: chain A residue 1243 THR Chi-restraints excluded: chain A residue 1289 ILE Chi-restraints excluded: chain A residue 1547 ASN Chi-restraints excluded: chain A residue 1587 HIS Chi-restraints excluded: chain A residue 1616 LEU Chi-restraints excluded: chain A residue 1756 ILE Chi-restraints excluded: chain A residue 1850 ILE Chi-restraints excluded: chain A residue 1930 LEU Chi-restraints excluded: chain A residue 1950 ILE Chi-restraints excluded: chain A residue 2094 ASP Chi-restraints excluded: chain A residue 2189 GLU Chi-restraints excluded: chain A residue 2205 VAL Chi-restraints excluded: chain K residue 140 LEU Chi-restraints excluded: chain K residue 158 ILE Chi-restraints excluded: chain K residue 171 VAL Chi-restraints excluded: chain K residue 202 ASP Chi-restraints excluded: chain K residue 255 LEU Chi-restraints excluded: chain K residue 375 THR Chi-restraints excluded: chain K residue 380 LEU Chi-restraints excluded: chain K residue 394 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 93 optimal weight: 0.5980 chunk 59 optimal weight: 0.9990 chunk 142 optimal weight: 0.2980 chunk 116 optimal weight: 0.8980 chunk 155 optimal weight: 0.9990 chunk 162 optimal weight: 2.9990 chunk 37 optimal weight: 0.0970 chunk 48 optimal weight: 9.9990 chunk 115 optimal weight: 1.9990 chunk 143 optimal weight: 0.5980 chunk 49 optimal weight: 0.6980 overall best weight: 0.4578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1174 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4557 r_free = 0.4557 target = 0.184547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.151435 restraints weight = 27142.531| |-----------------------------------------------------------------------------| r_work (start): 0.4171 rms_B_bonded: 2.72 r_work: 0.3989 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6981 moved from start: 0.2240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 16716 Z= 0.114 Angle : 0.611 15.438 22877 Z= 0.296 Chirality : 0.040 0.240 2595 Planarity : 0.005 0.078 2767 Dihedral : 8.195 104.422 2665 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.06 % Favored : 93.78 % Rotamer: Outliers : 2.21 % Allowed : 18.53 % Favored : 79.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.92 % Cis-general : 0.00 % Twisted Proline : 0.92 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.78 (0.20), residues: 1849 helix: 0.77 (0.18), residues: 847 sheet: -1.91 (0.35), residues: 208 loop : -1.51 (0.23), residues: 794 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1170 TYR 0.025 0.001 TYR A 529 PHE 0.024 0.001 PHE A2171 TRP 0.019 0.001 TRP K 313 HIS 0.006 0.001 HIS K 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.11 (16715) covalent geometry : angle 0.61071 / 0.30 (22877) hydrogen bonds : bond 0.03522 / 2.36 ( 702) hydrogen bonds : angle 4.36222 / 3.02 ( 2041) Misc. bond : bond 0.00057 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3698 Ramachandran restraints generated. 1849 Oldfield, 0 Emsley, 1849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3698 Ramachandran restraints generated. 1849 Oldfield, 0 Emsley, 1849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 148 time to evaluate : 0.482 Fit side-chains revert: symmetry clash REVERT: A 37 LEU cc_start: 0.5680 (OUTLIER) cc_final: 0.5329 (tt) REVERT: A 53 GLU cc_start: 0.7142 (OUTLIER) cc_final: 0.6736 (mt-10) REVERT: A 231 MET cc_start: 0.5059 (mmt) cc_final: 0.4504 (tpp) REVERT: A 284 ASN cc_start: 0.6407 (t0) cc_final: 0.6052 (p0) REVERT: A 518 ARG cc_start: 0.7136 (mmp80) cc_final: 0.6877 (mmp80) REVERT: A 1070 LEU cc_start: 0.6699 (OUTLIER) cc_final: 0.6447 (pp) REVERT: A 1208 TYR cc_start: 0.5589 (p90) cc_final: 0.5142 (p90) REVERT: A 1769 GLU cc_start: 0.6475 (pp20) cc_final: 0.6114 (pp20) REVERT: A 1850 ILE cc_start: 0.6452 (OUTLIER) cc_final: 0.6101 (tp) REVERT: A 2026 ASP cc_start: 0.7488 (t70) cc_final: 0.7252 (t70) REVERT: A 2189 GLU cc_start: 0.6171 (OUTLIER) cc_final: 0.5774 (tt0) REVERT: K 423 PHE cc_start: 0.8573 (m-80) cc_final: 0.7954 (m-80) outliers start: 37 outliers final: 24 residues processed: 176 average time/residue: 0.1210 time to fit residues: 32.7627 Evaluate side-chains 167 residues out of total 1673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 138 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 53 GLU Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 514 GLU Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 863 TYR Chi-restraints excluded: chain A residue 966 CYS Chi-restraints excluded: chain A residue 999 TYR Chi-restraints excluded: chain A residue 1031 VAL Chi-restraints excluded: chain A residue 1070 LEU Chi-restraints excluded: chain A residue 1174 HIS Chi-restraints excluded: chain A residue 1243 THR Chi-restraints excluded: chain A residue 1587 HIS Chi-restraints excluded: chain A residue 1616 LEU Chi-restraints excluded: chain A residue 1850 ILE Chi-restraints excluded: chain A residue 1930 LEU Chi-restraints excluded: chain A residue 2094 ASP Chi-restraints excluded: chain A residue 2189 GLU Chi-restraints excluded: chain A residue 2205 VAL Chi-restraints excluded: chain K residue 140 LEU Chi-restraints excluded: chain K residue 202 ASP Chi-restraints excluded: chain K residue 255 LEU Chi-restraints excluded: chain K residue 375 THR Chi-restraints excluded: chain K residue 380 LEU Chi-restraints excluded: chain K residue 394 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 29 optimal weight: 2.9990 chunk 191 optimal weight: 5.9990 chunk 102 optimal weight: 3.9990 chunk 112 optimal weight: 0.2980 chunk 192 optimal weight: 5.9990 chunk 124 optimal weight: 3.9990 chunk 119 optimal weight: 0.6980 chunk 52 optimal weight: 0.2980 chunk 109 optimal weight: 3.9990 chunk 104 optimal weight: 0.7980 chunk 58 optimal weight: 4.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 303 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1174 HIS A2223 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4534 r_free = 0.4534 target = 0.182448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.149657 restraints weight = 27186.633| |-----------------------------------------------------------------------------| r_work (start): 0.4146 rms_B_bonded: 2.93 r_work: 0.3943 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7056 moved from start: 0.2271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 16716 Z= 0.151 Angle : 0.643 17.254 22877 Z= 0.312 Chirality : 0.041 0.234 2595 Planarity : 0.005 0.071 2767 Dihedral : 8.156 104.743 2665 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.52 % Favored : 92.32 % Rotamer: Outliers : 2.33 % Allowed : 18.71 % Favored : 78.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.92 % Cis-general : 0.00 % Twisted Proline : 0.92 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.80 (0.20), residues: 1849 helix: 0.71 (0.18), residues: 840 sheet: -1.86 (0.35), residues: 208 loop : -1.48 (0.23), residues: 801 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG K 311 TYR 0.025 0.001 TYR A 529 PHE 0.022 0.002 PHE A2171 TRP 0.017 0.001 TRP K 313 HIS 0.007 0.001 HIS K 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.15 (16715) covalent geometry : angle 0.64283 / 0.31 (22877) hydrogen bonds : bond 0.03839 / 2.54 ( 702) hydrogen bonds : angle 4.44402 / 3.08 ( 2041) Misc. bond : bond 0.00099 / 0.05 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3698 Ramachandran restraints generated. 1849 Oldfield, 0 Emsley, 1849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3698 Ramachandran restraints generated. 1849 Oldfield, 0 Emsley, 1849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 139 time to evaluate : 0.514 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 37 LEU cc_start: 0.5884 (OUTLIER) cc_final: 0.5535 (tt) REVERT: A 84 MET cc_start: 0.7731 (mmm) cc_final: 0.7458 (mmt) REVERT: A 231 MET cc_start: 0.5105 (mmt) cc_final: 0.4585 (tpp) REVERT: A 284 ASN cc_start: 0.6366 (t0) cc_final: 0.6024 (p0) REVERT: A 518 ARG cc_start: 0.7067 (mmp80) cc_final: 0.6801 (mmp80) REVERT: A 1070 LEU cc_start: 0.6673 (OUTLIER) cc_final: 0.6347 (pp) REVERT: A 1208 TYR cc_start: 0.5635 (p90) cc_final: 0.5185 (p90) REVERT: A 1769 GLU cc_start: 0.6670 (pp20) cc_final: 0.6261 (pp20) REVERT: A 2026 ASP cc_start: 0.7641 (t70) cc_final: 0.7385 (t70) REVERT: A 2189 GLU cc_start: 0.6178 (OUTLIER) cc_final: 0.5780 (tt0) REVERT: K 423 PHE cc_start: 0.8597 (m-80) cc_final: 0.7959 (m-80) outliers start: 39 outliers final: 30 residues processed: 166 average time/residue: 0.1259 time to fit residues: 31.9940 Evaluate side-chains 170 residues out of total 1673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 137 time to evaluate : 0.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 53 GLU Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 514 GLU Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 966 CYS Chi-restraints excluded: chain A residue 999 TYR Chi-restraints excluded: chain A residue 1013 THR Chi-restraints excluded: chain A residue 1031 VAL Chi-restraints excluded: chain A residue 1070 LEU Chi-restraints excluded: chain A residue 1121 ARG Chi-restraints excluded: chain A residue 1174 HIS Chi-restraints excluded: chain A residue 1243 THR Chi-restraints excluded: chain A residue 1587 HIS Chi-restraints excluded: chain A residue 1616 LEU Chi-restraints excluded: chain A residue 1930 LEU Chi-restraints excluded: chain A residue 1950 ILE Chi-restraints excluded: chain A residue 2094 ASP Chi-restraints excluded: chain A residue 2189 GLU Chi-restraints excluded: chain A residue 2205 VAL Chi-restraints excluded: chain K residue 140 LEU Chi-restraints excluded: chain K residue 158 ILE Chi-restraints excluded: chain K residue 202 ASP Chi-restraints excluded: chain K residue 375 THR Chi-restraints excluded: chain K residue 380 LEU Chi-restraints excluded: chain K residue 394 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 41 optimal weight: 4.9990 chunk 54 optimal weight: 0.9990 chunk 149 optimal weight: 0.9990 chunk 121 optimal weight: 0.9990 chunk 119 optimal weight: 0.7980 chunk 127 optimal weight: 0.9990 chunk 72 optimal weight: 4.9990 chunk 50 optimal weight: 0.7980 chunk 15 optimal weight: 1.9990 chunk 31 optimal weight: 10.0000 chunk 182 optimal weight: 2.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 303 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1174 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4540 r_free = 0.4540 target = 0.182938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.150159 restraints weight = 27324.505| |-----------------------------------------------------------------------------| r_work (start): 0.4151 rms_B_bonded: 2.94 r_work: 0.3946 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7050 moved from start: 0.2317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 16716 Z= 0.145 Angle : 0.648 17.603 22877 Z= 0.313 Chirality : 0.041 0.229 2595 Planarity : 0.005 0.067 2767 Dihedral : 8.141 104.975 2665 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.19 % Favored : 92.64 % Rotamer: Outliers : 2.21 % Allowed : 18.83 % Favored : 78.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.92 % Cis-general : 0.00 % Twisted Proline : 0.92 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.79 (0.20), residues: 1849 helix: 0.70 (0.18), residues: 842 sheet: -1.87 (0.35), residues: 208 loop : -1.45 (0.23), residues: 799 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG K 306 TYR 0.027 0.001 TYR A 529 PHE 0.022 0.002 PHE A2171 TRP 0.017 0.001 TRP A 848 HIS 0.007 0.001 HIS A1174 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.15 (16715) covalent geometry : angle 0.64751 / 0.31 (22877) hydrogen bonds : bond 0.03786 / 2.51 ( 702) hydrogen bonds : angle 4.44725 / 3.09 ( 2041) Misc. bond : bond 0.00091 / 0.05 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3698 Ramachandran restraints generated. 1849 Oldfield, 0 Emsley, 1849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3698 Ramachandran restraints generated. 1849 Oldfield, 0 Emsley, 1849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 140 time to evaluate : 0.544 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 37 LEU cc_start: 0.5822 (OUTLIER) cc_final: 0.5459 (tt) REVERT: A 231 MET cc_start: 0.5097 (mmt) cc_final: 0.4597 (tpp) REVERT: A 284 ASN cc_start: 0.6451 (t0) cc_final: 0.6104 (p0) REVERT: A 518 ARG cc_start: 0.7054 (mmp80) cc_final: 0.6850 (mmp80) REVERT: A 1070 LEU cc_start: 0.6630 (OUTLIER) cc_final: 0.6404 (pp) REVERT: A 1208 TYR cc_start: 0.5656 (p90) cc_final: 0.5205 (p90) REVERT: A 1769 GLU cc_start: 0.6648 (pp20) cc_final: 0.6232 (pp20) REVERT: A 2026 ASP cc_start: 0.7620 (t70) cc_final: 0.7362 (t70) REVERT: A 2189 GLU cc_start: 0.6270 (OUTLIER) cc_final: 0.5764 (tt0) REVERT: K 423 PHE cc_start: 0.8618 (m-80) cc_final: 0.7974 (m-80) outliers start: 37 outliers final: 30 residues processed: 166 average time/residue: 0.1160 time to fit residues: 29.5383 Evaluate side-chains 172 residues out of total 1673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 139 time to evaluate : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 53 GLU Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 514 GLU Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 966 CYS Chi-restraints excluded: chain A residue 999 TYR Chi-restraints excluded: chain A residue 1013 THR Chi-restraints excluded: chain A residue 1031 VAL Chi-restraints excluded: chain A residue 1070 LEU Chi-restraints excluded: chain A residue 1121 ARG Chi-restraints excluded: chain A residue 1154 ILE Chi-restraints excluded: chain A residue 1174 HIS Chi-restraints excluded: chain A residue 1243 THR Chi-restraints excluded: chain A residue 1587 HIS Chi-restraints excluded: chain A residue 1616 LEU Chi-restraints excluded: chain A residue 1930 LEU Chi-restraints excluded: chain A residue 1950 ILE Chi-restraints excluded: chain A residue 2094 ASP Chi-restraints excluded: chain A residue 2189 GLU Chi-restraints excluded: chain A residue 2205 VAL Chi-restraints excluded: chain K residue 140 LEU Chi-restraints excluded: chain K residue 158 ILE Chi-restraints excluded: chain K residue 202 ASP Chi-restraints excluded: chain K residue 375 THR Chi-restraints excluded: chain K residue 380 LEU Chi-restraints excluded: chain K residue 394 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 114 optimal weight: 1.9990 chunk 105 optimal weight: 0.9990 chunk 111 optimal weight: 0.7980 chunk 1 optimal weight: 0.6980 chunk 131 optimal weight: 2.9990 chunk 61 optimal weight: 0.6980 chunk 4 optimal weight: 0.6980 chunk 191 optimal weight: 8.9990 chunk 47 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 151 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 303 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1174 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4546 r_free = 0.4546 target = 0.183545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.150681 restraints weight = 27108.968| |-----------------------------------------------------------------------------| r_work (start): 0.4155 rms_B_bonded: 2.89 r_work: 0.3959 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7022 moved from start: 0.2368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 16716 Z= 0.135 Angle : 0.642 17.520 22877 Z= 0.309 Chirality : 0.040 0.220 2595 Planarity : 0.005 0.067 2767 Dihedral : 8.096 104.975 2665 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.08 % Favored : 92.75 % Rotamer: Outliers : 2.21 % Allowed : 19.07 % Favored : 78.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.92 % Cis-general : 0.00 % Twisted Proline : 0.92 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.76 (0.20), residues: 1849 helix: 0.74 (0.18), residues: 844 sheet: -1.86 (0.35), residues: 208 loop : -1.46 (0.23), residues: 797 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1170 TYR 0.027 0.001 TYR A 529 PHE 0.022 0.001 PHE A2171 TRP 0.017 0.001 TRP A 848 HIS 0.009 0.001 HIS A1174 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.14 (16715) covalent geometry : angle 0.64173 / 0.31 (22877) hydrogen bonds : bond 0.03698 / 2.45 ( 702) hydrogen bonds : angle 4.41561 / 3.06 ( 2041) Misc. bond : bond 0.00081 / 0.04 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3878.00 seconds wall clock time: 67 minutes 20.69 seconds (4040.69 seconds total)