Starting phenix.real_space_refine on Sat Jul 4 00:20:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8dfv_27415/07_2026/8dfv_27415.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dfv_27415/07_2026/8dfv_27415.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.06 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8dfv_27415/07_2026/8dfv_27415.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dfv_27415/07_2026/8dfv_27415.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8dfv_27415/07_2026/8dfv_27415.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dfv_27415/07_2026/8dfv_27415.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8dfv_27415/07_2026/8dfv_27415.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8dfv_27415/07_2026/8dfv_27415.cif" } resolution = 3.06 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= -0.001 sd= 0.070 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 Ca 10 9.91 5 P 60 5.49 5 S 91 5.16 5 C 10365 2.51 5 N 2935 2.21 5 O 3249 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.02s 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: 16710 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 13422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1664, 13422 Classifications: {'peptide': 1664} Link IDs: {'PTRANS': 97, 'TRANS': 1566} Chain breaks: 12 Chain: "E" Number of atoms: 1266 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 1266 Classifications: {'RNA': 60} Modifications used: {'p5*END': 1, 'rna2p_pur': 1, 'rna2p_pyr': 1, 'rna3p_pur': 27, 'rna3p_pyr': 31} Link IDs: {'rna2p': 2, 'rna3p': 57} Chain: "K" Number of atoms: 2012 Number of conformers: 1 Conformer: "" Number of residues, atoms: 253, 2012 Classifications: {'peptide': 253} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 240} Chain breaks: 2 Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' CA': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "E" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Unusual residues: {' CA': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Time building chain proxies: 3.62, per 1000 atoms: 0.22 Number of scatterers: 16710 At special positions: 0 Unit cell: (156.88, 130.38, 146.28, 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) Ca 10 19.99 S 91 16.00 P 60 15.00 O 3249 8.00 N 2935 7.00 C 10365 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=0, symmetry=0 Time building additional restraints: 1.51 Conformation dependent library (CDL) restraints added in 621.1 milliseconds 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3660 Finding SS restraints... Secondary structure from input PDB file: 65 helices and 19 sheets defined 46.8% alpha, 9.0% beta 19 base pairs and 39 stacking pairs defined. Time for finding SS restraints: 2.03 Creating SS restraints... Processing helix chain 'A' and resid 19 through 31 removed outlier: 3.784A pdb=" N GLU A 23 " --> pdb=" O ASP A 19 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLU A 30 " --> pdb=" O ALA A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 39 through 59 Processing helix chain 'A' and resid 79 through 88 removed outlier: 4.256A pdb=" N THR A 83 " --> pdb=" O CYS A 79 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N MET A 84 " --> pdb=" O SER A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 111 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 removed outlier: 3.578A pdb=" N LEU A 192 " --> pdb=" O LEU A 188 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ALA A 193 " --> pdb=" O SER A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 215 removed outlier: 3.535A pdb=" N VAL A 212 " --> pdb=" O ASP A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 252 removed outlier: 3.840A pdb=" N ASP A 251 " --> pdb=" O SER A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 293 removed outlier: 4.535A pdb=" N VAL A 288 " --> pdb=" O ASN A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 313 removed outlier: 4.198A pdb=" N HIS A 304 " --> pdb=" O ARG A 300 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LYS A 311 " --> pdb=" O GLN A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 344 removed outlier: 3.738A pdb=" N ALA A 342 " --> pdb=" O LEU A 338 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N PHE A 343 " --> pdb=" O CYS A 339 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N HIS A 344 " --> pdb=" O GLU A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 361 Processing helix chain 'A' and resid 362 through 375 Processing helix chain 'A' and resid 501 through 517 Processing helix chain 'A' and resid 520 through 524 removed outlier: 3.837A pdb=" N LYS A 523 " --> pdb=" O PRO A 520 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N PHE A 524 " --> pdb=" O ASP A 521 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 520 through 524' Processing helix chain 'A' and resid 540 through 560 removed outlier: 3.907A pdb=" N ARG A 557 " --> pdb=" O GLU A 553 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ARG A 559 " --> pdb=" O LEU A 555 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N MET A 560 " --> pdb=" O LYS A 556 " (cutoff:3.500A) Processing helix chain 'A' and resid 569 through 573 removed outlier: 3.659A pdb=" N GLU A 573 " --> pdb=" O SER A 570 " (cutoff:3.500A) Processing helix chain 'A' and resid 592 through 601 removed outlier: 3.633A pdb=" N CYS A 599 " --> pdb=" O SER A 595 " (cutoff:3.500A) Processing helix chain 'A' and resid 629 through 639 Processing helix chain 'A' and resid 760 through 785 Processing helix chain 'A' and resid 791 through 801 removed outlier: 3.570A pdb=" N GLN A 795 " --> pdb=" O PRO A 791 " (cutoff:3.500A) Processing helix chain 'A' and resid 822 through 834 removed outlier: 4.091A pdb=" N ILE A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 884 through 904 Processing helix chain 'A' and resid 922 through 927 removed outlier: 3.516A pdb=" N GLU A 926 " --> pdb=" O PRO A 923 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N CYS A 927 " --> pdb=" O ASP A 924 " (cutoff:3.500A) Processing helix chain 'A' and resid 931 through 941 removed outlier: 3.792A pdb=" N GLU A 935 " --> pdb=" O GLU A 931 " (cutoff:3.500A) Processing helix chain 'A' and resid 1045 through 1062 removed outlier: 3.705A pdb=" N ILE A1049 " --> pdb=" O THR A1045 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N VAL A1050 " --> pdb=" O SER A1046 " (cutoff:3.500A) Processing helix chain 'A' and resid 1098 through 1108 Processing helix chain 'A' and resid 1117 through 1124 removed outlier: 3.735A pdb=" N ARG A1121 " --> pdb=" O PRO A1117 " (cutoff:3.500A) Processing helix chain 'A' and resid 1230 through 1234 removed outlier: 3.967A pdb=" N LYS A1234 " --> pdb=" O LEU A1231 " (cutoff:3.500A) Processing helix chain 'A' and resid 1238 through 1242 removed outlier: 3.776A pdb=" N CYS A1242 " --> pdb=" O PRO A1239 " (cutoff:3.500A) Processing helix chain 'A' and resid 1248 through 1282 Proline residue: A1259 - end of helix Processing helix chain 'A' and resid 1524 through 1546 removed outlier: 4.648A pdb=" N GLN A1541 " --> pdb=" O ALA A1537 " (cutoff:3.500A) Processing helix chain 'A' and resid 1568 through 1581 Processing helix chain 'A' and resid 1607 through 1616 Processing helix chain 'A' and resid 1620 through 1629 removed outlier: 4.053A pdb=" N LEU A1624 " --> pdb=" O ASN A1620 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N LYS A1626 " --> pdb=" O ASP A1622 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLY A1629 " --> pdb=" O ALA A1625 " (cutoff:3.500A) Processing helix chain 'A' and resid 1636 through 1650 removed outlier: 3.510A pdb=" N HIS A1650 " --> pdb=" O TRP A1646 " (cutoff:3.500A) Processing helix chain 'A' and resid 1722 through 1731 Processing helix chain 'A' and resid 1732 through 1736 removed outlier: 3.735A pdb=" N ASN A1736 " --> pdb=" O SER A1733 " (cutoff:3.500A) Processing helix chain 'A' and resid 1741 through 1764 Processing helix chain 'A' and resid 1768 through 1780 removed outlier: 3.775A 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 1793 through 1797 Processing helix chain 'A' and resid 1838 through 1842 removed outlier: 4.025A pdb=" N ASP A1841 " --> pdb=" O ASP A1838 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ILE A1842 " --> pdb=" O LEU A1839 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1838 through 1842' Processing helix chain 'A' and resid 1847 through 1852 Processing helix chain 'A' and resid 1900 through 1931 Proline residue: A1920 - end of helix Processing helix chain 'A' and resid 1981 through 1990 removed outlier: 3.526A pdb=" N LEU A1990 " --> pdb=" O LEU A1986 " (cutoff:3.500A) Processing helix chain 'A' and resid 1993 through 1999 Processing helix chain 'A' and resid 2007 through 2015 Processing helix chain 'A' and resid 2028 through 2049 removed outlier: 3.792A pdb=" N ALA A2037 " --> pdb=" O PHE A2033 " (cutoff:3.500A) Processing helix chain 'A' and resid 2055 through 2067 Processing helix chain 'A' and resid 2068 through 2079 Processing helix chain 'A' and resid 2089 through 2106 Processing helix chain 'A' and resid 2131 through 2149 removed outlier: 3.652A pdb=" N GLY A2135 " --> pdb=" O PRO A2131 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ALA A2142 " --> pdb=" O PHE A2138 " (cutoff:3.500A) Processing helix chain 'A' and resid 2155 through 2173 removed outlier: 3.696A pdb=" N VAL A2159 " --> pdb=" O VAL A2155 " (cutoff:3.500A) Proline residue: A2166 - end of helix removed outlier: 3.523A pdb=" N ASN A2173 " --> pdb=" O GLU A2169 " (cutoff:3.500A) Processing helix chain 'A' and resid 2178 through 2187 Processing helix chain 'A' and resid 2223 through 2239 Processing helix chain 'K' and resid 135 through 146 Processing helix chain 'K' and resid 188 through 204 Processing helix chain 'K' and resid 253 through 262 Processing helix chain 'K' and resid 300 through 319 Processing helix chain 'K' and resid 359 through 374 Processing helix chain 'K' and resid 376 through 384 removed outlier: 4.466A pdb=" N LEU K 380 " --> pdb=" O GLY K 376 " (cutoff:3.500A) Processing helix chain 'K' and resid 393 through 405 Processing helix chain 'K' and resid 443 through 464 Processing sheet with id=AA1, first strand: chain 'A' and resid 115 through 116 removed outlier: 7.831A pdb=" N LEU A 116 " --> pdb=" O SER A 65 " (cutoff:3.500A) removed outlier: 5.773A pdb=" N TYR A 67 " --> pdb=" O LEU A 116 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N VAL A 64 " --> pdb=" O GLU A 136 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N ILE A 138 " --> pdb=" O VAL A 64 " (cutoff:3.500A) removed outlier: 7.118A 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 220 through 221 removed outlier: 6.220A pdb=" N HIS A 220 " --> pdb=" O HIS A 610 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N ILE A 612 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N VAL A 224 " --> pdb=" O VAL A 614 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 220 through 221 removed outlier: 6.220A pdb=" N HIS A 220 " --> pdb=" O HIS A 610 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N ILE A 612 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N VAL A 584 " --> pdb=" O VAL A 611 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N LEU A 613 " --> pdb=" O VAL A 584 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N ARG A 586 " --> pdb=" O LEU A 613 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 527 through 529 Processing sheet with id=AA5, first strand: chain 'A' and resid 805 through 806 Processing sheet with id=AA6, first strand: chain 'A' and resid 847 through 850 Processing sheet with id=AA7, first strand: chain 'A' and resid 853 through 854 Processing sheet with id=AA8, first strand: chain 'A' and resid 952 through 956 removed outlier: 3.572A pdb=" N TYR A 955 " --> pdb=" O HIS A1896 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N HIS A1896 " --> pdb=" O TYR A 955 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1036 through 1042 removed outlier: 4.574A pdb=" N LEU A 976 " --> pdb=" O ALA A1038 " (cutoff:3.500A) removed outlier: 7.622A pdb=" N GLU A1040 " --> pdb=" O CYS A 974 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N CYS A 974 " --> pdb=" O GLU A1040 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 981 through 986 removed outlier: 6.626A pdb=" N GLU A1030 " --> pdb=" O GLN A 984 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 1072 through 1073 Processing sheet with id=AB3, first strand: chain 'A' and resid 1153 through 1155 removed outlier: 4.355A pdb=" N GLN A1235 " --> pdb=" O VAL A1194 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 1673 through 1674 removed outlier: 3.780A pdb=" N ASN A1674 " --> pdb=" O GLN A1679 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLN A1679 " --> pdb=" O ASN A1674 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 1937 through 1940 removed outlier: 4.038A pdb=" N VAL A1964 " --> pdb=" O THR A1938 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 2191 through 2193 removed outlier: 3.893A pdb=" N LYS A2192 " --> pdb=" O ASP A2210 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ASP A2210 " --> pdb=" O LYS A2192 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 2191 through 2193 removed outlier: 3.893A pdb=" N LYS A2192 " --> pdb=" O ASP A2210 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ASP A2210 " --> pdb=" O LYS A2192 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'K' and resid 152 through 160 removed outlier: 3.808A pdb=" N GLY K 152 " --> pdb=" O SER K 172 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N ARG K 168 " --> pdb=" O VAL K 156 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N ILE K 158 " --> pdb=" O THR K 166 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N THR K 166 " --> pdb=" O ILE K 158 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'K' and resid 268 through 273 removed outlier: 4.363A pdb=" N SER K 268 " --> pdb=" O SER K 288 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N SER K 288 " --> pdb=" O SER K 268 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N THR K 284 " --> pdb=" O GLU K 272 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'K' and resid 408 through 412 removed outlier: 4.205A pdb=" N GLU K 408 " --> pdb=" O SER K 430 " (cutoff:3.500A) 675 hydrogen bonds defined for protein. 1950 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 47 hydrogen bonds 94 hydrogen bond angles 0 basepair planarities 19 basepair parallelities 39 stacking parallelities Total time for adding SS restraints: 4.20 Time building geometry restraints manager: 1.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4007 1.33 - 1.45: 3761 1.45 - 1.57: 9176 1.57 - 1.69: 119 1.69 - 1.81: 126 Bond restraints: 17189 Sorted by residual: bond pdb=" CG ARG A 586 " pdb=" CD ARG A 586 " ideal model delta sigma weight residual 1.520 1.416 0.104 3.00e-02 1.11e+03 1.19e+01 bond pdb=" CD1 PHE A1996 " pdb=" CE1 PHE A1996 " ideal model delta sigma weight residual 1.382 1.286 0.096 3.00e-02 1.11e+03 1.02e+01 bond pdb=" CG1 ILE A2180 " pdb=" CD1 ILE A2180 " ideal model delta sigma weight residual 1.513 1.393 0.120 3.90e-02 6.57e+02 9.46e+00 bond pdb=" CG1 ILE A1898 " pdb=" CD1 ILE A1898 " ideal model delta sigma weight residual 1.513 1.399 0.114 3.90e-02 6.57e+02 8.49e+00 bond pdb=" CB PHE A1996 " pdb=" CG PHE A1996 " ideal model delta sigma weight residual 1.502 1.437 0.065 2.30e-02 1.89e+03 7.96e+00 ... (remaining 17184 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.83: 22800 2.83 - 5.66: 657 5.66 - 8.49: 92 8.49 - 11.33: 14 11.33 - 14.16: 6 Bond angle restraints: 23569 Sorted by residual: angle pdb=" OG1 THR A 851 " pdb=" CB THR A 851 " pdb=" CG2 THR A 851 " ideal model delta sigma weight residual 109.30 98.90 10.40 2.00e+00 2.50e-01 2.70e+01 angle pdb=" CB LEU A1930 " pdb=" CG LEU A1930 " pdb=" CD2 LEU A1930 " ideal model delta sigma weight residual 110.70 97.13 13.57 3.00e+00 1.11e-01 2.05e+01 angle pdb=" C PHE A 3 " pdb=" N HIS A 4 " pdb=" CA HIS A 4 " ideal model delta sigma weight residual 121.54 129.92 -8.38 1.91e+00 2.74e-01 1.93e+01 angle pdb=" C PHE K 173 " pdb=" N LYS K 174 " pdb=" CA LYS K 174 " ideal model delta sigma weight residual 121.54 129.86 -8.32 1.91e+00 2.74e-01 1.90e+01 angle pdb=" N LYS A1227 " pdb=" CA LYS A1227 " pdb=" C LYS A1227 " ideal model delta sigma weight residual 110.80 119.96 -9.16 2.13e+00 2.20e-01 1.85e+01 ... (remaining 23564 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.93: 10048 31.93 - 63.87: 270 63.87 - 95.80: 18 95.80 - 127.74: 0 127.74 - 159.67: 1 Dihedral angle restraints: 10337 sinusoidal: 4704 harmonic: 5633 Sorted by residual: dihedral pdb=" O4' U E 1 " pdb=" C1' U E 1 " pdb=" N1 U E 1 " pdb=" C2 U E 1 " ideal model delta sinusoidal sigma weight residual 232.00 72.33 159.67 1 1.70e+01 3.46e-03 6.44e+01 dihedral pdb=" CA GLY A1661 " pdb=" C GLY A1661 " pdb=" N ASP A1662 " pdb=" CA ASP A1662 " ideal model delta harmonic sigma weight residual -180.00 -145.34 -34.66 0 5.00e+00 4.00e-02 4.81e+01 dihedral pdb=" CA PRO A 912 " pdb=" C PRO A 912 " pdb=" N ILE A 913 " pdb=" CA ILE A 913 " ideal model delta harmonic sigma weight residual -180.00 -148.80 -31.20 0 5.00e+00 4.00e-02 3.89e+01 ... (remaining 10334 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.124: 2538 0.124 - 0.249: 128 0.249 - 0.373: 8 0.373 - 0.497: 0 0.497 - 0.622: 1 Chirality restraints: 2675 Sorted by residual: chirality pdb=" CB ILE A2180 " pdb=" CA ILE A2180 " pdb=" CG1 ILE A2180 " pdb=" CG2 ILE A2180 " both_signs ideal model delta sigma weight residual False 2.64 2.02 0.62 2.00e-01 2.50e+01 9.66e+00 chirality pdb=" CB VAL A2137 " pdb=" CA VAL A2137 " pdb=" CG1 VAL A2137 " pdb=" CG2 VAL A2137 " both_signs ideal model delta sigma weight residual False -2.63 -2.28 -0.35 2.00e-01 2.50e+01 3.05e+00 chirality pdb=" CB VAL A1934 " pdb=" CA VAL A1934 " pdb=" CG1 VAL A1934 " pdb=" CG2 VAL A1934 " both_signs ideal model delta sigma weight residual False -2.63 -2.29 -0.34 2.00e-01 2.50e+01 2.81e+00 ... (remaining 2672 not shown) Planarity restraints: 2827 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A1814 " -0.025 2.00e-02 2.50e+03 3.39e-02 2.30e+01 pdb=" CG TYR A1814 " 0.078 2.00e-02 2.50e+03 pdb=" CD1 TYR A1814 " -0.043 2.00e-02 2.50e+03 pdb=" CD2 TYR A1814 " -0.014 2.00e-02 2.50e+03 pdb=" CE1 TYR A1814 " 0.017 2.00e-02 2.50e+03 pdb=" CE2 TYR A1814 " -0.010 2.00e-02 2.50e+03 pdb=" CZ TYR A1814 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR A1814 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 863 " 0.032 2.00e-02 2.50e+03 2.87e-02 1.65e+01 pdb=" CG TYR A 863 " -0.068 2.00e-02 2.50e+03 pdb=" CD1 TYR A 863 " 0.025 2.00e-02 2.50e+03 pdb=" CD2 TYR A 863 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR A 863 " -0.008 2.00e-02 2.50e+03 pdb=" CE2 TYR A 863 " 0.015 2.00e-02 2.50e+03 pdb=" CZ TYR A 863 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR A 863 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A2020 " -0.060 5.00e-02 4.00e+02 8.95e-02 1.28e+01 pdb=" N PRO A2021 " 0.155 5.00e-02 4.00e+02 pdb=" CA PRO A2021 " -0.045 5.00e-02 4.00e+02 pdb=" CD PRO A2021 " -0.050 5.00e-02 4.00e+02 ... (remaining 2824 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.74: 1997 2.74 - 3.28: 16136 3.28 - 3.82: 29426 3.82 - 4.36: 35292 4.36 - 4.90: 57676 Nonbonded interactions: 140527 Sorted by model distance: nonbonded pdb=" O LEU A1727 " pdb=" OG1 THR A1731 " model vdw 2.206 3.040 nonbonded pdb=" O ILE A1950 " pdb=" OG SER A1953 " model vdw 2.223 3.040 nonbonded pdb=" OH TYR A 832 " pdb=" OG SER A 871 " model vdw 2.233 3.040 nonbonded pdb=" O SER A1162 " pdb=" OG1 THR A1171 " model vdw 2.236 3.040 nonbonded pdb=" OG SER A1999 " pdb=" O HIS A2079 " model vdw 2.265 3.040 ... (remaining 140522 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: 3.240 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.310 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 18.440 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:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7043 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 : 0.010 0.131 17189 Z= 0.419 Angle : 1.153 14.157 23569 Z= 0.589 Chirality : 0.064 0.622 2675 Planarity : 0.009 0.105 2827 Dihedral : 14.653 159.671 6677 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.32 % Allowed : 9.66 % Favored : 90.03 % Rotamer: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -2.99 (0.18), residues: 1885 helix: -1.54 (0.15), residues: 843 sheet: -2.30 (0.36), residues: 198 loop : -2.27 (0.21), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A1027 TYR 0.078 0.004 TYR A1814 PHE 0.054 0.005 PHE A2081 TRP 0.016 0.003 TRP K 254 HIS 0.031 0.002 HIS A1896 Details of bonding type rmsd/Z covalent geometry : bond 0.01010 / 0.42 (17189) covalent geometry : angle 1.15278 / 0.59 (23569) hydrogen bonds : bond 0.14451 / 10.18 ( 722) hydrogen bonds : angle 6.67804 / 4.78 ( 2044) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 1701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 294 time to evaluate : 0.622 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ILE cc_start: 0.7546 (tt) cc_final: 0.7148 (mt) REVERT: A 524 PHE cc_start: 0.6621 (p90) cc_final: 0.6262 (p90) REVERT: A 580 LYS cc_start: 0.6821 (pttt) cc_final: 0.6468 (mmtp) REVERT: A 1531 ILE cc_start: 0.5659 (mm) cc_final: 0.5431 (mt) REVERT: A 1818 LYS cc_start: 0.7669 (mttp) cc_final: 0.7398 (ptpt) REVERT: A 2067 VAL cc_start: 0.5822 (t) cc_final: 0.5540 (m) REVERT: K 176 LYS cc_start: 0.6323 (mmtt) cc_final: 0.6036 (ttpp) REVERT: K 311 ARG cc_start: 0.6867 (mtp85) cc_final: 0.6583 (mmm160) REVERT: K 369 LYS cc_start: 0.7885 (tmmt) cc_final: 0.7543 (tptp) REVERT: K 384 LYS cc_start: 0.8110 (mttp) cc_final: 0.7409 (tptt) outliers start: 0 outliers final: 0 residues processed: 294 average time/residue: 0.1569 time to fit residues: 67.0043 Evaluate side-chains 177 residues out of total 1701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 177 time to evaluate : 0.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 6.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 0.5980 chunk 91 optimal weight: 0.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 225 GLN ** A 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 245 HIS A 346 HIS A 773 GLN A1142 ASN A1235 GLN A1590 GLN A1784 ASN K 194 HIS ** K 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4455 r_free = 0.4455 target = 0.186008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.153279 restraints weight = 26179.412| |-----------------------------------------------------------------------------| r_work (start): 0.4087 rms_B_bonded: 2.40 r_work: 0.3920 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7095 moved from start: 0.1831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 17189 Z= 0.168 Angle : 0.723 11.956 23569 Z= 0.368 Chirality : 0.043 0.184 2675 Planarity : 0.006 0.063 2827 Dihedral : 9.971 155.689 2822 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 13.68 Ramachandran Plot: Outliers : 0.32 % Allowed : 7.37 % Favored : 92.31 % Rotamer: Outliers : 1.29 % Allowed : 8.05 % Favored : 90.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.96 (0.19), residues: 1885 helix: -0.42 (0.17), residues: 865 sheet: -2.34 (0.36), residues: 203 loop : -1.92 (0.22), residues: 817 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 218 TYR 0.024 0.002 TYR A 863 PHE 0.022 0.002 PHE A1707 TRP 0.014 0.001 TRP A 94 HIS 0.011 0.001 HIS A1768 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.17 (17189) covalent geometry : angle 0.72303 / 0.37 (23569) hydrogen bonds : bond 0.05174 / 3.59 ( 722) hydrogen bonds : angle 4.97560 / 3.59 ( 2044) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 215 time to evaluate : 0.605 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 GLU cc_start: 0.6234 (mm-30) cc_final: 0.5810 (mm-30) REVERT: A 81 ILE cc_start: 0.7488 (tt) cc_final: 0.7158 (tt) REVERT: A 191 MET cc_start: 0.6784 (ptp) cc_final: 0.6567 (ptp) REVERT: A 303 HIS cc_start: 0.6339 (OUTLIER) cc_final: 0.5434 (t70) REVERT: A 524 PHE cc_start: 0.6253 (p90) cc_final: 0.5941 (p90) REVERT: A 580 LYS cc_start: 0.7040 (pttt) cc_final: 0.6593 (mmtt) REVERT: A 930 LEU cc_start: 0.4623 (OUTLIER) cc_final: 0.4344 (pp) REVERT: A 1531 ILE cc_start: 0.5475 (mm) cc_final: 0.5268 (mt) REVERT: A 2197 GLU cc_start: 0.6196 (mm-30) cc_final: 0.5790 (mt-10) REVERT: K 176 LYS cc_start: 0.5755 (mmtt) cc_final: 0.5371 (ttpp) REVERT: K 311 ARG cc_start: 0.7533 (mtp85) cc_final: 0.6759 (mmm160) REVERT: K 312 MET cc_start: 0.4926 (tpp) cc_final: 0.4326 (tpp) REVERT: K 369 LYS cc_start: 0.7743 (tmmt) cc_final: 0.7439 (tptp) outliers start: 22 outliers final: 9 residues processed: 225 average time/residue: 0.1544 time to fit residues: 51.1195 Evaluate side-chains 187 residues out of total 1701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 176 time to evaluate : 0.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain A residue 303 HIS Chi-restraints excluded: chain A residue 813 HIS Chi-restraints excluded: chain A residue 930 LEU Chi-restraints excluded: chain A residue 1071 MET Chi-restraints excluded: chain A residue 1079 GLU Chi-restraints excluded: chain A residue 1927 MET Chi-restraints excluded: chain A residue 2097 ASP Chi-restraints excluded: chain A residue 2216 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 193 optimal weight: 0.8980 chunk 23 optimal weight: 3.9990 chunk 62 optimal weight: 0.9980 chunk 66 optimal weight: 5.9990 chunk 89 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 40 optimal weight: 5.9990 chunk 43 optimal weight: 2.9990 chunk 163 optimal weight: 0.8980 chunk 149 optimal weight: 0.9980 chunk 58 optimal weight: 3.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 243 ASN A 245 HIS A 984 GLN A1185 GLN A1806 HIS ** K 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4440 r_free = 0.4440 target = 0.184681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.151733 restraints weight = 26518.603| |-----------------------------------------------------------------------------| r_work (start): 0.4069 rms_B_bonded: 2.35 r_work: 0.3894 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7131 moved from start: 0.2160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 17189 Z= 0.181 Angle : 0.695 10.274 23569 Z= 0.352 Chirality : 0.043 0.202 2675 Planarity : 0.005 0.057 2827 Dihedral : 9.630 157.129 2822 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 13.10 Ramachandran Plot: Outliers : 0.32 % Allowed : 7.64 % Favored : 92.04 % Rotamer: Outliers : 1.82 % Allowed : 12.29 % Favored : 85.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.52 (0.19), residues: 1885 helix: 0.02 (0.17), residues: 867 sheet: -2.30 (0.36), residues: 204 loop : -1.74 (0.23), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 866 TYR 0.019 0.002 TYR A1914 PHE 0.022 0.002 PHE A1707 TRP 0.012 0.001 TRP A 5 HIS 0.009 0.001 HIS A1896 Details of bonding type rmsd/Z covalent geometry : bond 0.00416 / 0.18 (17189) covalent geometry : angle 0.69453 / 0.35 (23569) hydrogen bonds : bond 0.04997 / 3.48 ( 722) hydrogen bonds : angle 4.75515 / 3.42 ( 2044) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 202 time to evaluate : 0.454 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ILE cc_start: 0.7472 (tt) cc_final: 0.7174 (tt) REVERT: A 191 MET cc_start: 0.6766 (ptp) cc_final: 0.6520 (ptp) REVERT: A 303 HIS cc_start: 0.6264 (OUTLIER) cc_final: 0.5356 (t70) REVERT: A 341 HIS cc_start: 0.7056 (m-70) cc_final: 0.6714 (m90) REVERT: A 524 PHE cc_start: 0.6098 (p90) cc_final: 0.5751 (p90) REVERT: A 561 HIS cc_start: 0.6550 (m-70) cc_final: 0.6116 (m-70) REVERT: A 580 LYS cc_start: 0.7026 (pttt) cc_final: 0.6555 (mmtt) REVERT: A 890 ARG cc_start: 0.6627 (mtt-85) cc_final: 0.6398 (mtt-85) REVERT: A 930 LEU cc_start: 0.4664 (OUTLIER) cc_final: 0.4436 (pp) REVERT: A 991 GLN cc_start: 0.7373 (tp40) cc_final: 0.7081 (tp40) REVERT: A 1112 MET cc_start: 0.6553 (mpp) cc_final: 0.5871 (mpp) REVERT: A 2197 GLU cc_start: 0.6458 (mm-30) cc_final: 0.6041 (mt-10) REVERT: K 263 ARG cc_start: 0.4914 (mtp180) cc_final: 0.4288 (ptp-170) REVERT: K 311 ARG cc_start: 0.7450 (mtp85) cc_final: 0.6830 (mmm160) REVERT: K 312 MET cc_start: 0.4984 (tpp) cc_final: 0.4446 (tpp) REVERT: K 369 LYS cc_start: 0.7737 (tmmt) cc_final: 0.7354 (tptp) REVERT: K 397 LEU cc_start: 0.6109 (OUTLIER) cc_final: 0.5353 (mm) outliers start: 31 outliers final: 18 residues processed: 217 average time/residue: 0.1408 time to fit residues: 45.1900 Evaluate side-chains 193 residues out of total 1701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 172 time to evaluate : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain A residue 303 HIS Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 858 VAL Chi-restraints excluded: chain A residue 880 LEU Chi-restraints excluded: chain A residue 930 LEU Chi-restraints excluded: chain A residue 1071 MET Chi-restraints excluded: chain A residue 1587 HIS Chi-restraints excluded: chain A residue 1725 ILE Chi-restraints excluded: chain A residue 1816 VAL Chi-restraints excluded: chain A residue 1927 MET Chi-restraints excluded: chain A residue 2094 ASP Chi-restraints excluded: chain A residue 2097 ASP Chi-restraints excluded: chain A residue 2140 SER Chi-restraints excluded: chain A residue 2216 THR Chi-restraints excluded: chain K residue 150 THR Chi-restraints excluded: chain K residue 300 SER Chi-restraints excluded: chain K residue 397 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 109 optimal weight: 7.9990 chunk 136 optimal weight: 1.9990 chunk 95 optimal weight: 0.3980 chunk 17 optimal weight: 0.8980 chunk 76 optimal weight: 2.9990 chunk 111 optimal weight: 0.0570 chunk 48 optimal weight: 6.9990 chunk 196 optimal weight: 0.9980 chunk 21 optimal weight: 0.9980 chunk 131 optimal weight: 0.7980 chunk 116 optimal weight: 0.5980 overall best weight: 0.5498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 150 GLN A 245 HIS A1589 GLN A1656 ASN K 157 GLN K 383 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4473 r_free = 0.4473 target = 0.187881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.155160 restraints weight = 26317.163| |-----------------------------------------------------------------------------| r_work (start): 0.4108 rms_B_bonded: 2.43 r_work: 0.3942 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7051 moved from start: 0.2566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 17189 Z= 0.133 Angle : 0.643 9.319 23569 Z= 0.324 Chirality : 0.041 0.272 2675 Planarity : 0.005 0.055 2827 Dihedral : 9.402 159.291 2822 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.37 % Allowed : 6.10 % Favored : 93.53 % Rotamer: Outliers : 1.70 % Allowed : 14.17 % Favored : 84.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.04 (0.20), residues: 1885 helix: 0.48 (0.17), residues: 863 sheet: -2.15 (0.37), residues: 199 loop : -1.54 (0.23), residues: 823 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 354 TYR 0.022 0.001 TYR A 111 PHE 0.018 0.002 PHE K 367 TRP 0.011 0.001 TRP A 5 HIS 0.007 0.001 HIS A1896 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 (17189) covalent geometry : angle 0.64289 / 0.32 (23569) hydrogen bonds : bond 0.04321 / 3.03 ( 722) hydrogen bonds : angle 4.47331 / 3.23 ( 2044) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 207 time to evaluate : 0.486 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ILE cc_start: 0.7549 (tt) cc_final: 0.6976 (mt) REVERT: A 126 GLU cc_start: 0.6180 (mm-30) cc_final: 0.5910 (mm-30) REVERT: A 140 LEU cc_start: 0.8339 (OUTLIER) cc_final: 0.8106 (mt) REVERT: A 303 HIS cc_start: 0.6040 (OUTLIER) cc_final: 0.5272 (t70) REVERT: A 311 LYS cc_start: 0.8168 (mtmm) cc_final: 0.7474 (mptt) REVERT: A 341 HIS cc_start: 0.7056 (m-70) cc_final: 0.6624 (m90) REVERT: A 561 HIS cc_start: 0.6326 (m-70) cc_final: 0.6038 (m-70) REVERT: A 580 LYS cc_start: 0.6924 (pttt) cc_final: 0.6519 (mmtm) REVERT: A 930 LEU cc_start: 0.4592 (OUTLIER) cc_final: 0.4388 (pp) REVERT: A 969 VAL cc_start: 0.6424 (t) cc_final: 0.6155 (m) REVERT: A 977 TYR cc_start: 0.6486 (m-10) cc_final: 0.6219 (m-80) REVERT: A 1112 MET cc_start: 0.6715 (mpp) cc_final: 0.6502 (mpp) REVERT: A 1529 LEU cc_start: 0.6496 (mt) cc_final: 0.6042 (mp) REVERT: A 1666 ASN cc_start: 0.6801 (t0) cc_final: 0.6308 (t0) REVERT: A 2197 GLU cc_start: 0.6368 (mm-30) cc_final: 0.5963 (mt-10) REVERT: K 176 LYS cc_start: 0.5846 (mmtt) cc_final: 0.5280 (ttpp) REVERT: K 311 ARG cc_start: 0.7535 (mtp85) cc_final: 0.6879 (mmm160) REVERT: K 312 MET cc_start: 0.5088 (tpp) cc_final: 0.4502 (tpp) REVERT: K 369 LYS cc_start: 0.7721 (tmmt) cc_final: 0.7467 (tptt) outliers start: 29 outliers final: 14 residues processed: 222 average time/residue: 0.1290 time to fit residues: 43.0814 Evaluate side-chains 197 residues out of total 1701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 180 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 MET Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain A residue 303 HIS Chi-restraints excluded: chain A residue 521 ASP Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 858 VAL Chi-restraints excluded: chain A residue 930 LEU Chi-restraints excluded: chain A residue 1071 MET Chi-restraints excluded: chain A residue 1079 GLU Chi-restraints excluded: chain A residue 1583 MET Chi-restraints excluded: chain A residue 1927 MET Chi-restraints excluded: chain A residue 2094 ASP Chi-restraints excluded: chain A residue 2097 ASP Chi-restraints excluded: chain A residue 2216 THR Chi-restraints excluded: chain K residue 300 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 149 optimal weight: 4.9990 chunk 24 optimal weight: 8.9990 chunk 143 optimal weight: 0.9980 chunk 21 optimal weight: 0.9980 chunk 63 optimal weight: 0.5980 chunk 82 optimal weight: 0.4980 chunk 80 optimal weight: 0.9980 chunk 18 optimal weight: 5.9990 chunk 68 optimal weight: 8.9990 chunk 111 optimal weight: 0.0060 chunk 123 optimal weight: 1.9990 overall best weight: 0.6196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 150 GLN ** A 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 245 HIS A 341 HIS A1142 ASN A1656 ASN A2069 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4472 r_free = 0.4472 target = 0.187826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.155073 restraints weight = 26365.918| |-----------------------------------------------------------------------------| r_work (start): 0.4107 rms_B_bonded: 2.50 r_work: 0.3944 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7047 moved from start: 0.2767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 17189 Z= 0.134 Angle : 0.634 8.717 23569 Z= 0.318 Chirality : 0.041 0.237 2675 Planarity : 0.005 0.054 2827 Dihedral : 9.174 160.822 2822 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.37 % Allowed : 6.53 % Favored : 93.10 % Rotamer: Outliers : 2.00 % Allowed : 14.99 % Favored : 83.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.78 (0.20), residues: 1885 helix: 0.70 (0.18), residues: 862 sheet: -1.98 (0.38), residues: 192 loop : -1.43 (0.23), residues: 831 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1225 TYR 0.016 0.001 TYR A 111 PHE 0.023 0.002 PHE A2193 TRP 0.010 0.001 TRP A 5 HIS 0.011 0.001 HIS A1670 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.13 (17189) covalent geometry : angle 0.63364 / 0.32 (23569) hydrogen bonds : bond 0.04222 / 2.97 ( 722) hydrogen bonds : angle 4.38088 / 3.17 ( 2044) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 205 time to evaluate : 0.460 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ILE cc_start: 0.7366 (tt) cc_final: 0.6769 (mt) REVERT: A 104 PHE cc_start: 0.7323 (m-80) cc_final: 0.7027 (m-80) REVERT: A 140 LEU cc_start: 0.8314 (OUTLIER) cc_final: 0.8088 (mt) REVERT: A 303 HIS cc_start: 0.5956 (OUTLIER) cc_final: 0.5072 (t70) REVERT: A 311 LYS cc_start: 0.8198 (mtmm) cc_final: 0.7515 (mptt) REVERT: A 358 GLU cc_start: 0.6594 (tp30) cc_final: 0.5860 (mm-30) REVERT: A 561 HIS cc_start: 0.6269 (m-70) cc_final: 0.5976 (m-70) REVERT: A 580 LYS cc_start: 0.6906 (pttt) cc_final: 0.6494 (mmtm) REVERT: A 969 VAL cc_start: 0.6240 (t) cc_final: 0.6010 (m) REVERT: A 977 TYR cc_start: 0.6493 (m-10) cc_final: 0.6194 (m-80) REVERT: A 1083 PHE cc_start: 0.7210 (OUTLIER) cc_final: 0.6926 (m-10) REVERT: A 1112 MET cc_start: 0.6861 (mpp) cc_final: 0.6615 (mpp) REVERT: A 1124 GLN cc_start: 0.6816 (pm20) cc_final: 0.6446 (pm20) REVERT: A 1546 LYS cc_start: 0.4473 (mmtm) cc_final: 0.4169 (mtmt) REVERT: A 1959 GLU cc_start: 0.7117 (tp30) cc_final: 0.6831 (tt0) REVERT: A 2184 LEU cc_start: 0.6478 (OUTLIER) cc_final: 0.5994 (tt) REVERT: A 2197 GLU cc_start: 0.6387 (mm-30) cc_final: 0.6007 (mt-10) REVERT: K 176 LYS cc_start: 0.5955 (mmtt) cc_final: 0.5408 (ttpp) REVERT: K 301 LYS cc_start: 0.6043 (ptpt) cc_final: 0.5014 (ptpt) REVERT: K 311 ARG cc_start: 0.7586 (mtp85) cc_final: 0.6998 (mmm160) REVERT: K 312 MET cc_start: 0.5092 (tpp) cc_final: 0.4483 (tpp) outliers start: 34 outliers final: 18 residues processed: 224 average time/residue: 0.1536 time to fit residues: 50.8304 Evaluate side-chains 201 residues out of total 1701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 179 time to evaluate : 0.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 303 HIS Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 858 VAL Chi-restraints excluded: chain A residue 1071 MET Chi-restraints excluded: chain A residue 1083 PHE Chi-restraints excluded: chain A residue 1583 MET Chi-restraints excluded: chain A residue 1754 TYR Chi-restraints excluded: chain A residue 1816 VAL Chi-restraints excluded: chain A residue 1927 MET Chi-restraints excluded: chain A residue 2094 ASP Chi-restraints excluded: chain A residue 2097 ASP Chi-restraints excluded: chain A residue 2184 LEU Chi-restraints excluded: chain A residue 2209 VAL Chi-restraints excluded: chain A residue 2216 THR Chi-restraints excluded: chain K residue 144 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 78 optimal weight: 0.9990 chunk 77 optimal weight: 2.9990 chunk 57 optimal weight: 0.6980 chunk 159 optimal weight: 0.4980 chunk 18 optimal weight: 6.9990 chunk 27 optimal weight: 4.9990 chunk 35 optimal weight: 1.9990 chunk 139 optimal weight: 8.9990 chunk 80 optimal weight: 0.7980 chunk 138 optimal weight: 0.9980 chunk 189 optimal weight: 7.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 245 HIS A2016 HIS ** A2069 ASN ** 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 = 0.4470 r_free = 0.4470 target = 0.187488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.154474 restraints weight = 26360.198| |-----------------------------------------------------------------------------| r_work (start): 0.4094 rms_B_bonded: 2.51 r_work: 0.3935 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7056 moved from start: 0.2922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 17189 Z= 0.145 Angle : 0.644 8.341 23569 Z= 0.323 Chirality : 0.041 0.243 2675 Planarity : 0.005 0.057 2827 Dihedral : 9.068 160.673 2822 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.32 % Allowed : 6.42 % Favored : 93.26 % Rotamer: Outliers : 2.47 % Allowed : 15.81 % Favored : 81.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.70 (0.20), residues: 1885 helix: 0.78 (0.18), residues: 859 sheet: -1.90 (0.38), residues: 195 loop : -1.41 (0.23), residues: 831 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A1225 TYR 0.018 0.002 TYR A 111 PHE 0.020 0.002 PHE A2193 TRP 0.010 0.001 TRP A 5 HIS 0.008 0.001 HIS K 194 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.15 (17189) covalent geometry : angle 0.64406 / 0.32 (23569) hydrogen bonds : bond 0.04270 / 2.99 ( 722) hydrogen bonds : angle 4.33544 / 3.13 ( 2044) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 185 time to evaluate : 0.547 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ILE cc_start: 0.7318 (tt) cc_final: 0.6701 (mt) REVERT: A 104 PHE cc_start: 0.7313 (m-80) cc_final: 0.7021 (m-80) REVERT: A 140 LEU cc_start: 0.8328 (OUTLIER) cc_final: 0.8120 (mt) REVERT: A 303 HIS cc_start: 0.5977 (OUTLIER) cc_final: 0.5109 (t70) REVERT: A 311 LYS cc_start: 0.8186 (mtmm) cc_final: 0.7504 (mptt) REVERT: A 341 HIS cc_start: 0.7224 (m170) cc_final: 0.6892 (m90) REVERT: A 358 GLU cc_start: 0.6582 (tp30) cc_final: 0.5855 (mm-30) REVERT: A 561 HIS cc_start: 0.6265 (m-70) cc_final: 0.5974 (m-70) REVERT: A 580 LYS cc_start: 0.6921 (pttt) cc_final: 0.6493 (mmtm) REVERT: A 816 THR cc_start: 0.6097 (OUTLIER) cc_final: 0.5723 (p) REVERT: A 969 VAL cc_start: 0.6120 (t) cc_final: 0.5910 (m) REVERT: A 1083 PHE cc_start: 0.7191 (OUTLIER) cc_final: 0.6860 (m-10) REVERT: A 1112 MET cc_start: 0.6872 (mpp) cc_final: 0.6636 (mpp) REVERT: A 1546 LYS cc_start: 0.4525 (mmtm) cc_final: 0.4170 (mtmt) REVERT: A 1633 GLU cc_start: 0.6141 (OUTLIER) cc_final: 0.5852 (pm20) REVERT: A 1959 GLU cc_start: 0.7193 (tp30) cc_final: 0.6913 (tt0) REVERT: A 2171 PHE cc_start: 0.6358 (m-80) cc_final: 0.6150 (m-80) REVERT: A 2184 LEU cc_start: 0.6465 (OUTLIER) cc_final: 0.5921 (tt) REVERT: A 2197 GLU cc_start: 0.6412 (mm-30) cc_final: 0.6032 (mt-10) REVERT: K 176 LYS cc_start: 0.5967 (mmtt) cc_final: 0.5427 (ttpp) REVERT: K 263 ARG cc_start: 0.5059 (mtp180) cc_final: 0.4394 (ptp-170) REVERT: K 301 LYS cc_start: 0.5911 (ptpt) cc_final: 0.4653 (ptpp) REVERT: K 311 ARG cc_start: 0.7603 (mtp85) cc_final: 0.6940 (mmm160) outliers start: 42 outliers final: 21 residues processed: 212 average time/residue: 0.1361 time to fit residues: 43.1768 Evaluate side-chains 206 residues out of total 1701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 179 time to evaluate : 0.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 84 MET Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 303 HIS Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 816 THR Chi-restraints excluded: chain A residue 858 VAL Chi-restraints excluded: chain A residue 1051 CYS Chi-restraints excluded: chain A residue 1071 MET Chi-restraints excluded: chain A residue 1083 PHE Chi-restraints excluded: chain A residue 1223 THR Chi-restraints excluded: chain A residue 1583 MET Chi-restraints excluded: chain A residue 1633 GLU Chi-restraints excluded: chain A residue 1754 TYR Chi-restraints excluded: chain A residue 1816 VAL Chi-restraints excluded: chain A residue 1927 MET Chi-restraints excluded: chain A residue 2094 ASP Chi-restraints excluded: chain A residue 2097 ASP Chi-restraints excluded: chain A residue 2184 LEU Chi-restraints excluded: chain A residue 2209 VAL Chi-restraints excluded: chain A residue 2216 THR Chi-restraints excluded: chain K residue 144 LEU Chi-restraints excluded: chain K residue 150 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 176 optimal weight: 7.9990 chunk 130 optimal weight: 10.0000 chunk 78 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 chunk 43 optimal weight: 0.6980 chunk 12 optimal weight: 4.9990 chunk 71 optimal weight: 1.9990 chunk 72 optimal weight: 0.9990 chunk 8 optimal weight: 3.9990 chunk 128 optimal weight: 0.6980 chunk 15 optimal weight: 0.9980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 245 HIS ** A2069 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4456 r_free = 0.4456 target = 0.186515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.154486 restraints weight = 26145.272| |-----------------------------------------------------------------------------| r_work (start): 0.4092 rms_B_bonded: 2.47 r_work: 0.3912 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7099 moved from start: 0.2941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 17189 Z= 0.166 Angle : 0.669 11.382 23569 Z= 0.334 Chirality : 0.042 0.328 2675 Planarity : 0.005 0.049 2827 Dihedral : 9.007 159.592 2822 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 12.42 Ramachandran Plot: Outliers : 0.27 % Allowed : 6.90 % Favored : 92.84 % Rotamer: Outliers : 2.00 % Allowed : 16.17 % Favored : 81.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.73 (0.20), residues: 1885 helix: 0.73 (0.18), residues: 863 sheet: -1.93 (0.37), residues: 195 loop : -1.39 (0.23), residues: 827 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A1225 TYR 0.025 0.002 TYR A 306 PHE 0.030 0.002 PHE A 45 TRP 0.011 0.001 TRP A 5 HIS 0.007 0.001 HIS A 245 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.17 (17189) covalent geometry : angle 0.66860 / 0.33 (23569) hydrogen bonds : bond 0.04472 / 3.14 ( 722) hydrogen bonds : angle 4.40241 / 3.18 ( 2044) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 187 time to evaluate : 0.547 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 GLU cc_start: 0.6037 (tp30) cc_final: 0.5708 (mm-30) REVERT: A 81 ILE cc_start: 0.7346 (tt) cc_final: 0.6709 (mt) REVERT: A 104 PHE cc_start: 0.7274 (m-80) cc_final: 0.7014 (m-80) REVERT: A 140 LEU cc_start: 0.8379 (OUTLIER) cc_final: 0.8147 (mt) REVERT: A 303 HIS cc_start: 0.6035 (OUTLIER) cc_final: 0.5147 (t70) REVERT: A 306 TYR cc_start: 0.6052 (t80) cc_final: 0.5848 (t80) REVERT: A 311 LYS cc_start: 0.8188 (mtmm) cc_final: 0.7487 (mptt) REVERT: A 341 HIS cc_start: 0.7210 (m170) cc_final: 0.6786 (m90) REVERT: A 580 LYS cc_start: 0.6921 (pttt) cc_final: 0.6558 (mmtm) REVERT: A 816 THR cc_start: 0.6145 (OUTLIER) cc_final: 0.5767 (p) REVERT: A 1083 PHE cc_start: 0.7141 (OUTLIER) cc_final: 0.6793 (m-10) REVERT: A 1112 MET cc_start: 0.6882 (mpp) cc_final: 0.6646 (mpp) REVERT: A 1633 GLU cc_start: 0.6236 (OUTLIER) cc_final: 0.5908 (pm20) REVERT: A 1959 GLU cc_start: 0.7279 (tp30) cc_final: 0.7038 (tt0) REVERT: A 2094 ASP cc_start: 0.6690 (OUTLIER) cc_final: 0.6166 (t70) REVERT: A 2184 LEU cc_start: 0.6539 (OUTLIER) cc_final: 0.5953 (tt) REVERT: A 2197 GLU cc_start: 0.6429 (mm-30) cc_final: 0.6076 (mt-10) REVERT: K 176 LYS cc_start: 0.5955 (mmtt) cc_final: 0.5430 (ttpp) REVERT: K 301 LYS cc_start: 0.5892 (ptpt) cc_final: 0.4573 (ptpp) REVERT: K 311 ARG cc_start: 0.7671 (mtp85) cc_final: 0.7102 (mmm160) outliers start: 34 outliers final: 24 residues processed: 208 average time/residue: 0.1336 time to fit residues: 42.2721 Evaluate side-chains 205 residues out of total 1701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 174 time to evaluate : 0.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 84 MET Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 303 HIS Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 816 THR Chi-restraints excluded: chain A residue 858 VAL Chi-restraints excluded: chain A residue 1051 CYS Chi-restraints excluded: chain A residue 1071 MET Chi-restraints excluded: chain A residue 1074 ASP Chi-restraints excluded: chain A residue 1083 PHE Chi-restraints excluded: chain A residue 1124 GLN Chi-restraints excluded: chain A residue 1223 THR Chi-restraints excluded: chain A residue 1583 MET Chi-restraints excluded: chain A residue 1633 GLU Chi-restraints excluded: chain A residue 1754 TYR Chi-restraints excluded: chain A residue 1816 VAL Chi-restraints excluded: chain A residue 1927 MET Chi-restraints excluded: chain A residue 2094 ASP Chi-restraints excluded: chain A residue 2097 ASP Chi-restraints excluded: chain A residue 2140 SER Chi-restraints excluded: chain A residue 2184 LEU Chi-restraints excluded: chain A residue 2209 VAL Chi-restraints excluded: chain A residue 2216 THR Chi-restraints excluded: chain K residue 144 LEU Chi-restraints excluded: chain K residue 150 THR Chi-restraints excluded: chain K residue 440 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 73 optimal weight: 0.8980 chunk 64 optimal weight: 0.9980 chunk 35 optimal weight: 0.9980 chunk 102 optimal weight: 0.0970 chunk 132 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 182 optimal weight: 8.9990 chunk 118 optimal weight: 0.0980 chunk 72 optimal weight: 1.9990 chunk 134 optimal weight: 2.9990 chunk 171 optimal weight: 4.9990 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 245 HIS ** A 610 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1589 GLN A2069 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4484 r_free = 0.4484 target = 0.189259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.156405 restraints weight = 26456.312| |-----------------------------------------------------------------------------| r_work (start): 0.4109 rms_B_bonded: 2.42 r_work: 0.3948 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7043 moved from start: 0.3163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 17189 Z= 0.133 Angle : 0.644 11.012 23569 Z= 0.320 Chirality : 0.041 0.298 2675 Planarity : 0.005 0.050 2827 Dihedral : 8.884 161.582 2822 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.27 % Allowed : 6.15 % Favored : 93.58 % Rotamer: Outliers : 2.18 % Allowed : 16.40 % Favored : 81.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.60 (0.20), residues: 1885 helix: 0.87 (0.18), residues: 868 sheet: -1.90 (0.37), residues: 195 loop : -1.38 (0.23), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A2098 TYR 0.021 0.002 TYR A 111 PHE 0.033 0.002 PHE A2193 TRP 0.009 0.001 TRP A2157 HIS 0.007 0.001 HIS A 245 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.13 (17189) covalent geometry : angle 0.64416 / 0.32 (23569) hydrogen bonds : bond 0.04094 / 2.85 ( 722) hydrogen bonds : angle 4.27751 / 3.09 ( 2044) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 181 time to evaluate : 0.518 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ILE cc_start: 0.7359 (tt) cc_final: 0.6793 (mt) REVERT: A 104 PHE cc_start: 0.7223 (m-80) cc_final: 0.6917 (m-80) REVERT: A 303 HIS cc_start: 0.5992 (OUTLIER) cc_final: 0.5090 (t70) REVERT: A 306 TYR cc_start: 0.6123 (t80) cc_final: 0.5848 (t80) REVERT: A 341 HIS cc_start: 0.7172 (m170) cc_final: 0.6723 (m90) REVERT: A 557 ARG cc_start: 0.7627 (ptp90) cc_final: 0.7207 (ptm160) REVERT: A 561 HIS cc_start: 0.6064 (m-70) cc_final: 0.5792 (m-70) REVERT: A 580 LYS cc_start: 0.6889 (pttt) cc_final: 0.6578 (mmtm) REVERT: A 816 THR cc_start: 0.6042 (OUTLIER) cc_final: 0.5649 (p) REVERT: A 1083 PHE cc_start: 0.7152 (OUTLIER) cc_final: 0.6839 (m-10) REVERT: A 1112 MET cc_start: 0.6981 (mpp) cc_final: 0.6770 (mpp) REVERT: A 1633 GLU cc_start: 0.6346 (OUTLIER) cc_final: 0.6048 (pm20) REVERT: A 2184 LEU cc_start: 0.6551 (OUTLIER) cc_final: 0.6065 (tt) REVERT: A 2197 GLU cc_start: 0.6393 (mm-30) cc_final: 0.6066 (mt-10) REVERT: K 176 LYS cc_start: 0.5983 (mmtt) cc_final: 0.5402 (ttpp) REVERT: K 311 ARG cc_start: 0.7579 (mtp85) cc_final: 0.7053 (mmm160) REVERT: K 312 MET cc_start: 0.5913 (tpp) cc_final: 0.5242 (tpp) outliers start: 37 outliers final: 27 residues processed: 206 average time/residue: 0.1367 time to fit residues: 42.8385 Evaluate side-chains 202 residues out of total 1701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 170 time to evaluate : 0.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 TRP Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain A residue 84 MET Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain A residue 303 HIS Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 816 THR Chi-restraints excluded: chain A residue 858 VAL Chi-restraints excluded: chain A residue 913 ILE Chi-restraints excluded: chain A residue 1051 CYS Chi-restraints excluded: chain A residue 1071 MET Chi-restraints excluded: chain A residue 1074 ASP Chi-restraints excluded: chain A residue 1079 GLU Chi-restraints excluded: chain A residue 1083 PHE Chi-restraints excluded: chain A residue 1124 GLN Chi-restraints excluded: chain A residue 1583 MET Chi-restraints excluded: chain A residue 1633 GLU Chi-restraints excluded: chain A residue 1754 TYR Chi-restraints excluded: chain A residue 1816 VAL Chi-restraints excluded: chain A residue 1927 MET Chi-restraints excluded: chain A residue 2094 ASP Chi-restraints excluded: chain A residue 2097 ASP Chi-restraints excluded: chain A residue 2184 LEU Chi-restraints excluded: chain A residue 2209 VAL Chi-restraints excluded: chain A residue 2216 THR Chi-restraints excluded: chain K residue 144 LEU Chi-restraints excluded: chain K residue 150 THR Chi-restraints excluded: chain K residue 300 SER Chi-restraints excluded: chain K residue 440 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 184 optimal weight: 0.7980 chunk 90 optimal weight: 2.9990 chunk 58 optimal weight: 0.9990 chunk 20 optimal weight: 0.6980 chunk 52 optimal weight: 0.6980 chunk 35 optimal weight: 1.9990 chunk 104 optimal weight: 1.9990 chunk 57 optimal weight: 0.3980 chunk 171 optimal weight: 4.9990 chunk 74 optimal weight: 3.9990 chunk 41 optimal weight: 8.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 245 HIS A 341 HIS A1157 HIS ** A1666 ASN ** 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 = 0.4477 r_free = 0.4477 target = 0.188737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.156316 restraints weight = 26376.119| |-----------------------------------------------------------------------------| r_work (start): 0.4111 rms_B_bonded: 2.31 r_work: 0.3948 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7038 moved from start: 0.3206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 17189 Z= 0.140 Angle : 0.644 10.882 23569 Z= 0.320 Chirality : 0.041 0.322 2675 Planarity : 0.005 0.049 2827 Dihedral : 8.776 161.260 2822 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.32 % Allowed : 6.63 % Favored : 93.05 % Rotamer: Outliers : 1.88 % Allowed : 16.93 % Favored : 81.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.57 (0.20), residues: 1885 helix: 0.91 (0.18), residues: 869 sheet: -1.87 (0.37), residues: 195 loop : -1.39 (0.23), residues: 821 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A1114 TYR 0.027 0.002 TYR A 593 PHE 0.031 0.002 PHE A2171 TRP 0.009 0.001 TRP A 5 HIS 0.015 0.001 HIS A1157 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.14 (17189) covalent geometry : angle 0.64362 / 0.32 (23569) hydrogen bonds : bond 0.04161 / 2.93 ( 722) hydrogen bonds : angle 4.26201 / 3.08 ( 2044) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 178 time to evaluate : 0.645 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ILE cc_start: 0.7326 (tt) cc_final: 0.6716 (mt) REVERT: A 104 PHE cc_start: 0.7314 (m-80) cc_final: 0.7080 (m-80) REVERT: A 303 HIS cc_start: 0.6009 (OUTLIER) cc_final: 0.5140 (t70) REVERT: A 306 TYR cc_start: 0.6085 (t80) cc_final: 0.5824 (t80) REVERT: A 341 HIS cc_start: 0.7333 (m-70) cc_final: 0.6988 (m90) REVERT: A 557 ARG cc_start: 0.7569 (ptp90) cc_final: 0.7145 (ptm160) REVERT: A 561 HIS cc_start: 0.5995 (m-70) cc_final: 0.5693 (m-70) REVERT: A 580 LYS cc_start: 0.6888 (pttt) cc_final: 0.6573 (mmtm) REVERT: A 816 THR cc_start: 0.6149 (OUTLIER) cc_final: 0.5743 (p) REVERT: A 1083 PHE cc_start: 0.7137 (OUTLIER) cc_final: 0.6730 (m-10) REVERT: A 1112 MET cc_start: 0.6997 (mpp) cc_final: 0.6719 (mpp) REVERT: A 1223 THR cc_start: 0.6990 (OUTLIER) cc_final: 0.6742 (m) REVERT: A 1633 GLU cc_start: 0.6378 (OUTLIER) cc_final: 0.6067 (pm20) REVERT: A 2184 LEU cc_start: 0.6620 (OUTLIER) cc_final: 0.6178 (tt) REVERT: A 2197 GLU cc_start: 0.6355 (mm-30) cc_final: 0.6038 (mt-10) REVERT: K 176 LYS cc_start: 0.5974 (mmtt) cc_final: 0.5351 (mmtp) REVERT: K 301 LYS cc_start: 0.5582 (ptpt) cc_final: 0.5343 (pttt) REVERT: K 311 ARG cc_start: 0.7607 (mtp85) cc_final: 0.6966 (mmm160) REVERT: K 312 MET cc_start: 0.6011 (tpp) cc_final: 0.5280 (tpp) outliers start: 32 outliers final: 25 residues processed: 198 average time/residue: 0.1422 time to fit residues: 42.8377 Evaluate side-chains 203 residues out of total 1701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 172 time to evaluate : 0.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 TRP Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 84 MET Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain A residue 303 HIS Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 816 THR Chi-restraints excluded: chain A residue 858 VAL Chi-restraints excluded: chain A residue 1051 CYS Chi-restraints excluded: chain A residue 1071 MET Chi-restraints excluded: chain A residue 1074 ASP Chi-restraints excluded: chain A residue 1083 PHE Chi-restraints excluded: chain A residue 1124 GLN Chi-restraints excluded: chain A residue 1157 HIS Chi-restraints excluded: chain A residue 1223 THR Chi-restraints excluded: chain A residue 1545 THR Chi-restraints excluded: chain A residue 1583 MET Chi-restraints excluded: chain A residue 1633 GLU Chi-restraints excluded: chain A residue 1754 TYR Chi-restraints excluded: chain A residue 1816 VAL Chi-restraints excluded: chain A residue 1927 MET Chi-restraints excluded: chain A residue 2094 ASP Chi-restraints excluded: chain A residue 2097 ASP Chi-restraints excluded: chain A residue 2184 LEU Chi-restraints excluded: chain A residue 2209 VAL Chi-restraints excluded: chain A residue 2216 THR Chi-restraints excluded: chain K residue 144 LEU Chi-restraints excluded: chain K residue 150 THR Chi-restraints excluded: chain K residue 440 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 179 optimal weight: 5.9990 chunk 20 optimal weight: 2.9990 chunk 133 optimal weight: 0.7980 chunk 155 optimal weight: 0.8980 chunk 149 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 105 optimal weight: 0.8980 chunk 80 optimal weight: 0.2980 chunk 50 optimal weight: 0.6980 chunk 95 optimal weight: 0.9990 chunk 29 optimal weight: 10.0000 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 245 HIS A 341 HIS A1157 HIS ** A1666 ASN ** 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 = 0.4478 r_free = 0.4478 target = 0.188342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.155784 restraints weight = 26447.540| |-----------------------------------------------------------------------------| r_work (start): 0.4112 rms_B_bonded: 2.42 r_work: 0.3950 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7040 moved from start: 0.3266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 17189 Z= 0.141 Angle : 0.658 11.594 23569 Z= 0.326 Chirality : 0.042 0.360 2675 Planarity : 0.005 0.049 2827 Dihedral : 8.742 161.171 2822 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.27 % Allowed : 6.31 % Favored : 93.42 % Rotamer: Outliers : 1.88 % Allowed : 17.11 % Favored : 81.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.53 (0.20), residues: 1885 helix: 0.95 (0.18), residues: 869 sheet: -1.80 (0.38), residues: 193 loop : -1.39 (0.23), residues: 823 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A2098 TYR 0.029 0.002 TYR A 593 PHE 0.039 0.002 PHE A 45 TRP 0.010 0.001 TRP A 5 HIS 0.018 0.001 HIS A1157 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.14 (17189) covalent geometry : angle 0.65773 / 0.33 (23569) hydrogen bonds : bond 0.04151 / 2.92 ( 722) hydrogen bonds : angle 4.22888 / 3.06 ( 2044) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 175 time to evaluate : 0.616 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ILE cc_start: 0.7331 (tt) cc_final: 0.6725 (mt) REVERT: A 104 PHE cc_start: 0.7289 (m-80) cc_final: 0.7025 (m-80) REVERT: A 303 HIS cc_start: 0.6002 (OUTLIER) cc_final: 0.5140 (t70) REVERT: A 557 ARG cc_start: 0.7535 (ptp90) cc_final: 0.7119 (ptm160) REVERT: A 561 HIS cc_start: 0.5946 (m-70) cc_final: 0.5678 (m-70) REVERT: A 580 LYS cc_start: 0.6903 (pttt) cc_final: 0.6583 (mmtm) REVERT: A 816 THR cc_start: 0.6221 (OUTLIER) cc_final: 0.5821 (p) REVERT: A 1083 PHE cc_start: 0.7129 (OUTLIER) cc_final: 0.6723 (m-10) REVERT: A 1112 MET cc_start: 0.7015 (mpp) cc_final: 0.6753 (mpp) REVERT: A 1223 THR cc_start: 0.6927 (OUTLIER) cc_final: 0.6678 (m) REVERT: A 1589 GLN cc_start: 0.6877 (tt0) cc_final: 0.6627 (tt0) REVERT: A 1608 MET cc_start: 0.5844 (mmp) cc_final: 0.5311 (mmp) REVERT: A 1633 GLU cc_start: 0.6284 (OUTLIER) cc_final: 0.6000 (pm20) REVERT: A 2184 LEU cc_start: 0.6607 (OUTLIER) cc_final: 0.6172 (tt) REVERT: A 2197 GLU cc_start: 0.6359 (mm-30) cc_final: 0.6060 (mt-10) REVERT: K 176 LYS cc_start: 0.5969 (mmtt) cc_final: 0.5350 (mmtp) REVERT: K 311 ARG cc_start: 0.7587 (mtp85) cc_final: 0.6964 (mmm160) outliers start: 32 outliers final: 26 residues processed: 195 average time/residue: 0.1348 time to fit residues: 40.4666 Evaluate side-chains 203 residues out of total 1701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 171 time to evaluate : 0.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 TRP Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 84 MET Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain A residue 303 HIS Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 816 THR Chi-restraints excluded: chain A residue 858 VAL Chi-restraints excluded: chain A residue 913 ILE Chi-restraints excluded: chain A residue 1051 CYS Chi-restraints excluded: chain A residue 1071 MET Chi-restraints excluded: chain A residue 1074 ASP Chi-restraints excluded: chain A residue 1083 PHE Chi-restraints excluded: chain A residue 1124 GLN Chi-restraints excluded: chain A residue 1157 HIS Chi-restraints excluded: chain A residue 1223 THR Chi-restraints excluded: chain A residue 1545 THR Chi-restraints excluded: chain A residue 1583 MET Chi-restraints excluded: chain A residue 1633 GLU Chi-restraints excluded: chain A residue 1754 TYR Chi-restraints excluded: chain A residue 1816 VAL Chi-restraints excluded: chain A residue 1927 MET Chi-restraints excluded: chain A residue 2094 ASP Chi-restraints excluded: chain A residue 2097 ASP Chi-restraints excluded: chain A residue 2184 LEU Chi-restraints excluded: chain A residue 2209 VAL Chi-restraints excluded: chain A residue 2216 THR Chi-restraints excluded: chain K residue 144 LEU Chi-restraints excluded: chain K residue 150 THR Chi-restraints excluded: chain K residue 440 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 94 optimal weight: 1.9990 chunk 174 optimal weight: 3.9990 chunk 184 optimal weight: 0.9980 chunk 55 optimal weight: 0.0870 chunk 153 optimal weight: 2.9990 chunk 155 optimal weight: 0.3980 chunk 76 optimal weight: 1.9990 chunk 136 optimal weight: 0.6980 chunk 146 optimal weight: 0.5980 chunk 171 optimal weight: 4.9990 chunk 5 optimal weight: 0.0870 overall best weight: 0.3736 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 245 HIS ** A1157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1666 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4496 r_free = 0.4496 target = 0.190148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.157061 restraints weight = 26361.603| |-----------------------------------------------------------------------------| r_work (start): 0.4125 rms_B_bonded: 2.52 r_work: 0.3979 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6993 moved from start: 0.3436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 17189 Z= 0.123 Angle : 0.651 10.779 23569 Z= 0.321 Chirality : 0.041 0.378 2675 Planarity : 0.005 0.051 2827 Dihedral : 8.666 163.044 2822 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.27 % Allowed : 6.21 % Favored : 93.53 % Rotamer: Outliers : 2.00 % Allowed : 16.81 % Favored : 81.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.41 (0.20), residues: 1885 helix: 1.06 (0.18), residues: 870 sheet: -1.74 (0.38), residues: 193 loop : -1.33 (0.23), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A1972 TYR 0.030 0.001 TYR A 306 PHE 0.039 0.002 PHE A2171 TRP 0.010 0.001 TRP A2157 HIS 0.017 0.001 HIS A1157 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.12 (17189) covalent geometry : angle 0.65051 / 0.32 (23569) hydrogen bonds : bond 0.03912 / 2.75 ( 722) hydrogen bonds : angle 4.16765 / 3.01 ( 2044) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4160.21 seconds wall clock time: 72 minutes 22.03 seconds (4342.03 seconds total)