Starting phenix.real_space_refine on Wed Mar 4 22:07:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dg5_27416/03_2026/8dg5_27416.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dg5_27416/03_2026/8dg5_27416.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.26 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8dg5_27416/03_2026/8dg5_27416.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dg5_27416/03_2026/8dg5_27416.map" model { file = "/net/cci-nas-00/data/ceres_data/8dg5_27416/03_2026/8dg5_27416.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dg5_27416/03_2026/8dg5_27416.cif" } resolution = 3.26 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.039 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 51 5.49 5 Mg 11 5.21 5 S 88 5.16 5 C 10124 2.51 5 N 2859 2.21 5 O 3136 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16269 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 13175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1635, 13175 Classifications: {'peptide': 1635} Link IDs: {'PTRANS': 98, 'TRANS': 1536} Chain breaks: 14 Chain: "E" Number of atoms: 1057 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 1057 Classifications: {'RNA': 50} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 23, 'rna3p_pyr': 26} Link IDs: {'rna2p': 1, 'rna3p': 48} Chain breaks: 1 Chain: "K" Number of atoms: 2005 Number of conformers: 1 Conformer: "" Number of residues, atoms: 252, 2005 Classifications: {'peptide': 252} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 240} Chain breaks: 3 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 29 Unusual residues: {' MG': 8, 'U5P%rna2p': 1} Classifications: {'RNA_mixed': 1, 'undetermined': 8} Modifications used: {'rna2p': 1} Link IDs: {None: 8} Time building chain proxies: 3.04, per 1000 atoms: 0.19 Number of scatterers: 16269 At special positions: 0 Unit cell: (156.04, 128.65, 146.08, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 88 16.00 P 51 15.00 Mg 11 11.99 O 3136 8.00 N 2859 7.00 C 10124 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.33 Conformation dependent library (CDL) restraints added in 687.6 milliseconds 3698 Ramachandran restraints generated. 1849 Oldfield, 0 Emsley, 1849 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3602 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 15 sheets defined 47.9% alpha, 9.2% beta 17 base pairs and 32 stacking pairs defined. Time for finding SS restraints: 1.70 Creating SS restraints... Processing helix chain 'A' and resid 19 through 31 Processing helix chain 'A' and resid 39 through 59 Processing helix chain 'A' and resid 79 through 88 removed outlier: 3.879A pdb=" N THR A 83 " --> pdb=" O CYS A 79 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N MET A 84 " --> pdb=" O SER A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 127 Processing helix chain 'A' and resid 145 through 157 Proline residue: A 154 - end of helix Processing helix chain 'A' and resid 187 through 199 Processing helix chain 'A' and resid 232 through 251 removed outlier: 3.763A pdb=" N SER A 247 " --> pdb=" O ASN A 243 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N PHE A 248 " --> pdb=" O THR A 244 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LEU A 249 " --> pdb=" O HIS A 245 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N ASP A 251 " --> pdb=" O SER A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 285 Processing helix chain 'A' and resid 286 through 293 Processing helix chain 'A' and resid 294 through 311 removed outlier: 4.340A pdb=" N HIS A 304 " --> pdb=" O ARG A 300 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N PHE A 305 " --> pdb=" O ALA A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 346 removed outlier: 3.656A pdb=" N ARG A 345 " --> pdb=" O HIS A 341 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N HIS A 346 " --> pdb=" O ALA A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 360 Processing helix chain 'A' and resid 362 through 374 removed outlier: 3.673A pdb=" N ARG A 366 " --> pdb=" O SER A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 503 through 519 Processing helix chain 'A' and resid 520 through 523 removed outlier: 3.659A pdb=" N LYS A 523 " --> pdb=" O PRO A 520 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 520 through 523' Processing helix chain 'A' and resid 540 through 560 removed outlier: 3.740A pdb=" N ALA A 544 " --> pdb=" O GLU A 540 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ARG A 550 " --> pdb=" O LEU A 546 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N GLU A 553 " --> pdb=" O ARG A 549 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N MET A 560 " --> pdb=" O LYS A 556 " (cutoff:3.500A) Processing helix chain 'A' and resid 569 through 573 removed outlier: 3.711A pdb=" N GLU A 573 " --> pdb=" O SER A 570 " (cutoff:3.500A) Processing helix chain 'A' and resid 592 through 601 Processing helix chain 'A' and resid 629 through 639 Processing helix chain 'A' and resid 760 through 784 Processing helix chain 'A' and resid 791 through 802 removed outlier: 3.715A pdb=" N GLN A 795 " --> pdb=" O PRO A 791 " (cutoff:3.500A) Processing helix chain 'A' and resid 821 through 833 removed outlier: 3.610A pdb=" N ALA A 825 " --> pdb=" O ASP A 821 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ILE A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N ASN A 830 " --> pdb=" O ILE A 826 " (cutoff:3.500A) Processing helix chain 'A' and resid 884 through 904 removed outlier: 3.804A pdb=" N ALA A 888 " --> pdb=" O THR A 884 " (cutoff:3.500A) Processing helix chain 'A' and resid 931 through 941 removed outlier: 4.016A pdb=" N ILE A 937 " --> pdb=" O GLU A 933 " (cutoff:3.500A) Processing helix chain 'A' and resid 960 through 964 removed outlier: 3.746A pdb=" N CYS A 964 " --> pdb=" O SER A 961 " (cutoff:3.500A) Processing helix chain 'A' and resid 1047 through 1062 removed outlier: 3.537A pdb=" N CYS A1051 " --> pdb=" O GLU A1047 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ASN A1057 " --> pdb=" O ASN A1053 " (cutoff:3.500A) Processing helix chain 'A' and resid 1098 through 1108 removed outlier: 3.885A pdb=" N ASN A1108 " --> pdb=" O LEU A1104 " (cutoff:3.500A) Processing helix chain 'A' and resid 1117 through 1124 removed outlier: 4.650A pdb=" N ARG A1121 " --> pdb=" O PRO A1117 " (cutoff:3.500A) Processing helix chain 'A' and resid 1171 through 1179 Processing helix chain 'A' and resid 1220 through 1230 Processing helix chain 'A' and resid 1248 through 1282 Proline residue: A1259 - end of helix Processing helix chain 'A' and resid 1526 through 1533 Processing helix chain 'A' and resid 1535 through 1548 removed outlier: 3.740A pdb=" N ARG A1540 " --> pdb=" O ASN A1536 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLN A1541 " --> pdb=" O ALA A1537 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLN A1543 " --> pdb=" O GLU A1539 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N GLN A1544 " --> pdb=" O ARG A1540 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LYS A1546 " --> pdb=" O TYR A1542 " (cutoff:3.500A) Processing helix chain 'A' and resid 1567 through 1581 Processing helix chain 'A' and resid 1607 through 1616 Processing helix chain 'A' and resid 1624 through 1629 Processing helix chain 'A' and resid 1635 through 1650 Processing helix chain 'A' and resid 1722 through 1731 Processing helix chain 'A' and resid 1732 through 1736 removed outlier: 3.675A pdb=" N ASN A1736 " --> pdb=" O SER A1733 " (cutoff:3.500A) Processing helix chain 'A' and resid 1741 through 1764 removed outlier: 3.780A pdb=" N THR A1746 " --> pdb=" O GLU A1742 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N ILE A1747 " --> pdb=" O ARG A1743 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N TYR A1764 " --> pdb=" O LEU A1760 " (cutoff:3.500A) Processing helix chain 'A' and resid 1768 through 1780 removed outlier: 3.915A pdb=" N LEU A1772 " --> pdb=" O HIS A1768 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N HIS A1774 " --> pdb=" O GLY A1770 " (cutoff:3.500A) Processing helix chain 'A' and resid 1781 through 1792 Processing helix chain 'A' and resid 1794 through 1798 removed outlier: 4.024A pdb=" N MET A1798 " --> pdb=" O GLY A1795 " (cutoff:3.500A) Processing helix chain 'A' and resid 1819 through 1824 Processing helix chain 'A' and resid 1836 through 1846 Processing helix chain 'A' and resid 1847 through 1854 removed outlier: 3.626A pdb=" N CYS A1851 " --> pdb=" O SER A1847 " (cutoff:3.500A) Processing helix chain 'A' and resid 1900 through 1931 Proline residue: A1920 - end of helix Processing helix chain 'A' and resid 1981 through 1990 Processing helix chain 'A' and resid 1993 through 2001 Processing helix chain 'A' and resid 2006 through 2015 removed outlier: 4.038A pdb=" N LEU A2010 " --> pdb=" O ASP A2006 " (cutoff:3.500A) Processing helix chain 'A' and resid 2028 through 2049 removed outlier: 3.715A pdb=" N LEU A2034 " --> pdb=" O ARG A2030 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N ALA A2037 " --> pdb=" O PHE A2033 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLU A2049 " --> pdb=" O ARG A2045 " (cutoff:3.500A) Processing helix chain 'A' and resid 2055 through 2065 removed outlier: 3.923A pdb=" N ARG A2063 " --> pdb=" O LEU A2059 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA A2065 " --> pdb=" O ASP A2061 " (cutoff:3.500A) Processing helix chain 'A' and resid 2068 through 2079 Processing helix chain 'A' and resid 2089 through 2107 Processing helix chain 'A' and resid 2131 through 2149 removed outlier: 3.829A pdb=" N ALA A2142 " --> pdb=" O PHE A2138 " (cutoff:3.500A) Processing helix chain 'A' and resid 2153 through 2174 removed outlier: 4.147A pdb=" N ASN A2162 " --> pdb=" O HIS A2158 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N MET A2163 " --> pdb=" O VAL A2159 " (cutoff:3.500A) Proline residue: A2166 - end of helix Processing helix chain 'A' and resid 2178 through 2187 Processing helix chain 'A' and resid 2223 through 2240 removed outlier: 3.825A pdb=" N ALA A2227 " --> pdb=" O ASN A2223 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N LYS A2240 " --> pdb=" O LEU A2236 " (cutoff:3.500A) Processing helix chain 'K' and resid 135 through 145 Processing helix chain 'K' and resid 188 through 205 Processing helix chain 'K' and resid 252 through 262 removed outlier: 3.838A pdb=" N GLN K 256 " --> pdb=" O ILE K 252 " (cutoff:3.500A) Processing helix chain 'K' and resid 300 through 319 removed outlier: 3.821A pdb=" N THR K 319 " --> pdb=" O ARG K 315 " (cutoff:3.500A) Processing helix chain 'K' and resid 359 through 374 Processing helix chain 'K' and resid 376 through 385 removed outlier: 4.080A pdb=" N LEU K 380 " --> pdb=" O GLY K 376 " (cutoff:3.500A) Processing helix chain 'K' and resid 393 through 405 removed outlier: 3.737A pdb=" N LEU K 397 " --> pdb=" O ASP K 393 " (cutoff:3.500A) Processing helix chain 'K' and resid 443 through 464 Processing sheet with id=AA1, first strand: chain 'A' and resid 64 through 66 removed outlier: 7.780A pdb=" N VAL A 64 " --> pdb=" O GLU A 136 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ILE A 138 " --> pdb=" O VAL A 64 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N VAL A 66 " --> pdb=" O ILE A 138 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 583 through 586 removed outlier: 6.124A pdb=" N VAL A 584 " --> pdb=" O VAL A 611 " (cutoff:3.500A) removed outlier: 7.549A pdb=" N LEU A 613 " --> pdb=" O VAL A 584 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N ARG A 586 " --> pdb=" O LEU A 613 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N HIS A 220 " --> pdb=" O HIS A 610 " (cutoff:3.500A) removed outlier: 8.197A pdb=" N ILE A 612 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N TYR A 222 " --> pdb=" O ILE A 612 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N VAL A 614 " --> pdb=" O TYR A 222 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N VAL A 224 " --> pdb=" O VAL A 614 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL A1585 " --> pdb=" O ILE A 223 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLN A 225 " --> pdb=" O VAL A1585 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 852 through 855 Processing sheet with id=AA4, first strand: chain 'A' and resid 952 through 956 Processing sheet with id=AA5, first strand: chain 'A' and resid 1023 through 1026 removed outlier: 6.707A pdb=" N GLU A1030 " --> pdb=" O GLN A 984 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1023 through 1026 removed outlier: 6.707A pdb=" N GLU A1030 " --> pdb=" O GLN A 984 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N PHE A1008 " --> pdb=" O ILE A 979 " (cutoff:3.500A) removed outlier: 9.273A pdb=" N LEU A 981 " --> pdb=" O GLN A1006 " (cutoff:3.500A) removed outlier: 10.646A pdb=" N GLN A1006 " --> pdb=" O LEU A 981 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1072 through 1073 removed outlier: 3.974A pdb=" N LEU A1072 " --> pdb=" O TYR A1815 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1136 through 1138 removed outlier: 3.683A pdb=" N MET A1137 " --> pdb=" O THR A1243 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1153 through 1155 Processing sheet with id=AB1, first strand: chain 'A' and resid 1937 through 1941 removed outlier: 3.717A pdb=" N VAL A1964 " --> pdb=" O THR A1938 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 2125 through 2126 removed outlier: 3.581A pdb=" N ILE A2220 " --> pdb=" O ALA A2125 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 2192 through 2193 Processing sheet with id=AB4, first strand: chain 'K' and resid 152 through 159 removed outlier: 3.611A pdb=" N GLY K 152 " --> pdb=" O SER K 172 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N ARG K 168 " --> pdb=" O VAL K 156 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N ILE K 158 " --> pdb=" O THR K 166 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N THR K 166 " --> pdb=" O ILE K 158 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'K' and resid 268 through 273 removed outlier: 4.034A pdb=" N SER K 268 " --> pdb=" O SER K 288 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N THR K 284 " --> pdb=" O GLU K 272 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'K' and resid 409 through 413 673 hydrogen bonds defined for protein. 1965 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 40 hydrogen bonds 76 hydrogen bond angles 0 basepair planarities 17 basepair parallelities 32 stacking parallelities Total time for adding SS restraints: 3.64 Time building geometry restraints manager: 1.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.09 - 1.33: 3529 1.33 - 1.57: 12958 1.57 - 1.80: 200 1.80 - 2.04: 27 2.04 - 2.28: 1 Bond restraints: 16715 Sorted by residual: bond pdb=" CB PRO A2188 " pdb=" CG PRO A2188 " ideal model delta sigma weight residual 1.492 2.280 -0.788 5.00e-02 4.00e+02 2.49e+02 bond pdb=" CG PRO A2188 " pdb=" CD PRO A2188 " ideal model delta sigma weight residual 1.503 1.091 0.412 3.40e-02 8.65e+02 1.47e+02 bond pdb=" CG PRO K 251 " pdb=" CD PRO K 251 " ideal model delta sigma weight residual 1.503 1.094 0.409 3.40e-02 8.65e+02 1.45e+02 bond pdb=" CG PRO K 165 " pdb=" CD PRO K 165 " ideal model delta sigma weight residual 1.503 1.125 0.378 3.40e-02 8.65e+02 1.24e+02 bond pdb=" O5' U5P E 101 " pdb=" P U5P E 101 " ideal model delta sigma weight residual 1.711 1.588 0.123 2.00e-02 2.50e+03 3.78e+01 ... (remaining 16710 not shown) Histogram of bond angle deviations from ideal: 0.00 - 16.15: 22866 16.15 - 32.30: 9 32.30 - 48.46: 0 48.46 - 64.61: 0 64.61 - 80.76: 2 Bond angle restraints: 22877 Sorted by residual: angle pdb=" CB PRO A2188 " pdb=" CG PRO A2188 " pdb=" CD PRO A2188 " ideal model delta sigma weight residual 106.10 25.34 80.76 3.20e+00 9.77e-02 6.37e+02 angle pdb=" CB PRO K 251 " pdb=" CG PRO K 251 " pdb=" CD PRO K 251 " ideal model delta sigma weight residual 106.10 179.94 -73.84 3.20e+00 9.77e-02 5.32e+02 angle pdb=" CA PRO A2188 " pdb=" N PRO A2188 " pdb=" CD PRO A2188 " ideal model delta sigma weight residual 112.00 83.27 28.73 1.40e+00 5.10e-01 4.21e+02 angle pdb=" N PRO K 251 " pdb=" CD PRO K 251 " pdb=" CG PRO K 251 " ideal model delta sigma weight residual 103.20 72.61 30.59 1.50e+00 4.44e-01 4.16e+02 angle pdb=" N PRO K 165 " pdb=" CD PRO K 165 " pdb=" CG PRO K 165 " ideal model delta sigma weight residual 103.20 77.96 25.24 1.50e+00 4.44e-01 2.83e+02 ... (remaining 22872 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.56: 9617 27.56 - 55.12: 536 55.12 - 82.67: 75 82.67 - 110.23: 7 110.23 - 137.79: 1 Dihedral angle restraints: 10236 sinusoidal: 4695 harmonic: 5541 Sorted by residual: dihedral pdb=" CA ALA A 606 " pdb=" C ALA A 606 " pdb=" N PRO A 607 " pdb=" CA PRO A 607 " ideal model delta harmonic sigma weight residual 180.00 125.49 54.51 0 5.00e+00 4.00e-02 1.19e+02 dihedral pdb=" CA GLN A 862 " pdb=" C GLN A 862 " pdb=" N TYR A 863 " pdb=" CA TYR A 863 " ideal model delta harmonic sigma weight residual 180.00 130.97 49.03 0 5.00e+00 4.00e-02 9.62e+01 dihedral pdb=" N PRO A2188 " pdb=" CG PRO A2188 " pdb=" CD PRO A2188 " pdb=" CB PRO A2188 " ideal model delta sinusoidal sigma weight residual -30.00 -167.79 137.79 1 1.50e+01 4.44e-03 7.43e+01 ... (remaining 10233 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.098: 2364 0.098 - 0.195: 202 0.195 - 0.293: 15 0.293 - 0.390: 13 0.390 - 0.488: 1 Chirality restraints: 2595 Sorted by residual: chirality pdb=" CG LEU A 50 " pdb=" CB LEU A 50 " pdb=" CD1 LEU A 50 " pdb=" CD2 LEU A 50 " both_signs ideal model delta sigma weight residual False -2.59 -2.10 -0.49 2.00e-01 2.50e+01 5.95e+00 chirality pdb=" CB VAL A 14 " pdb=" CA VAL A 14 " pdb=" CG1 VAL A 14 " pdb=" CG2 VAL A 14 " both_signs ideal model delta sigma weight residual False -2.63 -2.25 -0.38 2.00e-01 2.50e+01 3.67e+00 chirality pdb=" CB VAL A 22 " pdb=" CA VAL A 22 " pdb=" CG1 VAL A 22 " pdb=" CG2 VAL A 22 " both_signs ideal model delta sigma weight residual False -2.63 -2.25 -0.38 2.00e-01 2.50e+01 3.59e+00 ... (remaining 2592 not shown) Planarity restraints: 2767 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN K 250 " 0.113 5.00e-02 4.00e+02 1.70e-01 4.63e+01 pdb=" N PRO K 251 " -0.294 5.00e-02 4.00e+02 pdb=" CA PRO K 251 " 0.102 5.00e-02 4.00e+02 pdb=" CD PRO K 251 " 0.079 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 863 " 0.034 2.00e-02 2.50e+03 2.90e-02 1.68e+01 pdb=" CG TYR A 863 " -0.070 2.00e-02 2.50e+03 pdb=" CD1 TYR A 863 " 0.020 2.00e-02 2.50e+03 pdb=" CD2 TYR A 863 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR A 863 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR A 863 " 0.017 2.00e-02 2.50e+03 pdb=" CZ TYR A 863 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR A 863 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER A2165 " 0.065 5.00e-02 4.00e+02 9.51e-02 1.45e+01 pdb=" N PRO A2166 " -0.164 5.00e-02 4.00e+02 pdb=" CA PRO A2166 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO A2166 " 0.056 5.00e-02 4.00e+02 ... (remaining 2764 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 185 2.59 - 3.17: 12802 3.17 - 3.75: 26738 3.75 - 4.32: 35343 4.32 - 4.90: 57531 Nonbonded interactions: 132599 Sorted by model distance: nonbonded pdb=" OD1 ASP A1749 " pdb="MG MG A2301 " model vdw 2.013 2.170 nonbonded pdb=" OP1 C E 39 " pdb="MG MG E 102 " model vdw 2.045 2.170 nonbonded pdb=" OP2 C E 39 " pdb="MG MG E 108 " model vdw 2.050 2.170 nonbonded pdb=" OP2 A E 10 " pdb="MG MG E 105 " model vdw 2.057 2.170 nonbonded pdb=" O ILE A 357 " pdb=" OG SER A 361 " model vdw 2.215 3.040 ... (remaining 132594 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.930 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: 0.330 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 16.690 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6777 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.788 16716 Z= 0.374 Angle : 1.416 80.760 22877 Z= 0.665 Chirality : 0.062 0.488 2595 Planarity : 0.009 0.170 2767 Dihedral : 16.313 137.790 6634 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.32 % Allowed : 7.95 % Favored : 91.73 % Rotamer: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.92 % Cis-general : 0.00 % Twisted Proline : 1.83 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.73 (0.18), residues: 1849 helix: -1.41 (0.16), residues: 810 sheet: -1.94 (0.34), residues: 202 loop : -2.09 (0.21), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 518 TYR 0.070 0.003 TYR A 863 PHE 0.056 0.003 PHE K 173 TRP 0.032 0.002 TRP A 848 HIS 0.024 0.002 HIS A1896 Details of bonding type rmsd covalent geometry : bond 0.01105 (16715) covalent geometry : angle 1.41635 (22877) hydrogen bonds : bond 0.13857 ( 702) hydrogen bonds : angle 7.17939 ( 2041) Misc. bond : bond 0.03985 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3698 Ramachandran restraints generated. 1849 Oldfield, 0 Emsley, 1849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3698 Ramachandran restraints generated. 1849 Oldfield, 0 Emsley, 1849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 183 time to evaluate : 0.461 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 529 TYR cc_start: 0.6776 (p90) cc_final: 0.6014 (p90) REVERT: A 1769 GLU cc_start: 0.6633 (pp20) cc_final: 0.6277 (pp20) REVERT: A 2166 PRO cc_start: 0.7639 (Cg_endo) cc_final: 0.7432 (Cg_exo) REVERT: K 314 MET cc_start: 0.5185 (pmm) cc_final: 0.4533 (pmm) outliers start: 0 outliers final: 0 residues processed: 183 average time/residue: 0.1270 time to fit residues: 35.1129 Evaluate side-chains 143 residues out of total 1673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 143 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 98 optimal weight: 0.6980 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 0.3980 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 0.3980 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 0.6980 chunk 91 optimal weight: 0.0370 chunk 149 optimal weight: 0.9990 overall best weight: 0.4458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 150 GLN A 502 ASN ** A 830 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1124 GLN A1235 GLN ** A1544 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4576 r_free = 0.4576 target = 0.185907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.152079 restraints weight = 26971.608| |-----------------------------------------------------------------------------| r_work (start): 0.4180 rms_B_bonded: 2.86 r_work: 0.3997 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6802 moved from start: 0.1261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.101 16716 Z= 0.127 Angle : 0.666 15.130 22877 Z= 0.331 Chirality : 0.040 0.229 2595 Planarity : 0.006 0.142 2767 Dihedral : 13.279 101.699 2845 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.65 % Favored : 93.13 % Rotamer: Outliers : 1.08 % Allowed : 8.37 % Favored : 90.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.92 % Cis-general : 0.00 % Twisted Proline : 0.92 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.68 (0.19), residues: 1849 helix: -0.22 (0.17), residues: 844 sheet: -2.17 (0.34), residues: 217 loop : -1.70 (0.22), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1790 TYR 0.037 0.001 TYR A 863 PHE 0.032 0.002 PHE A2171 TRP 0.010 0.001 TRP A 848 HIS 0.006 0.001 HIS A 303 Details of bonding type rmsd covalent geometry : bond 0.00293 (16715) covalent geometry : angle 0.66644 (22877) hydrogen bonds : bond 0.04127 ( 702) hydrogen bonds : angle 4.98753 ( 2041) Misc. bond : bond 0.00000 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3698 Ramachandran restraints generated. 1849 Oldfield, 0 Emsley, 1849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3698 Ramachandran restraints generated. 1849 Oldfield, 0 Emsley, 1849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 164 time to evaluate : 0.578 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 307 GLN cc_start: 0.6823 (mm110) cc_final: 0.6159 (mm-40) REVERT: A 863 TYR cc_start: 0.6863 (OUTLIER) cc_final: 0.6535 (m-80) REVERT: A 1769 GLU cc_start: 0.6567 (pp20) cc_final: 0.6092 (pp20) REVERT: K 258 MET cc_start: 0.3965 (OUTLIER) cc_final: 0.1458 (mmp) REVERT: K 295 MET cc_start: 0.1981 (mmp) cc_final: 0.1781 (mmp) outliers start: 18 outliers final: 8 residues processed: 174 average time/residue: 0.1254 time to fit residues: 32.8116 Evaluate side-chains 152 residues out of total 1673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 142 time to evaluate : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 84 MET Chi-restraints excluded: chain A residue 863 TYR Chi-restraints excluded: chain A residue 1154 ILE Chi-restraints excluded: chain A residue 1616 LEU Chi-restraints excluded: chain A residue 1950 ILE Chi-restraints excluded: chain A residue 2205 VAL Chi-restraints excluded: chain K residue 140 LEU Chi-restraints excluded: chain K residue 258 MET Chi-restraints excluded: chain K residue 380 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 117 optimal weight: 0.9980 chunk 153 optimal weight: 0.8980 chunk 83 optimal weight: 0.6980 chunk 15 optimal weight: 0.3980 chunk 43 optimal weight: 1.9990 chunk 184 optimal weight: 0.0670 chunk 72 optimal weight: 5.9990 chunk 134 optimal weight: 2.9990 chunk 48 optimal weight: 10.0000 chunk 62 optimal weight: 0.5980 chunk 158 optimal weight: 0.9990 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 303 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 344 HIS ** A 830 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1124 GLN A1287 GLN ** A1544 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4572 r_free = 0.4572 target = 0.185818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.152533 restraints weight = 27191.316| |-----------------------------------------------------------------------------| r_work (start): 0.4191 rms_B_bonded: 2.82 r_work: 0.4000 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.4000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6775 moved from start: 0.1651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 16716 Z= 0.118 Angle : 0.611 13.026 22877 Z= 0.299 Chirality : 0.040 0.261 2595 Planarity : 0.005 0.127 2767 Dihedral : 12.957 99.264 2845 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.38 % Favored : 93.40 % Rotamer: Outliers : 1.91 % Allowed : 11.24 % Favored : 86.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.92 % Cis-general : 0.00 % Twisted Proline : 0.92 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.14 (0.20), residues: 1849 helix: 0.37 (0.18), residues: 847 sheet: -1.98 (0.35), residues: 215 loop : -1.60 (0.22), residues: 787 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1141 TYR 0.037 0.001 TYR A 863 PHE 0.025 0.001 PHE A2171 TRP 0.010 0.001 TRP A 848 HIS 0.005 0.001 HIS A1896 Details of bonding type rmsd covalent geometry : bond 0.00265 (16715) covalent geometry : angle 0.61146 (22877) hydrogen bonds : bond 0.03824 ( 702) hydrogen bonds : angle 4.57846 ( 2041) Misc. bond : bond 0.00035 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3698 Ramachandran restraints generated. 1849 Oldfield, 0 Emsley, 1849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3698 Ramachandran restraints generated. 1849 Oldfield, 0 Emsley, 1849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 158 time to evaluate : 0.593 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 LEU cc_start: 0.5793 (OUTLIER) cc_final: 0.5493 (tt) REVERT: A 53 GLU cc_start: 0.7164 (OUTLIER) cc_final: 0.6900 (mt-10) REVERT: A 307 GLN cc_start: 0.6680 (mm110) cc_final: 0.6243 (mm-40) REVERT: A 567 ILE cc_start: 0.7402 (OUTLIER) cc_final: 0.7027 (pt) REVERT: A 1070 LEU cc_start: 0.6685 (OUTLIER) cc_final: 0.6249 (pp) REVERT: A 1208 TYR cc_start: 0.5372 (p90) cc_final: 0.4925 (p90) REVERT: A 1769 GLU cc_start: 0.6450 (pp20) cc_final: 0.6123 (pp20) REVERT: A 2053 GLN cc_start: 0.8300 (mt0) cc_final: 0.8074 (tt0) REVERT: K 258 MET cc_start: 0.3608 (OUTLIER) cc_final: 0.1011 (mmp) REVERT: K 423 PHE cc_start: 0.8558 (m-80) cc_final: 0.7991 (m-80) outliers start: 32 outliers final: 16 residues processed: 182 average time/residue: 0.1304 time to fit residues: 35.9396 Evaluate side-chains 163 residues out of total 1673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 142 time to evaluate : 0.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 53 GLU Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 567 ILE Chi-restraints excluded: chain A residue 999 TYR Chi-restraints excluded: chain A residue 1070 LEU Chi-restraints excluded: chain A residue 1243 THR Chi-restraints excluded: chain A residue 1289 ILE Chi-restraints excluded: chain A residue 1930 LEU Chi-restraints excluded: chain A residue 1950 ILE Chi-restraints excluded: chain A residue 2062 LEU Chi-restraints excluded: chain A residue 2205 VAL Chi-restraints excluded: chain K residue 202 ASP Chi-restraints excluded: chain K residue 258 MET Chi-restraints excluded: chain K residue 375 THR Chi-restraints excluded: chain K residue 380 LEU Chi-restraints excluded: chain K residue 394 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 65 optimal weight: 0.0060 chunk 22 optimal weight: 0.6980 chunk 69 optimal weight: 0.2980 chunk 129 optimal weight: 0.2980 chunk 19 optimal weight: 0.0270 chunk 7 optimal weight: 2.9990 chunk 97 optimal weight: 0.8980 chunk 118 optimal weight: 0.5980 chunk 49 optimal weight: 0.8980 chunk 91 optimal weight: 2.9990 chunk 188 optimal weight: 7.9990 overall best weight: 0.2454 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 303 HIS A 344 HIS ** A 830 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1174 HIS A1287 GLN ** A1544 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 448 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4602 r_free = 0.4602 target = 0.188789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4250 r_free = 0.4250 target = 0.155596 restraints weight = 27089.995| |-----------------------------------------------------------------------------| r_work (start): 0.4234 rms_B_bonded: 2.97 r_work: 0.4050 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.4050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6709 moved from start: 0.2045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 16716 Z= 0.101 Angle : 0.580 12.655 22877 Z= 0.282 Chirality : 0.039 0.254 2595 Planarity : 0.005 0.112 2767 Dihedral : 12.778 98.722 2845 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.57 % Favored : 94.27 % Rotamer: Outliers : 2.45 % Allowed : 12.73 % Favored : 84.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.92 % Cis-general : 0.00 % Twisted Proline : 0.92 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.70 (0.20), residues: 1849 helix: 0.75 (0.18), residues: 849 sheet: -1.66 (0.36), residues: 203 loop : -1.45 (0.23), residues: 797 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG K 311 TYR 0.017 0.001 TYR A 529 PHE 0.037 0.001 PHE A2171 TRP 0.015 0.001 TRP A1929 HIS 0.006 0.001 HIS A1174 Details of bonding type rmsd covalent geometry : bond 0.00221 (16715) covalent geometry : angle 0.57990 (22877) hydrogen bonds : bond 0.03321 ( 702) hydrogen bonds : angle 4.25305 ( 2041) Misc. bond : bond 0.00016 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3698 Ramachandran restraints generated. 1849 Oldfield, 0 Emsley, 1849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3698 Ramachandran restraints generated. 1849 Oldfield, 0 Emsley, 1849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 156 time to evaluate : 0.585 Fit side-chains revert: symmetry clash REVERT: A 37 LEU cc_start: 0.5652 (OUTLIER) cc_final: 0.5350 (tt) REVERT: A 53 GLU cc_start: 0.7015 (OUTLIER) cc_final: 0.6752 (mt-10) REVERT: A 231 MET cc_start: 0.4865 (mmt) cc_final: 0.4417 (tpp) REVERT: A 284 ASN cc_start: 0.6459 (t0) cc_final: 0.6095 (p0) REVERT: A 518 ARG cc_start: 0.7286 (mmp80) cc_final: 0.7048 (mmp80) REVERT: A 1070 LEU cc_start: 0.6693 (OUTLIER) cc_final: 0.6274 (pp) REVERT: A 1769 GLU cc_start: 0.6317 (pp20) cc_final: 0.6115 (pp20) REVERT: A 1850 ILE cc_start: 0.6445 (OUTLIER) cc_final: 0.5914 (tp) REVERT: A 2053 GLN cc_start: 0.8224 (mt0) cc_final: 0.8013 (tt0) REVERT: K 423 PHE cc_start: 0.8632 (m-80) cc_final: 0.8037 (m-80) outliers start: 41 outliers final: 19 residues processed: 186 average time/residue: 0.1284 time to fit residues: 36.8045 Evaluate side-chains 169 residues out of total 1673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 146 time to evaluate : 0.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 53 GLU Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 84 MET Chi-restraints excluded: chain A residue 1070 LEU Chi-restraints excluded: chain A residue 1174 HIS Chi-restraints excluded: chain A residue 1243 THR Chi-restraints excluded: chain A residue 1289 ILE Chi-restraints excluded: chain A residue 1616 LEU Chi-restraints excluded: chain A residue 1850 ILE Chi-restraints excluded: chain A residue 1930 LEU Chi-restraints excluded: chain A residue 2062 LEU Chi-restraints excluded: chain A residue 2168 ILE Chi-restraints excluded: chain A residue 2175 VAL Chi-restraints excluded: chain A residue 2205 VAL Chi-restraints excluded: chain A residue 2223 ASN Chi-restraints excluded: chain K residue 140 LEU Chi-restraints excluded: chain K residue 202 ASP Chi-restraints excluded: chain K residue 255 LEU Chi-restraints excluded: chain K residue 375 THR Chi-restraints excluded: chain K residue 380 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 41 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 128 optimal weight: 0.2980 chunk 106 optimal weight: 0.7980 chunk 81 optimal weight: 2.9990 chunk 97 optimal weight: 4.9990 chunk 135 optimal weight: 4.9990 chunk 63 optimal weight: 3.9990 chunk 58 optimal weight: 0.9990 chunk 42 optimal weight: 0.6980 chunk 23 optimal weight: 1.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 830 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1124 GLN A1174 HIS A1544 GLN A1782 ASN K 448 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4559 r_free = 0.4559 target = 0.184700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.151250 restraints weight = 27111.894| |-----------------------------------------------------------------------------| r_work (start): 0.4167 rms_B_bonded: 2.78 r_work: 0.3981 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6815 moved from start: 0.2025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 16716 Z= 0.145 Angle : 0.618 14.002 22877 Z= 0.303 Chirality : 0.041 0.242 2595 Planarity : 0.005 0.102 2767 Dihedral : 12.711 100.085 2845 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.08 % Favored : 92.70 % Rotamer: Outliers : 2.45 % Allowed : 14.64 % Favored : 82.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.92 % Cis-general : 0.00 % Twisted Proline : 0.92 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.70 (0.20), residues: 1849 helix: 0.78 (0.18), residues: 846 sheet: -1.81 (0.36), residues: 202 loop : -1.42 (0.23), residues: 801 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG K 311 TYR 0.020 0.001 TYR A 529 PHE 0.030 0.002 PHE A2171 TRP 0.012 0.001 TRP A 848 HIS 0.013 0.001 HIS A1174 Details of bonding type rmsd covalent geometry : bond 0.00335 (16715) covalent geometry : angle 0.61770 (22877) hydrogen bonds : bond 0.03772 ( 702) hydrogen bonds : angle 4.33997 ( 2041) Misc. bond : bond 0.00065 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3698 Ramachandran restraints generated. 1849 Oldfield, 0 Emsley, 1849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3698 Ramachandran restraints generated. 1849 Oldfield, 0 Emsley, 1849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 151 time to evaluate : 0.595 Fit side-chains revert: symmetry clash REVERT: A 37 LEU cc_start: 0.5849 (OUTLIER) cc_final: 0.5514 (tt) REVERT: A 53 GLU cc_start: 0.7178 (OUTLIER) cc_final: 0.6792 (mt-10) REVERT: A 231 MET cc_start: 0.4912 (mmt) cc_final: 0.4425 (tpp) REVERT: A 284 ASN cc_start: 0.6412 (t0) cc_final: 0.6031 (p0) REVERT: A 1208 TYR cc_start: 0.5439 (p90) cc_final: 0.4955 (p90) REVERT: A 1769 GLU cc_start: 0.6550 (pp20) cc_final: 0.6249 (pp20) REVERT: A 1850 ILE cc_start: 0.6383 (OUTLIER) cc_final: 0.6026 (tp) REVERT: A 2053 GLN cc_start: 0.8302 (mt0) cc_final: 0.8090 (tt0) REVERT: K 423 PHE cc_start: 0.8616 (m-80) cc_final: 0.8008 (m-80) outliers start: 41 outliers final: 25 residues processed: 179 average time/residue: 0.1277 time to fit residues: 35.1610 Evaluate side-chains 167 residues out of total 1673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 139 time to evaluate : 0.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 53 GLU Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 84 MET Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 1031 VAL Chi-restraints excluded: chain A residue 1243 THR Chi-restraints excluded: chain A residue 1289 ILE Chi-restraints excluded: chain A residue 1547 ASN Chi-restraints excluded: chain A residue 1587 HIS Chi-restraints excluded: chain A residue 1616 LEU Chi-restraints excluded: chain A residue 1850 ILE Chi-restraints excluded: chain A residue 1930 LEU Chi-restraints excluded: chain A residue 1950 ILE Chi-restraints excluded: chain A residue 2062 LEU Chi-restraints excluded: chain A residue 2094 ASP Chi-restraints excluded: chain A residue 2168 ILE Chi-restraints excluded: chain A residue 2175 VAL Chi-restraints excluded: chain A residue 2205 VAL Chi-restraints excluded: chain K residue 140 LEU Chi-restraints excluded: chain K residue 202 ASP Chi-restraints excluded: chain K residue 255 LEU Chi-restraints excluded: chain K residue 375 THR Chi-restraints excluded: chain K residue 380 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 166 optimal weight: 4.9990 chunk 152 optimal weight: 0.7980 chunk 83 optimal weight: 2.9990 chunk 113 optimal weight: 0.5980 chunk 94 optimal weight: 1.9990 chunk 136 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 chunk 108 optimal weight: 7.9990 chunk 60 optimal weight: 3.9990 chunk 160 optimal weight: 1.9990 chunk 30 optimal weight: 7.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 633 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1062 ASN ** A1544 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2223 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4520 r_free = 0.4520 target = 0.180970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.147670 restraints weight = 27361.465| |-----------------------------------------------------------------------------| r_work (start): 0.4121 rms_B_bonded: 2.95 r_work: 0.3913 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6925 moved from start: 0.2075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 16716 Z= 0.194 Angle : 0.671 16.034 22877 Z= 0.332 Chirality : 0.043 0.246 2595 Planarity : 0.005 0.092 2767 Dihedral : 12.787 104.514 2845 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 11.82 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.90 % Favored : 91.89 % Rotamer: Outliers : 2.63 % Allowed : 16.74 % Favored : 80.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.92 % Cis-general : 0.00 % Twisted Proline : 0.92 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.98 (0.20), residues: 1849 helix: 0.47 (0.18), residues: 850 sheet: -1.93 (0.36), residues: 202 loop : -1.49 (0.23), residues: 797 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 967 TYR 0.026 0.002 TYR A 529 PHE 0.026 0.002 PHE A2171 TRP 0.020 0.002 TRP K 313 HIS 0.007 0.001 HIS K 360 Details of bonding type rmsd covalent geometry : bond 0.00453 (16715) covalent geometry : angle 0.67107 (22877) hydrogen bonds : bond 0.04286 ( 702) hydrogen bonds : angle 4.61858 ( 2041) Misc. bond : bond 0.00086 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3698 Ramachandran restraints generated. 1849 Oldfield, 0 Emsley, 1849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3698 Ramachandran restraints generated. 1849 Oldfield, 0 Emsley, 1849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 143 time to evaluate : 0.643 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 LEU cc_start: 0.5970 (OUTLIER) cc_final: 0.5622 (tt) REVERT: A 84 MET cc_start: 0.7525 (OUTLIER) cc_final: 0.6886 (mmt) REVERT: A 231 MET cc_start: 0.5203 (mmt) cc_final: 0.4705 (tpp) REVERT: A 518 ARG cc_start: 0.7216 (mmp80) cc_final: 0.6945 (mmp80) REVERT: A 1070 LEU cc_start: 0.6737 (OUTLIER) cc_final: 0.6453 (pp) REVERT: A 1208 TYR cc_start: 0.5617 (p90) cc_final: 0.5160 (p90) REVERT: A 1769 GLU cc_start: 0.6769 (pp20) cc_final: 0.6244 (pp20) REVERT: A 1850 ILE cc_start: 0.6483 (OUTLIER) cc_final: 0.5867 (tp) REVERT: A 2097 ASP cc_start: 0.7165 (t0) cc_final: 0.6926 (t0) REVERT: A 2189 GLU cc_start: 0.6167 (OUTLIER) cc_final: 0.5710 (tt0) REVERT: K 170 ARG cc_start: 0.7393 (ttt-90) cc_final: 0.7167 (ttp-170) REVERT: K 423 PHE cc_start: 0.8655 (m-80) cc_final: 0.8027 (m-80) outliers start: 44 outliers final: 30 residues processed: 172 average time/residue: 0.1259 time to fit residues: 33.4914 Evaluate side-chains 168 residues out of total 1673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 133 time to evaluate : 0.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 53 GLU Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 84 MET Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 514 GLU Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 966 CYS Chi-restraints excluded: chain A residue 1031 VAL Chi-restraints excluded: chain A residue 1070 LEU Chi-restraints excluded: chain A residue 1084 ILE Chi-restraints excluded: chain A residue 1121 ARG Chi-restraints excluded: chain A residue 1243 THR Chi-restraints excluded: chain A residue 1247 PHE Chi-restraints excluded: chain A residue 1289 ILE Chi-restraints excluded: chain A residue 1547 ASN Chi-restraints excluded: chain A residue 1587 HIS Chi-restraints excluded: chain A residue 1616 LEU Chi-restraints excluded: chain A residue 1850 ILE Chi-restraints excluded: chain A residue 1930 LEU Chi-restraints excluded: chain A residue 1950 ILE Chi-restraints excluded: chain A residue 2094 ASP Chi-restraints excluded: chain A residue 2175 VAL Chi-restraints excluded: chain A residue 2189 GLU Chi-restraints excluded: chain A residue 2205 VAL Chi-restraints excluded: chain K residue 140 LEU Chi-restraints excluded: chain K residue 202 ASP Chi-restraints excluded: chain K residue 255 LEU Chi-restraints excluded: chain K residue 375 THR Chi-restraints excluded: chain K residue 380 LEU Chi-restraints excluded: chain K residue 394 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 115 optimal weight: 0.7980 chunk 2 optimal weight: 0.3980 chunk 100 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 41 optimal weight: 0.8980 chunk 50 optimal weight: 3.9990 chunk 108 optimal weight: 6.9990 chunk 88 optimal weight: 0.9980 chunk 34 optimal weight: 0.9990 chunk 167 optimal weight: 5.9990 chunk 139 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 303 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 830 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1544 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4546 r_free = 0.4546 target = 0.183481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.150642 restraints weight = 27126.479| |-----------------------------------------------------------------------------| r_work (start): 0.4162 rms_B_bonded: 2.96 r_work: 0.3960 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6846 moved from start: 0.2209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 16716 Z= 0.134 Angle : 0.618 15.059 22877 Z= 0.302 Chirality : 0.041 0.241 2595 Planarity : 0.005 0.082 2767 Dihedral : 12.672 105.119 2845 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.81 % Favored : 93.02 % Rotamer: Outliers : 2.39 % Allowed : 17.69 % Favored : 79.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.92 % Cis-general : 0.00 % Twisted Proline : 0.92 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.82 (0.20), residues: 1849 helix: 0.69 (0.18), residues: 847 sheet: -1.89 (0.36), residues: 200 loop : -1.49 (0.23), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG K 311 TYR 0.017 0.001 TYR A 529 PHE 0.025 0.002 PHE A2171 TRP 0.018 0.001 TRP K 313 HIS 0.006 0.001 HIS A1896 Details of bonding type rmsd covalent geometry : bond 0.00311 (16715) covalent geometry : angle 0.61804 (22877) hydrogen bonds : bond 0.03714 ( 702) hydrogen bonds : angle 4.42381 ( 2041) Misc. bond : bond 0.00056 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3698 Ramachandran restraints generated. 1849 Oldfield, 0 Emsley, 1849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3698 Ramachandran restraints generated. 1849 Oldfield, 0 Emsley, 1849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 142 time to evaluate : 0.647 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 LEU cc_start: 0.5756 (OUTLIER) cc_final: 0.5411 (tt) REVERT: A 84 MET cc_start: 0.7316 (OUTLIER) cc_final: 0.6785 (mmt) REVERT: A 231 MET cc_start: 0.5112 (mmt) cc_final: 0.4602 (tpp) REVERT: A 518 ARG cc_start: 0.7140 (mmp80) cc_final: 0.6863 (mmp80) REVERT: A 1070 LEU cc_start: 0.6659 (OUTLIER) cc_final: 0.6428 (pp) REVERT: A 1208 TYR cc_start: 0.5647 (p90) cc_final: 0.5196 (p90) REVERT: A 1769 GLU cc_start: 0.6659 (pp20) cc_final: 0.6238 (pp20) REVERT: A 1850 ILE cc_start: 0.6399 (OUTLIER) cc_final: 0.6044 (tp) REVERT: A 2053 GLN cc_start: 0.8377 (mt0) cc_final: 0.8139 (tt0) REVERT: A 2097 ASP cc_start: 0.7077 (t0) cc_final: 0.6845 (t0) REVERT: A 2189 GLU cc_start: 0.6194 (OUTLIER) cc_final: 0.5776 (tt0) REVERT: K 423 PHE cc_start: 0.8660 (m-80) cc_final: 0.8021 (m-80) outliers start: 40 outliers final: 27 residues processed: 171 average time/residue: 0.1295 time to fit residues: 34.1879 Evaluate side-chains 168 residues out of total 1673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 136 time to evaluate : 0.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 53 GLU Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 84 MET Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 514 GLU Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 966 CYS Chi-restraints excluded: chain A residue 1031 VAL Chi-restraints excluded: chain A residue 1070 LEU Chi-restraints excluded: chain A residue 1084 ILE Chi-restraints excluded: chain A residue 1243 THR Chi-restraints excluded: chain A residue 1289 ILE Chi-restraints excluded: chain A residue 1587 HIS Chi-restraints excluded: chain A residue 1616 LEU Chi-restraints excluded: chain A residue 1850 ILE Chi-restraints excluded: chain A residue 1930 LEU Chi-restraints excluded: chain A residue 1950 ILE Chi-restraints excluded: chain A residue 2094 ASP Chi-restraints excluded: chain A residue 2175 VAL Chi-restraints excluded: chain A residue 2189 GLU Chi-restraints excluded: chain A residue 2205 VAL Chi-restraints excluded: chain K residue 140 LEU Chi-restraints excluded: chain K residue 202 ASP Chi-restraints excluded: chain K residue 255 LEU Chi-restraints excluded: chain K residue 375 THR Chi-restraints excluded: chain K residue 380 LEU Chi-restraints excluded: chain K residue 394 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 93 optimal weight: 0.6980 chunk 59 optimal weight: 0.6980 chunk 142 optimal weight: 0.8980 chunk 116 optimal weight: 0.5980 chunk 155 optimal weight: 1.9990 chunk 162 optimal weight: 0.7980 chunk 37 optimal weight: 8.9990 chunk 48 optimal weight: 4.9990 chunk 115 optimal weight: 1.9990 chunk 143 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 225 GLN ** A 303 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1287 GLN ** A1544 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4553 r_free = 0.4553 target = 0.184118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.150713 restraints weight = 27284.544| |-----------------------------------------------------------------------------| r_work (start): 0.4155 rms_B_bonded: 2.81 r_work: 0.3968 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6820 moved from start: 0.2286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 16716 Z= 0.130 Angle : 0.616 16.081 22877 Z= 0.299 Chirality : 0.040 0.236 2595 Planarity : 0.004 0.073 2767 Dihedral : 12.584 104.973 2845 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.03 % Favored : 92.81 % Rotamer: Outliers : 2.39 % Allowed : 17.81 % Favored : 79.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.92 % Cis-general : 0.00 % Twisted Proline : 0.92 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.68 (0.20), residues: 1849 helix: 0.79 (0.18), residues: 843 sheet: -1.86 (0.37), residues: 190 loop : -1.41 (0.23), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 889 TYR 0.018 0.001 TYR A 529 PHE 0.023 0.002 PHE A2171 TRP 0.016 0.001 TRP A 848 HIS 0.005 0.001 HIS A1896 Details of bonding type rmsd covalent geometry : bond 0.00302 (16715) covalent geometry : angle 0.61606 (22877) hydrogen bonds : bond 0.03635 ( 702) hydrogen bonds : angle 4.34242 ( 2041) Misc. bond : bond 0.00049 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3698 Ramachandran restraints generated. 1849 Oldfield, 0 Emsley, 1849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3698 Ramachandran restraints generated. 1849 Oldfield, 0 Emsley, 1849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 139 time to evaluate : 0.413 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 LEU cc_start: 0.5742 (OUTLIER) cc_final: 0.5385 (tt) REVERT: A 231 MET cc_start: 0.5052 (mmt) cc_final: 0.4565 (tpp) REVERT: A 515 ILE cc_start: 0.9195 (mm) cc_final: 0.8921 (tt) REVERT: A 518 ARG cc_start: 0.7108 (mmp80) cc_final: 0.6820 (mmp80) REVERT: A 1070 LEU cc_start: 0.6583 (OUTLIER) cc_final: 0.6364 (pp) REVERT: A 1208 TYR cc_start: 0.5595 (p90) cc_final: 0.5157 (p90) REVERT: A 1769 GLU cc_start: 0.6589 (pp20) cc_final: 0.6228 (pp20) REVERT: A 1850 ILE cc_start: 0.6363 (OUTLIER) cc_final: 0.6008 (tp) REVERT: A 2053 GLN cc_start: 0.8349 (mt0) cc_final: 0.8120 (tt0) REVERT: A 2189 GLU cc_start: 0.6260 (OUTLIER) cc_final: 0.5813 (tt0) REVERT: K 423 PHE cc_start: 0.8646 (m-80) cc_final: 0.7987 (m-80) outliers start: 40 outliers final: 28 residues processed: 168 average time/residue: 0.1284 time to fit residues: 32.7647 Evaluate side-chains 166 residues out of total 1673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 134 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 53 GLU Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 514 GLU Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 966 CYS Chi-restraints excluded: chain A residue 1031 VAL Chi-restraints excluded: chain A residue 1070 LEU Chi-restraints excluded: chain A residue 1084 ILE Chi-restraints excluded: chain A residue 1243 THR Chi-restraints excluded: chain A residue 1247 PHE Chi-restraints excluded: chain A residue 1289 ILE Chi-restraints excluded: chain A residue 1587 HIS Chi-restraints excluded: chain A residue 1616 LEU Chi-restraints excluded: chain A residue 1850 ILE Chi-restraints excluded: chain A residue 1930 LEU Chi-restraints excluded: chain A residue 1950 ILE Chi-restraints excluded: chain A residue 2094 ASP Chi-restraints excluded: chain A residue 2175 VAL Chi-restraints excluded: chain A residue 2189 GLU Chi-restraints excluded: chain A residue 2205 VAL Chi-restraints excluded: chain K residue 140 LEU Chi-restraints excluded: chain K residue 202 ASP Chi-restraints excluded: chain K residue 255 LEU Chi-restraints excluded: chain K residue 375 THR Chi-restraints excluded: chain K residue 380 LEU Chi-restraints excluded: chain K residue 394 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 29 optimal weight: 2.9990 chunk 191 optimal weight: 2.9990 chunk 102 optimal weight: 0.2980 chunk 112 optimal weight: 0.5980 chunk 192 optimal weight: 8.9990 chunk 124 optimal weight: 0.7980 chunk 119 optimal weight: 0.5980 chunk 52 optimal weight: 0.0570 chunk 109 optimal weight: 3.9990 chunk 104 optimal weight: 0.7980 chunk 58 optimal weight: 0.9980 overall best weight: 0.4698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 303 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1287 GLN ** A1544 GLN ** 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 = 0.4574 r_free = 0.4574 target = 0.186067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.152255 restraints weight = 27063.771| |-----------------------------------------------------------------------------| r_work (start): 0.4174 rms_B_bonded: 3.00 r_work: 0.3992 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6766 moved from start: 0.2484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 16716 Z= 0.111 Angle : 0.604 15.593 22877 Z= 0.290 Chirality : 0.040 0.229 2595 Planarity : 0.004 0.066 2767 Dihedral : 12.448 103.644 2845 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.27 % Favored : 93.56 % Rotamer: Outliers : 1.91 % Allowed : 18.47 % Favored : 79.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.92 % Cis-general : 0.00 % Twisted Proline : 0.92 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.50 (0.20), residues: 1849 helix: 0.97 (0.18), residues: 842 sheet: -1.75 (0.36), residues: 200 loop : -1.33 (0.23), residues: 807 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG K 170 TYR 0.017 0.001 TYR K 458 PHE 0.022 0.001 PHE A2171 TRP 0.019 0.001 TRP K 313 HIS 0.003 0.001 HIS A 344 Details of bonding type rmsd covalent geometry : bond 0.00253 (16715) covalent geometry : angle 0.60445 (22877) hydrogen bonds : bond 0.03362 ( 702) hydrogen bonds : angle 4.18469 ( 2041) Misc. bond : bond 0.00042 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3698 Ramachandran restraints generated. 1849 Oldfield, 0 Emsley, 1849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3698 Ramachandran restraints generated. 1849 Oldfield, 0 Emsley, 1849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 150 time to evaluate : 0.613 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 37 LEU cc_start: 0.5677 (OUTLIER) cc_final: 0.5311 (tt) REVERT: A 53 GLU cc_start: 0.7128 (OUTLIER) cc_final: 0.6722 (mt-10) REVERT: A 231 MET cc_start: 0.4966 (mmt) cc_final: 0.4417 (tpp) REVERT: A 515 ILE cc_start: 0.9201 (mm) cc_final: 0.8958 (tt) REVERT: A 518 ARG cc_start: 0.7150 (mmp80) cc_final: 0.6888 (mmp80) REVERT: A 529 TYR cc_start: 0.6820 (p90) cc_final: 0.5883 (p90) REVERT: A 1070 LEU cc_start: 0.6552 (OUTLIER) cc_final: 0.6341 (pp) REVERT: A 1208 TYR cc_start: 0.5561 (p90) cc_final: 0.5128 (p90) REVERT: A 1769 GLU cc_start: 0.6475 (pp20) cc_final: 0.6157 (pp20) REVERT: A 2053 GLN cc_start: 0.8318 (mt0) cc_final: 0.8099 (tt0) REVERT: A 2189 GLU cc_start: 0.6345 (OUTLIER) cc_final: 0.5861 (tt0) REVERT: K 423 PHE cc_start: 0.8639 (m-80) cc_final: 0.7966 (m-80) outliers start: 32 outliers final: 23 residues processed: 175 average time/residue: 0.1304 time to fit residues: 34.8053 Evaluate side-chains 168 residues out of total 1673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 141 time to evaluate : 0.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 53 GLU Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 514 GLU Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 966 CYS Chi-restraints excluded: chain A residue 1031 VAL Chi-restraints excluded: chain A residue 1070 LEU Chi-restraints excluded: chain A residue 1243 THR Chi-restraints excluded: chain A residue 1587 HIS Chi-restraints excluded: chain A residue 1616 LEU Chi-restraints excluded: chain A residue 1930 LEU Chi-restraints excluded: chain A residue 2059 LEU Chi-restraints excluded: chain A residue 2175 VAL Chi-restraints excluded: chain A residue 2189 GLU Chi-restraints excluded: chain A residue 2205 VAL Chi-restraints excluded: chain K residue 140 LEU Chi-restraints excluded: chain K residue 202 ASP Chi-restraints excluded: chain K residue 255 LEU Chi-restraints excluded: chain K residue 375 THR Chi-restraints excluded: chain K residue 380 LEU Chi-restraints excluded: chain K residue 394 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 41 optimal weight: 6.9990 chunk 54 optimal weight: 4.9990 chunk 149 optimal weight: 0.9990 chunk 121 optimal weight: 0.9990 chunk 119 optimal weight: 0.6980 chunk 127 optimal weight: 6.9990 chunk 72 optimal weight: 3.9990 chunk 50 optimal weight: 0.9980 chunk 15 optimal weight: 0.1980 chunk 31 optimal weight: 6.9990 chunk 182 optimal weight: 6.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 303 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1544 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1782 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4556 r_free = 0.4556 target = 0.184401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.151801 restraints weight = 27229.402| |-----------------------------------------------------------------------------| r_work (start): 0.4174 rms_B_bonded: 2.83 r_work: 0.3986 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6807 moved from start: 0.2493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 16716 Z= 0.132 Angle : 0.632 16.535 22877 Z= 0.303 Chirality : 0.041 0.285 2595 Planarity : 0.004 0.067 2767 Dihedral : 12.422 103.896 2845 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.71 % Favored : 93.13 % Rotamer: Outliers : 2.09 % Allowed : 18.23 % Favored : 79.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.92 % Cis-general : 0.00 % Twisted Proline : 0.92 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.55 (0.20), residues: 1849 helix: 0.91 (0.18), residues: 840 sheet: -1.73 (0.37), residues: 200 loop : -1.34 (0.23), residues: 809 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG K 306 TYR 0.018 0.001 TYR A1890 PHE 0.042 0.002 PHE A 20 TRP 0.021 0.001 TRP K 313 HIS 0.004 0.001 HIS A1896 Details of bonding type rmsd covalent geometry : bond 0.00310 (16715) covalent geometry : angle 0.63179 (22877) hydrogen bonds : bond 0.03603 ( 702) hydrogen bonds : angle 4.26589 ( 2041) Misc. bond : bond 0.00048 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3698 Ramachandran restraints generated. 1849 Oldfield, 0 Emsley, 1849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3698 Ramachandran restraints generated. 1849 Oldfield, 0 Emsley, 1849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 142 time to evaluate : 0.623 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 37 LEU cc_start: 0.5710 (OUTLIER) cc_final: 0.5323 (tt) REVERT: A 53 GLU cc_start: 0.7081 (OUTLIER) cc_final: 0.6786 (mt-10) REVERT: A 231 MET cc_start: 0.4952 (mmt) cc_final: 0.4475 (tpp) REVERT: A 515 ILE cc_start: 0.9203 (mm) cc_final: 0.8979 (tt) REVERT: A 518 ARG cc_start: 0.7119 (mmp80) cc_final: 0.6842 (mmp80) REVERT: A 529 TYR cc_start: 0.6953 (p90) cc_final: 0.6002 (p90) REVERT: A 1070 LEU cc_start: 0.6669 (OUTLIER) cc_final: 0.6455 (pp) REVERT: A 1208 TYR cc_start: 0.5596 (p90) cc_final: 0.5149 (p90) REVERT: A 1769 GLU cc_start: 0.6528 (pp20) cc_final: 0.6139 (pp20) REVERT: A 1850 ILE cc_start: 0.6439 (OUTLIER) cc_final: 0.6177 (tp) REVERT: A 2053 GLN cc_start: 0.8333 (mt0) cc_final: 0.8120 (tt0) REVERT: A 2075 LEU cc_start: 0.8147 (OUTLIER) cc_final: 0.7919 (mp) REVERT: A 2189 GLU cc_start: 0.6303 (OUTLIER) cc_final: 0.5953 (tt0) REVERT: K 423 PHE cc_start: 0.8589 (m-80) cc_final: 0.7928 (m-80) outliers start: 35 outliers final: 22 residues processed: 167 average time/residue: 0.1319 time to fit residues: 33.8218 Evaluate side-chains 165 residues out of total 1673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 137 time to evaluate : 0.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 53 GLU Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 514 GLU Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 966 CYS Chi-restraints excluded: chain A residue 1013 THR Chi-restraints excluded: chain A residue 1031 VAL Chi-restraints excluded: chain A residue 1070 LEU Chi-restraints excluded: chain A residue 1243 THR Chi-restraints excluded: chain A residue 1247 PHE Chi-restraints excluded: chain A residue 1587 HIS Chi-restraints excluded: chain A residue 1616 LEU Chi-restraints excluded: chain A residue 1850 ILE Chi-restraints excluded: chain A residue 1930 LEU Chi-restraints excluded: chain A residue 2075 LEU Chi-restraints excluded: chain A residue 2175 VAL Chi-restraints excluded: chain A residue 2189 GLU Chi-restraints excluded: chain A residue 2205 VAL Chi-restraints excluded: chain K residue 140 LEU Chi-restraints excluded: chain K residue 202 ASP Chi-restraints excluded: chain K residue 375 THR Chi-restraints excluded: chain K residue 394 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 114 optimal weight: 0.0770 chunk 105 optimal weight: 0.8980 chunk 111 optimal weight: 0.7980 chunk 1 optimal weight: 0.4980 chunk 131 optimal weight: 2.9990 chunk 61 optimal weight: 0.8980 chunk 4 optimal weight: 0.9990 chunk 191 optimal weight: 20.0000 chunk 47 optimal weight: 6.9990 chunk 54 optimal weight: 2.9990 chunk 151 optimal weight: 0.6980 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 303 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1544 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4567 r_free = 0.4567 target = 0.185484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.152338 restraints weight = 27028.296| |-----------------------------------------------------------------------------| r_work (start): 0.4177 rms_B_bonded: 3.00 r_work: 0.3989 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6807 moved from start: 0.2585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 16716 Z= 0.120 Angle : 0.627 16.400 22877 Z= 0.299 Chirality : 0.040 0.325 2595 Planarity : 0.004 0.066 2767 Dihedral : 12.391 103.830 2845 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.27 % Favored : 93.56 % Rotamer: Outliers : 1.91 % Allowed : 19.01 % Favored : 79.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.92 % Cis-general : 0.00 % Twisted Proline : 0.92 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.45 (0.20), residues: 1849 helix: 1.01 (0.18), residues: 839 sheet: -1.68 (0.37), residues: 200 loop : -1.31 (0.23), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG K 306 TYR 0.019 0.001 TYR K 458 PHE 0.039 0.001 PHE A 20 TRP 0.018 0.001 TRP A 848 HIS 0.004 0.001 HIS A1896 Details of bonding type rmsd covalent geometry : bond 0.00278 (16715) covalent geometry : angle 0.62750 (22877) hydrogen bonds : bond 0.03403 ( 702) hydrogen bonds : angle 4.21041 ( 2041) Misc. bond : bond 0.00043 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4183.43 seconds wall clock time: 72 minutes 27.00 seconds (4347.00 seconds total)