Starting phenix.real_space_refine on Sun Jun 15 02:07:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dg5_27416/06_2025/8dg5_27416.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dg5_27416/06_2025/8dg5_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_27416/06_2025/8dg5_27416.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dg5_27416/06_2025/8dg5_27416.map" model { file = "/net/cci-nas-00/data/ceres_data/8dg5_27416/06_2025/8dg5_27416.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dg5_27416/06_2025/8dg5_27416.cif" } resolution = 3.26 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 10.35, per 1000 atoms: 0.64 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: 3.88 Conformation dependent library (CDL) restraints added in 1.9 seconds 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: 5.34 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: 8.04 Time building geometry restraints manager: 4.65 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: 5.550 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: 1.000 Check model and map are aligned: 0.420 Set scattering table: 0.380 Process input model: 43.950 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.080 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: 0.010 Load rotamer database and sin/cos tables:3.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.800 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.032 0.002 TRP A 848 HIS 0.024 0.002 HIS A1896 PHE 0.056 0.003 PHE K 173 TYR 0.070 0.003 TYR A 863 ARG 0.010 0.001 ARG A 518 Details of bonding type rmsd hydrogen bonds : bond 0.13857 ( 702) hydrogen bonds : angle 7.17939 ( 2041) covalent geometry : bond 0.01105 (16715) covalent geometry : angle 1.41635 (22877) 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 : 1.887 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: 0.2980 time to fit residues: 82.1825 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 : 1.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 162 optimal weight: 1.9990 chunk 146 optimal weight: 0.7980 chunk 81 optimal weight: 5.9990 chunk 49 optimal weight: 0.0670 chunk 98 optimal weight: 0.5980 chunk 78 optimal weight: 0.8980 chunk 151 optimal weight: 0.7980 chunk 58 optimal weight: 2.9990 chunk 91 optimal weight: 0.5980 chunk 112 optimal weight: 2.9990 chunk 175 optimal weight: 0.9990 overall best weight: 0.5718 ------------------------------------------------------------------------------- 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 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 = 0.4568 r_free = 0.4568 target = 0.185256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.150920 restraints weight = 26783.811| |-----------------------------------------------------------------------------| r_work (start): 0.4165 rms_B_bonded: 3.01 r_work: 0.3976 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6822 moved from start: 0.1257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 16716 Z= 0.131 Angle : 0.662 14.187 22877 Z= 0.330 Chirality : 0.041 0.226 2595 Planarity : 0.006 0.142 2767 Dihedral : 13.276 101.883 2845 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.71 % Favored : 93.08 % Rotamer: Outliers : 1.14 % Allowed : 8.19 % Favored : 90.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.92 % Cis-general : 0.00 % Twisted Proline : 0.92 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.68 (0.19), residues: 1849 helix: -0.20 (0.17), residues: 843 sheet: -2.18 (0.34), residues: 217 loop : -1.72 (0.22), residues: 789 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 848 HIS 0.006 0.001 HIS A 303 PHE 0.032 0.002 PHE A2171 TYR 0.038 0.001 TYR A 863 ARG 0.004 0.000 ARG A1065 Details of bonding type rmsd hydrogen bonds : bond 0.04083 ( 702) hydrogen bonds : angle 4.97759 ( 2041) covalent geometry : bond 0.00299 (16715) covalent geometry : angle 0.66211 (22877) Misc. bond : bond 0.00039 ( 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: 19 poor density : 163 time to evaluate : 1.851 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 307 GLN cc_start: 0.6754 (mm110) cc_final: 0.6088 (mm-40) REVERT: A 863 TYR cc_start: 0.6933 (OUTLIER) cc_final: 0.6568 (m-80) REVERT: A 1208 TYR cc_start: 0.5379 (p90) cc_final: 0.4952 (p90) REVERT: A 1769 GLU cc_start: 0.6614 (pp20) cc_final: 0.6101 (pp20) REVERT: K 258 MET cc_start: 0.3947 (OUTLIER) cc_final: 0.1443 (mmp) outliers start: 19 outliers final: 9 residues processed: 174 average time/residue: 0.2970 time to fit residues: 77.8915 Evaluate side-chains 153 residues out of total 1673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 142 time to evaluate : 1.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 84 MET Chi-restraints excluded: chain A residue 863 TYR Chi-restraints excluded: chain A residue 1154 ILE Chi-restraints excluded: chain A residue 1616 LEU Chi-restraints excluded: chain A residue 1950 ILE Chi-restraints excluded: chain A residue 2205 VAL Chi-restraints excluded: chain K residue 140 LEU Chi-restraints excluded: chain K residue 258 MET Chi-restraints excluded: chain K residue 380 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 30 optimal weight: 9.9990 chunk 171 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 chunk 150 optimal weight: 2.9990 chunk 147 optimal weight: 2.9990 chunk 7 optimal weight: 0.0770 chunk 36 optimal weight: 0.4980 chunk 136 optimal weight: 0.3980 chunk 20 optimal weight: 0.5980 chunk 141 optimal weight: 0.4980 overall best weight: 0.4138 ------------------------------------------------------------------------------- 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 = 0.4579 r_free = 0.4579 target = 0.186455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.152626 restraints weight = 26786.094| |-----------------------------------------------------------------------------| r_work (start): 0.4194 rms_B_bonded: 3.04 r_work: 0.4008 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.4008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6777 moved from start: 0.1667 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= 0.112 Angle : 0.605 12.947 22877 Z= 0.296 Chirality : 0.039 0.261 2595 Planarity : 0.005 0.128 2767 Dihedral : 12.957 99.202 2845 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.27 % Favored : 93.51 % Rotamer: Outliers : 1.85 % Allowed : 10.94 % Favored : 87.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.92 % Cis-general : 0.00 % Twisted Proline : 0.92 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.14 (0.20), residues: 1849 helix: 0.37 (0.18), residues: 847 sheet: -1.98 (0.35), residues: 215 loop : -1.59 (0.22), residues: 787 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 848 HIS 0.005 0.001 HIS A1896 PHE 0.025 0.001 PHE A2171 TYR 0.036 0.001 TYR A 863 ARG 0.006 0.000 ARG A1141 Details of bonding type rmsd hydrogen bonds : bond 0.03745 ( 702) hydrogen bonds : angle 4.55899 ( 2041) covalent geometry : bond 0.00249 (16715) covalent geometry : angle 0.60542 (22877) Misc. bond : bond 0.00038 ( 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 189 residues out of total 1673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 158 time to evaluate : 1.916 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 37 LEU cc_start: 0.5744 (OUTLIER) cc_final: 0.5452 (tt) REVERT: A 53 GLU cc_start: 0.7077 (OUTLIER) cc_final: 0.6765 (mt-10) REVERT: A 284 ASN cc_start: 0.6528 (t0) cc_final: 0.6136 (p0) REVERT: A 307 GLN cc_start: 0.6705 (mm110) cc_final: 0.6265 (mm-40) REVERT: A 567 ILE cc_start: 0.7410 (OUTLIER) cc_final: 0.7035 (pt) REVERT: A 1769 GLU cc_start: 0.6419 (pp20) cc_final: 0.6141 (pp20) REVERT: A 2053 GLN cc_start: 0.8294 (mt0) cc_final: 0.8070 (tt0) REVERT: K 258 MET cc_start: 0.3611 (OUTLIER) cc_final: 0.1039 (mmp) REVERT: K 423 PHE cc_start: 0.8582 (m-80) cc_final: 0.8015 (m-80) outliers start: 31 outliers final: 14 residues processed: 181 average time/residue: 0.2991 time to fit residues: 82.4803 Evaluate side-chains 161 residues out of total 1673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 143 time to evaluate : 1.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 104 optimal weight: 0.8980 chunk 191 optimal weight: 0.5980 chunk 91 optimal weight: 0.9980 chunk 88 optimal weight: 9.9990 chunk 129 optimal weight: 0.0050 chunk 2 optimal weight: 0.4980 chunk 30 optimal weight: 0.9990 chunk 179 optimal weight: 10.0000 chunk 190 optimal weight: 9.9990 chunk 80 optimal weight: 0.9990 chunk 155 optimal weight: 1.9990 overall best weight: 0.5994 ------------------------------------------------------------------------------- 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** A1174 HIS A1287 GLN ** A1544 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 448 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4570 r_free = 0.4570 target = 0.185714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.152631 restraints weight = 27068.211| |-----------------------------------------------------------------------------| r_work (start): 0.4192 rms_B_bonded: 3.00 r_work: 0.3995 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6780 moved from start: 0.1852 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= 0.121 Angle : 0.600 13.376 22877 Z= 0.292 Chirality : 0.040 0.260 2595 Planarity : 0.005 0.114 2767 Dihedral : 12.817 99.837 2845 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.49 % Favored : 93.35 % Rotamer: Outliers : 2.27 % Allowed : 13.33 % Favored : 84.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.92 % Cis-general : 0.00 % Twisted Proline : 0.92 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.20), residues: 1849 helix: 0.62 (0.18), residues: 847 sheet: -1.89 (0.35), residues: 212 loop : -1.47 (0.23), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1929 HIS 0.008 0.001 HIS A1174 PHE 0.038 0.001 PHE A2171 TYR 0.012 0.001 TYR A 529 ARG 0.006 0.000 ARG K 311 Details of bonding type rmsd hydrogen bonds : bond 0.03619 ( 702) hydrogen bonds : angle 4.39864 ( 2041) covalent geometry : bond 0.00274 (16715) covalent geometry : angle 0.59983 (22877) Misc. bond : bond 0.00045 ( 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 184 residues out of total 1673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 146 time to evaluate : 1.869 Fit side-chains revert: symmetry clash REVERT: A 37 LEU cc_start: 0.5796 (OUTLIER) cc_final: 0.5467 (tt) REVERT: A 53 GLU cc_start: 0.7148 (OUTLIER) cc_final: 0.6773 (mt-10) REVERT: A 231 MET cc_start: 0.4973 (mmt) cc_final: 0.4465 (tpp) REVERT: A 284 ASN cc_start: 0.6439 (t0) cc_final: 0.6073 (p0) REVERT: A 518 ARG cc_start: 0.7291 (mmp80) cc_final: 0.7037 (mmp80) REVERT: A 1070 LEU cc_start: 0.6683 (OUTLIER) cc_final: 0.6291 (pp) REVERT: A 1208 TYR cc_start: 0.5412 (p90) cc_final: 0.4953 (p90) REVERT: A 1769 GLU cc_start: 0.6500 (pp20) cc_final: 0.6207 (pp20) REVERT: A 1850 ILE cc_start: 0.6472 (OUTLIER) cc_final: 0.6071 (tp) REVERT: A 2053 GLN cc_start: 0.8310 (mt0) cc_final: 0.8072 (tt0) REVERT: K 423 PHE cc_start: 0.8609 (m-80) cc_final: 0.8017 (m-80) outliers start: 38 outliers final: 22 residues processed: 175 average time/residue: 0.2822 time to fit residues: 76.6682 Evaluate side-chains 165 residues out of total 1673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 139 time to evaluate : 1.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 53 GLU Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 84 MET Chi-restraints excluded: chain A residue 514 GLU Chi-restraints excluded: chain A residue 999 TYR 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 1950 ILE Chi-restraints excluded: chain A residue 2062 LEU 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 Chi-restraints excluded: chain K residue 394 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 113 optimal weight: 0.9990 chunk 38 optimal weight: 0.0270 chunk 177 optimal weight: 2.9990 chunk 78 optimal weight: 0.8980 chunk 36 optimal weight: 2.9990 chunk 162 optimal weight: 0.6980 chunk 97 optimal weight: 0.8980 chunk 54 optimal weight: 0.9980 chunk 131 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 26 optimal weight: 5.9990 overall best weight: 0.7038 ------------------------------------------------------------------------------- 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** A1062 ASN A1174 HIS A1544 GLN ** K 448 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 = 0.4567 r_free = 0.4567 target = 0.185440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.152169 restraints weight = 27347.169| |-----------------------------------------------------------------------------| r_work (start): 0.4180 rms_B_bonded: 2.82 r_work: 0.3996 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6789 moved from start: 0.1976 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= 0.124 Angle : 0.597 14.756 22877 Z= 0.291 Chirality : 0.040 0.243 2595 Planarity : 0.005 0.104 2767 Dihedral : 12.747 100.483 2845 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.71 % Favored : 93.13 % Rotamer: Outliers : 2.45 % Allowed : 14.29 % Favored : 83.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.92 % Cis-general : 0.00 % Twisted Proline : 0.92 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.20), residues: 1849 helix: 0.72 (0.18), residues: 847 sheet: -1.83 (0.36), residues: 202 loop : -1.46 (0.23), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 848 HIS 0.014 0.001 HIS A1174 PHE 0.033 0.001 PHE A2171 TYR 0.014 0.001 TYR A 529 ARG 0.006 0.000 ARG A1170 Details of bonding type rmsd hydrogen bonds : bond 0.03616 ( 702) hydrogen bonds : angle 4.34368 ( 2041) covalent geometry : bond 0.00283 (16715) covalent geometry : angle 0.59718 (22877) Misc. bond : bond 0.00053 ( 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 194 residues out of total 1673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 153 time to evaluate : 1.693 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 37 LEU cc_start: 0.5837 (OUTLIER) cc_final: 0.5488 (tt) REVERT: A 191 MET cc_start: 0.8075 (mmt) cc_final: 0.7863 (mmt) REVERT: A 231 MET cc_start: 0.4949 (mmt) cc_final: 0.4459 (tpp) REVERT: A 284 ASN cc_start: 0.6414 (t0) cc_final: 0.6031 (p0) REVERT: A 1070 LEU cc_start: 0.6718 (OUTLIER) cc_final: 0.6204 (pp) REVERT: A 1208 TYR cc_start: 0.5413 (p90) cc_final: 0.4938 (p90) REVERT: A 1769 GLU cc_start: 0.6521 (pp20) cc_final: 0.6210 (pp20) REVERT: A 1850 ILE cc_start: 0.6416 (OUTLIER) cc_final: 0.6035 (tp) REVERT: A 2053 GLN cc_start: 0.8315 (mt0) cc_final: 0.8081 (tt0) REVERT: K 423 PHE cc_start: 0.8612 (m-80) cc_final: 0.8014 (m-80) outliers start: 41 outliers final: 27 residues processed: 179 average time/residue: 0.2811 time to fit residues: 76.8105 Evaluate side-chains 170 residues out of total 1673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 140 time to evaluate : 1.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 53 GLU Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 84 MET Chi-restraints excluded: chain A residue 514 GLU Chi-restraints excluded: chain A residue 546 LEU 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 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 2175 VAL Chi-restraints excluded: chain A residue 2205 VAL Chi-restraints excluded: chain K residue 140 LEU Chi-restraints excluded: chain K residue 171 VAL Chi-restraints excluded: chain K residue 202 ASP Chi-restraints excluded: chain K residue 255 LEU Chi-restraints excluded: chain K residue 375 THR Chi-restraints excluded: chain K residue 380 LEU Chi-restraints excluded: chain K residue 394 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 99 optimal weight: 0.7980 chunk 131 optimal weight: 0.4980 chunk 53 optimal weight: 1.9990 chunk 155 optimal weight: 1.9990 chunk 158 optimal weight: 0.9990 chunk 103 optimal weight: 0.8980 chunk 113 optimal weight: 1.9990 chunk 163 optimal weight: 6.9990 chunk 27 optimal weight: 1.9990 chunk 171 optimal weight: 7.9990 chunk 137 optimal weight: 0.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- 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** A1287 GLN K 448 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4555 r_free = 0.4555 target = 0.184254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.150906 restraints weight = 27072.396| |-----------------------------------------------------------------------------| r_work (start): 0.4166 rms_B_bonded: 2.78 r_work: 0.3978 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6820 moved from start: 0.2054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 16716 Z= 0.135 Angle : 0.609 15.323 22877 Z= 0.298 Chirality : 0.040 0.242 2595 Planarity : 0.005 0.095 2767 Dihedral : 12.688 101.954 2845 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.87 % Favored : 92.97 % Rotamer: Outliers : 2.45 % Allowed : 15.84 % Favored : 81.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.92 % Cis-general : 0.00 % Twisted Proline : 0.92 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.20), residues: 1849 helix: 0.75 (0.18), residues: 848 sheet: -1.81 (0.36), residues: 198 loop : -1.45 (0.23), residues: 803 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 848 HIS 0.005 0.001 HIS A1896 PHE 0.026 0.002 PHE A2171 TYR 0.016 0.001 TYR A 529 ARG 0.004 0.000 ARG K 311 Details of bonding type rmsd hydrogen bonds : bond 0.03676 ( 702) hydrogen bonds : angle 4.32997 ( 2041) covalent geometry : bond 0.00312 (16715) covalent geometry : angle 0.60912 (22877) Misc. bond : bond 0.00052 ( 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 182 residues out of total 1673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 141 time to evaluate : 1.743 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 LEU cc_start: 0.5956 (OUTLIER) cc_final: 0.5609 (tt) REVERT: A 84 MET cc_start: 0.7219 (OUTLIER) cc_final: 0.6604 (mmt) REVERT: A 191 MET cc_start: 0.8031 (mmt) cc_final: 0.7817 (mmt) REVERT: A 231 MET cc_start: 0.4981 (mmt) cc_final: 0.4428 (tpp) REVERT: A 284 ASN cc_start: 0.6478 (t0) cc_final: 0.6124 (p0) REVERT: A 1070 LEU cc_start: 0.6670 (OUTLIER) cc_final: 0.6399 (pp) REVERT: A 1208 TYR cc_start: 0.5539 (p90) cc_final: 0.5086 (p90) REVERT: A 1769 GLU cc_start: 0.6578 (pp20) cc_final: 0.6240 (pp20) REVERT: A 1850 ILE cc_start: 0.6457 (OUTLIER) cc_final: 0.5805 (tp) REVERT: A 2053 GLN cc_start: 0.8321 (mt0) cc_final: 0.8106 (tt0) REVERT: A 2097 ASP cc_start: 0.6944 (t0) cc_final: 0.6643 (t0) REVERT: A 2189 GLU cc_start: 0.6178 (OUTLIER) cc_final: 0.5768 (tt0) REVERT: K 423 PHE cc_start: 0.8615 (m-80) cc_final: 0.7994 (m-80) outliers start: 41 outliers final: 26 residues processed: 170 average time/residue: 0.2868 time to fit residues: 75.1516 Evaluate side-chains 168 residues out of total 1673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 137 time to evaluate : 1.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 53 GLU Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 84 MET Chi-restraints excluded: chain A residue 514 GLU Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 966 CYS 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 171 VAL Chi-restraints excluded: chain K residue 202 ASP Chi-restraints excluded: chain K residue 255 LEU Chi-restraints excluded: chain K residue 375 THR Chi-restraints excluded: chain K residue 380 LEU Chi-restraints excluded: chain K residue 394 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 171 optimal weight: 7.9990 chunk 69 optimal weight: 0.7980 chunk 111 optimal weight: 0.3980 chunk 95 optimal weight: 0.9980 chunk 179 optimal weight: 2.9990 chunk 155 optimal weight: 1.9990 chunk 176 optimal weight: 6.9990 chunk 45 optimal weight: 0.0870 chunk 167 optimal weight: 5.9990 chunk 160 optimal weight: 0.9990 chunk 161 optimal weight: 0.9990 overall best weight: 0.6560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 303 HIS ** A 830 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1006 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1287 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4563 r_free = 0.4563 target = 0.185005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.152234 restraints weight = 27158.617| |-----------------------------------------------------------------------------| r_work (start): 0.4180 rms_B_bonded: 2.95 r_work: 0.3981 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6804 moved from start: 0.2182 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= 0.123 Angle : 0.604 15.960 22877 Z= 0.293 Chirality : 0.040 0.237 2595 Planarity : 0.005 0.087 2767 Dihedral : 12.628 102.395 2845 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.60 % Favored : 93.19 % Rotamer: Outliers : 2.57 % Allowed : 16.80 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.20), residues: 1849 helix: 0.84 (0.18), residues: 847 sheet: -1.82 (0.36), residues: 198 loop : -1.41 (0.23), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP K 313 HIS 0.005 0.001 HIS A1896 PHE 0.024 0.001 PHE A2171 TYR 0.023 0.001 TYR A 529 ARG 0.008 0.000 ARG K 311 Details of bonding type rmsd hydrogen bonds : bond 0.03544 ( 702) hydrogen bonds : angle 4.29191 ( 2041) covalent geometry : bond 0.00281 (16715) covalent geometry : angle 0.60357 (22877) Misc. bond : bond 0.00049 ( 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 191 residues out of total 1673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 148 time to evaluate : 1.736 Fit side-chains revert: symmetry clash REVERT: A 37 LEU cc_start: 0.5781 (OUTLIER) cc_final: 0.5431 (tt) REVERT: A 53 GLU cc_start: 0.7110 (OUTLIER) cc_final: 0.6868 (mt-10) REVERT: A 84 MET cc_start: 0.7122 (OUTLIER) cc_final: 0.6579 (mmt) REVERT: A 191 MET cc_start: 0.8061 (mmt) cc_final: 0.7831 (mmt) REVERT: A 231 MET cc_start: 0.5010 (mmt) cc_final: 0.4473 (tpp) REVERT: A 518 ARG cc_start: 0.7196 (mmp80) cc_final: 0.6960 (mmp80) REVERT: A 935 GLU cc_start: 0.6520 (tt0) cc_final: 0.5733 (mt-10) REVERT: A 1070 LEU cc_start: 0.6616 (OUTLIER) cc_final: 0.6367 (pp) REVERT: A 1208 TYR cc_start: 0.5545 (p90) cc_final: 0.5074 (p90) REVERT: A 1769 GLU cc_start: 0.6548 (pp20) cc_final: 0.6146 (pp20) REVERT: A 1850 ILE cc_start: 0.6422 (OUTLIER) cc_final: 0.6057 (tp) REVERT: A 2026 ASP cc_start: 0.7582 (t70) cc_final: 0.7310 (t70) REVERT: A 2053 GLN cc_start: 0.8336 (mt0) cc_final: 0.8120 (tt0) REVERT: A 2097 ASP cc_start: 0.6939 (t0) cc_final: 0.6671 (t0) REVERT: A 2189 GLU cc_start: 0.6260 (OUTLIER) cc_final: 0.5793 (tt0) REVERT: K 423 PHE cc_start: 0.8662 (m-80) cc_final: 0.8028 (m-80) outliers start: 43 outliers final: 28 residues processed: 176 average time/residue: 0.2818 time to fit residues: 76.3565 Evaluate side-chains 176 residues out of total 1673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 142 time to evaluate : 1.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 53 GLU Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 84 MET Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 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 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 171 VAL Chi-restraints excluded: chain K residue 202 ASP Chi-restraints excluded: chain K residue 255 LEU Chi-restraints excluded: chain K residue 375 THR Chi-restraints excluded: chain K residue 380 LEU Chi-restraints excluded: chain K residue 394 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 20 optimal weight: 0.5980 chunk 11 optimal weight: 4.9990 chunk 176 optimal weight: 5.9990 chunk 55 optimal weight: 0.5980 chunk 146 optimal weight: 0.9990 chunk 92 optimal weight: 7.9990 chunk 98 optimal weight: 0.7980 chunk 160 optimal weight: 0.5980 chunk 143 optimal weight: 1.9990 chunk 122 optimal weight: 3.9990 chunk 21 optimal weight: 4.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 303 HIS A1006 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4560 r_free = 0.4560 target = 0.184714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.151063 restraints weight = 27137.234| |-----------------------------------------------------------------------------| r_work (start): 0.4165 rms_B_bonded: 2.87 r_work: 0.3979 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6824 moved from start: 0.2244 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= 0.126 Angle : 0.607 16.205 22877 Z= 0.295 Chirality : 0.040 0.234 2595 Planarity : 0.004 0.079 2767 Dihedral : 12.559 103.094 2845 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.76 % Favored : 93.08 % Rotamer: Outliers : 2.63 % Allowed : 17.10 % Favored : 80.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.92 % Cis-general : 0.00 % Twisted Proline : 0.92 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.20), residues: 1849 helix: 0.87 (0.18), residues: 843 sheet: -1.80 (0.37), residues: 198 loop : -1.37 (0.23), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP K 313 HIS 0.009 0.001 HIS A 303 PHE 0.022 0.001 PHE A2171 TYR 0.023 0.001 TYR A 529 ARG 0.004 0.000 ARG K 311 Details of bonding type rmsd hydrogen bonds : bond 0.03567 ( 702) hydrogen bonds : angle 4.27734 ( 2041) covalent geometry : bond 0.00291 (16715) covalent geometry : angle 0.60723 (22877) Misc. bond : bond 0.00050 ( 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 194 residues out of total 1673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 150 time to evaluate : 1.730 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 37 LEU cc_start: 0.5748 (OUTLIER) cc_final: 0.5403 (tt) REVERT: A 53 GLU cc_start: 0.7066 (OUTLIER) cc_final: 0.6822 (mt-10) REVERT: A 84 MET cc_start: 0.7126 (OUTLIER) cc_final: 0.6659 (mmt) REVERT: A 191 MET cc_start: 0.8030 (mmt) cc_final: 0.7786 (mmt) REVERT: A 231 MET cc_start: 0.4947 (mmt) cc_final: 0.4421 (tpp) REVERT: A 518 ARG cc_start: 0.7186 (mmp80) cc_final: 0.6946 (mmp80) REVERT: A 1070 LEU cc_start: 0.6613 (OUTLIER) cc_final: 0.6379 (pp) REVERT: A 1208 TYR cc_start: 0.5600 (p90) cc_final: 0.5145 (p90) REVERT: A 1769 GLU cc_start: 0.6559 (pp20) cc_final: 0.6221 (pp20) REVERT: A 1850 ILE cc_start: 0.6389 (OUTLIER) cc_final: 0.6002 (tp) REVERT: A 2026 ASP cc_start: 0.7590 (t70) cc_final: 0.7326 (t70) REVERT: A 2053 GLN cc_start: 0.8318 (mt0) cc_final: 0.8115 (tt0) REVERT: A 2097 ASP cc_start: 0.6943 (t0) cc_final: 0.6698 (t0) REVERT: A 2189 GLU cc_start: 0.6293 (OUTLIER) cc_final: 0.5891 (tt0) REVERT: K 423 PHE cc_start: 0.8617 (m-80) cc_final: 0.7971 (m-80) outliers start: 44 outliers final: 30 residues processed: 180 average time/residue: 0.2905 time to fit residues: 80.7361 Evaluate side-chains 178 residues out of total 1673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 142 time to evaluate : 1.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 53 GLU Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 84 MET Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 514 GLU Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 966 CYS Chi-restraints excluded: chain A residue 999 TYR Chi-restraints excluded: chain A residue 1031 VAL Chi-restraints excluded: chain A residue 1070 LEU Chi-restraints excluded: chain A residue 1084 ILE 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 1950 ILE Chi-restraints excluded: chain A residue 2059 LEU 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 171 VAL Chi-restraints excluded: chain K residue 202 ASP Chi-restraints excluded: chain K residue 255 LEU Chi-restraints excluded: chain K residue 375 THR Chi-restraints excluded: chain K residue 380 LEU Chi-restraints excluded: chain K residue 394 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 34 optimal weight: 0.9980 chunk 77 optimal weight: 0.9990 chunk 65 optimal weight: 0.0030 chunk 112 optimal weight: 0.7980 chunk 71 optimal weight: 0.9980 chunk 183 optimal weight: 1.9990 chunk 30 optimal weight: 9.9990 chunk 164 optimal weight: 4.9990 chunk 130 optimal weight: 0.5980 chunk 124 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 overall best weight: 0.6790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1287 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4563 r_free = 0.4563 target = 0.184937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.150617 restraints weight = 27043.344| |-----------------------------------------------------------------------------| r_work (start): 0.4164 rms_B_bonded: 2.85 r_work: 0.3985 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6812 moved from start: 0.2350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 16716 Z= 0.126 Angle : 0.619 16.029 22877 Z= 0.299 Chirality : 0.040 0.228 2595 Planarity : 0.004 0.071 2767 Dihedral : 12.504 103.424 2845 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.38 % Favored : 93.46 % Rotamer: Outliers : 2.33 % Allowed : 17.51 % Favored : 80.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.92 % Cis-general : 0.00 % Twisted Proline : 0.92 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.20), residues: 1849 helix: 0.87 (0.18), residues: 843 sheet: -1.78 (0.37), residues: 198 loop : -1.35 (0.23), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 848 HIS 0.008 0.001 HIS K 360 PHE 0.021 0.001 PHE A2171 TYR 0.020 0.001 TYR A 529 ARG 0.003 0.000 ARG K 170 Details of bonding type rmsd hydrogen bonds : bond 0.03548 ( 702) hydrogen bonds : angle 4.25892 ( 2041) covalent geometry : bond 0.00293 (16715) covalent geometry : angle 0.61919 (22877) Misc. bond : bond 0.00043 ( 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 187 residues out of total 1673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 148 time to evaluate : 1.655 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 37 LEU cc_start: 0.5697 (OUTLIER) cc_final: 0.5333 (tt) REVERT: A 53 GLU cc_start: 0.7062 (OUTLIER) cc_final: 0.6839 (mt-10) REVERT: A 231 MET cc_start: 0.5031 (mmt) cc_final: 0.4537 (tpp) REVERT: A 1208 TYR cc_start: 0.5574 (p90) cc_final: 0.5122 (p90) REVERT: A 1769 GLU cc_start: 0.6540 (pp20) cc_final: 0.6173 (pp20) REVERT: A 1850 ILE cc_start: 0.6350 (OUTLIER) cc_final: 0.6093 (tp) REVERT: A 2053 GLN cc_start: 0.8323 (mt0) cc_final: 0.8112 (tt0) REVERT: A 2189 GLU cc_start: 0.6323 (OUTLIER) cc_final: 0.5914 (tt0) REVERT: K 170 ARG cc_start: 0.7005 (ttt-90) cc_final: 0.6792 (ttp-170) REVERT: K 423 PHE cc_start: 0.8647 (m-80) cc_final: 0.7995 (m-80) outliers start: 39 outliers final: 27 residues processed: 174 average time/residue: 0.2880 time to fit residues: 76.2643 Evaluate side-chains 175 residues out of total 1673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 144 time to evaluate : 1.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 53 GLU Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 514 GLU Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 966 CYS Chi-restraints excluded: chain A residue 1031 VAL 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 98 optimal weight: 0.9990 chunk 169 optimal weight: 10.0000 chunk 106 optimal weight: 6.9990 chunk 49 optimal weight: 0.8980 chunk 109 optimal weight: 3.9990 chunk 184 optimal weight: 30.0000 chunk 166 optimal weight: 4.9990 chunk 88 optimal weight: 3.9990 chunk 28 optimal weight: 6.9990 chunk 188 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 225 GLN A1124 GLN A1287 GLN A2223 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4510 r_free = 0.4510 target = 0.180112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.146810 restraints weight = 27322.930| |-----------------------------------------------------------------------------| r_work (start): 0.4109 rms_B_bonded: 2.92 r_work: 0.3900 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6943 moved from start: 0.2303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 16716 Z= 0.217 Angle : 0.712 17.313 22877 Z= 0.348 Chirality : 0.044 0.220 2595 Planarity : 0.005 0.067 2767 Dihedral : 12.652 106.924 2845 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 12.26 Ramachandran Plot: Outliers : 0.16 % Allowed : 8.27 % Favored : 91.56 % Rotamer: Outliers : 2.15 % Allowed : 17.93 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.20), residues: 1849 helix: 0.47 (0.18), residues: 849 sheet: -1.97 (0.35), residues: 208 loop : -1.53 (0.23), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 848 HIS 0.008 0.001 HIS K 360 PHE 0.022 0.002 PHE A2171 TYR 0.022 0.002 TYR A 529 ARG 0.007 0.001 ARG K 306 Details of bonding type rmsd hydrogen bonds : bond 0.04407 ( 702) hydrogen bonds : angle 4.63211 ( 2041) covalent geometry : bond 0.00513 (16715) covalent geometry : angle 0.71195 (22877) Misc. bond : bond 0.00085 ( 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 178 residues out of total 1673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 142 time to evaluate : 1.689 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 37 LEU cc_start: 0.5984 (OUTLIER) cc_final: 0.5644 (tt) REVERT: A 53 GLU cc_start: 0.7130 (OUTLIER) cc_final: 0.6783 (mt-10) REVERT: A 84 MET cc_start: 0.7799 (mmm) cc_final: 0.7482 (mmt) REVERT: A 191 MET cc_start: 0.8144 (mmt) cc_final: 0.7900 (mmt) REVERT: A 231 MET cc_start: 0.4946 (mmt) cc_final: 0.4442 (tpp) REVERT: A 515 ILE cc_start: 0.9199 (mm) cc_final: 0.8975 (tt) REVERT: A 1208 TYR cc_start: 0.5608 (p90) cc_final: 0.5184 (p90) REVERT: A 1769 GLU cc_start: 0.6834 (pp20) cc_final: 0.6283 (pp20) REVERT: A 1850 ILE cc_start: 0.6443 (OUTLIER) cc_final: 0.6200 (tp) REVERT: A 2189 GLU cc_start: 0.6309 (OUTLIER) cc_final: 0.5916 (tt0) REVERT: K 423 PHE cc_start: 0.8641 (m-80) cc_final: 0.7982 (m-80) outliers start: 36 outliers final: 27 residues processed: 167 average time/residue: 0.2758 time to fit residues: 70.6927 Evaluate side-chains 167 residues out of total 1673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 136 time to evaluate : 1.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 53 GLU Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 514 GLU Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 966 CYS Chi-restraints excluded: chain A residue 1031 VAL Chi-restraints excluded: chain A residue 1084 ILE Chi-restraints excluded: chain A residue 1243 THR 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 105 optimal weight: 0.6980 chunk 177 optimal weight: 0.0060 chunk 76 optimal weight: 3.9990 chunk 192 optimal weight: 5.9990 chunk 170 optimal weight: 0.2980 chunk 26 optimal weight: 0.9980 chunk 129 optimal weight: 2.9990 chunk 173 optimal weight: 5.9990 chunk 4 optimal weight: 0.9990 chunk 183 optimal weight: 1.9990 chunk 5 optimal weight: 0.1980 overall best weight: 0.4396 ------------------------------------------------------------------------------- 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** A1287 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4571 r_free = 0.4571 target = 0.185805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.152139 restraints weight = 27148.758| |-----------------------------------------------------------------------------| r_work (start): 0.4174 rms_B_bonded: 2.82 r_work: 0.3994 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6789 moved from start: 0.2508 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= 0.115 Angle : 0.631 16.240 22877 Z= 0.302 Chirality : 0.040 0.213 2595 Planarity : 0.004 0.066 2767 Dihedral : 12.535 105.844 2845 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.90 % Favored : 93.94 % Rotamer: Outliers : 1.79 % Allowed : 18.35 % Favored : 79.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.92 % Cis-general : 0.00 % Twisted Proline : 0.92 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.20), residues: 1849 helix: 0.86 (0.18), residues: 843 sheet: -1.82 (0.37), residues: 198 loop : -1.38 (0.23), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 848 HIS 0.005 0.001 HIS K 360 PHE 0.022 0.001 PHE A2171 TYR 0.020 0.001 TYR K 458 ARG 0.003 0.000 ARG A 889 Details of bonding type rmsd hydrogen bonds : bond 0.03404 ( 702) hydrogen bonds : angle 4.28245 ( 2041) covalent geometry : bond 0.00263 (16715) covalent geometry : angle 0.63071 (22877) Misc. bond : bond 0.00063 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8936.21 seconds wall clock time: 153 minutes 43.34 seconds (9223.34 seconds total)