Starting phenix.real_space_refine on Tue Dec 31 21:56:13 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dg5_27416/12_2024/8dg5_27416.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dg5_27416/12_2024/8dg5_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_27416/12_2024/8dg5_27416.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dg5_27416/12_2024/8dg5_27416.map" model { file = "/net/cci-nas-00/data/ceres_data/8dg5_27416/12_2024/8dg5_27416.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dg5_27416/12_2024/8dg5_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-5532/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} Classifications: {'RNA': 1, 'undetermined': 8} Modifications used: {'rna2p': 1} Link IDs: {None: 8} Time building chain proxies: 10.11, per 1000 atoms: 0.62 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: 4.12 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: 5.99 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: 8.15 Time building geometry restraints manager: 4.78 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=" CB PRO K 251 " pdb=" CG PRO K 251 " ideal model delta sigma weight residual 1.492 1.206 0.286 5.00e-02 4.00e+02 3.27e+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: 9619 27.56 - 55.12: 534 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: 2367 0.098 - 0.195: 200 0.195 - 0.293: 14 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: 5.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.680 Check model and map are aligned: 0.110 Set scattering table: 0.150 Process input model: 43.480 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.750 ------------------------------------------------------------------------------- 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 16715 Z= 0.748 Angle : 1.416 80.760 22877 Z= 0.665 Chirality : 0.061 0.488 2595 Planarity : 0.009 0.170 2767 Dihedral : 16.301 137.790 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 *********************** 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 : 1.735 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: 0.3076 time to fit residues: 84.4972 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 : 1.626 ------------------------------------------------------------------------------- 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 ** A 830 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1124 GLN A1235 GLN ** A1544 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6714 moved from start: 0.1287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.103 16715 Z= 0.202 Angle : 0.672 14.803 22877 Z= 0.334 Chirality : 0.041 0.226 2595 Planarity : 0.007 0.143 2767 Dihedral : 13.562 101.802 2845 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.65 % Favored : 93.13 % Rotamer: Outliers : 1.08 % Allowed : 8.37 % Favored : 90.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.92 % Cis-general : 0.00 % Twisted Proline : 0.92 % Twisted General : 0.06 % Rama-Z (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: -0.22 (0.17), residues: 844 sheet: -2.18 (0.34), residues: 217 loop : -1.71 (0.22), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 848 HIS 0.006 0.001 HIS A 303 PHE 0.033 0.002 PHE A2171 TYR 0.038 0.001 TYR A 863 ARG 0.005 0.000 ARG A1065 *********************** 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 181 residues out of total 1673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 163 time to evaluate : 1.697 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 307 GLN cc_start: 0.7247 (mm110) cc_final: 0.6564 (mm-40) REVERT: A 863 TYR cc_start: 0.6981 (OUTLIER) cc_final: 0.6646 (m-80) REVERT: A 1208 TYR cc_start: 0.5571 (p90) cc_final: 0.5107 (p90) REVERT: A 1769 GLU cc_start: 0.6473 (pp20) cc_final: 0.6074 (pp20) outliers start: 18 outliers final: 9 residues processed: 173 average time/residue: 0.3135 time to fit residues: 81.7991 Evaluate side-chains 151 residues out of total 1673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 141 time to evaluate : 1.751 ------------------------------------------------------------------------------- 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 380 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 97 optimal weight: 3.9990 chunk 54 optimal weight: 0.7980 chunk 145 optimal weight: 0.9990 chunk 119 optimal weight: 0.5980 chunk 48 optimal weight: 9.9990 chunk 175 optimal weight: 9.9990 chunk 189 optimal weight: 20.0000 chunk 156 optimal weight: 0.9980 chunk 174 optimal weight: 2.9990 chunk 59 optimal weight: 0.7980 chunk 140 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 A1124 GLN ** A1544 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6751 moved from start: 0.1557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 16715 Z= 0.209 Angle : 0.632 13.504 22877 Z= 0.310 Chirality : 0.041 0.258 2595 Planarity : 0.005 0.129 2767 Dihedral : 13.338 100.780 2845 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.76 % Favored : 93.02 % Rotamer: Outliers : 2.03 % Allowed : 11.78 % Favored : 86.19 % 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: -1.29 (0.20), residues: 1849 helix: 0.19 (0.18), residues: 852 sheet: -2.06 (0.35), residues: 212 loop : -1.62 (0.22), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP K 313 HIS 0.005 0.001 HIS A1896 PHE 0.025 0.002 PHE A2171 TYR 0.038 0.002 TYR A 863 ARG 0.007 0.000 ARG A1141 *********************** 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 185 residues out of total 1673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 151 time to evaluate : 1.629 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 LEU cc_start: 0.5796 (OUTLIER) cc_final: 0.5513 (tt) REVERT: A 231 MET cc_start: 0.5289 (mmt) cc_final: 0.4810 (tpp) REVERT: A 307 GLN cc_start: 0.7244 (mm110) cc_final: 0.6852 (mm-40) REVERT: A 567 ILE cc_start: 0.7727 (OUTLIER) cc_final: 0.7328 (pt) REVERT: A 863 TYR cc_start: 0.6712 (OUTLIER) cc_final: 0.6441 (m-80) REVERT: A 1070 LEU cc_start: 0.6641 (OUTLIER) cc_final: 0.6217 (pp) REVERT: A 1208 TYR cc_start: 0.5673 (p90) cc_final: 0.5176 (p90) REVERT: A 1769 GLU cc_start: 0.6542 (pp20) cc_final: 0.6229 (pp20) REVERT: K 258 MET cc_start: 0.3186 (OUTLIER) cc_final: 0.0803 (mmm) outliers start: 34 outliers final: 18 residues processed: 176 average time/residue: 0.3039 time to fit residues: 81.4421 Evaluate side-chains 164 residues out of total 1673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 141 time to evaluate : 2.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 53 GLU Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 567 ILE Chi-restraints excluded: chain A residue 863 TYR Chi-restraints excluded: chain A residue 999 TYR Chi-restraints excluded: chain A residue 1070 LEU Chi-restraints excluded: chain A residue 1243 THR Chi-restraints excluded: chain A residue 1289 ILE Chi-restraints excluded: chain A residue 1930 LEU Chi-restraints excluded: chain A residue 1950 ILE Chi-restraints excluded: chain A residue 2062 LEU Chi-restraints excluded: chain A residue 2168 ILE 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 173 optimal weight: 6.9990 chunk 132 optimal weight: 0.9990 chunk 91 optimal weight: 4.9990 chunk 19 optimal weight: 3.9990 chunk 83 optimal weight: 0.7980 chunk 117 optimal weight: 0.7980 chunk 176 optimal weight: 4.9990 chunk 186 optimal weight: 4.9990 chunk 92 optimal weight: 4.9990 chunk 167 optimal weight: 5.9990 chunk 50 optimal weight: 3.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 303 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 633 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1062 ASN ** A1124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1174 HIS A1544 GLN A2223 ASN K 448 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6931 moved from start: 0.1882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 16715 Z= 0.388 Angle : 0.748 11.917 22877 Z= 0.373 Chirality : 0.045 0.261 2595 Planarity : 0.006 0.113 2767 Dihedral : 13.451 106.732 2845 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 13.29 Ramachandran Plot: Outliers : 0.16 % Allowed : 8.98 % Favored : 90.86 % Rotamer: Outliers : 3.05 % Allowed : 15.42 % Favored : 81.53 % 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: -1.66 (0.19), residues: 1849 helix: -0.07 (0.17), residues: 846 sheet: -1.92 (0.36), residues: 210 loop : -1.98 (0.22), residues: 793 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 848 HIS 0.007 0.001 HIS A1896 PHE 0.033 0.003 PHE A2171 TYR 0.041 0.002 TYR A 863 ARG 0.008 0.001 ARG A 967 *********************** 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 195 residues out of total 1673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 144 time to evaluate : 1.649 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 37 LEU cc_start: 0.6045 (OUTLIER) cc_final: 0.5731 (tt) REVERT: A 53 GLU cc_start: 0.7286 (OUTLIER) cc_final: 0.6882 (mt-10) REVERT: A 518 ARG cc_start: 0.7246 (mmp80) cc_final: 0.6994 (mmp80) REVERT: A 529 TYR cc_start: 0.7252 (p90) cc_final: 0.5868 (p90) REVERT: A 567 ILE cc_start: 0.8021 (OUTLIER) cc_final: 0.7677 (pt) REVERT: A 863 TYR cc_start: 0.7425 (OUTLIER) cc_final: 0.6930 (m-80) REVERT: A 1208 TYR cc_start: 0.5852 (p90) cc_final: 0.5367 (p90) REVERT: A 1769 GLU cc_start: 0.6948 (pp20) cc_final: 0.6431 (pp20) REVERT: A 1850 ILE cc_start: 0.6517 (OUTLIER) cc_final: 0.5833 (tp) REVERT: A 1927 MET cc_start: 0.7939 (mtp) cc_final: 0.7699 (mtm) REVERT: A 2151 MET cc_start: 0.7546 (mtt) cc_final: 0.7333 (mtm) outliers start: 51 outliers final: 30 residues processed: 179 average time/residue: 0.3066 time to fit residues: 82.7658 Evaluate side-chains 169 residues out of total 1673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 134 time to evaluate : 2.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 53 GLU Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 84 MET Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 567 ILE Chi-restraints excluded: chain A residue 863 TYR Chi-restraints excluded: chain A residue 993 THR Chi-restraints excluded: chain A residue 999 TYR Chi-restraints excluded: chain A residue 1031 VAL Chi-restraints excluded: chain A residue 1084 ILE Chi-restraints excluded: chain A residue 1154 ILE Chi-restraints excluded: chain A residue 1174 HIS Chi-restraints excluded: chain A residue 1243 THR Chi-restraints excluded: chain A residue 1289 ILE Chi-restraints excluded: chain A residue 1616 LEU Chi-restraints excluded: chain A residue 1756 ILE Chi-restraints excluded: chain A residue 1850 ILE Chi-restraints excluded: chain A residue 1930 LEU Chi-restraints excluded: chain A residue 1950 ILE Chi-restraints excluded: chain A residue 2062 LEU Chi-restraints excluded: chain A residue 2094 ASP Chi-restraints excluded: chain A residue 2168 ILE Chi-restraints excluded: chain A residue 2205 VAL Chi-restraints excluded: chain K residue 140 LEU Chi-restraints excluded: chain K residue 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 155 optimal weight: 0.5980 chunk 105 optimal weight: 0.0670 chunk 2 optimal weight: 0.5980 chunk 138 optimal weight: 0.0770 chunk 76 optimal weight: 3.9990 chunk 159 optimal weight: 5.9990 chunk 128 optimal weight: 5.9990 chunk 0 optimal weight: 2.9990 chunk 95 optimal weight: 5.9990 chunk 167 optimal weight: 5.9990 chunk 47 optimal weight: 7.9990 overall best weight: 0.8678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 304 HIS A1124 GLN A1174 HIS ** K 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6814 moved from start: 0.1951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 16715 Z= 0.215 Angle : 0.636 9.839 22877 Z= 0.314 Chirality : 0.041 0.252 2595 Planarity : 0.005 0.102 2767 Dihedral : 13.336 106.364 2845 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.14 % Favored : 92.70 % Rotamer: Outliers : 2.75 % Allowed : 16.62 % 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: -1.24 (0.20), residues: 1849 helix: 0.33 (0.18), residues: 849 sheet: -2.01 (0.35), residues: 210 loop : -1.72 (0.22), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 848 HIS 0.011 0.001 HIS K 360 PHE 0.032 0.002 PHE A2171 TYR 0.038 0.002 TYR A 863 ARG 0.004 0.000 ARG A1065 *********************** 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 189 residues out of total 1673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 143 time to evaluate : 1.719 Fit side-chains revert: symmetry clash REVERT: A 37 LEU cc_start: 0.5751 (OUTLIER) cc_final: 0.5430 (tt) REVERT: A 53 GLU cc_start: 0.7089 (OUTLIER) cc_final: 0.6746 (mt-10) REVERT: A 231 MET cc_start: 0.5348 (mmt) cc_final: 0.4844 (tpp) REVERT: A 567 ILE cc_start: 0.7713 (OUTLIER) cc_final: 0.7336 (pt) REVERT: A 863 TYR cc_start: 0.6996 (OUTLIER) cc_final: 0.6620 (m-80) REVERT: A 1070 LEU cc_start: 0.6546 (OUTLIER) cc_final: 0.6246 (pp) REVERT: A 1208 TYR cc_start: 0.5848 (p90) cc_final: 0.5387 (p90) REVERT: A 1769 GLU cc_start: 0.6659 (pp20) cc_final: 0.6290 (pp20) REVERT: A 1850 ILE cc_start: 0.6459 (OUTLIER) cc_final: 0.6010 (tp) REVERT: K 258 MET cc_start: 0.2787 (OUTLIER) cc_final: 0.0451 (mmm) REVERT: K 295 MET cc_start: 0.1635 (mmp) cc_final: 0.1419 (mmp) outliers start: 46 outliers final: 30 residues processed: 173 average time/residue: 0.2959 time to fit residues: 78.5560 Evaluate side-chains 171 residues out of total 1673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 134 time to evaluate : 1.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 53 GLU Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 514 GLU Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 567 ILE Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 863 TYR Chi-restraints excluded: chain A residue 966 CYS Chi-restraints excluded: chain A residue 999 TYR Chi-restraints excluded: chain A residue 1070 LEU Chi-restraints excluded: chain A residue 1084 ILE Chi-restraints excluded: chain A residue 1174 HIS Chi-restraints excluded: chain A residue 1243 THR Chi-restraints excluded: chain A residue 1247 PHE Chi-restraints excluded: chain A residue 1289 ILE Chi-restraints excluded: chain A residue 1587 HIS Chi-restraints excluded: chain A residue 1616 LEU Chi-restraints excluded: chain A residue 1650 HIS Chi-restraints excluded: chain A residue 1850 ILE Chi-restraints excluded: chain A residue 1925 LEU Chi-restraints excluded: chain A residue 1930 LEU Chi-restraints excluded: chain A residue 1950 ILE Chi-restraints excluded: chain A residue 2168 ILE Chi-restraints excluded: chain A residue 2175 VAL Chi-restraints excluded: chain A residue 2205 VAL Chi-restraints excluded: chain K residue 140 LEU Chi-restraints excluded: chain K residue 202 ASP Chi-restraints excluded: chain K residue 255 LEU Chi-restraints excluded: chain K residue 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 62 optimal weight: 0.5980 chunk 168 optimal weight: 0.8980 chunk 36 optimal weight: 0.0980 chunk 109 optimal weight: 0.9980 chunk 46 optimal weight: 2.9990 chunk 186 optimal weight: 10.0000 chunk 155 optimal weight: 1.9990 chunk 86 optimal weight: 3.9990 chunk 15 optimal weight: 0.9980 chunk 61 optimal weight: 0.9980 chunk 98 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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** A1174 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6782 moved from start: 0.2044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 16715 Z= 0.196 Angle : 0.624 15.710 22877 Z= 0.304 Chirality : 0.040 0.247 2595 Planarity : 0.005 0.093 2767 Dihedral : 13.225 105.641 2845 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.25 % Favored : 92.59 % Rotamer: Outliers : 3.05 % Allowed : 17.63 % Favored : 79.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.92 % Cis-general : 0.00 % Twisted Proline : 0.92 % Twisted General : 0.00 % Rama-Z (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: 0.57 (0.18), residues: 844 sheet: -1.94 (0.36), residues: 210 loop : -1.66 (0.23), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 848 HIS 0.009 0.001 HIS A1174 PHE 0.026 0.001 PHE A2171 TYR 0.037 0.001 TYR A 863 ARG 0.003 0.000 ARG A 889 *********************** 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 194 residues out of total 1673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 143 time to evaluate : 1.718 Fit side-chains revert: symmetry clash REVERT: A 37 LEU cc_start: 0.5722 (OUTLIER) cc_final: 0.5391 (tt) REVERT: A 53 GLU cc_start: 0.7096 (OUTLIER) cc_final: 0.6748 (mt-10) REVERT: A 231 MET cc_start: 0.5504 (mmt) cc_final: 0.4984 (tpp) REVERT: A 567 ILE cc_start: 0.7745 (OUTLIER) cc_final: 0.7524 (mt) REVERT: A 863 TYR cc_start: 0.6862 (OUTLIER) cc_final: 0.6636 (m-80) REVERT: A 1070 LEU cc_start: 0.6614 (OUTLIER) cc_final: 0.6316 (pp) REVERT: A 1208 TYR cc_start: 0.5834 (p90) cc_final: 0.5386 (p90) REVERT: A 1850 ILE cc_start: 0.6508 (OUTLIER) cc_final: 0.5712 (tp) REVERT: K 258 MET cc_start: 0.2652 (OUTLIER) cc_final: 0.0426 (mmm) REVERT: K 259 CYS cc_start: 0.4941 (OUTLIER) cc_final: 0.4200 (m) outliers start: 51 outliers final: 34 residues processed: 179 average time/residue: 0.2874 time to fit residues: 79.7942 Evaluate side-chains 174 residues out of total 1673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 132 time to evaluate : 1.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 53 GLU Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 514 GLU Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 567 ILE Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 863 TYR Chi-restraints excluded: chain A residue 966 CYS Chi-restraints excluded: chain A residue 999 TYR Chi-restraints excluded: chain A residue 1013 THR Chi-restraints excluded: chain A residue 1031 VAL Chi-restraints excluded: chain A residue 1070 LEU Chi-restraints excluded: chain A residue 1084 ILE Chi-restraints excluded: chain A residue 1174 HIS Chi-restraints excluded: chain A residue 1243 THR Chi-restraints excluded: chain A residue 1247 PHE 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 1925 LEU Chi-restraints excluded: chain A residue 1930 LEU Chi-restraints excluded: chain A residue 1950 ILE Chi-restraints excluded: chain A residue 2094 ASP Chi-restraints excluded: chain A residue 2168 ILE Chi-restraints excluded: chain A residue 2175 VAL Chi-restraints excluded: chain A residue 2205 VAL Chi-restraints excluded: chain K residue 140 LEU Chi-restraints excluded: chain K residue 158 ILE Chi-restraints excluded: chain K residue 202 ASP Chi-restraints excluded: chain K residue 255 LEU Chi-restraints excluded: chain K residue 258 MET Chi-restraints excluded: chain K residue 259 CYS 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 180 optimal weight: 5.9990 chunk 21 optimal weight: 4.9990 chunk 106 optimal weight: 7.9990 chunk 136 optimal weight: 0.8980 chunk 105 optimal weight: 3.9990 chunk 157 optimal weight: 2.9990 chunk 104 optimal weight: 0.9990 chunk 186 optimal weight: 9.9990 chunk 116 optimal weight: 0.0470 chunk 113 optimal weight: 3.9990 chunk 85 optimal weight: 0.0040 overall best weight: 0.9894 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 11 HIS ** A 303 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1174 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6805 moved from start: 0.2142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 16715 Z= 0.227 Angle : 0.643 15.923 22877 Z= 0.313 Chirality : 0.041 0.244 2595 Planarity : 0.005 0.085 2767 Dihedral : 13.164 105.747 2845 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.46 % Favored : 92.37 % Rotamer: Outliers : 3.11 % Allowed : 18.47 % Favored : 78.42 % 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: -0.99 (0.20), residues: 1849 helix: 0.59 (0.18), residues: 843 sheet: -1.83 (0.36), residues: 208 loop : -1.66 (0.23), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 848 HIS 0.007 0.001 HIS A1174 PHE 0.023 0.002 PHE A2171 TYR 0.037 0.002 TYR A 863 ARG 0.006 0.000 ARG K 311 *********************** 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 187 residues out of total 1673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 135 time to evaluate : 1.823 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 37 LEU cc_start: 0.5766 (OUTLIER) cc_final: 0.5458 (tt) REVERT: A 84 MET cc_start: 0.7777 (mmm) cc_final: 0.7480 (mmt) REVERT: A 284 ASN cc_start: 0.6612 (t0) cc_final: 0.6300 (p0) REVERT: A 863 TYR cc_start: 0.6978 (OUTLIER) cc_final: 0.6616 (m-80) REVERT: A 1070 LEU cc_start: 0.6596 (OUTLIER) cc_final: 0.6309 (pp) REVERT: A 1208 TYR cc_start: 0.5823 (p90) cc_final: 0.5370 (p90) REVERT: A 1769 GLU cc_start: 0.6490 (pp20) cc_final: 0.6280 (pp20) REVERT: A 1850 ILE cc_start: 0.6418 (OUTLIER) cc_final: 0.5942 (tp) REVERT: K 258 MET cc_start: 0.2827 (OUTLIER) cc_final: 0.0547 (mmm) REVERT: K 259 CYS cc_start: 0.4961 (OUTLIER) cc_final: 0.4362 (m) outliers start: 52 outliers final: 36 residues processed: 173 average time/residue: 0.2986 time to fit residues: 78.6343 Evaluate side-chains 172 residues out of total 1673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 130 time to evaluate : 1.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 53 GLU Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 514 GLU Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 863 TYR Chi-restraints excluded: chain A residue 966 CYS Chi-restraints excluded: chain A residue 999 TYR Chi-restraints excluded: chain A residue 1013 THR Chi-restraints excluded: chain A residue 1031 VAL Chi-restraints excluded: chain A residue 1070 LEU Chi-restraints excluded: chain A residue 1084 ILE Chi-restraints excluded: chain A residue 1121 ARG Chi-restraints excluded: chain A residue 1174 HIS Chi-restraints excluded: chain A residue 1243 THR Chi-restraints excluded: chain A residue 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 1925 LEU Chi-restraints excluded: chain A residue 1930 LEU Chi-restraints excluded: chain A residue 1950 ILE Chi-restraints excluded: chain A residue 2094 ASP Chi-restraints excluded: chain A residue 2168 ILE Chi-restraints excluded: chain A residue 2175 VAL Chi-restraints excluded: chain A residue 2205 VAL Chi-restraints excluded: chain K residue 140 LEU Chi-restraints excluded: chain K residue 158 ILE Chi-restraints excluded: chain K residue 202 ASP Chi-restraints excluded: chain K residue 255 LEU Chi-restraints excluded: chain K residue 258 MET Chi-restraints excluded: chain K residue 259 CYS 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 115 optimal weight: 0.9980 chunk 74 optimal weight: 2.9990 chunk 111 optimal weight: 1.9990 chunk 56 optimal weight: 0.0270 chunk 36 optimal weight: 0.0060 chunk 118 optimal weight: 0.6980 chunk 126 optimal weight: 0.0980 chunk 91 optimal weight: 4.9990 chunk 17 optimal weight: 0.6980 chunk 146 optimal weight: 2.9990 chunk 169 optimal weight: 0.0060 overall best weight: 0.1670 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 303 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6657 moved from start: 0.2356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 16715 Z= 0.151 Angle : 0.613 15.682 22877 Z= 0.294 Chirality : 0.039 0.241 2595 Planarity : 0.005 0.078 2767 Dihedral : 13.016 103.765 2845 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.73 % Favored : 94.10 % Rotamer: Outliers : 2.39 % Allowed : 19.31 % Favored : 78.30 % 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: -0.58 (0.20), residues: 1849 helix: 0.92 (0.18), residues: 846 sheet: -1.71 (0.37), residues: 200 loop : -1.43 (0.23), residues: 803 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 848 HIS 0.016 0.001 HIS A1174 PHE 0.022 0.001 PHE A2171 TYR 0.035 0.001 TYR A 863 ARG 0.005 0.000 ARG K 311 *********************** 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 195 residues out of total 1673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 155 time to evaluate : 1.881 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 37 LEU cc_start: 0.5438 (OUTLIER) cc_final: 0.5054 (tt) REVERT: A 53 GLU cc_start: 0.7057 (OUTLIER) cc_final: 0.6833 (mt-10) REVERT: A 284 ASN cc_start: 0.6467 (t0) cc_final: 0.6195 (p0) REVERT: A 518 ARG cc_start: 0.6994 (mmp80) cc_final: 0.6745 (mmp80) REVERT: A 1208 TYR cc_start: 0.5748 (p90) cc_final: 0.5305 (p90) REVERT: A 1769 GLU cc_start: 0.6382 (pp20) cc_final: 0.6172 (pp20) REVERT: A 1850 ILE cc_start: 0.6396 (OUTLIER) cc_final: 0.5923 (tp) REVERT: K 258 MET cc_start: 0.2485 (OUTLIER) cc_final: 0.0296 (mmm) REVERT: K 259 CYS cc_start: 0.4873 (OUTLIER) cc_final: 0.4112 (m) outliers start: 40 outliers final: 25 residues processed: 183 average time/residue: 0.2922 time to fit residues: 82.3917 Evaluate side-chains 168 residues out of total 1673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 138 time to evaluate : 1.921 ------------------------------------------------------------------------------- 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 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 1013 THR Chi-restraints excluded: chain A residue 1031 VAL Chi-restraints excluded: chain A residue 1121 ARG Chi-restraints excluded: chain A residue 1243 THR Chi-restraints excluded: chain A residue 1587 HIS Chi-restraints excluded: chain A residue 1616 LEU Chi-restraints excluded: chain A residue 1850 ILE Chi-restraints excluded: chain A residue 1930 LEU Chi-restraints excluded: chain A residue 2094 ASP Chi-restraints excluded: chain A residue 2175 VAL Chi-restraints excluded: chain A residue 2205 VAL Chi-restraints excluded: chain K residue 140 LEU Chi-restraints excluded: chain K residue 158 ILE Chi-restraints excluded: chain K residue 202 ASP Chi-restraints excluded: chain K residue 255 LEU Chi-restraints excluded: chain K residue 258 MET Chi-restraints excluded: chain K residue 259 CYS 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 178 optimal weight: 7.9990 chunk 162 optimal weight: 2.9990 chunk 173 optimal weight: 6.9990 chunk 104 optimal weight: 0.0980 chunk 75 optimal weight: 0.6980 chunk 136 optimal weight: 2.9990 chunk 53 optimal weight: 6.9990 chunk 156 optimal weight: 0.6980 chunk 163 optimal weight: 3.9990 chunk 172 optimal weight: 5.9990 chunk 113 optimal weight: 3.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1174 HIS A1287 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6835 moved from start: 0.2311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 16715 Z= 0.296 Angle : 0.691 17.311 22877 Z= 0.335 Chirality : 0.043 0.235 2595 Planarity : 0.005 0.070 2767 Dihedral : 13.016 105.749 2845 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 12.47 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.95 % Favored : 91.89 % Rotamer: Outliers : 2.27 % Allowed : 20.02 % Favored : 77.70 % 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: -0.94 (0.20), residues: 1849 helix: 0.58 (0.18), residues: 848 sheet: -1.85 (0.36), residues: 208 loop : -1.58 (0.23), residues: 793 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 848 HIS 0.006 0.001 HIS K 360 PHE 0.020 0.002 PHE A2171 TYR 0.025 0.002 TYR A 529 ARG 0.005 0.000 ARG K 311 *********************** 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 174 residues out of total 1673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 136 time to evaluate : 1.999 Fit side-chains revert: symmetry clash REVERT: A 37 LEU cc_start: 0.5813 (OUTLIER) cc_final: 0.5504 (tt) REVERT: A 53 GLU cc_start: 0.7236 (OUTLIER) cc_final: 0.6881 (mt-10) REVERT: A 231 MET cc_start: 0.5155 (mmt) cc_final: 0.4678 (tpp) REVERT: A 284 ASN cc_start: 0.6558 (t0) cc_final: 0.6254 (p0) REVERT: A 1208 TYR cc_start: 0.5817 (p90) cc_final: 0.5399 (p90) REVERT: A 1850 ILE cc_start: 0.6444 (OUTLIER) cc_final: 0.6139 (tp) REVERT: K 258 MET cc_start: 0.2603 (OUTLIER) cc_final: 0.0317 (mmm) REVERT: K 259 CYS cc_start: 0.4934 (OUTLIER) cc_final: 0.4226 (m) outliers start: 38 outliers final: 31 residues processed: 164 average time/residue: 0.2870 time to fit residues: 72.4758 Evaluate side-chains 168 residues out of total 1673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 132 time to evaluate : 1.846 ------------------------------------------------------------------------------- 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 369 LEU Chi-restraints excluded: chain A residue 514 GLU Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 966 CYS Chi-restraints excluded: chain A residue 999 TYR Chi-restraints excluded: chain A residue 1013 THR Chi-restraints excluded: chain A residue 1031 VAL Chi-restraints excluded: chain A residue 1121 ARG Chi-restraints excluded: chain A residue 1174 HIS Chi-restraints excluded: chain A residue 1243 THR Chi-restraints excluded: chain A residue 1289 ILE Chi-restraints excluded: chain A residue 1547 ASN Chi-restraints excluded: chain A residue 1587 HIS Chi-restraints excluded: chain A residue 1616 LEU Chi-restraints excluded: chain A residue 1850 ILE Chi-restraints excluded: chain A residue 1930 LEU Chi-restraints excluded: chain A residue 2025 THR Chi-restraints excluded: chain A residue 2094 ASP Chi-restraints excluded: chain A residue 2175 VAL Chi-restraints excluded: chain A residue 2205 VAL Chi-restraints excluded: chain A residue 2236 LEU Chi-restraints excluded: chain K residue 140 LEU Chi-restraints excluded: chain K residue 158 ILE Chi-restraints excluded: chain K residue 202 ASP Chi-restraints excluded: chain K residue 255 LEU Chi-restraints excluded: chain K residue 258 MET Chi-restraints excluded: chain K residue 259 CYS 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 183 optimal weight: 0.2980 chunk 111 optimal weight: 4.9990 chunk 86 optimal weight: 0.3980 chunk 127 optimal weight: 2.9990 chunk 192 optimal weight: 0.9990 chunk 176 optimal weight: 7.9990 chunk 153 optimal weight: 0.9990 chunk 15 optimal weight: 0.0040 chunk 118 optimal weight: 0.9990 chunk 93 optimal weight: 0.0470 chunk 121 optimal weight: 0.5980 overall best weight: 0.2690 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 502 ASN ** A1174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1287 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6673 moved from start: 0.2510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 16715 Z= 0.164 Angle : 0.649 16.348 22877 Z= 0.308 Chirality : 0.040 0.231 2595 Planarity : 0.004 0.066 2767 Dihedral : 12.952 104.708 2845 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.68 % Favored : 94.16 % Rotamer: Outliers : 1.85 % Allowed : 20.38 % Favored : 77.76 % 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: -0.62 (0.20), residues: 1849 helix: 0.86 (0.18), residues: 847 sheet: -1.74 (0.37), residues: 202 loop : -1.42 (0.23), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 848 HIS 0.010 0.001 HIS A1174 PHE 0.020 0.001 PHE A2171 TYR 0.030 0.001 TYR A1175 ARG 0.005 0.000 ARG K 311 ********************** 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 171 residues out of total 1673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 140 time to evaluate : 1.891 Fit side-chains revert: symmetry clash REVERT: A 231 MET cc_start: 0.4919 (mmt) cc_final: 0.4434 (tpp) REVERT: A 284 ASN cc_start: 0.6506 (t0) cc_final: 0.6229 (p0) REVERT: A 343 PHE cc_start: 0.5551 (p90) cc_final: 0.5227 (p90) REVERT: A 1208 TYR cc_start: 0.5743 (p90) cc_final: 0.5298 (p90) REVERT: K 258 MET cc_start: 0.2396 (OUTLIER) cc_final: 0.0156 (mmm) REVERT: K 259 CYS cc_start: 0.4787 (OUTLIER) cc_final: 0.4037 (m) outliers start: 31 outliers final: 25 residues processed: 164 average time/residue: 0.2920 time to fit residues: 73.4893 Evaluate side-chains 162 residues out of total 1673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 135 time to evaluate : 1.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 514 GLU Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 966 CYS Chi-restraints excluded: chain A residue 999 TYR Chi-restraints excluded: chain A residue 1013 THR Chi-restraints excluded: chain A residue 1031 VAL Chi-restraints excluded: chain A residue 1121 ARG Chi-restraints excluded: chain A residue 1174 HIS Chi-restraints excluded: chain A residue 1243 THR Chi-restraints excluded: chain A residue 1274 ILE Chi-restraints excluded: chain A residue 1587 HIS Chi-restraints excluded: chain A residue 1616 LEU Chi-restraints excluded: chain A residue 1930 LEU Chi-restraints excluded: chain A residue 2094 ASP Chi-restraints excluded: chain A residue 2175 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 258 MET Chi-restraints excluded: chain K residue 259 CYS 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 163 optimal weight: 6.9990 chunk 46 optimal weight: 0.9990 chunk 141 optimal weight: 2.9990 chunk 22 optimal weight: 0.0870 chunk 42 optimal weight: 0.1980 chunk 153 optimal weight: 0.8980 chunk 64 optimal weight: 1.9990 chunk 157 optimal weight: 0.8980 chunk 19 optimal weight: 0.8980 chunk 28 optimal weight: 0.5980 chunk 134 optimal weight: 0.3980 overall best weight: 0.4358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1174 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4571 r_free = 0.4571 target = 0.185876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.152698 restraints weight = 27166.615| |-----------------------------------------------------------------------------| r_work (start): 0.4182 rms_B_bonded: 2.98 r_work: 0.3992 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6769 moved from start: 0.2598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 16715 Z= 0.176 Angle : 0.649 16.213 22877 Z= 0.308 Chirality : 0.040 0.218 2595 Planarity : 0.004 0.067 2767 Dihedral : 12.853 103.818 2845 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.38 % Favored : 93.40 % Rotamer: Outliers : 2.09 % Allowed : 20.02 % Favored : 77.88 % 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: -0.52 (0.20), residues: 1849 helix: 0.94 (0.18), residues: 845 sheet: -1.73 (0.37), residues: 198 loop : -1.34 (0.23), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 848 HIS 0.007 0.001 HIS K 360 PHE 0.019 0.001 PHE A2171 TYR 0.025 0.001 TYR A 529 ARG 0.004 0.000 ARG K 311 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3338.22 seconds wall clock time: 62 minutes 23.38 seconds (3743.38 seconds total)