Starting phenix.real_space_refine on Sun Jun 15 08:42:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dfv_27415/06_2025/8dfv_27415.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dfv_27415/06_2025/8dfv_27415.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.06 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8dfv_27415/06_2025/8dfv_27415.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dfv_27415/06_2025/8dfv_27415.map" model { file = "/net/cci-nas-00/data/ceres_data/8dfv_27415/06_2025/8dfv_27415.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dfv_27415/06_2025/8dfv_27415.cif" } resolution = 3.06 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= -0.001 sd= 0.070 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Ca 10 9.91 5 P 60 5.49 5 S 91 5.16 5 C 10365 2.51 5 N 2935 2.21 5 O 3249 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 16710 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 13422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1664, 13422 Classifications: {'peptide': 1664} Link IDs: {'PTRANS': 97, 'TRANS': 1566} Chain breaks: 12 Chain: "E" Number of atoms: 1266 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 1266 Classifications: {'RNA': 60} Modifications used: {'p5*END': 1, 'rna2p_pur': 1, 'rna2p_pyr': 1, 'rna3p_pur': 27, 'rna3p_pyr': 31} Link IDs: {'rna2p': 2, 'rna3p': 57} Chain: "K" Number of atoms: 2012 Number of conformers: 1 Conformer: "" Number of residues, atoms: 253, 2012 Classifications: {'peptide': 253} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 240} Chain breaks: 2 Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' CA': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "E" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Unusual residues: {' CA': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Time building chain proxies: 9.78, per 1000 atoms: 0.59 Number of scatterers: 16710 At special positions: 0 Unit cell: (156.88, 130.38, 146.28, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 10 19.99 S 91 16.00 P 60 15.00 O 3249 8.00 N 2935 7.00 C 10365 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.97 Conformation dependent library (CDL) restraints added in 1.9 seconds 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3660 Finding SS restraints... Secondary structure from input PDB file: 65 helices and 19 sheets defined 46.8% alpha, 9.0% beta 19 base pairs and 39 stacking pairs defined. Time for finding SS restraints: 5.53 Creating SS restraints... Processing helix chain 'A' and resid 19 through 31 removed outlier: 3.784A pdb=" N GLU A 23 " --> pdb=" O ASP A 19 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLU A 30 " --> pdb=" O ALA A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 39 through 59 Processing helix chain 'A' and resid 79 through 88 removed outlier: 4.256A pdb=" N THR A 83 " --> pdb=" O CYS A 79 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N MET A 84 " --> pdb=" O SER A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 111 Processing helix chain 'A' and resid 117 through 127 Processing helix chain 'A' and resid 145 through 157 Proline residue: A 154 - end of helix Processing helix chain 'A' and resid 187 through 199 removed outlier: 3.578A pdb=" N LEU A 192 " --> pdb=" O LEU A 188 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ALA A 193 " --> pdb=" O SER A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 215 removed outlier: 3.535A pdb=" N VAL A 212 " --> pdb=" O ASP A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 252 removed outlier: 3.840A pdb=" N ASP A 251 " --> pdb=" O SER A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 293 removed outlier: 4.535A pdb=" N VAL A 288 " --> pdb=" O ASN A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 313 removed outlier: 4.198A pdb=" N HIS A 304 " --> pdb=" O ARG A 300 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LYS A 311 " --> pdb=" O GLN A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 344 removed outlier: 3.738A pdb=" N ALA A 342 " --> pdb=" O LEU A 338 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N PHE A 343 " --> pdb=" O CYS A 339 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N HIS A 344 " --> pdb=" O GLU A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 361 Processing helix chain 'A' and resid 362 through 375 Processing helix chain 'A' and resid 501 through 517 Processing helix chain 'A' and resid 520 through 524 removed outlier: 3.837A pdb=" N LYS A 523 " --> pdb=" O PRO A 520 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N PHE A 524 " --> pdb=" O ASP A 521 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 520 through 524' Processing helix chain 'A' and resid 540 through 560 removed outlier: 3.907A pdb=" N ARG A 557 " --> pdb=" O GLU A 553 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ARG A 559 " --> pdb=" O LEU A 555 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N MET A 560 " --> pdb=" O LYS A 556 " (cutoff:3.500A) Processing helix chain 'A' and resid 569 through 573 removed outlier: 3.659A pdb=" N GLU A 573 " --> pdb=" O SER A 570 " (cutoff:3.500A) Processing helix chain 'A' and resid 592 through 601 removed outlier: 3.633A pdb=" N CYS A 599 " --> pdb=" O SER A 595 " (cutoff:3.500A) Processing helix chain 'A' and resid 629 through 639 Processing helix chain 'A' and resid 760 through 785 Processing helix chain 'A' and resid 791 through 801 removed outlier: 3.570A pdb=" N GLN A 795 " --> pdb=" O PRO A 791 " (cutoff:3.500A) Processing helix chain 'A' and resid 822 through 834 removed outlier: 4.091A pdb=" N ILE A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 884 through 904 Processing helix chain 'A' and resid 922 through 927 removed outlier: 3.516A pdb=" N GLU A 926 " --> pdb=" O PRO A 923 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N CYS A 927 " --> pdb=" O ASP A 924 " (cutoff:3.500A) Processing helix chain 'A' and resid 931 through 941 removed outlier: 3.792A pdb=" N GLU A 935 " --> pdb=" O GLU A 931 " (cutoff:3.500A) Processing helix chain 'A' and resid 1045 through 1062 removed outlier: 3.705A pdb=" N ILE A1049 " --> pdb=" O THR A1045 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N VAL A1050 " --> pdb=" O SER A1046 " (cutoff:3.500A) Processing helix chain 'A' and resid 1098 through 1108 Processing helix chain 'A' and resid 1117 through 1124 removed outlier: 3.735A pdb=" N ARG A1121 " --> pdb=" O PRO A1117 " (cutoff:3.500A) Processing helix chain 'A' and resid 1230 through 1234 removed outlier: 3.967A pdb=" N LYS A1234 " --> pdb=" O LEU A1231 " (cutoff:3.500A) Processing helix chain 'A' and resid 1238 through 1242 removed outlier: 3.776A pdb=" N CYS A1242 " --> pdb=" O PRO A1239 " (cutoff:3.500A) Processing helix chain 'A' and resid 1248 through 1282 Proline residue: A1259 - end of helix Processing helix chain 'A' and resid 1524 through 1546 removed outlier: 4.648A pdb=" N GLN A1541 " --> pdb=" O ALA A1537 " (cutoff:3.500A) Processing helix chain 'A' and resid 1568 through 1581 Processing helix chain 'A' and resid 1607 through 1616 Processing helix chain 'A' and resid 1620 through 1629 removed outlier: 4.053A pdb=" N LEU A1624 " --> pdb=" O ASN A1620 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N LYS A1626 " --> pdb=" O ASP A1622 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLY A1629 " --> pdb=" O ALA A1625 " (cutoff:3.500A) Processing helix chain 'A' and resid 1636 through 1650 removed outlier: 3.510A pdb=" N HIS A1650 " --> pdb=" O TRP A1646 " (cutoff:3.500A) Processing helix chain 'A' and resid 1722 through 1731 Processing helix chain 'A' and resid 1732 through 1736 removed outlier: 3.735A pdb=" N ASN A1736 " --> pdb=" O SER A1733 " (cutoff:3.500A) Processing helix chain 'A' and resid 1741 through 1764 Processing helix chain 'A' and resid 1768 through 1780 removed outlier: 3.775A pdb=" N HIS A1774 " --> pdb=" O GLY A1770 " (cutoff:3.500A) Processing helix chain 'A' and resid 1781 through 1792 Processing helix chain 'A' and resid 1793 through 1797 Processing helix chain 'A' and resid 1838 through 1842 removed outlier: 4.025A pdb=" N ASP A1841 " --> pdb=" O ASP A1838 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ILE A1842 " --> pdb=" O LEU A1839 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1838 through 1842' Processing helix chain 'A' and resid 1847 through 1852 Processing helix chain 'A' and resid 1900 through 1931 Proline residue: A1920 - end of helix Processing helix chain 'A' and resid 1981 through 1990 removed outlier: 3.526A pdb=" N LEU A1990 " --> pdb=" O LEU A1986 " (cutoff:3.500A) Processing helix chain 'A' and resid 1993 through 1999 Processing helix chain 'A' and resid 2007 through 2015 Processing helix chain 'A' and resid 2028 through 2049 removed outlier: 3.792A pdb=" N ALA A2037 " --> pdb=" O PHE A2033 " (cutoff:3.500A) Processing helix chain 'A' and resid 2055 through 2067 Processing helix chain 'A' and resid 2068 through 2079 Processing helix chain 'A' and resid 2089 through 2106 Processing helix chain 'A' and resid 2131 through 2149 removed outlier: 3.652A pdb=" N GLY A2135 " --> pdb=" O PRO A2131 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ALA A2142 " --> pdb=" O PHE A2138 " (cutoff:3.500A) Processing helix chain 'A' and resid 2155 through 2173 removed outlier: 3.696A pdb=" N VAL A2159 " --> pdb=" O VAL A2155 " (cutoff:3.500A) Proline residue: A2166 - end of helix removed outlier: 3.523A pdb=" N ASN A2173 " --> pdb=" O GLU A2169 " (cutoff:3.500A) Processing helix chain 'A' and resid 2178 through 2187 Processing helix chain 'A' and resid 2223 through 2239 Processing helix chain 'K' and resid 135 through 146 Processing helix chain 'K' and resid 188 through 204 Processing helix chain 'K' and resid 253 through 262 Processing helix chain 'K' and resid 300 through 319 Processing helix chain 'K' and resid 359 through 374 Processing helix chain 'K' and resid 376 through 384 removed outlier: 4.466A pdb=" N LEU K 380 " --> pdb=" O GLY K 376 " (cutoff:3.500A) Processing helix chain 'K' and resid 393 through 405 Processing helix chain 'K' and resid 443 through 464 Processing sheet with id=AA1, first strand: chain 'A' and resid 115 through 116 removed outlier: 7.831A pdb=" N LEU A 116 " --> pdb=" O SER A 65 " (cutoff:3.500A) removed outlier: 5.773A pdb=" N TYR A 67 " --> pdb=" O LEU A 116 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N VAL A 64 " --> pdb=" O GLU A 136 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N ILE A 138 " --> pdb=" O VAL A 64 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N VAL A 66 " --> pdb=" O ILE A 138 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 220 through 221 removed outlier: 6.220A pdb=" N HIS A 220 " --> pdb=" O HIS A 610 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N ILE A 612 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N VAL A 224 " --> pdb=" O VAL A 614 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 220 through 221 removed outlier: 6.220A pdb=" N HIS A 220 " --> pdb=" O HIS A 610 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N ILE A 612 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N VAL A 584 " --> pdb=" O VAL A 611 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N LEU A 613 " --> pdb=" O VAL A 584 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N ARG A 586 " --> pdb=" O LEU A 613 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 527 through 529 Processing sheet with id=AA5, first strand: chain 'A' and resid 805 through 806 Processing sheet with id=AA6, first strand: chain 'A' and resid 847 through 850 Processing sheet with id=AA7, first strand: chain 'A' and resid 853 through 854 Processing sheet with id=AA8, first strand: chain 'A' and resid 952 through 956 removed outlier: 3.572A pdb=" N TYR A 955 " --> pdb=" O HIS A1896 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N HIS A1896 " --> pdb=" O TYR A 955 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1036 through 1042 removed outlier: 4.574A pdb=" N LEU A 976 " --> pdb=" O ALA A1038 " (cutoff:3.500A) removed outlier: 7.622A pdb=" N GLU A1040 " --> pdb=" O CYS A 974 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N CYS A 974 " --> pdb=" O GLU A1040 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 981 through 986 removed outlier: 6.626A pdb=" N GLU A1030 " --> pdb=" O GLN A 984 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 1072 through 1073 Processing sheet with id=AB3, first strand: chain 'A' and resid 1153 through 1155 removed outlier: 4.355A pdb=" N GLN A1235 " --> pdb=" O VAL A1194 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 1673 through 1674 removed outlier: 3.780A pdb=" N ASN A1674 " --> pdb=" O GLN A1679 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLN A1679 " --> pdb=" O ASN A1674 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 1937 through 1940 removed outlier: 4.038A pdb=" N VAL A1964 " --> pdb=" O THR A1938 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 2191 through 2193 removed outlier: 3.893A pdb=" N LYS A2192 " --> pdb=" O ASP A2210 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ASP A2210 " --> pdb=" O LYS A2192 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 2191 through 2193 removed outlier: 3.893A pdb=" N LYS A2192 " --> pdb=" O ASP A2210 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ASP A2210 " --> pdb=" O LYS A2192 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'K' and resid 152 through 160 removed outlier: 3.808A pdb=" N GLY K 152 " --> pdb=" O SER K 172 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N ARG K 168 " --> pdb=" O VAL K 156 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N ILE K 158 " --> pdb=" O THR K 166 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N THR K 166 " --> pdb=" O ILE K 158 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'K' and resid 268 through 273 removed outlier: 4.363A pdb=" N SER K 268 " --> pdb=" O SER K 288 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N SER K 288 " --> pdb=" O SER K 268 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N THR K 284 " --> pdb=" O GLU K 272 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'K' and resid 408 through 412 removed outlier: 4.205A pdb=" N GLU K 408 " --> pdb=" O SER K 430 " (cutoff:3.500A) 675 hydrogen bonds defined for protein. 1950 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 47 hydrogen bonds 94 hydrogen bond angles 0 basepair planarities 19 basepair parallelities 39 stacking parallelities Total time for adding SS restraints: 7.85 Time building geometry restraints manager: 4.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4007 1.33 - 1.45: 3761 1.45 - 1.57: 9176 1.57 - 1.69: 119 1.69 - 1.81: 126 Bond restraints: 17189 Sorted by residual: bond pdb=" CG ARG A 586 " pdb=" CD ARG A 586 " ideal model delta sigma weight residual 1.520 1.416 0.104 3.00e-02 1.11e+03 1.19e+01 bond pdb=" CD1 PHE A1996 " pdb=" CE1 PHE A1996 " ideal model delta sigma weight residual 1.382 1.286 0.096 3.00e-02 1.11e+03 1.02e+01 bond pdb=" CG1 ILE A2180 " pdb=" CD1 ILE A2180 " ideal model delta sigma weight residual 1.513 1.393 0.120 3.90e-02 6.57e+02 9.46e+00 bond pdb=" CG1 ILE A1898 " pdb=" CD1 ILE A1898 " ideal model delta sigma weight residual 1.513 1.399 0.114 3.90e-02 6.57e+02 8.49e+00 bond pdb=" CB PHE A1996 " pdb=" CG PHE A1996 " ideal model delta sigma weight residual 1.502 1.437 0.065 2.30e-02 1.89e+03 7.96e+00 ... (remaining 17184 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.83: 22800 2.83 - 5.66: 657 5.66 - 8.49: 92 8.49 - 11.33: 14 11.33 - 14.16: 6 Bond angle restraints: 23569 Sorted by residual: angle pdb=" OG1 THR A 851 " pdb=" CB THR A 851 " pdb=" CG2 THR A 851 " ideal model delta sigma weight residual 109.30 98.90 10.40 2.00e+00 2.50e-01 2.70e+01 angle pdb=" CB LEU A1930 " pdb=" CG LEU A1930 " pdb=" CD2 LEU A1930 " ideal model delta sigma weight residual 110.70 97.13 13.57 3.00e+00 1.11e-01 2.05e+01 angle pdb=" C PHE A 3 " pdb=" N HIS A 4 " pdb=" CA HIS A 4 " ideal model delta sigma weight residual 121.54 129.92 -8.38 1.91e+00 2.74e-01 1.93e+01 angle pdb=" C PHE K 173 " pdb=" N LYS K 174 " pdb=" CA LYS K 174 " ideal model delta sigma weight residual 121.54 129.86 -8.32 1.91e+00 2.74e-01 1.90e+01 angle pdb=" N LYS A1227 " pdb=" CA LYS A1227 " pdb=" C LYS A1227 " ideal model delta sigma weight residual 110.80 119.96 -9.16 2.13e+00 2.20e-01 1.85e+01 ... (remaining 23564 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.93: 10132 31.93 - 63.87: 351 63.87 - 95.80: 35 95.80 - 127.74: 0 127.74 - 159.67: 1 Dihedral angle restraints: 10519 sinusoidal: 4886 harmonic: 5633 Sorted by residual: dihedral pdb=" O4' U E 1 " pdb=" C1' U E 1 " pdb=" N1 U E 1 " pdb=" C2 U E 1 " ideal model delta sinusoidal sigma weight residual 232.00 72.33 159.67 1 1.70e+01 3.46e-03 6.44e+01 dihedral pdb=" CA GLY A1661 " pdb=" C GLY A1661 " pdb=" N ASP A1662 " pdb=" CA ASP A1662 " ideal model delta harmonic sigma weight residual -180.00 -145.34 -34.66 0 5.00e+00 4.00e-02 4.81e+01 dihedral pdb=" CA PRO A 912 " pdb=" C PRO A 912 " pdb=" N ILE A 913 " pdb=" CA ILE A 913 " ideal model delta harmonic sigma weight residual -180.00 -148.80 -31.20 0 5.00e+00 4.00e-02 3.89e+01 ... (remaining 10516 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.124: 2538 0.124 - 0.249: 128 0.249 - 0.373: 8 0.373 - 0.497: 0 0.497 - 0.622: 1 Chirality restraints: 2675 Sorted by residual: chirality pdb=" CB ILE A2180 " pdb=" CA ILE A2180 " pdb=" CG1 ILE A2180 " pdb=" CG2 ILE A2180 " both_signs ideal model delta sigma weight residual False 2.64 2.02 0.62 2.00e-01 2.50e+01 9.66e+00 chirality pdb=" CB VAL A2137 " pdb=" CA VAL A2137 " pdb=" CG1 VAL A2137 " pdb=" CG2 VAL A2137 " both_signs ideal model delta sigma weight residual False -2.63 -2.28 -0.35 2.00e-01 2.50e+01 3.05e+00 chirality pdb=" CB VAL A1934 " pdb=" CA VAL A1934 " pdb=" CG1 VAL A1934 " pdb=" CG2 VAL A1934 " both_signs ideal model delta sigma weight residual False -2.63 -2.29 -0.34 2.00e-01 2.50e+01 2.81e+00 ... (remaining 2672 not shown) Planarity restraints: 2827 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A1814 " -0.025 2.00e-02 2.50e+03 3.39e-02 2.30e+01 pdb=" CG TYR A1814 " 0.078 2.00e-02 2.50e+03 pdb=" CD1 TYR A1814 " -0.043 2.00e-02 2.50e+03 pdb=" CD2 TYR A1814 " -0.014 2.00e-02 2.50e+03 pdb=" CE1 TYR A1814 " 0.017 2.00e-02 2.50e+03 pdb=" CE2 TYR A1814 " -0.010 2.00e-02 2.50e+03 pdb=" CZ TYR A1814 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR A1814 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 863 " 0.032 2.00e-02 2.50e+03 2.87e-02 1.65e+01 pdb=" CG TYR A 863 " -0.068 2.00e-02 2.50e+03 pdb=" CD1 TYR A 863 " 0.025 2.00e-02 2.50e+03 pdb=" CD2 TYR A 863 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR A 863 " -0.008 2.00e-02 2.50e+03 pdb=" CE2 TYR A 863 " 0.015 2.00e-02 2.50e+03 pdb=" CZ TYR A 863 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR A 863 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A2020 " -0.060 5.00e-02 4.00e+02 8.95e-02 1.28e+01 pdb=" N PRO A2021 " 0.155 5.00e-02 4.00e+02 pdb=" CA PRO A2021 " -0.045 5.00e-02 4.00e+02 pdb=" CD PRO A2021 " -0.050 5.00e-02 4.00e+02 ... (remaining 2824 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.74: 1997 2.74 - 3.28: 16136 3.28 - 3.82: 29426 3.82 - 4.36: 35292 4.36 - 4.90: 57676 Nonbonded interactions: 140527 Sorted by model distance: nonbonded pdb=" O LEU A1727 " pdb=" OG1 THR A1731 " model vdw 2.206 3.040 nonbonded pdb=" O ILE A1950 " pdb=" OG SER A1953 " model vdw 2.223 3.040 nonbonded pdb=" OH TYR A 832 " pdb=" OG SER A 871 " model vdw 2.233 3.040 nonbonded pdb=" O SER A1162 " pdb=" OG1 THR A1171 " model vdw 2.236 3.040 nonbonded pdb=" OG SER A1999 " pdb=" O HIS A2079 " model vdw 2.265 3.040 ... (remaining 140522 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.640 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: 0.630 Check model and map are aligned: 0.120 Set scattering table: 0.150 Process input model: 43.750 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.060 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:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6886 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.131 17189 Z= 0.419 Angle : 1.153 14.157 23569 Z= 0.589 Chirality : 0.064 0.622 2675 Planarity : 0.009 0.105 2827 Dihedral : 16.023 159.671 6859 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.32 % Allowed : 9.66 % Favored : 90.03 % Rotamer: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z (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: -2.99 (0.18), residues: 1885 helix: -1.54 (0.15), residues: 843 sheet: -2.30 (0.36), residues: 198 loop : -2.27 (0.21), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP K 254 HIS 0.031 0.002 HIS A1896 PHE 0.054 0.005 PHE A2081 TYR 0.078 0.004 TYR A1814 ARG 0.016 0.001 ARG A1027 Details of bonding type rmsd hydrogen bonds : bond 0.14451 ( 722) hydrogen bonds : angle 6.67804 ( 2044) covalent geometry : bond 0.01010 (17189) covalent geometry : angle 1.15278 (23569) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 1701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 294 time to evaluate : 1.636 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ILE cc_start: 0.7547 (tt) cc_final: 0.6985 (mt) REVERT: A 524 PHE cc_start: 0.6621 (p90) cc_final: 0.6262 (p90) REVERT: A 580 LYS cc_start: 0.6821 (pttt) cc_final: 0.6470 (mmtp) REVERT: A 936 GLN cc_start: 0.7473 (tp40) cc_final: 0.7259 (tp-100) REVERT: A 1531 ILE cc_start: 0.5659 (mm) cc_final: 0.5430 (mt) REVERT: A 1818 LYS cc_start: 0.7669 (mttp) cc_final: 0.7398 (ptpt) REVERT: A 2067 VAL cc_start: 0.5822 (t) cc_final: 0.5544 (m) REVERT: K 176 LYS cc_start: 0.6323 (mmtt) cc_final: 0.6036 (ttpp) REVERT: K 311 ARG cc_start: 0.6867 (mtp85) cc_final: 0.6582 (mmm160) REVERT: K 369 LYS cc_start: 0.7885 (tmmt) cc_final: 0.7542 (tptp) REVERT: K 384 LYS cc_start: 0.8110 (mttp) cc_final: 0.7410 (tptt) outliers start: 0 outliers final: 0 residues processed: 294 average time/residue: 0.3345 time to fit residues: 141.7860 Evaluate side-chains 176 residues out of total 1701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 176 time to evaluate : 1.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 166 optimal weight: 4.9990 chunk 149 optimal weight: 0.8980 chunk 82 optimal weight: 1.9990 chunk 51 optimal weight: 0.6980 chunk 100 optimal weight: 0.6980 chunk 79 optimal weight: 0.9990 chunk 154 optimal weight: 4.9990 chunk 59 optimal weight: 3.9990 chunk 93 optimal weight: 0.7980 chunk 114 optimal weight: 0.5980 chunk 178 optimal weight: 8.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 225 GLN ** A 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 245 HIS A 346 HIS A 773 GLN A1142 ASN A1185 GLN A1235 GLN A1590 GLN A1784 ASN K 194 HIS ** K 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4456 r_free = 0.4456 target = 0.186087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.153127 restraints weight = 26090.778| |-----------------------------------------------------------------------------| r_work (start): 0.4086 rms_B_bonded: 2.46 r_work: 0.3921 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6939 moved from start: 0.1817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 17189 Z= 0.164 Angle : 0.725 11.957 23569 Z= 0.368 Chirality : 0.043 0.184 2675 Planarity : 0.006 0.063 2827 Dihedral : 14.254 156.307 3004 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 12.97 Ramachandran Plot: Outliers : 0.32 % Allowed : 7.37 % Favored : 92.31 % Rotamer: Outliers : 1.35 % Allowed : 8.23 % Favored : 90.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.95 (0.19), residues: 1885 helix: -0.42 (0.17), residues: 865 sheet: -2.32 (0.36), residues: 203 loop : -1.91 (0.22), residues: 817 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 94 HIS 0.012 0.001 HIS A1768 PHE 0.028 0.002 PHE A2171 TYR 0.025 0.002 TYR A 863 ARG 0.006 0.001 ARG K 146 Details of bonding type rmsd hydrogen bonds : bond 0.05181 ( 722) hydrogen bonds : angle 4.97959 ( 2044) covalent geometry : bond 0.00367 (17189) covalent geometry : angle 0.72482 (23569) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 223 time to evaluate : 1.676 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 GLU cc_start: 0.6445 (mm-30) cc_final: 0.6033 (mm-30) REVERT: A 81 ILE cc_start: 0.7625 (OUTLIER) cc_final: 0.7260 (tt) REVERT: A 303 HIS cc_start: 0.6284 (OUTLIER) cc_final: 0.5379 (t70) REVERT: A 524 PHE cc_start: 0.6200 (p90) cc_final: 0.5910 (p90) REVERT: A 580 LYS cc_start: 0.7029 (pttt) cc_final: 0.6573 (mmtt) REVERT: A 930 LEU cc_start: 0.4613 (OUTLIER) cc_final: 0.4341 (pp) REVERT: A 977 TYR cc_start: 0.6484 (m-10) cc_final: 0.6251 (m-10) REVERT: A 2177 LYS cc_start: 0.7626 (mmtp) cc_final: 0.7101 (mmmt) REVERT: A 2182 GLU cc_start: 0.6536 (tp30) cc_final: 0.6321 (tp30) REVERT: A 2197 GLU cc_start: 0.6198 (mm-30) cc_final: 0.5787 (mt-10) REVERT: K 176 LYS cc_start: 0.5953 (mmtt) cc_final: 0.5552 (ttpp) REVERT: K 311 ARG cc_start: 0.7466 (mtp85) cc_final: 0.6728 (mmm160) REVERT: K 312 MET cc_start: 0.4905 (tpp) cc_final: 0.4309 (tpp) REVERT: K 369 LYS cc_start: 0.7740 (tmmt) cc_final: 0.7434 (tptp) outliers start: 23 outliers final: 9 residues processed: 231 average time/residue: 0.3185 time to fit residues: 108.0300 Evaluate side-chains 188 residues out of total 1701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 176 time to evaluate : 1.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 81 ILE Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain A residue 303 HIS Chi-restraints excluded: chain A residue 813 HIS Chi-restraints excluded: chain A residue 930 LEU Chi-restraints excluded: chain A residue 1071 MET Chi-restraints excluded: chain A residue 1079 GLU Chi-restraints excluded: chain A residue 1927 MET Chi-restraints excluded: chain A residue 2097 ASP Chi-restraints excluded: chain A residue 2216 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 92 optimal weight: 7.9990 chunk 13 optimal weight: 0.1980 chunk 21 optimal weight: 0.9990 chunk 145 optimal weight: 0.0770 chunk 10 optimal weight: 0.5980 chunk 20 optimal weight: 0.4980 chunk 36 optimal weight: 3.9990 chunk 111 optimal weight: 1.9990 chunk 153 optimal weight: 0.9980 chunk 52 optimal weight: 0.9980 chunk 159 optimal weight: 1.9990 overall best weight: 0.4738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 243 ASN A 245 HIS A 341 HIS A1142 ASN A1589 GLN A1806 HIS ** K 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4475 r_free = 0.4475 target = 0.188035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.155703 restraints weight = 26038.952| |-----------------------------------------------------------------------------| r_work (start): 0.4115 rms_B_bonded: 2.36 r_work: 0.3949 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6894 moved from start: 0.2308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 17189 Z= 0.134 Angle : 0.655 10.537 23569 Z= 0.330 Chirality : 0.041 0.200 2675 Planarity : 0.005 0.058 2827 Dihedral : 13.983 159.837 3004 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.32 % Allowed : 7.27 % Favored : 92.41 % Rotamer: Outliers : 1.53 % Allowed : 11.52 % Favored : 86.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -1.36 (0.19), residues: 1885 helix: 0.18 (0.17), residues: 867 sheet: -2.24 (0.36), residues: 203 loop : -1.69 (0.23), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1646 HIS 0.007 0.001 HIS A1896 PHE 0.020 0.002 PHE A1707 TYR 0.018 0.002 TYR A 863 ARG 0.004 0.000 ARG A1114 Details of bonding type rmsd hydrogen bonds : bond 0.04495 ( 722) hydrogen bonds : angle 4.60873 ( 2044) covalent geometry : bond 0.00296 (17189) covalent geometry : angle 0.65510 (23569) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 209 time to evaluate : 1.623 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ILE cc_start: 0.7552 (tt) cc_final: 0.7096 (mt) REVERT: A 303 HIS cc_start: 0.6092 (OUTLIER) cc_final: 0.5176 (t70) REVERT: A 341 HIS cc_start: 0.7041 (m-70) cc_final: 0.6735 (m90) REVERT: A 580 LYS cc_start: 0.6980 (pttt) cc_final: 0.6535 (mmtt) REVERT: A 930 LEU cc_start: 0.4546 (OUTLIER) cc_final: 0.4335 (pp) REVERT: A 977 TYR cc_start: 0.6506 (m-10) cc_final: 0.6238 (m-80) REVERT: A 2177 LYS cc_start: 0.7639 (mmtp) cc_final: 0.7120 (mmmt) REVERT: A 2182 GLU cc_start: 0.6557 (tp30) cc_final: 0.6307 (tp30) REVERT: A 2197 GLU cc_start: 0.6358 (mm-30) cc_final: 0.6024 (mt-10) REVERT: K 176 LYS cc_start: 0.5756 (mmtt) cc_final: 0.5382 (ttpp) REVERT: K 263 ARG cc_start: 0.4819 (mtp180) cc_final: 0.4217 (ptp-170) REVERT: K 311 ARG cc_start: 0.7429 (mtp85) cc_final: 0.6783 (mmm160) REVERT: K 312 MET cc_start: 0.4991 (tpp) cc_final: 0.4438 (tpp) REVERT: K 369 LYS cc_start: 0.7715 (tmmt) cc_final: 0.7406 (tptp) outliers start: 26 outliers final: 10 residues processed: 223 average time/residue: 0.3199 time to fit residues: 104.5997 Evaluate side-chains 190 residues out of total 1701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 178 time to evaluate : 1.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain A residue 303 HIS Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 930 LEU Chi-restraints excluded: chain A residue 1079 GLU Chi-restraints excluded: chain A residue 1587 HIS Chi-restraints excluded: chain A residue 1927 MET Chi-restraints excluded: chain A residue 2094 ASP Chi-restraints excluded: chain A residue 2097 ASP Chi-restraints excluded: chain A residue 2216 THR Chi-restraints excluded: chain K residue 150 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 62.1479 > 50: distance: 40 - 45: 7.936 distance: 45 - 46: 14.973 distance: 46 - 47: 8.292 distance: 46 - 49: 12.860 distance: 47 - 48: 8.823 distance: 47 - 52: 15.501 distance: 49 - 50: 25.237 distance: 49 - 51: 33.899 distance: 52 - 53: 15.569 distance: 53 - 54: 20.539 distance: 53 - 56: 10.027 distance: 54 - 55: 33.683 distance: 54 - 57: 30.182 distance: 57 - 58: 30.817 distance: 57 - 196: 28.056 distance: 58 - 59: 21.735 distance: 59 - 60: 32.750 distance: 59 - 66: 23.770 distance: 60 - 193: 26.721 distance: 61 - 62: 19.418 distance: 62 - 63: 20.866 distance: 63 - 64: 27.873 distance: 63 - 65: 6.178 distance: 66 - 67: 40.343 distance: 67 - 68: 30.280 distance: 67 - 70: 26.014 distance: 68 - 69: 27.361 distance: 68 - 74: 29.343 distance: 70 - 71: 16.889 distance: 70 - 72: 21.567 distance: 71 - 73: 19.067 distance: 74 - 75: 31.712 distance: 74 - 182: 28.928 distance: 75 - 76: 47.127 distance: 75 - 78: 32.007 distance: 76 - 77: 39.091 distance: 76 - 80: 48.464 distance: 77 - 179: 19.147 distance: 78 - 79: 30.429 distance: 80 - 81: 19.895 distance: 80 - 86: 30.295 distance: 81 - 82: 28.575 distance: 81 - 84: 34.800 distance: 82 - 83: 13.858 distance: 82 - 87: 21.926 distance: 84 - 85: 12.766 distance: 85 - 86: 30.921 distance: 87 - 88: 33.511 distance: 88 - 89: 42.614 distance: 88 - 91: 38.656 distance: 89 - 90: 25.887 distance: 89 - 97: 45.569 distance: 91 - 92: 17.912 distance: 92 - 93: 13.456 distance: 92 - 94: 19.612 distance: 93 - 95: 21.425 distance: 94 - 96: 13.915 distance: 95 - 96: 12.608 distance: 97 - 98: 26.539 distance: 98 - 99: 29.074 distance: 98 - 101: 17.009 distance: 99 - 100: 27.692 distance: 99 - 105: 27.240 distance: 101 - 102: 30.670 distance: 102 - 103: 21.163 distance: 102 - 104: 29.450 distance: 105 - 106: 8.634 distance: 106 - 109: 7.716 distance: 107 - 108: 21.006 distance: 107 - 111: 20.482 distance: 109 - 110: 3.006 distance: 111 - 112: 18.446 distance: 111 - 117: 7.750 distance: 112 - 113: 19.750 distance: 112 - 115: 27.052 distance: 113 - 114: 20.532 distance: 113 - 118: 21.296 distance: 115 - 116: 16.025 distance: 116 - 117: 15.428