Starting phenix.real_space_refine on Sun Jan 19 13:30:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dgi_27423/01_2025/8dgi_27423.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dgi_27423/01_2025/8dgi_27423.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.94 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8dgi_27423/01_2025/8dgi_27423.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dgi_27423/01_2025/8dgi_27423.map" model { file = "/net/cci-nas-00/data/ceres_data/8dgi_27423/01_2025/8dgi_27423.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dgi_27423/01_2025/8dgi_27423.cif" } resolution = 3.94 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= 0.008 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: 4 Type Number sf(0) Gaussians S 74 5.16 5 C 8608 2.51 5 N 2384 2.21 5 O 2514 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 60 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 13580 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 12733 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1582, 12733 Classifications: {'peptide': 1582} Link IDs: {'PTRANS': 96, 'TRANS': 1485} Chain breaks: 9 Chain: "N" Number of atoms: 847 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 847 Classifications: {'peptide': 108} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 1, 'TRANS': 105} Time building chain proxies: 8.97, per 1000 atoms: 0.66 Number of scatterers: 13580 At special positions: 0 Unit cell: (153.12, 134.85, 135.72, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 74 16.00 O 2514 8.00 N 2384 7.00 C 8608 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: 3.05 Conformation dependent library (CDL) restraints added in 1.8 seconds 3336 Ramachandran restraints generated. 1668 Oldfield, 0 Emsley, 1668 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3222 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 10 sheets defined 51.0% alpha, 9.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.74 Creating SS restraints... Processing helix chain 'A' and resid 22 through 31 removed outlier: 3.774A pdb=" N ARG A 31 " --> pdb=" O THR A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 39 through 61 removed outlier: 3.823A pdb=" N LYS A 43 " --> pdb=" O HIS A 39 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ARG A 56 " --> pdb=" O GLN A 52 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N ARG A 57 " --> pdb=" O GLU A 53 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N ARG A 60 " --> pdb=" O ARG A 56 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N HIS A 61 " --> pdb=" O ARG A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 88 Processing helix chain 'A' and resid 117 through 127 Processing helix chain 'A' and resid 131 through 135 removed outlier: 3.737A pdb=" N VAL A 135 " --> pdb=" O LEU A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 160 Proline residue: A 154 - end of helix removed outlier: 3.593A pdb=" N HIS A 159 " --> pdb=" O LEU A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 168 removed outlier: 3.535A pdb=" N ARG A 168 " --> pdb=" O PRO A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 181 Processing helix chain 'A' and resid 184 through 200 Processing helix chain 'A' and resid 207 through 215 Processing helix chain 'A' and resid 232 through 252 Processing helix chain 'A' and resid 255 through 260 Processing helix chain 'A' and resid 267 through 272 removed outlier: 4.004A pdb=" N ASP A 271 " --> pdb=" O ASP A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 293 Processing helix chain 'A' and resid 294 through 316 removed outlier: 4.114A pdb=" N LYS A 311 " --> pdb=" O GLN A 307 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N THR A 316 " --> pdb=" O LEU A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 346 removed outlier: 3.515A pdb=" N TYR A 322 " --> pdb=" O HIS A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 361 removed outlier: 3.508A pdb=" N TYR A 360 " --> pdb=" O THR A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 374 Processing helix chain 'A' and resid 501 through 517 Processing helix chain 'A' and resid 540 through 560 removed outlier: 3.855A pdb=" N MET A 560 " --> pdb=" O LYS A 556 " (cutoff:3.500A) Processing helix chain 'A' and resid 569 through 573 Processing helix chain 'A' and resid 592 through 603 removed outlier: 3.857A pdb=" N ALA A 603 " --> pdb=" O CYS A 599 " (cutoff:3.500A) Processing helix chain 'A' and resid 763 through 783 Processing helix chain 'A' and resid 791 through 802 Processing helix chain 'A' and resid 824 through 835 Processing helix chain 'A' and resid 884 through 904 Processing helix chain 'A' and resid 921 through 929 removed outlier: 5.266A pdb=" N GLU A 926 " --> pdb=" O PRO A 923 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N CYS A 927 " --> pdb=" O ASP A 924 " (cutoff:3.500A) Processing helix chain 'A' and resid 1045 through 1062 Processing helix chain 'A' and resid 1098 through 1108 Processing helix chain 'A' and resid 1117 through 1123 Processing helix chain 'A' and resid 1171 through 1180 Processing helix chain 'A' and resid 1204 through 1208 Processing helix chain 'A' and resid 1223 through 1231 Processing helix chain 'A' and resid 1238 through 1240 No H-bonds generated for 'chain 'A' and resid 1238 through 1240' Processing helix chain 'A' and resid 1248 through 1256 Processing helix chain 'A' and resid 1261 through 1268 removed outlier: 3.566A pdb=" N ILE A1265 " --> pdb=" O ILE A1261 " (cutoff:3.500A) Processing helix chain 'A' and resid 1269 through 1283 Processing helix chain 'A' and resid 1519 through 1535 removed outlier: 4.240A pdb=" N THR A1535 " --> pdb=" O ILE A1531 " (cutoff:3.500A) Processing helix chain 'A' and resid 1537 through 1547 removed outlier: 3.612A pdb=" N GLN A1541 " --> pdb=" O ALA A1537 " (cutoff:3.500A) Processing helix chain 'A' and resid 1562 through 1579 removed outlier: 3.516A pdb=" N ARG A1566 " --> pdb=" O PRO A1562 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N SER A1570 " --> pdb=" O ARG A1566 " (cutoff:3.500A) Processing helix chain 'A' and resid 1608 through 1616 Processing helix chain 'A' and resid 1620 through 1629 removed outlier: 3.722A pdb=" N LEU A1624 " --> pdb=" O ASN A1620 " (cutoff:3.500A) Processing helix chain 'A' and resid 1635 through 1650 Processing helix chain 'A' and resid 1665 through 1669 removed outlier: 4.481A pdb=" N ASN A1668 " --> pdb=" O ASP A1665 " (cutoff:3.500A) Processing helix chain 'A' and resid 1722 through 1731 removed outlier: 4.027A pdb=" N ILE A1726 " --> pdb=" O SER A1722 " (cutoff:3.500A) Processing helix chain 'A' and resid 1741 through 1764 removed outlier: 3.674A pdb=" N THR A1746 " --> pdb=" O GLU A1742 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N ILE A1747 " --> pdb=" O ARG A1743 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N SER A1750 " --> pdb=" O THR A1746 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LYS A1753 " --> pdb=" O ASP A1749 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N TYR A1754 " --> pdb=" O SER A1750 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N THR A1758 " --> pdb=" O TYR A1754 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N TYR A1759 " --> pdb=" O ALA A1755 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N TYR A1764 " --> pdb=" O LEU A1760 " (cutoff:3.500A) Processing helix chain 'A' and resid 1768 through 1780 removed outlier: 3.939A pdb=" N LEU A1772 " --> pdb=" O HIS A1768 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N HIS A1774 " --> pdb=" O GLY A1770 " (cutoff:3.500A) Processing helix chain 'A' and resid 1781 through 1792 removed outlier: 3.806A pdb=" N LYS A1792 " --> pdb=" O LEU A1788 " (cutoff:3.500A) Processing helix chain 'A' and resid 1899 through 1914 removed outlier: 3.504A pdb=" N ILE A1903 " --> pdb=" O PRO A1899 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ALA A1904 " --> pdb=" O ASP A1900 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ALA A1909 " --> pdb=" O ASP A1905 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ILE A1911 " --> pdb=" O VAL A1907 " (cutoff:3.500A) Processing helix chain 'A' and resid 1920 through 1931 removed outlier: 3.581A pdb=" N MET A1927 " --> pdb=" O ALA A1923 " (cutoff:3.500A) Processing helix chain 'A' and resid 1981 through 1990 removed outlier: 4.340A pdb=" N LEU A1990 " --> pdb=" O LEU A1986 " (cutoff:3.500A) Processing helix chain 'A' and resid 1992 through 2001 removed outlier: 3.600A pdb=" N PHE A1996 " --> pdb=" O GLY A1992 " (cutoff:3.500A) Processing helix chain 'A' and resid 2007 through 2014 Processing helix chain 'A' and resid 2030 through 2050 removed outlier: 3.750A pdb=" N LEU A2034 " --> pdb=" O ARG A2030 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N ALA A2037 " --> pdb=" O PHE A2033 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ASP A2050 " --> pdb=" O HIS A2046 " (cutoff:3.500A) Processing helix chain 'A' and resid 2055 through 2067 Processing helix chain 'A' and resid 2068 through 2079 removed outlier: 3.934A pdb=" N PHE A2072 " --> pdb=" O ASN A2068 " (cutoff:3.500A) Processing helix chain 'A' and resid 2091 through 2107 Processing helix chain 'A' and resid 2110 through 2121 removed outlier: 5.117A pdb=" N SER A2118 " --> pdb=" O TYR A2114 " (cutoff:3.500A) Processing helix chain 'A' and resid 2132 through 2149 removed outlier: 3.941A pdb=" N PHE A2138 " --> pdb=" O LEU A2134 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N ALA A2142 " --> pdb=" O PHE A2138 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLY A2143 " --> pdb=" O GLU A2139 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N SER A2149 " --> pdb=" O ILE A2145 " (cutoff:3.500A) Processing helix chain 'A' and resid 2152 through 2172 removed outlier: 3.567A pdb=" N VAL A2156 " --> pdb=" O SER A2152 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N ASN A2162 " --> pdb=" O HIS A2158 " (cutoff:3.500A) removed outlier: 5.043A 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 Processing helix chain 'N' and resid 359 through 372 Processing helix chain 'N' and resid 376 through 385 Processing helix chain 'N' and resid 394 through 405 Processing helix chain 'N' and resid 443 through 463 Processing sheet with id=AA1, first strand: chain 'A' and resid 137 through 140 removed outlier: 5.435A pdb=" N ILE A 34 " --> pdb=" O GLU A 204 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 65 through 68 removed outlier: 6.438A pdb=" N SER A 65 " --> pdb=" O SER A 114 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N LEU A 116 " --> pdb=" O SER A 65 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N TYR A 67 " --> pdb=" O LEU A 116 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 527 through 529 removed outlier: 6.771A pdb=" N GLN A 528 " --> pdb=" O ILE A 567 " (cutoff:3.500A) removed outlier: 8.142A pdb=" N VAL A1585 " --> pdb=" O GLU A 221 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N ILE A 223 " --> pdb=" O VAL A1585 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 847 through 855 Processing sheet with id=AA5, first strand: chain 'A' and resid 1022 through 1026 removed outlier: 3.942A pdb=" N PHE A1022 " --> pdb=" O VAL A1033 " (cutoff:3.500A) removed outlier: 5.874A pdb=" N LYS A1032 " --> pdb=" O LEU A 983 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N LEU A 983 " --> pdb=" O LYS A1032 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N SER A1034 " --> pdb=" O LEU A 981 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N LEU A 981 " --> pdb=" O SER A1034 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N GLU A1036 " --> pdb=" O ILE A 979 " (cutoff:3.500A) removed outlier: 5.663A pdb=" N ILE A 979 " --> pdb=" O GLU A1036 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N PHE A1008 " --> pdb=" O ILE A 979 " (cutoff:3.500A) removed outlier: 8.495A pdb=" N LEU A 981 " --> pdb=" O GLN A1006 " (cutoff:3.500A) removed outlier: 10.060A pdb=" N GLN A1006 " --> pdb=" O LEU A 981 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1236 through 1237 removed outlier: 7.273A pdb=" N LEU A1191 " --> pdb=" O ILE A1154 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N ILE A1154 " --> pdb=" O LEU A1191 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N ASP A1193 " --> pdb=" O ALA A1152 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1937 through 1940 Processing sheet with id=AA8, first strand: chain 'A' and resid 2191 through 2193 Processing sheet with id=AA9, first strand: chain 'A' and resid 2191 through 2193 Processing sheet with id=AB1, first strand: chain 'N' and resid 409 through 414 removed outlier: 4.551A pdb=" N GLN N 424 " --> pdb=" O ILE N 414 " (cutoff:3.500A) 640 hydrogen bonds defined for protein. 1839 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.33 Time building geometry restraints manager: 3.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4471 1.34 - 1.46: 2789 1.46 - 1.58: 6516 1.58 - 1.70: 3 1.70 - 1.82: 100 Bond restraints: 13879 Sorted by residual: bond pdb=" C GLU A 922 " pdb=" N PRO A 923 " ideal model delta sigma weight residual 1.336 1.376 -0.040 1.08e-02 8.57e+03 1.36e+01 bond pdb=" C LYS A2083 " pdb=" N PHE A2084 " ideal model delta sigma weight residual 1.332 1.374 -0.041 1.40e-02 5.10e+03 8.64e+00 bond pdb=" C VAL A2175 " pdb=" N PRO A2176 " ideal model delta sigma weight residual 1.334 1.401 -0.067 2.34e-02 1.83e+03 8.22e+00 bond pdb=" N ASP A 90 " pdb=" CA ASP A 90 " ideal model delta sigma weight residual 1.463 1.434 0.029 1.23e-02 6.61e+03 5.65e+00 bond pdb=" C VAL A2130 " pdb=" N PRO A2131 " ideal model delta sigma weight residual 1.334 1.386 -0.052 2.34e-02 1.83e+03 4.89e+00 ... (remaining 13874 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.42: 18426 3.42 - 6.83: 305 6.83 - 10.25: 67 10.25 - 13.66: 13 13.66 - 17.08: 5 Bond angle restraints: 18816 Sorted by residual: angle pdb=" N ARG A2030 " pdb=" CA ARG A2030 " pdb=" C ARG A2030 " ideal model delta sigma weight residual 114.75 106.58 8.17 1.26e+00 6.30e-01 4.20e+01 angle pdb=" CA ARG A1566 " pdb=" CB ARG A1566 " pdb=" CG ARG A1566 " ideal model delta sigma weight residual 114.10 125.30 -11.20 2.00e+00 2.50e-01 3.14e+01 angle pdb=" N PRO A 256 " pdb=" CD PRO A 256 " pdb=" CG PRO A 256 " ideal model delta sigma weight residual 103.20 95.23 7.97 1.50e+00 4.44e-01 2.82e+01 angle pdb=" CA PRO A 256 " pdb=" N PRO A 256 " pdb=" CD PRO A 256 " ideal model delta sigma weight residual 112.00 104.70 7.30 1.40e+00 5.10e-01 2.72e+01 angle pdb=" CA GLN N 406 " pdb=" CB GLN N 406 " pdb=" CG GLN N 406 " ideal model delta sigma weight residual 114.10 124.32 -10.22 2.00e+00 2.50e-01 2.61e+01 ... (remaining 18811 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.22: 7380 18.22 - 36.45: 888 36.45 - 54.67: 160 54.67 - 72.90: 30 72.90 - 91.12: 11 Dihedral angle restraints: 8469 sinusoidal: 3504 harmonic: 4965 Sorted by residual: dihedral pdb=" CA THR A1205 " pdb=" C THR A1205 " pdb=" N PRO A1206 " pdb=" CA PRO A1206 " ideal model delta harmonic sigma weight residual -180.00 -133.56 -46.44 0 5.00e+00 4.00e-02 8.63e+01 dihedral pdb=" CA LEU A2116 " pdb=" C LEU A2116 " pdb=" N LEU A2117 " pdb=" CA LEU A2117 " ideal model delta harmonic sigma weight residual 180.00 148.49 31.51 0 5.00e+00 4.00e-02 3.97e+01 dihedral pdb=" CA ILE A2110 " pdb=" C ILE A2110 " pdb=" N SER A2111 " pdb=" CA SER A2111 " ideal model delta harmonic sigma weight residual -180.00 -151.47 -28.53 0 5.00e+00 4.00e-02 3.26e+01 ... (remaining 8466 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 1750 0.069 - 0.139: 292 0.139 - 0.208: 45 0.208 - 0.278: 7 0.278 - 0.347: 4 Chirality restraints: 2098 Sorted by residual: chirality pdb=" CB VAL A 554 " pdb=" CA VAL A 554 " pdb=" CG1 VAL A 554 " pdb=" CG2 VAL A 554 " both_signs ideal model delta sigma weight residual False -2.63 -2.28 -0.35 2.00e-01 2.50e+01 3.01e+00 chirality pdb=" CA MET A 161 " pdb=" N MET A 161 " pdb=" C MET A 161 " pdb=" CB MET A 161 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.30 2.00e-01 2.50e+01 2.18e+00 chirality pdb=" CA TYR A2041 " pdb=" N TYR A2041 " pdb=" C TYR A2041 " pdb=" CB TYR A2041 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.16e+00 ... (remaining 2095 not shown) Planarity restraints: 2448 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A2041 " 0.039 2.00e-02 2.50e+03 2.30e-02 1.06e+01 pdb=" CG TYR A2041 " -0.034 2.00e-02 2.50e+03 pdb=" CD1 TYR A2041 " -0.030 2.00e-02 2.50e+03 pdb=" CD2 TYR A2041 " -0.009 2.00e-02 2.50e+03 pdb=" CE1 TYR A2041 " 0.022 2.00e-02 2.50e+03 pdb=" CE2 TYR A2041 " -0.002 2.00e-02 2.50e+03 pdb=" CZ TYR A2041 " 0.007 2.00e-02 2.50e+03 pdb=" OH TYR A2041 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 532 " -0.016 2.00e-02 2.50e+03 3.11e-02 9.69e+00 pdb=" C ASP A 532 " 0.054 2.00e-02 2.50e+03 pdb=" O ASP A 532 " -0.021 2.00e-02 2.50e+03 pdb=" N ARG A 533 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU N 432 " 0.051 5.00e-02 4.00e+02 7.76e-02 9.65e+00 pdb=" N PRO N 433 " -0.134 5.00e-02 4.00e+02 pdb=" CA PRO N 433 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO N 433 " 0.038 5.00e-02 4.00e+02 ... (remaining 2445 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 3153 2.79 - 3.32: 12530 3.32 - 3.85: 23811 3.85 - 4.37: 26896 4.37 - 4.90: 43684 Nonbonded interactions: 110074 Sorted by model distance: nonbonded pdb=" OG SER A1750 " pdb=" OD2 ASP A2040 " model vdw 2.263 3.040 nonbonded pdb=" O ASP A2040 " pdb=" OG1 THR A2044 " model vdw 2.268 3.040 nonbonded pdb=" OE1 GLU A 221 " pdb=" OH TYR A 596 " model vdw 2.275 3.040 nonbonded pdb=" O PRO A 868 " pdb=" OG SER A 871 " model vdw 2.291 3.040 nonbonded pdb=" OH TYR A2002 " pdb=" OD1 ASP A2148 " model vdw 2.306 3.040 ... (remaining 110069 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 group one per residue 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: 4.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.550 Check model and map are aligned: 0.090 Set scattering table: 0.150 Process input model: 33.720 Find NCS groups from input model: 0.140 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:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5162 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 : 0.005 0.094 13879 Z= 0.356 Angle : 1.162 17.078 18816 Z= 0.605 Chirality : 0.055 0.347 2098 Planarity : 0.009 0.087 2448 Dihedral : 15.934 91.123 5247 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.30 % Allowed : 5.88 % Favored : 93.82 % Rotamer: Outliers : 0.67 % Allowed : 21.65 % Favored : 77.68 % Cbeta Deviations : 0.25 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 1.03 % 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: -2.32 (0.18), residues: 1668 helix: -1.62 (0.15), residues: 791 sheet: -0.16 (0.38), residues: 189 loop : -1.68 (0.22), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A1968 HIS 0.015 0.001 HIS A 87 PHE 0.037 0.003 PHE A2072 TYR 0.039 0.002 TYR A2041 ARG 0.016 0.001 ARG A1566 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3336 Ramachandran restraints generated. 1668 Oldfield, 0 Emsley, 1668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3336 Ramachandran restraints generated. 1668 Oldfield, 0 Emsley, 1668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 132 time to evaluate : 1.406 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 315 LYS cc_start: 0.8179 (tmtt) cc_final: 0.7832 (tptp) outliers start: 10 outliers final: 3 residues processed: 137 average time/residue: 0.2843 time to fit residues: 57.2631 Evaluate side-chains 121 residues out of total 1501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 118 time to evaluate : 1.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ARG Chi-restraints excluded: chain A residue 841 PHE Chi-restraints excluded: chain A residue 2054 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 141 optimal weight: 0.0870 chunk 127 optimal weight: 0.6980 chunk 70 optimal weight: 20.0000 chunk 43 optimal weight: 0.8980 chunk 85 optimal weight: 40.0000 chunk 68 optimal weight: 0.9990 chunk 131 optimal weight: 4.9990 chunk 50 optimal weight: 2.9990 chunk 80 optimal weight: 20.0000 chunk 98 optimal weight: 3.9990 chunk 152 optimal weight: 7.9990 overall best weight: 1.1362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 548 HIS A 773 GLN A 895 GLN ** A1235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1774 HIS ** A2012 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2029 GLN A2054 HIS N 389 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5159 r_free = 0.5159 target = 0.194306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4938 r_free = 0.4938 target = 0.174977 restraints weight = 38285.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4900 r_free = 0.4900 target = 0.174479 restraints weight = 41764.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4917 r_free = 0.4917 target = 0.175872 restraints weight = 37110.844| |-----------------------------------------------------------------------------| r_work (final): 0.4946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4883 moved from start: 0.1212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 13879 Z= 0.229 Angle : 0.705 11.013 18816 Z= 0.356 Chirality : 0.043 0.168 2098 Planarity : 0.006 0.069 2448 Dihedral : 5.663 43.418 1864 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 13.65 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.28 % Favored : 94.48 % Rotamer: Outliers : 3.00 % Allowed : 18.65 % Favored : 78.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 1.03 % 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: -1.18 (0.20), residues: 1668 helix: -0.40 (0.17), residues: 805 sheet: -0.21 (0.38), residues: 193 loop : -1.29 (0.24), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 848 HIS 0.009 0.001 HIS A2087 PHE 0.023 0.002 PHE A2085 TYR 0.032 0.002 TYR A2041 ARG 0.005 0.000 ARG A 170 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3336 Ramachandran restraints generated. 1668 Oldfield, 0 Emsley, 1668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3336 Ramachandran restraints generated. 1668 Oldfield, 0 Emsley, 1668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 127 time to evaluate : 1.568 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 LEU cc_start: 0.5407 (OUTLIER) cc_final: 0.4839 (pp) REVERT: A 286 LEU cc_start: 0.4736 (mt) cc_final: 0.4348 (mt) REVERT: A 1137 MET cc_start: 0.2021 (OUTLIER) cc_final: 0.1521 (mmp) REVERT: A 1975 LEU cc_start: 0.4990 (tp) cc_final: 0.4496 (mt) REVERT: A 2138 PHE cc_start: 0.4387 (t80) cc_final: 0.3558 (t80) outliers start: 45 outliers final: 22 residues processed: 162 average time/residue: 0.2974 time to fit residues: 69.6772 Evaluate side-chains 138 residues out of total 1501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 114 time to evaluate : 1.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 81 ILE Chi-restraints excluded: chain A residue 90 ASP Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 201 CYS Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain A residue 768 VAL Chi-restraints excluded: chain A residue 1137 MET Chi-restraints excluded: chain A residue 1261 ILE Chi-restraints excluded: chain A residue 1747 ILE Chi-restraints excluded: chain A residue 1768 HIS Chi-restraints excluded: chain A residue 1780 VAL Chi-restraints excluded: chain A residue 1973 SER Chi-restraints excluded: chain A residue 2028 TYR Chi-restraints excluded: chain A residue 2034 LEU Chi-restraints excluded: chain A residue 2046 HIS Chi-restraints excluded: chain A residue 2069 ASN Chi-restraints excluded: chain A residue 2070 THR Chi-restraints excluded: chain A residue 2089 SER Chi-restraints excluded: chain A residue 2100 VAL Chi-restraints excluded: chain N residue 392 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 164 optimal weight: 0.9990 chunk 29 optimal weight: 6.9990 chunk 91 optimal weight: 0.0040 chunk 113 optimal weight: 5.9990 chunk 51 optimal weight: 1.9990 chunk 154 optimal weight: 0.1980 chunk 131 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 chunk 73 optimal weight: 20.0000 chunk 94 optimal weight: 3.9990 chunk 4 optimal weight: 0.7980 overall best weight: 0.5794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 548 HIS A1067 GLN ** A1235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1668 ASN ** A2012 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2054 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5179 r_free = 0.5179 target = 0.195903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4959 r_free = 0.4959 target = 0.176411 restraints weight = 38353.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4936 r_free = 0.4936 target = 0.177036 restraints weight = 38675.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4951 r_free = 0.4951 target = 0.178401 restraints weight = 30389.014| |-----------------------------------------------------------------------------| r_work (final): 0.4980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4803 moved from start: 0.1664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13879 Z= 0.181 Angle : 0.647 11.248 18816 Z= 0.318 Chirality : 0.043 0.179 2098 Planarity : 0.005 0.066 2448 Dihedral : 5.096 44.236 1856 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 12.32 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.58 % Favored : 94.30 % Rotamer: Outliers : 3.33 % Allowed : 18.19 % Favored : 78.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 1.03 % 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: -0.60 (0.21), residues: 1668 helix: 0.18 (0.18), residues: 809 sheet: -0.28 (0.38), residues: 187 loop : -1.03 (0.25), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1139 HIS 0.010 0.001 HIS A2087 PHE 0.019 0.001 PHE A2085 TYR 0.016 0.001 TYR A2028 ARG 0.005 0.000 ARG A 550 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3336 Ramachandran restraints generated. 1668 Oldfield, 0 Emsley, 1668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3336 Ramachandran restraints generated. 1668 Oldfield, 0 Emsley, 1668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 121 time to evaluate : 1.612 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 LEU cc_start: 0.5301 (OUTLIER) cc_final: 0.4767 (pp) REVERT: A 286 LEU cc_start: 0.4684 (mt) cc_final: 0.4274 (mt) REVERT: A 572 LEU cc_start: 0.6809 (OUTLIER) cc_final: 0.6453 (tt) REVERT: A 1137 MET cc_start: 0.1878 (OUTLIER) cc_final: 0.1408 (mmp) REVERT: A 1543 GLN cc_start: 0.6463 (OUTLIER) cc_final: 0.6224 (tm-30) REVERT: A 1749 ASP cc_start: 0.7433 (t0) cc_final: 0.6938 (t0) REVERT: A 1975 LEU cc_start: 0.4943 (tp) cc_final: 0.4414 (mt) REVERT: A 2020 THR cc_start: 0.6430 (OUTLIER) cc_final: 0.5901 (p) REVERT: N 462 MET cc_start: 0.7200 (OUTLIER) cc_final: 0.6991 (mtt) outliers start: 50 outliers final: 24 residues processed: 161 average time/residue: 0.2687 time to fit residues: 64.6386 Evaluate side-chains 136 residues out of total 1501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 106 time to evaluate : 1.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ARG Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 83 THR Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 90 ASP Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 297 CYS Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 764 THR Chi-restraints excluded: chain A residue 782 LEU Chi-restraints excluded: chain A residue 1137 MET Chi-restraints excluded: chain A residue 1261 ILE Chi-restraints excluded: chain A residue 1282 LEU Chi-restraints excluded: chain A residue 1543 GLN Chi-restraints excluded: chain A residue 1747 ILE Chi-restraints excluded: chain A residue 1768 HIS Chi-restraints excluded: chain A residue 1769 GLU Chi-restraints excluded: chain A residue 1780 VAL Chi-restraints excluded: chain A residue 1927 MET Chi-restraints excluded: chain A residue 1973 SER Chi-restraints excluded: chain A residue 2020 THR Chi-restraints excluded: chain A residue 2046 HIS Chi-restraints excluded: chain A residue 2070 THR Chi-restraints excluded: chain A residue 2089 SER Chi-restraints excluded: chain A residue 2100 VAL Chi-restraints excluded: chain A residue 2158 HIS Chi-restraints excluded: chain N residue 462 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 89 optimal weight: 6.9990 chunk 25 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 77 optimal weight: 20.0000 chunk 20 optimal weight: 0.9980 chunk 98 optimal weight: 10.0000 chunk 34 optimal weight: 2.9990 chunk 31 optimal weight: 8.9990 chunk 51 optimal weight: 7.9990 chunk 123 optimal weight: 6.9990 chunk 13 optimal weight: 0.8980 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 548 HIS ** A 610 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 875 HIS ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1533 GLN ** A1977 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2012 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2093 ASN ** A2104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5108 r_free = 0.5108 target = 0.189829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4867 r_free = 0.4867 target = 0.169949 restraints weight = 38011.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4840 r_free = 0.4840 target = 0.169678 restraints weight = 41697.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4854 r_free = 0.4854 target = 0.170934 restraints weight = 38247.249| |-----------------------------------------------------------------------------| r_work (final): 0.4882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5086 moved from start: 0.2478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 13879 Z= 0.300 Angle : 0.745 11.184 18816 Z= 0.373 Chirality : 0.045 0.190 2098 Planarity : 0.005 0.068 2448 Dihedral : 5.385 44.794 1856 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 18.37 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.31 % Favored : 92.57 % Rotamer: Outliers : 4.66 % Allowed : 18.25 % Favored : 77.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 1.03 % 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: -0.71 (0.21), residues: 1668 helix: 0.14 (0.18), residues: 804 sheet: -0.63 (0.39), residues: 180 loop : -1.05 (0.25), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 848 HIS 0.007 0.001 HIS A 179 PHE 0.026 0.002 PHE A2138 TYR 0.037 0.002 TYR A2028 ARG 0.008 0.001 ARG A 594 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3336 Ramachandran restraints generated. 1668 Oldfield, 0 Emsley, 1668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3336 Ramachandran restraints generated. 1668 Oldfield, 0 Emsley, 1668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 119 time to evaluate : 1.591 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 LEU cc_start: 0.5758 (OUTLIER) cc_final: 0.5267 (pp) REVERT: A 572 LEU cc_start: 0.7094 (OUTLIER) cc_final: 0.6800 (tt) REVERT: A 994 ARG cc_start: -0.3489 (OUTLIER) cc_final: -0.4212 (mpt180) REVERT: A 1041 ARG cc_start: 0.6988 (OUTLIER) cc_final: 0.6773 (mmp-170) REVERT: A 1137 MET cc_start: 0.1999 (mmp) cc_final: 0.1292 (mmm) REVERT: A 1749 ASP cc_start: 0.7659 (t0) cc_final: 0.7361 (t0) REVERT: A 2041 TYR cc_start: 0.5711 (t80) cc_final: 0.5297 (t80) REVERT: A 2094 ASP cc_start: 0.4754 (OUTLIER) cc_final: 0.4473 (p0) REVERT: A 2177 LYS cc_start: 0.5004 (OUTLIER) cc_final: 0.4761 (mmmt) outliers start: 70 outliers final: 46 residues processed: 176 average time/residue: 0.2675 time to fit residues: 70.4421 Evaluate side-chains 158 residues out of total 1501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 106 time to evaluate : 1.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ASP Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 81 ILE Chi-restraints excluded: chain A residue 83 THR Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 90 ASP Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 297 CYS Chi-restraints excluded: chain A residue 303 HIS Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 521 ASP Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 563 CYS Chi-restraints excluded: chain A residue 571 VAL Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain A residue 768 VAL Chi-restraints excluded: chain A residue 781 LEU Chi-restraints excluded: chain A residue 782 LEU Chi-restraints excluded: chain A residue 871 SER Chi-restraints excluded: chain A residue 994 ARG Chi-restraints excluded: chain A residue 1041 ARG Chi-restraints excluded: chain A residue 1088 VAL Chi-restraints excluded: chain A residue 1192 LEU Chi-restraints excluded: chain A residue 1238 VAL Chi-restraints excluded: chain A residue 1261 ILE Chi-restraints excluded: chain A residue 1282 LEU Chi-restraints excluded: chain A residue 1747 ILE Chi-restraints excluded: chain A residue 1762 ILE Chi-restraints excluded: chain A residue 1768 HIS Chi-restraints excluded: chain A residue 1769 GLU Chi-restraints excluded: chain A residue 1780 VAL Chi-restraints excluded: chain A residue 1917 GLU Chi-restraints excluded: chain A residue 1927 MET Chi-restraints excluded: chain A residue 1968 TRP Chi-restraints excluded: chain A residue 2015 THR Chi-restraints excluded: chain A residue 2028 TYR Chi-restraints excluded: chain A residue 2046 HIS Chi-restraints excluded: chain A residue 2069 ASN Chi-restraints excluded: chain A residue 2070 THR Chi-restraints excluded: chain A residue 2071 ILE Chi-restraints excluded: chain A residue 2094 ASP Chi-restraints excluded: chain A residue 2100 VAL Chi-restraints excluded: chain A residue 2113 GLU Chi-restraints excluded: chain A residue 2158 HIS Chi-restraints excluded: chain A residue 2177 LYS Chi-restraints excluded: chain N residue 392 ILE Chi-restraints excluded: chain N residue 462 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 19 optimal weight: 0.8980 chunk 75 optimal weight: 20.0000 chunk 110 optimal weight: 4.9990 chunk 126 optimal weight: 0.0070 chunk 157 optimal weight: 1.9990 chunk 83 optimal weight: 3.9990 chunk 158 optimal weight: 5.9990 chunk 21 optimal weight: 4.9990 chunk 50 optimal weight: 0.9990 chunk 152 optimal weight: 0.3980 chunk 99 optimal weight: 0.8980 overall best weight: 0.6400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 548 HIS ** A 862 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1559 GLN A1671 HIS ** A1977 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2012 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2093 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5152 r_free = 0.5152 target = 0.193639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4921 r_free = 0.4921 target = 0.173518 restraints weight = 38061.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4896 r_free = 0.4896 target = 0.173809 restraints weight = 39416.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4911 r_free = 0.4911 target = 0.175157 restraints weight = 31871.512| |-----------------------------------------------------------------------------| r_work (final): 0.4940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4949 moved from start: 0.2557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13879 Z= 0.189 Angle : 0.653 11.921 18816 Z= 0.320 Chirality : 0.043 0.192 2098 Planarity : 0.005 0.066 2448 Dihedral : 5.035 44.730 1856 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 13.87 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.94 % Favored : 94.00 % Rotamer: Outliers : 3.73 % Allowed : 19.39 % Favored : 76.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 1.03 % 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: -0.43 (0.21), residues: 1668 helix: 0.44 (0.18), residues: 805 sheet: -0.61 (0.38), residues: 180 loop : -0.97 (0.25), residues: 683 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1139 HIS 0.009 0.001 HIS A2087 PHE 0.023 0.001 PHE A2138 TYR 0.018 0.001 TYR A 863 ARG 0.003 0.000 ARG A 550 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3336 Ramachandran restraints generated. 1668 Oldfield, 0 Emsley, 1668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3336 Ramachandran restraints generated. 1668 Oldfield, 0 Emsley, 1668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 117 time to evaluate : 1.484 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 LEU cc_start: 0.5832 (OUTLIER) cc_final: 0.5345 (pp) REVERT: A 286 LEU cc_start: 0.4959 (mt) cc_final: 0.4543 (mt) REVERT: A 873 LEU cc_start: 0.5002 (OUTLIER) cc_final: 0.4668 (mp) REVERT: A 930 LEU cc_start: 0.3656 (OUTLIER) cc_final: 0.2154 (mp) REVERT: A 994 ARG cc_start: -0.3686 (OUTLIER) cc_final: -0.4078 (mpt90) REVERT: A 1137 MET cc_start: 0.2497 (OUTLIER) cc_final: 0.1949 (mmp) REVERT: A 1633 GLU cc_start: 0.7882 (OUTLIER) cc_final: 0.7255 (pp20) REVERT: A 1749 ASP cc_start: 0.7580 (t0) cc_final: 0.7280 (t0) REVERT: A 2088 LEU cc_start: 0.4339 (OUTLIER) cc_final: 0.3954 (tt) REVERT: A 2153 LEU cc_start: 0.3062 (OUTLIER) cc_final: 0.2483 (mt) outliers start: 56 outliers final: 31 residues processed: 166 average time/residue: 0.2627 time to fit residues: 65.4670 Evaluate side-chains 147 residues out of total 1501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 108 time to evaluate : 1.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 45 PHE Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 83 THR Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 90 ASP Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 297 CYS Chi-restraints excluded: chain A residue 303 HIS Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain A residue 781 LEU Chi-restraints excluded: chain A residue 801 PHE Chi-restraints excluded: chain A residue 873 LEU Chi-restraints excluded: chain A residue 930 LEU Chi-restraints excluded: chain A residue 994 ARG Chi-restraints excluded: chain A residue 1137 MET Chi-restraints excluded: chain A residue 1192 LEU Chi-restraints excluded: chain A residue 1261 ILE Chi-restraints excluded: chain A residue 1282 LEU Chi-restraints excluded: chain A residue 1633 GLU Chi-restraints excluded: chain A residue 1747 ILE Chi-restraints excluded: chain A residue 1768 HIS Chi-restraints excluded: chain A residue 1769 GLU Chi-restraints excluded: chain A residue 1780 VAL Chi-restraints excluded: chain A residue 1927 MET Chi-restraints excluded: chain A residue 1968 TRP Chi-restraints excluded: chain A residue 2020 THR Chi-restraints excluded: chain A residue 2028 TYR Chi-restraints excluded: chain A residue 2046 HIS Chi-restraints excluded: chain A residue 2070 THR Chi-restraints excluded: chain A residue 2088 LEU Chi-restraints excluded: chain A residue 2100 VAL Chi-restraints excluded: chain A residue 2134 LEU Chi-restraints excluded: chain A residue 2139 GLU Chi-restraints excluded: chain A residue 2153 LEU Chi-restraints excluded: chain A residue 2158 HIS Chi-restraints excluded: chain N residue 392 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 11 optimal weight: 9.9990 chunk 114 optimal weight: 9.9990 chunk 127 optimal weight: 0.8980 chunk 92 optimal weight: 6.9990 chunk 117 optimal weight: 0.9990 chunk 29 optimal weight: 6.9990 chunk 132 optimal weight: 0.0770 chunk 156 optimal weight: 9.9990 chunk 73 optimal weight: 0.2980 chunk 138 optimal weight: 1.9990 chunk 50 optimal weight: 0.2980 overall best weight: 0.5140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 548 HIS ** A 862 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1782 ASN ** A1977 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2012 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5142 r_free = 0.5142 target = 0.192786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4900 r_free = 0.4900 target = 0.170959 restraints weight = 37848.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4857 r_free = 0.4857 target = 0.170655 restraints weight = 31102.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4877 r_free = 0.4877 target = 0.172459 restraints weight = 25757.207| |-----------------------------------------------------------------------------| r_work (final): 0.4928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5024 moved from start: 0.2684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13879 Z= 0.177 Angle : 0.655 12.990 18816 Z= 0.320 Chirality : 0.043 0.351 2098 Planarity : 0.004 0.065 2448 Dihedral : 4.921 44.494 1856 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 14.35 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.88 % Favored : 94.06 % Rotamer: Outliers : 3.66 % Allowed : 19.39 % Favored : 76.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 1.03 % 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: -0.26 (0.21), residues: 1668 helix: 0.59 (0.18), residues: 805 sheet: -0.60 (0.38), residues: 180 loop : -0.89 (0.25), residues: 683 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1139 HIS 0.008 0.001 HIS A2087 PHE 0.016 0.001 PHE A2138 TYR 0.025 0.001 TYR A1542 ARG 0.004 0.000 ARG A1566 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3336 Ramachandran restraints generated. 1668 Oldfield, 0 Emsley, 1668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3336 Ramachandran restraints generated. 1668 Oldfield, 0 Emsley, 1668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 120 time to evaluate : 1.516 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 LEU cc_start: 0.5794 (OUTLIER) cc_final: 0.5327 (pp) REVERT: A 286 LEU cc_start: 0.5001 (mt) cc_final: 0.4551 (mt) REVERT: A 873 LEU cc_start: 0.4983 (OUTLIER) cc_final: 0.4560 (mp) REVERT: A 930 LEU cc_start: 0.3755 (OUTLIER) cc_final: 0.2179 (mp) REVERT: A 994 ARG cc_start: -0.3838 (OUTLIER) cc_final: -0.4284 (mpt180) REVERT: A 1137 MET cc_start: 0.2397 (OUTLIER) cc_final: 0.1668 (mmp) REVERT: A 1633 GLU cc_start: 0.7849 (OUTLIER) cc_final: 0.7198 (pp20) REVERT: A 2088 LEU cc_start: 0.4207 (OUTLIER) cc_final: 0.3816 (tt) REVERT: A 2153 LEU cc_start: 0.3007 (OUTLIER) cc_final: 0.2329 (mp) REVERT: A 2182 GLU cc_start: 0.8531 (mm-30) cc_final: 0.8262 (mm-30) outliers start: 55 outliers final: 32 residues processed: 168 average time/residue: 0.2533 time to fit residues: 63.6947 Evaluate side-chains 152 residues out of total 1501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 112 time to evaluate : 1.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 81 ILE Chi-restraints excluded: chain A residue 83 THR Chi-restraints excluded: chain A residue 90 ASP Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 297 CYS Chi-restraints excluded: chain A residue 303 HIS Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain A residue 781 LEU Chi-restraints excluded: chain A residue 801 PHE Chi-restraints excluded: chain A residue 873 LEU Chi-restraints excluded: chain A residue 930 LEU Chi-restraints excluded: chain A residue 994 ARG Chi-restraints excluded: chain A residue 1137 MET Chi-restraints excluded: chain A residue 1192 LEU Chi-restraints excluded: chain A residue 1238 VAL Chi-restraints excluded: chain A residue 1261 ILE Chi-restraints excluded: chain A residue 1282 LEU Chi-restraints excluded: chain A residue 1633 GLU Chi-restraints excluded: chain A residue 1747 ILE Chi-restraints excluded: chain A residue 1768 HIS Chi-restraints excluded: chain A residue 1769 GLU Chi-restraints excluded: chain A residue 1896 HIS Chi-restraints excluded: chain A residue 1927 MET Chi-restraints excluded: chain A residue 1968 TRP Chi-restraints excluded: chain A residue 2020 THR Chi-restraints excluded: chain A residue 2028 TYR Chi-restraints excluded: chain A residue 2046 HIS Chi-restraints excluded: chain A residue 2070 THR Chi-restraints excluded: chain A residue 2088 LEU Chi-restraints excluded: chain A residue 2089 SER Chi-restraints excluded: chain A residue 2100 VAL Chi-restraints excluded: chain A residue 2134 LEU Chi-restraints excluded: chain A residue 2153 LEU Chi-restraints excluded: chain A residue 2158 HIS Chi-restraints excluded: chain N residue 392 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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-5571/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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-5571/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-5571/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-5571/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-5571/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-5571/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-5571/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-5571/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-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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-5571/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-5571/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-5571/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-5571/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: 71.0471 > 50: distance: 74 - 160: 36.947 distance: 77 - 157: 29.823 distance: 137 - 143: 31.641 distance: 143 - 144: 52.870 distance: 144 - 145: 40.147 distance: 144 - 147: 46.863 distance: 145 - 146: 46.085 distance: 145 - 151: 33.650 distance: 147 - 148: 45.688 distance: 148 - 149: 41.679 distance: 148 - 150: 48.913 distance: 151 - 152: 12.484 distance: 152 - 153: 56.333 distance: 152 - 155: 22.476 distance: 153 - 157: 46.045 distance: 155 - 156: 47.468 distance: 157 - 158: 36.187 distance: 158 - 159: 30.406 distance: 158 - 161: 13.652 distance: 159 - 164: 39.815 distance: 161 - 162: 40.378 distance: 161 - 163: 39.116 distance: 164 - 165: 18.927 distance: 165 - 166: 53.191 distance: 165 - 168: 19.137 distance: 166 - 167: 39.359 distance: 166 - 171: 56.223 distance: 168 - 169: 32.922 distance: 168 - 170: 31.756 distance: 171 - 172: 57.409 distance: 172 - 173: 40.826 distance: 172 - 175: 51.294 distance: 173 - 174: 55.942 distance: 173 - 181: 53.770 distance: 175 - 176: 37.170 distance: 176 - 177: 37.205 distance: 176 - 178: 40.196 distance: 177 - 179: 43.616 distance: 178 - 180: 61.118 distance: 179 - 180: 43.041 distance: 181 - 182: 48.356 distance: 181 - 187: 41.077 distance: 182 - 183: 42.404 distance: 182 - 185: 43.341 distance: 183 - 184: 22.823 distance: 183 - 188: 12.844 distance: 185 - 186: 38.509 distance: 186 - 187: 58.135 distance: 188 - 189: 52.537 distance: 189 - 190: 59.061 distance: 189 - 192: 45.489 distance: 190 - 191: 62.881 distance: 190 - 199: 58.537 distance: 193 - 194: 47.849 distance: 194 - 196: 25.658 distance: 195 - 197: 6.069 distance: 197 - 198: 39.260 distance: 199 - 200: 42.159 distance: 199 - 205: 62.840 distance: 200 - 201: 22.333 distance: 200 - 203: 59.908 distance: 201 - 202: 25.522 distance: 201 - 206: 47.722 distance: 202 - 225: 32.336 distance: 204 - 205: 39.642 distance: 206 - 207: 27.424 distance: 207 - 208: 54.783 distance: 207 - 210: 12.512 distance: 208 - 209: 8.073 distance: 208 - 211: 51.234 distance: 209 - 235: 31.907 distance: 211 - 212: 48.738 distance: 212 - 213: 27.156 distance: 212 - 215: 29.632 distance: 213 - 214: 50.155 distance: 213 - 217: 25.421 distance: 214 - 246: 31.530 distance: 215 - 216: 56.515