Starting phenix.real_space_refine on Sun Aug 24 03:58:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ki7_37253/08_2025/8ki7_37253.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ki7_37253/08_2025/8ki7_37253.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ki7_37253/08_2025/8ki7_37253.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ki7_37253/08_2025/8ki7_37253.map" model { file = "/net/cci-nas-00/data/ceres_data/8ki7_37253/08_2025/8ki7_37253.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ki7_37253/08_2025/8ki7_37253.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.064 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: 5 Type Number sf(0) Gaussians P 32 5.49 5 S 105 5.16 5 C 10557 2.51 5 N 2801 2.21 5 O 3289 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 36 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16784 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 16102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2003, 16102 Classifications: {'peptide': 2003} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 53, 'TRANS': 1949} Chain breaks: 6 Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 2, 'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 24 Chain: "E" Number of atoms: 217 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 217 Classifications: {'RNA': 10} Modifications used: {'p5*END': 1, 'rna2p_pur': 2, 'rna2p_pyr': 1, 'rna3p_pur': 5, 'rna3p_pyr': 2} Link IDs: {'rna2p': 2, 'rna3p': 7} Chain: "B" Number of atoms: 195 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 195 Classifications: {'RNA': 9} Modifications used: {'rna3p_pur': 6, 'rna3p_pyr': 3} Link IDs: {'rna3p': 8} Chain: "F" Number of atoms: 270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 270 Classifications: {'RNA': 13} Modifications used: {'rna2p_pyr': 2, 'rna3p_pur': 4, 'rna3p_pyr': 7} Link IDs: {'rna2p': 1, 'rna3p': 11} Time building chain proxies: 3.68, per 1000 atoms: 0.22 Number of scatterers: 16784 At special positions: 0 Unit cell: (116.48, 110.24, 143.52, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 105 16.00 P 32 15.00 O 3289 8.00 N 2801 7.00 C 10557 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: 1.27 Conformation dependent library (CDL) restraints added in 708.4 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 3978 Ramachandran restraints generated. 1989 Oldfield, 0 Emsley, 1989 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3848 Finding SS restraints... Secondary structure from input PDB file: 90 helices and 9 sheets defined 58.7% alpha, 5.4% beta 11 base pairs and 21 stacking pairs defined. Time for finding SS restraints: 1.62 Creating SS restraints... Processing helix chain 'A' and resid 2 through 12 removed outlier: 4.136A pdb=" N ILE A 10 " --> pdb=" O ILE A 6 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLU A 11 " --> pdb=" O GLN A 7 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ASN A 12 " --> pdb=" O LYS A 8 " (cutoff:3.500A) Processing helix chain 'A' and resid 12 through 38 removed outlier: 3.861A pdb=" N ARG A 37 " --> pdb=" O ASP A 33 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 69 removed outlier: 4.414A pdb=" N VAL A 46 " --> pdb=" O ILE A 42 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N ILE A 47 " --> pdb=" O PRO A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 111 Processing helix chain 'A' and resid 125 through 140 Processing helix chain 'A' and resid 147 through 158 removed outlier: 4.173A pdb=" N GLU A 152 " --> pdb=" O ASP A 148 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N ARG A 153 " --> pdb=" O ASP A 149 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ILE A 154 " --> pdb=" O GLU A 150 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ASN A 155 " --> pdb=" O PHE A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 210 Processing helix chain 'A' and resid 220 through 224 Processing helix chain 'A' and resid 251 through 258 Proline residue: A 256 - end of helix Processing helix chain 'A' and resid 259 through 268 Processing helix chain 'A' and resid 277 through 281 Processing helix chain 'A' and resid 285 through 307 removed outlier: 3.671A pdb=" N ILE A 299 " --> pdb=" O ASN A 295 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N GLU A 302 " --> pdb=" O LYS A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 347 Processing helix chain 'A' and resid 352 through 363 Processing helix chain 'A' and resid 367 through 371 removed outlier: 3.629A pdb=" N THR A 370 " --> pdb=" O HIS A 367 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N MET A 371 " --> pdb=" O ILE A 368 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 367 through 371' Processing helix chain 'A' and resid 374 through 390 Processing helix chain 'A' and resid 397 through 413 Processing helix chain 'A' and resid 415 through 432 removed outlier: 3.673A pdb=" N LYS A 432 " --> pdb=" O ARG A 428 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 455 Processing helix chain 'A' and resid 462 through 466 removed outlier: 3.606A pdb=" N THR A 466 " --> pdb=" O LEU A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 491 through 502 Processing helix chain 'A' and resid 521 through 536 Processing helix chain 'A' and resid 567 through 571 removed outlier: 3.943A pdb=" N GLU A 570 " --> pdb=" O LYS A 567 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N TRP A 571 " --> pdb=" O SER A 568 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 567 through 571' Processing helix chain 'A' and resid 591 through 606 Processing helix chain 'A' and resid 610 through 626 removed outlier: 3.762A pdb=" N LYS A 622 " --> pdb=" O LYS A 618 " (cutoff:3.500A) Processing helix chain 'A' and resid 663 through 682 removed outlier: 3.661A pdb=" N ASN A 682 " --> pdb=" O PHE A 678 " (cutoff:3.500A) Processing helix chain 'A' and resid 690 through 700 removed outlier: 3.558A pdb=" N VAL A 694 " --> pdb=" O LYS A 690 " (cutoff:3.500A) Processing helix chain 'A' and resid 701 through 706 removed outlier: 3.837A pdb=" N CYS A 704 " --> pdb=" O ASN A 701 " (cutoff:3.500A) Processing helix chain 'A' and resid 713 through 729 Processing helix chain 'A' and resid 730 through 748 Processing helix chain 'A' and resid 796 through 804 Processing helix chain 'A' and resid 828 through 837 Processing helix chain 'A' and resid 837 through 853 Proline residue: A 843 - end of helix Processing helix chain 'A' and resid 853 through 863 Processing helix chain 'A' and resid 874 through 893 Processing helix chain 'A' and resid 896 through 908 removed outlier: 3.887A pdb=" N MET A 900 " --> pdb=" O LYS A 896 " (cutoff:3.500A) Processing helix chain 'A' and resid 921 through 927 Processing helix chain 'A' and resid 937 through 953 Processing helix chain 'A' and resid 991 through 1005 removed outlier: 3.668A pdb=" N LEU A 995 " --> pdb=" O THR A 991 " (cutoff:3.500A) Processing helix chain 'A' and resid 1012 through 1036 Proline residue: A1024 - end of helix removed outlier: 4.114A pdb=" N PHE A1031 " --> pdb=" O TRP A1027 " (cutoff:3.500A) Processing helix chain 'A' and resid 1060 through 1075 Processing helix chain 'A' and resid 1077 through 1089 Processing helix chain 'A' and resid 1094 through 1097 Processing helix chain 'A' and resid 1098 through 1103 Processing helix chain 'A' and resid 1114 through 1124 Processing helix chain 'A' and resid 1126 through 1130 removed outlier: 3.714A pdb=" N ILE A1130 " --> pdb=" O ILE A1127 " (cutoff:3.500A) Processing helix chain 'A' and resid 1135 through 1151 Processing helix chain 'A' and resid 1151 through 1163 removed outlier: 3.956A pdb=" N LEU A1155 " --> pdb=" O GLU A1151 " (cutoff:3.500A) Processing helix chain 'A' and resid 1165 through 1178 removed outlier: 3.838A pdb=" N LEU A1169 " --> pdb=" O ASN A1165 " (cutoff:3.500A) Processing helix chain 'A' and resid 1188 through 1195 removed outlier: 3.736A pdb=" N ILE A1193 " --> pdb=" O THR A1189 " (cutoff:3.500A) Processing helix chain 'A' and resid 1197 through 1209 removed outlier: 3.968A pdb=" N VAL A1201 " --> pdb=" O HIS A1197 " (cutoff:3.500A) Processing helix chain 'A' and resid 1222 through 1235 Processing helix chain 'A' and resid 1241 through 1247 removed outlier: 3.662A pdb=" N VAL A1245 " --> pdb=" O ASP A1241 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N MET A1246 " --> pdb=" O LEU A1242 " (cutoff:3.500A) Processing helix chain 'A' and resid 1258 through 1271 Processing helix chain 'A' and resid 1300 through 1313 Processing helix chain 'A' and resid 1314 through 1320 Processing helix chain 'A' and resid 1331 through 1353 removed outlier: 4.148A pdb=" N ARG A1335 " --> pdb=" O ASP A1331 " (cutoff:3.500A) Processing helix chain 'A' and resid 1377 through 1385 removed outlier: 3.771A pdb=" N VAL A1381 " --> pdb=" O THR A1377 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N ILE A1385 " --> pdb=" O VAL A1381 " (cutoff:3.500A) Processing helix chain 'A' and resid 1394 through 1408 Processing helix chain 'A' and resid 1414 through 1428 Processing helix chain 'A' and resid 1434 through 1439 Processing helix chain 'A' and resid 1460 through 1478 Processing helix chain 'A' and resid 1505 through 1513 Processing helix chain 'A' and resid 1517 through 1532 Processing helix chain 'A' and resid 1565 through 1572 Processing helix chain 'A' and resid 1580 through 1598 removed outlier: 3.617A pdb=" N HIS A1591 " --> pdb=" O SER A1587 " (cutoff:3.500A) Processing helix chain 'A' and resid 1604 through 1620 Processing helix chain 'A' and resid 1630 through 1638 Processing helix chain 'A' and resid 1647 through 1651 Processing helix chain 'A' and resid 1657 through 1664 Processing helix chain 'A' and resid 1667 through 1682 Processing helix chain 'A' and resid 1686 through 1696 removed outlier: 4.033A pdb=" N SER A1696 " --> pdb=" O ASP A1692 " (cutoff:3.500A) Processing helix chain 'A' and resid 1699 through 1714 Processing helix chain 'A' and resid 1717 through 1732 Processing helix chain 'A' and resid 1763 through 1770 removed outlier: 3.671A pdb=" N LEU A1767 " --> pdb=" O ASN A1763 " (cutoff:3.500A) Processing helix chain 'A' and resid 1770 through 1780 Processing helix chain 'A' and resid 1814 through 1829 removed outlier: 3.679A pdb=" N ASN A1829 " --> pdb=" O ILE A1825 " (cutoff:3.500A) Processing helix chain 'A' and resid 1830 through 1835 removed outlier: 3.839A pdb=" N ILE A1835 " --> pdb=" O GLU A1831 " (cutoff:3.500A) Processing helix chain 'A' and resid 1843 through 1850 Processing helix chain 'A' and resid 1867 through 1877 removed outlier: 3.950A pdb=" N ASP A1871 " --> pdb=" O LYS A1867 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N LYS A1877 " --> pdb=" O VAL A1873 " (cutoff:3.500A) Processing helix chain 'A' and resid 1891 through 1904 Processing helix chain 'A' and resid 1910 through 1923 Processing helix chain 'A' and resid 1924 through 1936 Proline residue: A1932 - end of helix Processing helix chain 'A' and resid 1951 through 1965 removed outlier: 4.670A pdb=" N LYS A1957 " --> pdb=" O PHE A1953 " (cutoff:3.500A) Proline residue: A1960 - end of helix Processing helix chain 'A' and resid 1986 through 2008 Processing helix chain 'A' and resid 2018 through 2030 removed outlier: 3.980A pdb=" N ASN A2030 " --> pdb=" O PHE A2026 " (cutoff:3.500A) Processing helix chain 'A' and resid 2031 through 2043 Processing helix chain 'A' and resid 2052 through 2058 removed outlier: 3.775A pdb=" N ARG A2058 " --> pdb=" O THR A2054 " (cutoff:3.500A) Processing helix chain 'A' and resid 2059 through 2066 Processing helix chain 'A' and resid 2067 through 2069 No H-bonds generated for 'chain 'A' and resid 2067 through 2069' Processing sheet with id=AA1, first strand: chain 'A' and resid 167 through 172 removed outlier: 3.587A pdb=" N CYS A 180 " --> pdb=" O TYR A 171 " (cutoff:3.500A) removed outlier: 8.416A pdb=" N PHE A 227 " --> pdb=" O LEU A 179 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N LEU A 181 " --> pdb=" O PHE A 227 " (cutoff:3.500A) removed outlier: 7.436A pdb=" N SER A 229 " --> pdb=" O LEU A 181 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N ILE A 183 " --> pdb=" O SER A 229 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N VAL A 231 " --> pdb=" O ILE A 183 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N ASP A 185 " --> pdb=" O VAL A 231 " (cutoff:3.500A) removed outlier: 8.336A pdb=" N LEU A 233 " --> pdb=" O ASP A 185 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 214 through 215 Processing sheet with id=AA3, first strand: chain 'A' and resid 508 through 509 removed outlier: 6.914A pdb=" N ILE A 821 " --> pdb=" O TYR A 809 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N TYR A 811 " --> pdb=" O ILE A 819 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N ILE A 819 " --> pdb=" O TYR A 811 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N ARG A 813 " --> pdb=" O ASN A 817 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N ASN A 817 " --> pdb=" O ARG A 813 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N ALA A 788 " --> pdb=" O MET A 822 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N MET A 768 " --> pdb=" O LEU A 789 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1109 through 1110 removed outlier: 3.629A pdb=" N GLN A1109 " --> pdb=" O LYS A1219 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1295 through 1299 removed outlier: 6.765A pdb=" N VAL A1281 " --> pdb=" O CYS A1412 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1484 through 1486 Processing sheet with id=AA7, first strand: chain 'A' and resid 1484 through 1486 Processing sheet with id=AA8, first strand: chain 'A' and resid 1548 through 1549 Processing sheet with id=AA9, first strand: chain 'A' and resid 1974 through 1975 removed outlier: 6.882A pdb=" N VAL A1974 " --> pdb=" O THR A2083 " (cutoff:3.500A) 832 hydrogen bonds defined for protein. 2433 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 28 hydrogen bonds 52 hydrogen bond angles 0 basepair planarities 11 basepair parallelities 21 stacking parallelities Total time for adding SS restraints: 3.19 Time building geometry restraints manager: 1.73 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: 4123 1.33 - 1.46: 3648 1.46 - 1.58: 9142 1.58 - 1.70: 61 1.70 - 1.82: 173 Bond restraints: 17147 Sorted by residual: bond pdb=" C LEU A 912 " pdb=" N PRO A 913 " ideal model delta sigma weight residual 1.337 1.380 -0.044 9.80e-03 1.04e+04 1.98e+01 bond pdb=" C SER A1965 " pdb=" N PRO A1966 " ideal model delta sigma weight residual 1.334 1.397 -0.063 2.34e-02 1.83e+03 7.20e+00 bond pdb=" CB ILE A1724 " pdb=" CG2 ILE A1724 " ideal model delta sigma weight residual 1.521 1.459 0.062 3.30e-02 9.18e+02 3.57e+00 bond pdb=" CB GLU A 715 " pdb=" CG GLU A 715 " ideal model delta sigma weight residual 1.520 1.574 -0.054 3.00e-02 1.11e+03 3.28e+00 bond pdb=" CB PHE A2026 " pdb=" CG PHE A2026 " ideal model delta sigma weight residual 1.502 1.542 -0.040 2.30e-02 1.89e+03 2.99e+00 ... (remaining 17142 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.59: 22882 3.59 - 7.19: 294 7.19 - 10.78: 56 10.78 - 14.38: 9 14.38 - 17.97: 3 Bond angle restraints: 23244 Sorted by residual: angle pdb=" N ILE A 299 " pdb=" CA ILE A 299 " pdb=" C ILE A 299 " ideal model delta sigma weight residual 113.71 106.69 7.02 9.50e-01 1.11e+00 5.46e+01 angle pdb=" CB MET A2042 " pdb=" CG MET A2042 " pdb=" SD MET A2042 " ideal model delta sigma weight residual 112.70 130.67 -17.97 3.00e+00 1.11e-01 3.59e+01 angle pdb=" CG1 ILE A 791 " pdb=" CB ILE A 791 " pdb=" CG2 ILE A 791 " ideal model delta sigma weight residual 110.70 93.94 16.76 3.00e+00 1.11e-01 3.12e+01 angle pdb=" N ILE A 555 " pdb=" CA ILE A 555 " pdb=" C ILE A 555 " ideal model delta sigma weight residual 111.48 106.39 5.09 9.40e-01 1.13e+00 2.94e+01 angle pdb=" C PRO A 456 " pdb=" N ASN A 457 " pdb=" CA ASN A 457 " ideal model delta sigma weight residual 122.46 129.73 -7.27 1.41e+00 5.03e-01 2.66e+01 ... (remaining 23239 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.40: 9601 26.40 - 52.80: 854 52.80 - 79.20: 88 79.20 - 105.59: 7 105.59 - 131.99: 1 Dihedral angle restraints: 10551 sinusoidal: 4626 harmonic: 5925 Sorted by residual: dihedral pdb=" O4' C F 12 " pdb=" C1' C F 12 " pdb=" N1 C F 12 " pdb=" C2 C F 12 " ideal model delta sinusoidal sigma weight residual 200.00 68.01 131.99 1 1.50e+01 4.44e-03 7.12e+01 dihedral pdb=" CA TYR A1044 " pdb=" C TYR A1044 " pdb=" N PRO A1045 " pdb=" CA PRO A1045 " ideal model delta harmonic sigma weight residual -180.00 -153.31 -26.69 0 5.00e+00 4.00e-02 2.85e+01 dihedral pdb=" CA GLY A1393 " pdb=" C GLY A1393 " pdb=" N GLU A1394 " pdb=" CA GLU A1394 " ideal model delta harmonic sigma weight residual 180.00 154.75 25.25 0 5.00e+00 4.00e-02 2.55e+01 ... (remaining 10548 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.088: 2390 0.088 - 0.177: 249 0.177 - 0.265: 18 0.265 - 0.353: 3 0.353 - 0.441: 2 Chirality restraints: 2662 Sorted by residual: chirality pdb=" CG LEU A1510 " pdb=" CB LEU A1510 " pdb=" CD1 LEU A1510 " pdb=" CD2 LEU A1510 " both_signs ideal model delta sigma weight residual False -2.59 -2.15 -0.44 2.00e-01 2.50e+01 4.87e+00 chirality pdb=" CB ILE A 791 " pdb=" CA ILE A 791 " pdb=" CG1 ILE A 791 " pdb=" CG2 ILE A 791 " both_signs ideal model delta sigma weight residual False 2.64 3.00 -0.36 2.00e-01 2.50e+01 3.21e+00 chirality pdb=" CB ILE A 188 " pdb=" CA ILE A 188 " pdb=" CG1 ILE A 188 " pdb=" CG2 ILE A 188 " both_signs ideal model delta sigma weight residual False 2.64 2.30 0.35 2.00e-01 2.50e+01 2.99e+00 ... (remaining 2659 not shown) Planarity restraints: 2811 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASP A 737 " 0.021 2.00e-02 2.50e+03 4.24e-02 1.80e+01 pdb=" CG ASP A 737 " -0.073 2.00e-02 2.50e+03 pdb=" OD1 ASP A 737 " 0.026 2.00e-02 2.50e+03 pdb=" OD2 ASP A 737 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 363 " 0.016 2.00e-02 2.50e+03 3.19e-02 1.02e+01 pdb=" C ASN A 363 " -0.055 2.00e-02 2.50e+03 pdb=" O ASN A 363 " 0.021 2.00e-02 2.50e+03 pdb=" N PHE A 364 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A1738 " -0.015 2.00e-02 2.50e+03 3.03e-02 9.17e+00 pdb=" C ASP A1738 " 0.052 2.00e-02 2.50e+03 pdb=" O ASP A1738 " -0.020 2.00e-02 2.50e+03 pdb=" N SER A1739 " -0.017 2.00e-02 2.50e+03 ... (remaining 2808 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 2098 2.76 - 3.29: 16478 3.29 - 3.83: 29477 3.83 - 4.36: 33137 4.36 - 4.90: 56789 Nonbonded interactions: 137979 Sorted by model distance: nonbonded pdb=" O PHE A2061 " pdb=" OG SER A2065 " model vdw 2.221 3.040 nonbonded pdb=" O MET A 472 " pdb=" OH TYR A 786 " model vdw 2.222 3.040 nonbonded pdb=" OH TYR A1773 " pdb=" O LYS A1785 " model vdw 2.278 3.040 nonbonded pdb=" O GLY A1251 " pdb=" ND2 ASN A1839 " model vdw 2.288 3.120 nonbonded pdb=" OG SER A 477 " pdb=" O LEU A 680 " model vdw 2.291 3.040 ... (remaining 137974 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: 0.670 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: 0.000 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 16.070 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7070 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 0.063 17147 Z= 0.232 Angle : 1.069 17.974 23244 Z= 0.557 Chirality : 0.056 0.441 2662 Planarity : 0.006 0.075 2811 Dihedral : 18.157 131.992 6703 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.20 % Allowed : 7.34 % Favored : 92.46 % Rotamer: Outliers : 3.86 % Allowed : 23.19 % Favored : 72.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.08 (0.17), residues: 1989 helix: -0.89 (0.14), residues: 1050 sheet: 0.55 (0.54), residues: 100 loop : -2.22 (0.20), residues: 839 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A1679 TYR 0.025 0.002 TYR A1938 PHE 0.051 0.003 PHE A1234 TRP 0.025 0.002 TRP A 474 HIS 0.014 0.002 HIS A1529 Details of bonding type rmsd covalent geometry : bond 0.00480 (17147) covalent geometry : angle 1.06859 (23244) hydrogen bonds : bond 0.07230 ( 856) hydrogen bonds : angle 5.80709 ( 2485) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3978 Ramachandran restraints generated. 1989 Oldfield, 0 Emsley, 1989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3978 Ramachandran restraints generated. 1989 Oldfield, 0 Emsley, 1989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 612 residues out of total 1848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 541 time to evaluate : 0.472 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 309 ASP cc_start: 0.6885 (m-30) cc_final: 0.6534 (m-30) REVERT: A 822 MET cc_start: 0.8598 (mmt) cc_final: 0.8391 (mmm) REVERT: A 833 LEU cc_start: 0.8900 (tp) cc_final: 0.8627 (tt) REVERT: A 1028 GLU cc_start: 0.6857 (tm-30) cc_final: 0.6653 (tm-30) REVERT: A 1084 GLU cc_start: 0.7024 (pt0) cc_final: 0.6307 (pt0) REVERT: A 1376 LEU cc_start: 0.8109 (OUTLIER) cc_final: 0.7873 (mt) REVERT: A 1534 CYS cc_start: 0.7585 (t) cc_final: 0.7242 (t) REVERT: A 1728 ASN cc_start: 0.7363 (t0) cc_final: 0.5486 (t0) REVERT: A 1747 LYS cc_start: 0.7636 (OUTLIER) cc_final: 0.6856 (pttt) REVERT: A 1992 ASP cc_start: 0.7181 (m-30) cc_final: 0.6886 (m-30) REVERT: A 2063 PHE cc_start: 0.5673 (t80) cc_final: 0.5101 (t80) outliers start: 71 outliers final: 28 residues processed: 581 average time/residue: 0.1208 time to fit residues: 105.2556 Evaluate side-chains 362 residues out of total 1848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 332 time to evaluate : 0.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 365 CYS Chi-restraints excluded: chain A residue 374 GLN Chi-restraints excluded: chain A residue 562 VAL Chi-restraints excluded: chain A residue 571 TRP Chi-restraints excluded: chain A residue 585 PHE Chi-restraints excluded: chain A residue 607 ILE Chi-restraints excluded: chain A residue 654 HIS Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain A residue 681 HIS Chi-restraints excluded: chain A residue 701 ASN Chi-restraints excluded: chain A residue 805 THR Chi-restraints excluded: chain A residue 1058 ILE Chi-restraints excluded: chain A residue 1245 VAL Chi-restraints excluded: chain A residue 1307 LEU Chi-restraints excluded: chain A residue 1339 THR Chi-restraints excluded: chain A residue 1376 LEU Chi-restraints excluded: chain A residue 1382 LEU Chi-restraints excluded: chain A residue 1385 ILE Chi-restraints excluded: chain A residue 1446 THR Chi-restraints excluded: chain A residue 1464 VAL Chi-restraints excluded: chain A residue 1627 VAL Chi-restraints excluded: chain A residue 1661 LEU Chi-restraints excluded: chain A residue 1747 LYS Chi-restraints excluded: chain A residue 1779 LEU Chi-restraints excluded: chain A residue 1822 VAL Chi-restraints excluded: chain A residue 1998 LEU Chi-restraints excluded: chain A residue 2061 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 98 optimal weight: 9.9990 chunk 194 optimal weight: 9.9990 chunk 107 optimal weight: 8.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 6.9990 chunk 200 optimal weight: 0.7980 chunk 77 optimal weight: 8.9990 chunk 122 optimal weight: 7.9990 overall best weight: 4.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 38 ASN A 103 HIS A 266 HIS A 358 HIS A 404 HIS A 491 ASN A 697 ASN ** A 790 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 919 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1063 ASN A1312 HIS A1457 ASN A1628 ASN A1683 ASN A1749 GLN A1863 GLN A1947 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.116147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.089411 restraints weight = 43970.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.092426 restraints weight = 22481.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.094463 restraints weight = 14413.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.095856 restraints weight = 10656.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.096586 restraints weight = 8699.030| |-----------------------------------------------------------------------------| r_work (final): 0.3515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.3166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.119 17147 Z= 0.306 Angle : 0.844 13.240 23244 Z= 0.441 Chirality : 0.049 0.283 2662 Planarity : 0.005 0.063 2811 Dihedral : 12.664 142.320 2678 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 17.46 Ramachandran Plot: Outliers : 0.20 % Allowed : 7.99 % Favored : 91.80 % Rotamer: Outliers : 6.75 % Allowed : 23.68 % Favored : 69.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.22 (0.18), residues: 1989 helix: 0.05 (0.15), residues: 1076 sheet: 0.50 (0.50), residues: 100 loop : -2.18 (0.21), residues: 813 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A1294 TYR 0.030 0.002 TYR A1675 PHE 0.044 0.003 PHE A 741 TRP 0.027 0.003 TRP A 474 HIS 0.008 0.002 HIS A1578 Details of bonding type rmsd covalent geometry : bond 0.00657 (17147) covalent geometry : angle 0.84432 (23244) hydrogen bonds : bond 0.04622 ( 856) hydrogen bonds : angle 4.84069 ( 2485) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3978 Ramachandran restraints generated. 1989 Oldfield, 0 Emsley, 1989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3978 Ramachandran restraints generated. 1989 Oldfield, 0 Emsley, 1989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 457 residues out of total 1848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 333 time to evaluate : 0.638 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: symmetry clash revert: symmetry clash REVERT: A 30 LEU cc_start: 0.9273 (tp) cc_final: 0.9062 (mp) REVERT: A 140 LYS cc_start: 0.8771 (mttt) cc_final: 0.8322 (ttpp) REVERT: A 199 MET cc_start: 0.9303 (tpp) cc_final: 0.8836 (ttt) REVERT: A 266 HIS cc_start: 0.8953 (OUTLIER) cc_final: 0.8742 (t-170) REVERT: A 378 ASP cc_start: 0.7920 (t0) cc_final: 0.7439 (t0) REVERT: A 472 MET cc_start: 0.7366 (mpp) cc_final: 0.6921 (mpp) REVERT: A 480 LYS cc_start: 0.7072 (tmtt) cc_final: 0.6773 (tmtt) REVERT: A 536 GLU cc_start: 0.8264 (mt-10) cc_final: 0.8011 (tm-30) REVERT: A 684 ASP cc_start: 0.6979 (OUTLIER) cc_final: 0.6365 (m-30) REVERT: A 809 TYR cc_start: 0.7089 (OUTLIER) cc_final: 0.6659 (m-80) REVERT: A 822 MET cc_start: 0.9115 (mmt) cc_final: 0.8378 (mmm) REVERT: A 882 ILE cc_start: 0.9403 (mt) cc_final: 0.9173 (mt) REVERT: A 900 MET cc_start: 0.7553 (mpp) cc_final: 0.7069 (mpp) REVERT: A 904 ASP cc_start: 0.8258 (m-30) cc_final: 0.7943 (m-30) REVERT: A 982 CYS cc_start: 0.8062 (m) cc_final: 0.7610 (m) REVERT: A 1262 MET cc_start: 0.8592 (tpp) cc_final: 0.8299 (tpp) REVERT: A 1267 MET cc_start: 0.8969 (mmm) cc_final: 0.8714 (mmt) REVERT: A 1285 GLU cc_start: 0.7982 (pt0) cc_final: 0.7748 (pt0) REVERT: A 1398 MET cc_start: 0.7748 (tpp) cc_final: 0.7124 (mtt) REVERT: A 1475 LYS cc_start: 0.8655 (OUTLIER) cc_final: 0.7845 (ttmm) REVERT: A 1534 CYS cc_start: 0.8041 (t) cc_final: 0.7632 (t) REVERT: A 1554 GLU cc_start: 0.7396 (mt-10) cc_final: 0.6597 (mt-10) REVERT: A 1620 TYR cc_start: 0.6424 (m-80) cc_final: 0.6168 (m-80) REVERT: A 1691 LYS cc_start: 0.9296 (ptmt) cc_final: 0.9025 (ptpp) REVERT: A 1747 LYS cc_start: 0.8642 (OUTLIER) cc_final: 0.8271 (pttt) REVERT: A 1850 MET cc_start: 0.8362 (ttp) cc_final: 0.8142 (ttp) REVERT: A 1929 MET cc_start: 0.8783 (mtp) cc_final: 0.7768 (ptt) REVERT: A 1986 LYS cc_start: 0.8158 (tptp) cc_final: 0.7928 (tptp) outliers start: 124 outliers final: 64 residues processed: 421 average time/residue: 0.1056 time to fit residues: 70.6346 Evaluate side-chains 369 residues out of total 1848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 300 time to evaluate : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 THR Chi-restraints excluded: chain A residue 15 THR Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 223 ASP Chi-restraints excluded: chain A residue 239 MET Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 266 HIS Chi-restraints excluded: chain A residue 320 HIS Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 358 HIS Chi-restraints excluded: chain A residue 371 MET Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 442 THR Chi-restraints excluded: chain A residue 507 VAL Chi-restraints excluded: chain A residue 551 ASP Chi-restraints excluded: chain A residue 566 LYS Chi-restraints excluded: chain A residue 571 TRP Chi-restraints excluded: chain A residue 579 THR Chi-restraints excluded: chain A residue 585 PHE Chi-restraints excluded: chain A residue 654 HIS Chi-restraints excluded: chain A residue 670 CYS Chi-restraints excluded: chain A residue 681 HIS Chi-restraints excluded: chain A residue 684 ASP Chi-restraints excluded: chain A residue 753 THR Chi-restraints excluded: chain A residue 792 VAL Chi-restraints excluded: chain A residue 809 TYR Chi-restraints excluded: chain A residue 821 ILE Chi-restraints excluded: chain A residue 842 VAL Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 887 SER Chi-restraints excluded: chain A residue 895 THR Chi-restraints excluded: chain A residue 995 LEU Chi-restraints excluded: chain A residue 1017 LEU Chi-restraints excluded: chain A residue 1023 VAL Chi-restraints excluded: chain A residue 1215 VAL Chi-restraints excluded: chain A residue 1223 VAL Chi-restraints excluded: chain A residue 1245 VAL Chi-restraints excluded: chain A residue 1307 LEU Chi-restraints excluded: chain A residue 1310 ILE Chi-restraints excluded: chain A residue 1339 THR Chi-restraints excluded: chain A residue 1348 TYR Chi-restraints excluded: chain A residue 1359 SER Chi-restraints excluded: chain A residue 1376 LEU Chi-restraints excluded: chain A residue 1382 LEU Chi-restraints excluded: chain A residue 1391 THR Chi-restraints excluded: chain A residue 1397 LEU Chi-restraints excluded: chain A residue 1411 VAL Chi-restraints excluded: chain A residue 1444 THR Chi-restraints excluded: chain A residue 1446 THR Chi-restraints excluded: chain A residue 1468 CYS Chi-restraints excluded: chain A residue 1475 LYS Chi-restraints excluded: chain A residue 1536 THR Chi-restraints excluded: chain A residue 1580 SER Chi-restraints excluded: chain A residue 1596 LEU Chi-restraints excluded: chain A residue 1663 ILE Chi-restraints excluded: chain A residue 1747 LYS Chi-restraints excluded: chain A residue 1751 MET Chi-restraints excluded: chain A residue 1756 ILE Chi-restraints excluded: chain A residue 1770 MET Chi-restraints excluded: chain A residue 1880 THR Chi-restraints excluded: chain A residue 1917 CYS Chi-restraints excluded: chain A residue 1931 ILE Chi-restraints excluded: chain A residue 1955 THR Chi-restraints excluded: chain A residue 1974 VAL Chi-restraints excluded: chain A residue 1998 LEU Chi-restraints excluded: chain A residue 2061 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 74 optimal weight: 4.9990 chunk 35 optimal weight: 6.9990 chunk 77 optimal weight: 7.9990 chunk 86 optimal weight: 0.7980 chunk 21 optimal weight: 6.9990 chunk 91 optimal weight: 3.9990 chunk 98 optimal weight: 0.4980 chunk 13 optimal weight: 6.9990 chunk 42 optimal weight: 0.9990 chunk 41 optimal weight: 0.9980 chunk 145 optimal weight: 6.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 ASN A 103 HIS A 260 HIS A 358 HIS ** A 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 919 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1063 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1728 ASN A1749 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.119279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.092188 restraints weight = 44758.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.095347 restraints weight = 22863.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.097461 restraints weight = 14681.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.098677 restraints weight = 10898.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.099678 restraints weight = 9083.055| |-----------------------------------------------------------------------------| r_work (final): 0.3556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.3450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 17147 Z= 0.158 Angle : 0.722 11.690 23244 Z= 0.370 Chirality : 0.045 0.230 2662 Planarity : 0.004 0.049 2811 Dihedral : 12.347 136.782 2655 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 16.41 Ramachandran Plot: Outliers : 0.20 % Allowed : 7.34 % Favored : 92.46 % Rotamer: Outliers : 5.23 % Allowed : 24.93 % Favored : 69.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.91 (0.18), residues: 1989 helix: 0.34 (0.15), residues: 1083 sheet: 0.44 (0.49), residues: 112 loop : -2.11 (0.21), residues: 794 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 268 TYR 0.017 0.001 TYR A1948 PHE 0.032 0.002 PHE A1950 TRP 0.038 0.002 TRP A1958 HIS 0.005 0.001 HIS A1529 Details of bonding type rmsd covalent geometry : bond 0.00359 (17147) covalent geometry : angle 0.72234 (23244) hydrogen bonds : bond 0.03997 ( 856) hydrogen bonds : angle 4.68713 ( 2485) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3978 Ramachandran restraints generated. 1989 Oldfield, 0 Emsley, 1989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3978 Ramachandran restraints generated. 1989 Oldfield, 0 Emsley, 1989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 431 residues out of total 1848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 335 time to evaluate : 0.454 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 MET cc_start: 0.8159 (mtp) cc_final: 0.7930 (mtp) REVERT: A 140 LYS cc_start: 0.8727 (mttt) cc_final: 0.8318 (ttpp) REVERT: A 199 MET cc_start: 0.9296 (tpp) cc_final: 0.8861 (ttt) REVERT: A 378 ASP cc_start: 0.7921 (t0) cc_final: 0.7432 (t0) REVERT: A 450 GLU cc_start: 0.8758 (tt0) cc_final: 0.8344 (tp30) REVERT: A 472 MET cc_start: 0.7262 (mpp) cc_final: 0.6935 (mpp) REVERT: A 480 LYS cc_start: 0.7144 (tmtt) cc_final: 0.6696 (tmtt) REVERT: A 536 GLU cc_start: 0.8276 (mt-10) cc_final: 0.7991 (tm-30) REVERT: A 684 ASP cc_start: 0.6618 (OUTLIER) cc_final: 0.6378 (m-30) REVERT: A 878 LYS cc_start: 0.9377 (tttt) cc_final: 0.9133 (ttpp) REVERT: A 882 ILE cc_start: 0.9413 (mt) cc_final: 0.9187 (mt) REVERT: A 890 MET cc_start: 0.8646 (tpp) cc_final: 0.8378 (tpp) REVERT: A 900 MET cc_start: 0.7329 (mpp) cc_final: 0.6881 (mpp) REVERT: A 982 CYS cc_start: 0.8164 (m) cc_final: 0.7940 (m) REVERT: A 985 THR cc_start: 0.8643 (m) cc_final: 0.8406 (p) REVERT: A 1086 GLU cc_start: 0.6240 (mt-10) cc_final: 0.5795 (mt-10) REVERT: A 1262 MET cc_start: 0.8675 (tpp) cc_final: 0.8175 (tpp) REVERT: A 1361 LEU cc_start: 0.8996 (tp) cc_final: 0.8771 (tp) REVERT: A 1398 MET cc_start: 0.7835 (tpp) cc_final: 0.7336 (mtp) REVERT: A 1403 LEU cc_start: 0.8674 (mm) cc_final: 0.8242 (tp) REVERT: A 1470 MET cc_start: 0.8732 (tpp) cc_final: 0.8420 (tpp) REVERT: A 1475 LYS cc_start: 0.8560 (OUTLIER) cc_final: 0.8272 (mtpp) REVERT: A 1534 CYS cc_start: 0.8009 (OUTLIER) cc_final: 0.7679 (t) REVERT: A 1675 TYR cc_start: 0.8743 (t80) cc_final: 0.8496 (t80) REVERT: A 1691 LYS cc_start: 0.9275 (ptmt) cc_final: 0.9064 (ptpp) REVERT: A 1747 LYS cc_start: 0.8699 (OUTLIER) cc_final: 0.8382 (pttp) REVERT: A 1748 PHE cc_start: 0.7626 (m-80) cc_final: 0.7215 (m-10) REVERT: A 1749 GLN cc_start: 0.8407 (mm-40) cc_final: 0.8187 (mm-40) REVERT: A 1850 MET cc_start: 0.8425 (ttp) cc_final: 0.8210 (ttp) REVERT: A 1929 MET cc_start: 0.8633 (mtp) cc_final: 0.7775 (ptt) REVERT: A 1958 TRP cc_start: 0.6128 (m-90) cc_final: 0.5738 (m-90) outliers start: 96 outliers final: 57 residues processed: 397 average time/residue: 0.1071 time to fit residues: 67.8178 Evaluate side-chains 361 residues out of total 1848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 300 time to evaluate : 0.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 171 TYR Chi-restraints excluded: chain A residue 223 ASP Chi-restraints excluded: chain A residue 239 MET Chi-restraints excluded: chain A residue 320 HIS Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 356 ILE Chi-restraints excluded: chain A residue 358 HIS Chi-restraints excluded: chain A residue 374 GLN Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 473 THR Chi-restraints excluded: chain A residue 474 TRP Chi-restraints excluded: chain A residue 562 VAL Chi-restraints excluded: chain A residue 566 LYS Chi-restraints excluded: chain A residue 571 TRP Chi-restraints excluded: chain A residue 585 PHE Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 607 ILE Chi-restraints excluded: chain A residue 610 SER Chi-restraints excluded: chain A residue 654 HIS Chi-restraints excluded: chain A residue 670 CYS Chi-restraints excluded: chain A residue 681 HIS Chi-restraints excluded: chain A residue 684 ASP Chi-restraints excluded: chain A residue 753 THR Chi-restraints excluded: chain A residue 768 MET Chi-restraints excluded: chain A residue 842 VAL Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 912 LEU Chi-restraints excluded: chain A residue 1023 VAL Chi-restraints excluded: chain A residue 1199 LEU Chi-restraints excluded: chain A residue 1218 LEU Chi-restraints excluded: chain A residue 1245 VAL Chi-restraints excluded: chain A residue 1307 LEU Chi-restraints excluded: chain A residue 1310 ILE Chi-restraints excluded: chain A residue 1339 THR Chi-restraints excluded: chain A residue 1348 TYR Chi-restraints excluded: chain A residue 1359 SER Chi-restraints excluded: chain A residue 1365 SER Chi-restraints excluded: chain A residue 1376 LEU Chi-restraints excluded: chain A residue 1382 LEU Chi-restraints excluded: chain A residue 1390 LEU Chi-restraints excluded: chain A residue 1391 THR Chi-restraints excluded: chain A residue 1411 VAL Chi-restraints excluded: chain A residue 1446 THR Chi-restraints excluded: chain A residue 1475 LYS Chi-restraints excluded: chain A residue 1534 CYS Chi-restraints excluded: chain A residue 1596 LEU Chi-restraints excluded: chain A residue 1663 ILE Chi-restraints excluded: chain A residue 1747 LYS Chi-restraints excluded: chain A residue 1756 ILE Chi-restraints excluded: chain A residue 1770 MET Chi-restraints excluded: chain A residue 1779 LEU Chi-restraints excluded: chain A residue 1832 THR Chi-restraints excluded: chain A residue 1863 GLN Chi-restraints excluded: chain A residue 1917 CYS Chi-restraints excluded: chain A residue 1920 LEU Chi-restraints excluded: chain A residue 1931 ILE Chi-restraints excluded: chain A residue 1974 VAL Chi-restraints excluded: chain A residue 1998 LEU Chi-restraints excluded: chain A residue 2061 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 134 optimal weight: 0.8980 chunk 19 optimal weight: 10.0000 chunk 80 optimal weight: 0.6980 chunk 117 optimal weight: 0.0670 chunk 33 optimal weight: 8.9990 chunk 146 optimal weight: 0.7980 chunk 66 optimal weight: 0.6980 chunk 84 optimal weight: 3.9990 chunk 199 optimal weight: 1.9990 chunk 187 optimal weight: 10.0000 chunk 77 optimal weight: 6.9990 overall best weight: 0.6318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 38 ASN A 103 HIS ** A 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 919 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1063 ASN ** A2030 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.120931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.094129 restraints weight = 44421.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.097397 restraints weight = 22417.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.099552 restraints weight = 14221.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.100965 restraints weight = 10463.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.101771 restraints weight = 8585.362| |-----------------------------------------------------------------------------| r_work (final): 0.3602 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.3673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 17147 Z= 0.137 Angle : 0.707 13.604 23244 Z= 0.358 Chirality : 0.044 0.339 2662 Planarity : 0.004 0.042 2811 Dihedral : 12.209 136.239 2655 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 15.55 Ramachandran Plot: Outliers : 0.20 % Allowed : 7.64 % Favored : 92.16 % Rotamer: Outliers : 5.12 % Allowed : 25.20 % Favored : 69.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.75 (0.19), residues: 1989 helix: 0.51 (0.15), residues: 1088 sheet: 0.61 (0.47), residues: 119 loop : -2.18 (0.21), residues: 782 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 580 TYR 0.016 0.001 TYR A1447 PHE 0.027 0.001 PHE A1950 TRP 0.016 0.001 TRP A1958 HIS 0.015 0.001 HIS A 358 Details of bonding type rmsd covalent geometry : bond 0.00302 (17147) covalent geometry : angle 0.70660 (23244) hydrogen bonds : bond 0.03812 ( 856) hydrogen bonds : angle 4.58533 ( 2485) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3978 Ramachandran restraints generated. 1989 Oldfield, 0 Emsley, 1989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3978 Ramachandran restraints generated. 1989 Oldfield, 0 Emsley, 1989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 432 residues out of total 1848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 338 time to evaluate : 0.654 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 LEU cc_start: 0.8224 (OUTLIER) cc_final: 0.7958 (mm) REVERT: A 140 LYS cc_start: 0.8727 (mttt) cc_final: 0.8322 (ttpp) REVERT: A 199 MET cc_start: 0.9251 (tpp) cc_final: 0.8789 (ttt) REVERT: A 298 LYS cc_start: 0.9343 (mttt) cc_final: 0.8823 (pttp) REVERT: A 378 ASP cc_start: 0.7897 (t0) cc_final: 0.7434 (t70) REVERT: A 450 GLU cc_start: 0.8758 (tt0) cc_final: 0.8379 (tp30) REVERT: A 472 MET cc_start: 0.7076 (mpp) cc_final: 0.6869 (mpp) REVERT: A 480 LYS cc_start: 0.6993 (tmtt) cc_final: 0.6562 (tmtt) REVERT: A 536 GLU cc_start: 0.8292 (mt-10) cc_final: 0.7973 (tm-30) REVERT: A 550 GLU cc_start: 0.6080 (pm20) cc_final: 0.5855 (pm20) REVERT: A 684 ASP cc_start: 0.6458 (OUTLIER) cc_final: 0.6196 (m-30) REVERT: A 767 MET cc_start: 0.6533 (mmt) cc_final: 0.5921 (mmm) REVERT: A 878 LYS cc_start: 0.9360 (tttt) cc_final: 0.9118 (ttpp) REVERT: A 882 ILE cc_start: 0.9409 (mt) cc_final: 0.9170 (mt) REVERT: A 890 MET cc_start: 0.8586 (tpp) cc_final: 0.8303 (tpp) REVERT: A 900 MET cc_start: 0.7406 (mpp) cc_final: 0.6989 (mpp) REVERT: A 985 THR cc_start: 0.8503 (m) cc_final: 0.8256 (p) REVERT: A 1262 MET cc_start: 0.8589 (tpp) cc_final: 0.8096 (tpp) REVERT: A 1348 TYR cc_start: 0.7666 (OUTLIER) cc_final: 0.7362 (t80) REVERT: A 1376 LEU cc_start: 0.7842 (OUTLIER) cc_final: 0.7515 (tt) REVERT: A 1398 MET cc_start: 0.7741 (tpp) cc_final: 0.7061 (mtp) REVERT: A 1403 LEU cc_start: 0.8541 (OUTLIER) cc_final: 0.8081 (tp) REVERT: A 1470 MET cc_start: 0.8661 (tpp) cc_final: 0.8258 (tpp) REVERT: A 1475 LYS cc_start: 0.8507 (OUTLIER) cc_final: 0.8166 (mtpp) REVERT: A 1534 CYS cc_start: 0.7954 (OUTLIER) cc_final: 0.7684 (t) REVERT: A 1598 LYS cc_start: 0.8094 (OUTLIER) cc_final: 0.7426 (mmmt) REVERT: A 1691 LYS cc_start: 0.9307 (ptmt) cc_final: 0.9060 (ptpp) REVERT: A 1747 LYS cc_start: 0.8664 (OUTLIER) cc_final: 0.8371 (pttp) REVERT: A 1748 PHE cc_start: 0.7629 (m-80) cc_final: 0.7326 (m-10) REVERT: A 1841 ARG cc_start: 0.7896 (OUTLIER) cc_final: 0.7522 (tmm-80) REVERT: A 1850 MET cc_start: 0.8430 (ttp) cc_final: 0.8227 (ttp) REVERT: A 1929 MET cc_start: 0.8453 (mtp) cc_final: 0.7756 (ptt) REVERT: A 1953 PHE cc_start: 0.6916 (m-80) cc_final: 0.6403 (m-80) outliers start: 94 outliers final: 51 residues processed: 404 average time/residue: 0.1033 time to fit residues: 66.8676 Evaluate side-chains 363 residues out of total 1848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 302 time to evaluate : 0.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 150 GLU Chi-restraints excluded: chain A residue 223 ASP Chi-restraints excluded: chain A residue 239 MET Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 374 GLN Chi-restraints excluded: chain A residue 442 THR Chi-restraints excluded: chain A residue 473 THR Chi-restraints excluded: chain A residue 534 LEU Chi-restraints excluded: chain A residue 562 VAL Chi-restraints excluded: chain A residue 571 TRP Chi-restraints excluded: chain A residue 585 PHE Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 607 ILE Chi-restraints excluded: chain A residue 610 SER Chi-restraints excluded: chain A residue 654 HIS Chi-restraints excluded: chain A residue 670 CYS Chi-restraints excluded: chain A residue 681 HIS Chi-restraints excluded: chain A residue 684 ASP Chi-restraints excluded: chain A residue 745 LEU Chi-restraints excluded: chain A residue 768 MET Chi-restraints excluded: chain A residue 842 VAL Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 912 LEU Chi-restraints excluded: chain A residue 1023 VAL Chi-restraints excluded: chain A residue 1216 THR Chi-restraints excluded: chain A residue 1220 SER Chi-restraints excluded: chain A residue 1245 VAL Chi-restraints excluded: chain A residue 1307 LEU Chi-restraints excluded: chain A residue 1310 ILE Chi-restraints excluded: chain A residue 1339 THR Chi-restraints excluded: chain A residue 1348 TYR Chi-restraints excluded: chain A residue 1359 SER Chi-restraints excluded: chain A residue 1376 LEU Chi-restraints excluded: chain A residue 1382 LEU Chi-restraints excluded: chain A residue 1391 THR Chi-restraints excluded: chain A residue 1403 LEU Chi-restraints excluded: chain A residue 1446 THR Chi-restraints excluded: chain A residue 1464 VAL Chi-restraints excluded: chain A residue 1468 CYS Chi-restraints excluded: chain A residue 1475 LYS Chi-restraints excluded: chain A residue 1534 CYS Chi-restraints excluded: chain A residue 1596 LEU Chi-restraints excluded: chain A residue 1598 LYS Chi-restraints excluded: chain A residue 1747 LYS Chi-restraints excluded: chain A residue 1756 ILE Chi-restraints excluded: chain A residue 1770 MET Chi-restraints excluded: chain A residue 1779 LEU Chi-restraints excluded: chain A residue 1822 VAL Chi-restraints excluded: chain A residue 1832 THR Chi-restraints excluded: chain A residue 1841 ARG Chi-restraints excluded: chain A residue 1917 CYS Chi-restraints excluded: chain A residue 1920 LEU Chi-restraints excluded: chain A residue 1931 ILE Chi-restraints excluded: chain A residue 1950 PHE Chi-restraints excluded: chain A residue 1961 VAL Chi-restraints excluded: chain A residue 1974 VAL Chi-restraints excluded: chain A residue 1998 LEU Chi-restraints excluded: chain A residue 2061 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 70.438 > 50: distance: 37 - 172: 25.806 distance: 40 - 169: 32.062 distance: 77 - 94: 25.788 distance: 89 - 94: 23.472 distance: 94 - 95: 19.014 distance: 95 - 96: 24.031 distance: 95 - 98: 26.729 distance: 96 - 97: 56.318 distance: 96 - 99: 33.656 distance: 99 - 100: 10.301 distance: 100 - 101: 31.947 distance: 100 - 103: 58.533 distance: 101 - 102: 39.380 distance: 103 - 104: 19.484 distance: 104 - 105: 27.133 distance: 107 - 108: 39.995 distance: 108 - 109: 42.490 distance: 108 - 111: 56.051 distance: 109 - 110: 40.200 distance: 109 - 118: 38.724 distance: 111 - 112: 57.205 distance: 112 - 113: 30.146 distance: 113 - 114: 40.021 distance: 114 - 115: 37.350 distance: 115 - 116: 21.645 distance: 115 - 117: 36.026 distance: 118 - 119: 40.796 distance: 119 - 120: 6.367 distance: 119 - 122: 39.475 distance: 120 - 121: 49.384 distance: 120 - 130: 3.826 distance: 122 - 123: 20.436 distance: 123 - 124: 43.986 distance: 123 - 125: 21.978 distance: 124 - 126: 40.440 distance: 125 - 127: 32.637 distance: 126 - 128: 54.515 distance: 127 - 128: 16.092 distance: 128 - 129: 27.531 distance: 130 - 131: 40.296 distance: 131 - 132: 45.893 distance: 131 - 134: 41.010 distance: 132 - 133: 13.365 distance: 132 - 138: 32.240 distance: 134 - 135: 40.496 distance: 135 - 136: 24.956 distance: 136 - 137: 42.931 distance: 138 - 139: 56.882 distance: 139 - 140: 25.824 distance: 139 - 142: 41.275 distance: 140 - 141: 12.579 distance: 140 - 145: 47.704 distance: 142 - 144: 40.309 distance: 145 - 146: 49.987 distance: 146 - 147: 46.380 distance: 146 - 149: 10.126 distance: 147 - 148: 21.462 distance: 147 - 154: 9.561 distance: 149 - 150: 28.001 distance: 150 - 151: 12.882 distance: 151 - 152: 34.645 distance: 152 - 153: 59.373 distance: 154 - 155: 32.466 distance: 155 - 156: 23.860 distance: 156 - 157: 18.629 distance: 156 - 163: 25.941 distance: 158 - 159: 33.196 distance: 159 - 160: 10.754 distance: 160 - 161: 19.861 distance: 160 - 162: 32.381 distance: 163 - 164: 19.183 distance: 164 - 165: 44.523 distance: 164 - 167: 20.062 distance: 169 - 170: 38.721 distance: 170 - 171: 35.659 distance: 170 - 173: 18.105 distance: 171 - 172: 42.287 distance: 171 - 180: 14.815 distance: 173 - 174: 21.892 distance: 174 - 175: 52.663 distance: 175 - 177: 17.584 distance: 177 - 179: 37.305 distance: 178 - 179: 28.110