Starting phenix.real_space_refine on Thu Feb 5 21:45:57 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9do8_47074/02_2026/9do8_47074_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9do8_47074/02_2026/9do8_47074.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.75 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9do8_47074/02_2026/9do8_47074.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9do8_47074/02_2026/9do8_47074.map" model { file = "/net/cci-nas-00/data/ceres_data/9do8_47074/02_2026/9do8_47074_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9do8_47074/02_2026/9do8_47074_neut.cif" } resolution = 2.75 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= 0.000 sd= 0.012 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 S 24 5.16 5 C 6295 2.51 5 N 1723 2.21 5 O 1941 1.98 5 H 9847 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19830 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2046 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 2046 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 3, 'TRANS': 131} Chain: "B" Number of atoms: 2046 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 2046 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 3, 'TRANS': 131} Chain: "C" Number of atoms: 5831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 5831 Classifications: {'peptide': 375} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 346} Chain breaks: 4 Chain: "D" Number of atoms: 2046 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 2046 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 3, 'TRANS': 131} Chain: "E" Number of atoms: 2046 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 2046 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 3, 'TRANS': 131} Chain: "F" Number of atoms: 5815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 374, 5815 Classifications: {'peptide': 374} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 345} Chain breaks: 4 Time building chain proxies: 3.34, per 1000 atoms: 0.17 Number of scatterers: 19830 At special positions: 0 Unit cell: (110.39, 94.62, 116.2, 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 24 16.00 O 1941 8.00 N 1723 7.00 C 6295 6.00 H 9847 1.00 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: 1.53 Conformation dependent library (CDL) restraints added in 468.5 milliseconds 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2358 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 21 sheets defined 16.4% alpha, 30.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.40 Creating SS restraints... Processing helix chain 'A' and resid 42 through 46 Processing helix chain 'B' and resid 42 through 46 Processing helix chain 'C' and resid 54 through 60 Processing helix chain 'C' and resid 61 through 72 Processing helix chain 'C' and resid 177 through 181 Processing helix chain 'C' and resid 189 through 201 Processing helix chain 'C' and resid 204 through 220 Processing helix chain 'C' and resid 298 through 302 Processing helix chain 'C' and resid 304 through 312 Processing helix chain 'C' and resid 313 through 318 removed outlier: 6.348A pdb=" N GLU C 316 " --> pdb=" O ASN C 313 " (cutoff:3.500A) Processing helix chain 'C' and resid 330 through 333 Processing helix chain 'C' and resid 334 through 345 Processing helix chain 'C' and resid 444 through 447 Processing helix chain 'D' and resid 42 through 46 Processing helix chain 'D' and resid 80 through 83 removed outlier: 4.231A pdb=" N GLY D 83 " --> pdb=" O PRO D 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 80 through 83' Processing helix chain 'E' and resid 42 through 46 Processing helix chain 'F' and resid 54 through 60 Processing helix chain 'F' and resid 61 through 72 Processing helix chain 'F' and resid 177 through 181 Processing helix chain 'F' and resid 189 through 201 Processing helix chain 'F' and resid 204 through 220 Processing helix chain 'F' and resid 298 through 302 removed outlier: 3.504A pdb=" N ILE F 302 " --> pdb=" O TYR F 299 " (cutoff:3.500A) Processing helix chain 'F' and resid 304 through 311 Processing helix chain 'F' and resid 312 through 318 removed outlier: 5.775A pdb=" N SER F 315 " --> pdb=" O THR F 312 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N GLU F 316 " --> pdb=" O ASN F 313 " (cutoff:3.500A) Processing helix chain 'F' and resid 330 through 333 Processing helix chain 'F' and resid 334 through 345 removed outlier: 3.660A pdb=" N GLN F 340 " --> pdb=" O PRO F 336 " (cutoff:3.500A) Processing helix chain 'F' and resid 444 through 447 removed outlier: 3.525A pdb=" N THR F 447 " --> pdb=" O PRO F 444 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 444 through 447' Processing sheet with id=AA1, first strand: chain 'A' and resid 40 through 41 removed outlier: 4.088A pdb=" N LEU A 31 " --> pdb=" O VAL A 41 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N ASN A 60 " --> pdb=" O HIS A 32 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N TRP A 6 " --> pdb=" O GLY A 127 " (cutoff:3.500A) removed outlier: 8.064A pdb=" N ILE A 129 " --> pdb=" O TRP A 6 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N ILE A 8 " --> pdb=" O ILE A 129 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N VAL A 131 " --> pdb=" O ILE A 8 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N ILE A 10 " --> pdb=" O VAL A 131 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N THR A 133 " --> pdb=" O ILE A 10 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N HIS A 12 " --> pdb=" O THR A 133 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 50 through 51 removed outlier: 3.615A pdb=" N VAL A 19 " --> pdb=" O VAL A 51 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N LYS A 22 " --> pdb=" O VAL A 78 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N VAL A 78 " --> pdb=" O LYS A 22 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N LEU A 24 " --> pdb=" O ASP A 76 " (cutoff:3.500A) removed outlier: 7.974A pdb=" N ASP A 76 " --> pdb=" O LEU A 24 " (cutoff:3.500A) removed outlier: 5.423A pdb=" N ALA A 26 " --> pdb=" O THR A 74 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N THR A 74 " --> pdb=" O ALA A 26 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N THR A 71 " --> pdb=" O ASP A 93 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N ASP A 93 " --> pdb=" O THR A 71 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N GLY A 73 " --> pdb=" O TYR A 91 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N TYR A 91 " --> pdb=" O GLY A 73 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N PHE A 75 " --> pdb=" O HIS A 89 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N HIS A 89 " --> pdb=" O PHE A 75 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N LEU A 77 " --> pdb=" O VAL A 87 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 36 through 41 removed outlier: 6.368A pdb=" N ALA B 39 " --> pdb=" O ALA B 33 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N LEU B 31 " --> pdb=" O VAL B 41 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N ASN B 60 " --> pdb=" O HIS B 32 " (cutoff:3.500A) removed outlier: 8.088A pdb=" N ILE B 129 " --> pdb=" O TRP B 6 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N ILE B 8 " --> pdb=" O ILE B 129 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N VAL B 131 " --> pdb=" O ILE B 8 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N ILE B 10 " --> pdb=" O VAL B 131 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N THR B 133 " --> pdb=" O ILE B 10 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N HIS B 12 " --> pdb=" O THR B 133 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 50 through 51 removed outlier: 6.896A pdb=" N THR B 71 " --> pdb=" O ASP B 93 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N ASP B 93 " --> pdb=" O THR B 71 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N GLY B 73 " --> pdb=" O TYR B 91 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N TYR B 91 " --> pdb=" O GLY B 73 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N PHE B 75 " --> pdb=" O HIS B 89 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N HIS B 89 " --> pdb=" O PHE B 75 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N LEU B 77 " --> pdb=" O VAL B 87 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 76 through 79 removed outlier: 5.198A pdb=" N GLY C 77 " --> pdb=" O SER C 88 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 103 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 100 through 103 current: chain 'C' and resid 162 through 174 removed outlier: 5.983A pdb=" N SER C 163 " --> pdb=" O THR C 237 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N THR C 237 " --> pdb=" O SER C 163 " (cutoff:3.500A) removed outlier: 5.390A pdb=" N ARG C 165 " --> pdb=" O ALA C 235 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N ALA C 235 " --> pdb=" O ARG C 165 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N LEU C 167 " --> pdb=" O LEU C 233 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N LEU C 233 " --> pdb=" O LEU C 167 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N GLY C 231 " --> pdb=" O PRO C 169 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLY C 171 " --> pdb=" O ILE C 229 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 291 through 295 current: chain 'F' and resid 161 through 174 removed outlier: 6.547A pdb=" N ILE F 229 " --> pdb=" O GLN F 170 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N ARG F 172 " --> pdb=" O VAL F 227 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N VAL F 227 " --> pdb=" O ARG F 172 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N ASP F 174 " --> pdb=" O THR F 225 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N THR F 225 " --> pdb=" O ASP F 174 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 380 through 381 Processing sheet with id=AA8, first strand: chain 'C' and resid 355 through 357 Processing sheet with id=AA9, first strand: chain 'C' and resid 421 through 423 Processing sheet with id=AB1, first strand: chain 'C' and resid 456 through 458 Processing sheet with id=AB2, first strand: chain 'C' and resid 460 through 464 removed outlier: 3.689A pdb=" N SER C 492 " --> pdb=" O THR C 475 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 30 through 32 removed outlier: 4.505A pdb=" N ASN D 60 " --> pdb=" O HIS D 32 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N TRP D 6 " --> pdb=" O GLY D 127 " (cutoff:3.500A) removed outlier: 7.998A pdb=" N ILE D 129 " --> pdb=" O TRP D 6 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N ILE D 8 " --> pdb=" O ILE D 129 " (cutoff:3.500A) removed outlier: 7.466A pdb=" N VAL D 131 " --> pdb=" O ILE D 8 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N ILE D 10 " --> pdb=" O VAL D 131 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N THR D 133 " --> pdb=" O ILE D 10 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N HIS D 12 " --> pdb=" O THR D 133 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 50 through 51 removed outlier: 3.554A pdb=" N VAL D 19 " --> pdb=" O VAL D 51 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N LEU D 24 " --> pdb=" O THR D 74 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N THR D 74 " --> pdb=" O LEU D 24 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N ALA D 26 " --> pdb=" O THR D 72 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N THR D 72 " --> pdb=" O ALA D 26 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N THR D 71 " --> pdb=" O ASP D 93 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N ASP D 93 " --> pdb=" O THR D 71 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N GLY D 73 " --> pdb=" O TYR D 91 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N TYR D 91 " --> pdb=" O GLY D 73 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N PHE D 75 " --> pdb=" O HIS D 89 " (cutoff:3.500A) removed outlier: 5.138A pdb=" N HIS D 89 " --> pdb=" O PHE D 75 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N LEU D 77 " --> pdb=" O VAL D 87 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 40 through 41 removed outlier: 4.116A pdb=" N LEU E 31 " --> pdb=" O VAL E 41 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N ASN E 60 " --> pdb=" O HIS E 32 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N TRP E 6 " --> pdb=" O GLY E 127 " (cutoff:3.500A) removed outlier: 8.150A pdb=" N ILE E 129 " --> pdb=" O TRP E 6 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N ILE E 8 " --> pdb=" O ILE E 129 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N VAL E 131 " --> pdb=" O ILE E 8 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N ILE E 10 " --> pdb=" O VAL E 131 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N THR E 133 " --> pdb=" O ILE E 10 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N HIS E 12 " --> pdb=" O THR E 133 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 50 through 51 removed outlier: 4.410A pdb=" N LEU E 24 " --> pdb=" O THR E 74 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N THR E 74 " --> pdb=" O LEU E 24 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N ALA E 26 " --> pdb=" O THR E 72 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N THR E 72 " --> pdb=" O ALA E 26 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N THR E 71 " --> pdb=" O ASP E 93 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N ASP E 93 " --> pdb=" O THR E 71 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N GLY E 73 " --> pdb=" O TYR E 91 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N TYR E 91 " --> pdb=" O GLY E 73 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N PHE E 75 " --> pdb=" O HIS E 89 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N HIS E 89 " --> pdb=" O PHE E 75 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N LEU E 77 " --> pdb=" O VAL E 87 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 76 through 79 removed outlier: 5.067A pdb=" N GLY F 77 " --> pdb=" O SER F 88 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 380 through 381 Processing sheet with id=AB9, first strand: chain 'F' and resid 355 through 357 Processing sheet with id=AC1, first strand: chain 'F' and resid 421 through 423 Processing sheet with id=AC2, first strand: chain 'F' and resid 456 through 458 Processing sheet with id=AC3, first strand: chain 'F' and resid 460 through 464 removed outlier: 3.862A pdb=" N SER F 492 " --> pdb=" O THR F 475 " (cutoff:3.500A) 312 hydrogen bonds defined for protein. 789 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: 3.95 Time building geometry restraints manager: 2.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.02: 9841 1.02 - 1.22: 21 1.22 - 1.42: 4167 1.42 - 1.62: 5975 1.62 - 1.82: 42 Bond restraints: 20046 Sorted by residual: bond pdb=" CA LYS D 135 " pdb=" C LYS D 135 " ideal model delta sigma weight residual 1.524 1.461 0.063 1.27e-02 6.20e+03 2.44e+01 bond pdb=" CA LYS A 135 " pdb=" C LYS A 135 " ideal model delta sigma weight residual 1.526 1.470 0.056 1.30e-02 5.92e+03 1.83e+01 bond pdb=" CA ALA A 67 " pdb=" C ALA A 67 " ideal model delta sigma weight residual 1.521 1.477 0.044 1.21e-02 6.83e+03 1.33e+01 bond pdb=" NZ LYS B 135 " pdb=" HZ3 LYS B 135 " ideal model delta sigma weight residual 0.890 0.961 -0.071 2.00e-02 2.50e+03 1.26e+01 bond pdb=" NZ LYS B 136 " pdb=" HZ2 LYS B 136 " ideal model delta sigma weight residual 0.890 0.961 -0.071 2.00e-02 2.50e+03 1.25e+01 ... (remaining 20041 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.60: 32346 1.60 - 3.21: 3562 3.21 - 4.81: 312 4.81 - 6.42: 64 6.42 - 8.02: 6 Bond angle restraints: 36290 Sorted by residual: angle pdb=" N LYS B 135 " pdb=" CA LYS B 135 " pdb=" C LYS B 135 " ideal model delta sigma weight residual 113.18 119.62 -6.44 1.21e+00 6.83e-01 2.84e+01 angle pdb=" N ALA E 26 " pdb=" CA ALA E 26 " pdb=" C ALA E 26 " ideal model delta sigma weight residual 108.90 116.92 -8.02 1.63e+00 3.76e-01 2.42e+01 angle pdb=" N GLY F 521 " pdb=" CA GLY F 521 " pdb=" C GLY F 521 " ideal model delta sigma weight residual 115.32 108.94 6.38 1.38e+00 5.25e-01 2.13e+01 angle pdb=" N PHE D 90 " pdb=" CA PHE D 90 " pdb=" C PHE D 90 " ideal model delta sigma weight residual 109.50 115.94 -6.44 1.58e+00 4.01e-01 1.66e+01 angle pdb=" N VAL E 87 " pdb=" CA VAL E 87 " pdb=" C VAL E 87 " ideal model delta sigma weight residual 111.45 107.79 3.66 9.30e-01 1.16e+00 1.55e+01 ... (remaining 36285 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.72: 8655 17.72 - 35.44: 496 35.44 - 53.17: 212 53.17 - 70.89: 51 70.89 - 88.61: 9 Dihedral angle restraints: 9423 sinusoidal: 5168 harmonic: 4255 Sorted by residual: dihedral pdb=" CA ARG B 64 " pdb=" C ARG B 64 " pdb=" N SER B 65 " pdb=" CA SER B 65 " ideal model delta harmonic sigma weight residual -180.00 -161.39 -18.61 0 5.00e+00 4.00e-02 1.38e+01 dihedral pdb=" CA TYR F 461 " pdb=" C TYR F 461 " pdb=" N GLU F 462 " pdb=" CA GLU F 462 " ideal model delta harmonic sigma weight residual 180.00 162.10 17.90 0 5.00e+00 4.00e-02 1.28e+01 dihedral pdb=" CA TYR F 473 " pdb=" C TYR F 473 " pdb=" N VAL F 474 " pdb=" CA VAL F 474 " ideal model delta harmonic sigma weight residual 180.00 163.51 16.49 0 5.00e+00 4.00e-02 1.09e+01 ... (remaining 9420 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 1142 0.040 - 0.081: 236 0.081 - 0.121: 142 0.121 - 0.161: 29 0.161 - 0.201: 1 Chirality restraints: 1550 Sorted by residual: chirality pdb=" CA LYS B 135 " pdb=" N LYS B 135 " pdb=" C LYS B 135 " pdb=" CB LYS B 135 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.01e+00 chirality pdb=" CA ILE E 59 " pdb=" N ILE E 59 " pdb=" C ILE E 59 " pdb=" CB ILE E 59 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.01e-01 chirality pdb=" CA ASP C 174 " pdb=" N ASP C 174 " pdb=" C ASP C 174 " pdb=" CB ASP C 174 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.14e-01 ... (remaining 1547 not shown) Planarity restraints: 2988 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN F 413 " -0.032 2.00e-02 2.50e+03 3.24e-02 1.57e+01 pdb=" CD GLN F 413 " 0.008 2.00e-02 2.50e+03 pdb=" OE1 GLN F 413 " 0.027 2.00e-02 2.50e+03 pdb=" NE2 GLN F 413 " -0.000 2.00e-02 2.50e+03 pdb="HE21 GLN F 413 " 0.046 2.00e-02 2.50e+03 pdb="HE22 GLN F 413 " -0.049 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR F 112 " -0.012 2.00e-02 2.50e+03 2.30e-02 5.29e+00 pdb=" C THR F 112 " 0.040 2.00e-02 2.50e+03 pdb=" O THR F 112 " -0.015 2.00e-02 2.50e+03 pdb=" N THR F 113 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL F 478 " 0.011 2.00e-02 2.50e+03 2.15e-02 4.63e+00 pdb=" C VAL F 478 " -0.037 2.00e-02 2.50e+03 pdb=" O VAL F 478 " 0.014 2.00e-02 2.50e+03 pdb=" N ASP F 479 " 0.012 2.00e-02 2.50e+03 ... (remaining 2985 not shown) Histogram of nonbonded interaction distances: 1.62 - 2.22: 1409 2.22 - 2.81: 42373 2.81 - 3.41: 52692 3.41 - 4.00: 73566 4.00 - 4.60: 110210 Nonbonded interactions: 280250 Sorted by model distance: nonbonded pdb=" O ASN A 13 " pdb=" H ASP A 54 " model vdw 1.620 2.450 nonbonded pdb=" O ASP C 384 " pdb=" HG SER C 432 " model vdw 1.624 2.450 nonbonded pdb=" HH TYR F 461 " pdb=" O PRO F 507 " model vdw 1.628 2.450 nonbonded pdb=" O TYR D 3 " pdb=" HZ3 LYS D 37 " model vdw 1.634 2.450 nonbonded pdb="HD22 ASN C 304 " pdb=" OE2 GLU C 307 " model vdw 1.666 2.450 ... (remaining 280245 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 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'D' selection = chain 'E' } ncs_group { reference = (chain 'C' and (resid 52 through 479 or resid 484 through 522)) selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.740 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: 0.130 Extract box with map and model: 0.310 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 17.520 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.020 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:6.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6954 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 : 0.004 0.063 10199 Z= 0.250 Angle : 0.620 8.020 13850 Z= 0.368 Chirality : 0.046 0.201 1550 Planarity : 0.004 0.045 1781 Dihedral : 11.641 88.611 3722 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 2.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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 are not related in a simple way. whole: 0.32 (0.23), residues: 1261 helix: 1.30 (0.47), residues: 139 sheet: -0.28 (0.25), residues: 424 loop : 0.49 (0.23), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 404 TYR 0.022 0.001 TYR C 161 PHE 0.008 0.001 PHE A 75 TRP 0.007 0.001 TRP D 96 HIS 0.007 0.001 HIS A 12 Details of bonding type rmsd covalent geometry : bond 0.00394 (10199) covalent geometry : angle 0.62040 (13850) hydrogen bonds : bond 0.15540 ( 312) hydrogen bonds : angle 6.42598 ( 789) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 326 time to evaluate : 0.478 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 ASP cc_start: 0.7328 (m-30) cc_final: 0.6921 (m-30) REVERT: A 102 THR cc_start: 0.6907 (m) cc_final: 0.6476 (p) REVERT: B 51 VAL cc_start: 0.6470 (t) cc_final: 0.6186 (m) REVERT: B 57 LEU cc_start: 0.7547 (tp) cc_final: 0.7344 (tm) REVERT: B 101 ASN cc_start: 0.7510 (m-40) cc_final: 0.7098 (m-40) REVERT: B 119 GLN cc_start: 0.7241 (pm20) cc_final: 0.6951 (pm20) REVERT: B 121 LEU cc_start: 0.7044 (mt) cc_final: 0.6693 (mm) REVERT: C 60 GLN cc_start: 0.8248 (mm-40) cc_final: 0.8034 (mm-40) REVERT: C 71 ASP cc_start: 0.8115 (m-30) cc_final: 0.7888 (m-30) REVERT: C 165 ARG cc_start: 0.7520 (ttt-90) cc_final: 0.7294 (ttt-90) REVERT: C 186 ILE cc_start: 0.7856 (pt) cc_final: 0.7539 (pp) REVERT: C 187 LYS cc_start: 0.8477 (mtmt) cc_final: 0.8114 (mtmt) REVERT: C 197 GLN cc_start: 0.8036 (mm-40) cc_final: 0.7734 (mp10) REVERT: C 354 ASP cc_start: 0.7784 (p0) cc_final: 0.7417 (p0) REVERT: C 372 LYS cc_start: 0.7526 (ttpp) cc_final: 0.7176 (ttpp) REVERT: C 425 LEU cc_start: 0.7816 (mm) cc_final: 0.7557 (mt) REVERT: C 491 LYS cc_start: 0.7985 (mtmm) cc_final: 0.7783 (mtmm) REVERT: D 23 ASN cc_start: 0.7721 (m-40) cc_final: 0.7207 (m-40) REVERT: D 76 ASP cc_start: 0.6416 (m-30) cc_final: 0.5858 (m-30) REVERT: D 93 ASP cc_start: 0.5994 (t0) cc_final: 0.5638 (t0) REVERT: D 126 LEU cc_start: 0.6680 (tp) cc_final: 0.6473 (tp) REVERT: D 134 LEU cc_start: 0.7246 (tp) cc_final: 0.7025 (tp) REVERT: E 17 GLN cc_start: 0.6382 (mp10) cc_final: 0.6151 (mp10) REVERT: E 101 ASN cc_start: 0.7069 (m-40) cc_final: 0.6564 (m-40) REVERT: F 110 GLU cc_start: 0.8146 (tt0) cc_final: 0.7866 (tp30) REVERT: F 210 GLU cc_start: 0.7512 (mm-30) cc_final: 0.7222 (mm-30) REVERT: F 304 ASN cc_start: 0.8149 (t0) cc_final: 0.7907 (t0) REVERT: F 463 MET cc_start: 0.7507 (ttm) cc_final: 0.7300 (ttt) REVERT: F 464 HIS cc_start: 0.7328 (m90) cc_final: 0.7058 (m170) REVERT: F 491 LYS cc_start: 0.8047 (mtpt) cc_final: 0.7834 (mtpp) REVERT: F 515 MET cc_start: 0.8278 (mmp) cc_final: 0.7750 (mmt) outliers start: 0 outliers final: 0 residues processed: 326 average time/residue: 0.9003 time to fit residues: 320.8658 Evaluate side-chains 299 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 299 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 108 optimal weight: 0.0060 chunk 49 optimal weight: 0.0770 chunk 97 optimal weight: 0.9980 chunk 113 optimal weight: 0.9980 chunk 53 optimal weight: 0.3980 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 0.1980 chunk 123 optimal weight: 0.8980 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 0.6980 overall best weight: 0.2754 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 45 ASN F 295 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.135661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.121108 restraints weight = 42591.252| |-----------------------------------------------------------------------------| r_work (start): 0.3592 rms_B_bonded: 2.10 r_work: 0.3500 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3364 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 moved from start: 0.1555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 10199 Z= 0.127 Angle : 0.500 4.270 13850 Z= 0.263 Chirality : 0.045 0.160 1550 Planarity : 0.004 0.028 1781 Dihedral : 4.586 18.769 1361 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 1.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.28 % Allowed : 9.61 % Favored : 89.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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 are not related in a simple way. whole: 0.34 (0.23), residues: 1261 helix: 1.28 (0.45), residues: 142 sheet: 0.00 (0.25), residues: 396 loop : 0.28 (0.22), residues: 723 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 452 TYR 0.014 0.001 TYR D 46 PHE 0.010 0.001 PHE E 90 TRP 0.009 0.001 TRP E 92 HIS 0.010 0.001 HIS C 412 Details of bonding type rmsd covalent geometry : bond 0.00291 (10199) covalent geometry : angle 0.49990 (13850) hydrogen bonds : bond 0.03577 ( 312) hydrogen bonds : angle 5.30696 ( 789) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 307 time to evaluate : 0.347 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: A 25 LYS cc_start: 0.7598 (ttpp) cc_final: 0.7289 (ttpp) REVERT: A 102 THR cc_start: 0.8161 (m) cc_final: 0.7938 (p) REVERT: B 119 GLN cc_start: 0.8206 (pm20) cc_final: 0.7913 (pm20) REVERT: C 186 ILE cc_start: 0.7967 (pt) cc_final: 0.7718 (pp) REVERT: C 187 LYS cc_start: 0.8597 (mtmt) cc_final: 0.8308 (mtmt) REVERT: C 197 GLN cc_start: 0.8057 (mm-40) cc_final: 0.7839 (mp10) REVERT: C 210 GLU cc_start: 0.7759 (mm-30) cc_final: 0.7510 (mm-30) REVERT: C 218 GLU cc_start: 0.6658 (pt0) cc_final: 0.6391 (pt0) REVERT: C 307 GLU cc_start: 0.7867 (mt-10) cc_final: 0.7574 (mt-10) REVERT: C 372 LYS cc_start: 0.8006 (ttpp) cc_final: 0.7707 (ttpp) REVERT: F 210 GLU cc_start: 0.7902 (mm-30) cc_final: 0.7656 (mm-30) REVERT: F 515 MET cc_start: 0.8632 (mmp) cc_final: 0.7977 (mmt) outliers start: 14 outliers final: 8 residues processed: 309 average time/residue: 0.8643 time to fit residues: 294.0451 Evaluate side-chains 311 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 303 time to evaluate : 0.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 176 THR Chi-restraints excluded: chain C residue 363 SER Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain E residue 50 ILE Chi-restraints excluded: chain E residue 102 THR Chi-restraints excluded: chain E residue 115 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/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-2.0-5952/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-2.0-5952/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-2.0-5952/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-2.0-5952/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-2.0-5952/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-2.0-5952/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-2.0-5952/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-2.0-5952/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-2.0-5952/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-2.0-5952/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-2.0-5952/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-2.0-5952/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-2.0-5952/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-2.0-5952/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-2.0-5952/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-2.0-5952/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-2.0-5952/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-2.0-5952/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-2.0-5952/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: 71.2451 > 50: distance: 159 - 173: 21.835 distance: 173 - 174: 40.802 distance: 173 - 181: 36.489 distance: 174 - 175: 54.204 distance: 174 - 177: 38.697 distance: 174 - 182: 29.163 distance: 175 - 176: 57.623 distance: 177 - 178: 41.131 distance: 177 - 183: 18.124 distance: 177 - 184: 45.889 distance: 178 - 179: 28.816 distance: 178 - 180: 18.196 distance: 185 - 193: 41.383 distance: 186 - 187: 57.832 distance: 186 - 189: 47.267 distance: 186 - 194: 39.940 distance: 187 - 188: 31.478 distance: 187 - 204: 33.660 distance: 189 - 190: 40.903 distance: 189 - 195: 58.418 distance: 189 - 196: 47.118 distance: 190 - 191: 31.937 distance: 190 - 192: 42.538 distance: 190 - 197: 32.492 distance: 191 - 198: 23.786 distance: 191 - 199: 27.595 distance: 191 - 200: 23.281 distance: 192 - 201: 27.061 distance: 192 - 202: 18.246 distance: 192 - 203: 17.033 distance: 204 - 205: 20.388 distance: 204 - 210: 32.406 distance: 205 - 206: 48.413 distance: 205 - 208: 19.759 distance: 205 - 211: 57.153 distance: 206 - 207: 11.865 distance: 206 - 218: 34.216 distance: 208 - 209: 22.544 distance: 208 - 212: 23.562 distance: 208 - 213: 31.887 distance: 209 - 210: 13.359 distance: 209 - 214: 9.189 distance: 209 - 215: 30.720 distance: 210 - 216: 13.389 distance: 210 - 217: 41.860 distance: 218 - 219: 37.147 distance: 218 - 227: 37.734 distance: 219 - 220: 43.870 distance: 219 - 222: 28.979 distance: 219 - 228: 42.582 distance: 220 - 221: 35.637 distance: 220 - 235: 52.198 distance: 222 - 223: 17.604 distance: 222 - 229: 21.939 distance: 222 - 230: 35.419 distance: 223 - 224: 12.890 distance: 223 - 231: 17.681 distance: 223 - 232: 45.607 distance: 224 - 225: 23.139 distance: 224 - 226: 18.138 distance: 226 - 233: 21.007 distance: 226 - 234: 29.066 distance: 235 - 236: 24.582 distance: 235 - 247: 46.651 distance: 236 - 237: 21.521 distance: 236 - 239: 15.327 distance: 236 - 248: 36.221 distance: 237 - 238: 51.106 distance: 237 - 256: 28.230 distance: 239 - 240: 21.492 distance: 239 - 249: 30.036 distance: 239 - 250: 24.158 distance: 240 - 241: 15.175 distance: 240 - 242: 13.086 distance: 241 - 243: 9.882 distance: 241 - 251: 10.381 distance: 242 - 244: 17.898 distance: 242 - 252: 19.032 distance: 243 - 245: 14.070 distance: 243 - 253: 8.710 distance: 244 - 245: 13.055 distance: 244 - 254: 9.236 distance: 245 - 246: 17.358 distance: 246 - 255: 23.880 distance: 256 - 257: 20.938 distance: 256 - 265: 20.538 distance: 257 - 258: 27.885 distance: 257 - 260: 18.841 distance: 257 - 266: 30.200 distance: 258 - 259: 45.837 distance: 258 - 273: 27.331 distance: 260 - 261: 17.697 distance: 260 - 267: 39.906 distance: 260 - 268: 47.883 distance: 261 - 262: 20.952 distance: 261 - 269: 46.129 distance: 261 - 270: 18.897 distance: 262 - 263: 23.589 distance: 262 - 264: 26.218 distance: 264 - 271: 12.266 distance: 264 - 272: 18.079 distance: 273 - 274: 33.549 distance: 273 - 285: 26.637 distance: 274 - 275: 20.554 distance: 274 - 277: 21.381 distance: 274 - 286: 33.051 distance: 275 - 294: 31.372 distance: 277 - 278: 39.012 distance: 277 - 287: 17.109 distance: 277 - 288: 38.715 distance: 278 - 280: 3.937 distance: 279 - 281: 8.449 distance: 279 - 289: 10.699 distance: 280 - 282: 11.201 distance: 280 - 290: 13.149 distance: 281 - 283: 15.341 distance: 281 - 291: 6.254 distance: 282 - 283: 14.644 distance: 282 - 292: 11.907 distance: 283 - 284: 20.752 distance: 284 - 293: 13.639 distance: 294 - 295: 12.461 distance: 294 - 302: 35.407 distance: 295 - 296: 38.647 distance: 295 - 298: 24.687 distance: 295 - 303: 26.622 distance: 296 - 297: 29.337 distance: 296 - 313: 34.726 distance: 298 - 299: 20.379 distance: 298 - 304: 19.460 distance: 298 - 305: 13.761 distance: 299 - 300: 10.093 distance: 299 - 301: 7.594 distance: 299 - 306: 7.775 distance: 300 - 307: 3.116 distance: 300 - 308: 7.374 distance: 300 - 309: 3.760 distance: 301 - 310: 11.077 distance: 301 - 311: 9.035 distance: 301 - 312: 9.206 distance: 313 - 314: 13.141 distance: 313 - 319: 23.175 distance: 314 - 315: 7.574 distance: 314 - 317: 7.427 distance: 314 - 320: 24.823 distance: 315 - 316: 12.778 distance: 315 - 324: 11.772 distance: 317 - 318: 8.187 distance: 317 - 321: 11.757 distance: 317 - 322: 8.058 distance: 318 - 323: 7.994 distance: 324 - 325: 8.304 distance: 324 - 331: 13.745 distance: 325 - 326: 11.569 distance: 325 - 328: 6.827 distance: 325 - 332: 11.660 distance: 326 - 327: 16.942 distance: 326 - 338: 9.499 distance: 328 - 329: 3.867 distance: 328 - 330: 6.713 distance: 329 - 334: 5.627 distance: 330 - 335: 9.767 distance: 330 - 336: 5.896