Starting phenix.real_space_refine on Fri Aug 22 18:16:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gfz_29989/08_2025/8gfz_29989.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gfz_29989/08_2025/8gfz_29989.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8gfz_29989/08_2025/8gfz_29989.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gfz_29989/08_2025/8gfz_29989.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8gfz_29989/08_2025/8gfz_29989.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gfz_29989/08_2025/8gfz_29989.map" } resolution = 3.0 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= 0.034 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 3 5.49 5 S 45 5.16 5 C 4311 2.51 5 N 1154 2.21 5 O 1231 1.98 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-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6744 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1763 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1763 Classifications: {'peptide': 230} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'PTRANS': 6, 'TRANS': 223} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 150 Unresolved non-hydrogen angles: 182 Unresolved non-hydrogen dihedrals: 121 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 6, 'GLU:plan': 12, 'PHE:plan': 1, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 107 Chain: "B" Number of atoms: 2433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2433 Classifications: {'peptide': 331} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 5, 'TRANS': 325} Chain breaks: 1 Unresolved non-hydrogen bonds: 111 Unresolved non-hydrogen angles: 134 Unresolved non-hydrogen dihedrals: 88 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 4, 'ARG:plan': 8, 'GLU:plan': 4, 'ASN:plan1': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 87 Chain: "G" Number of atoms: 349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 349 Classifications: {'peptide': 52} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 4, 'TRANS': 47} Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 65 Unresolved non-hydrogen dihedrals: 47 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 2, 'GLU:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 29 Chain: "R" Number of atoms: 2147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 278, 2147 Classifications: {'peptide': 278} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 7, 'TRANS': 270} Chain breaks: 1 Unresolved non-hydrogen bonds: 98 Unresolved non-hydrogen angles: 119 Unresolved non-hydrogen dihedrals: 83 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 5, 'ASN:plan1': 2, 'GLN:plan1': 3, 'HIS:plan': 2, 'ASP:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 65 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GTP': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 20 Unusual residues: {'G1I': 1} Classifications: {'undetermined': 1, 'water': 5} Link IDs: {None: 5} Time building chain proxies: 1.99, per 1000 atoms: 0.30 Number of scatterers: 6744 At special positions: 0 Unit cell: (85.0346, 132.758, 98.0501, 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 45 16.00 P 3 15.00 O 1231 8.00 N 1154 7.00 C 4311 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 106 " - pdb=" SG CYS R 191 " distance=2.03 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: 0.62 Conformation dependent library (CDL) restraints added in 558.7 milliseconds Enol-peptide restraints added in 1.2 microseconds 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1688 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 8 sheets defined 47.4% alpha, 18.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.20 Creating SS restraints... Processing helix chain 'A' and resid 12 through 39 removed outlier: 3.570A pdb=" N GLU A 16 " --> pdb=" O GLN A 12 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LYS A 17 " --> pdb=" O ARG A 13 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LYS A 32 " --> pdb=" O LYS A 28 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLN A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 59 Processing helix chain 'A' and resid 232 through 238 removed outlier: 3.527A pdb=" N ILE A 235 " --> pdb=" O ARG A 232 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N GLN A 236 " --> pdb=" O LYS A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 278 Processing helix chain 'A' and resid 293 through 303 removed outlier: 3.696A pdb=" N LEU A 297 " --> pdb=" O LYS A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 311 Processing helix chain 'A' and resid 312 through 318 removed outlier: 3.604A pdb=" N TYR A 318 " --> pdb=" O PHE A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 352 removed outlier: 3.649A pdb=" N THR A 335 " --> pdb=" O ASP A 331 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ARG A 336 " --> pdb=" O PRO A 332 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N PHE A 345 " --> pdb=" O ILE A 341 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 removed outlier: 3.605A pdb=" N ARG A 374 " --> pdb=" O GLU A 370 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N VAL A 375 " --> pdb=" O ASN A 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 7 through 24 removed outlier: 3.528A pdb=" N GLU B 12 " --> pdb=" O ARG B 8 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ARG B 19 " --> pdb=" O LYS B 15 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'G' and resid 12 through 24 removed outlier: 3.623A pdb=" N VAL G 16 " --> pdb=" O ALA G 12 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 45 removed outlier: 3.648A pdb=" N ALA G 33 " --> pdb=" O LYS G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 46 through 48 No H-bonds generated for 'chain 'G' and resid 46 through 48' Processing helix chain 'R' and resid 37 through 61 Processing helix chain 'R' and resid 66 through 97 removed outlier: 4.083A pdb=" N PHE R 71 " --> pdb=" O VAL R 67 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ILE R 72 " --> pdb=" O THR R 68 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N VAL R 87 " --> pdb=" O GLY R 83 " (cutoff:3.500A) Proline residue: R 88 - end of helix Processing helix chain 'R' and resid 104 through 137 removed outlier: 3.598A pdb=" N THR R 123 " --> pdb=" O ALA R 119 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LEU R 124 " --> pdb=" O SER R 120 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N CYS R 125 " --> pdb=" O ILE R 121 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N VAL R 126 " --> pdb=" O GLU R 122 " (cutoff:3.500A) Processing helix chain 'R' and resid 140 through 145 Processing helix chain 'R' and resid 146 through 164 Processing helix chain 'R' and resid 165 through 171 removed outlier: 3.606A pdb=" N ILE R 169 " --> pdb=" O SER R 165 " (cutoff:3.500A) Processing helix chain 'R' and resid 178 through 187 Processing helix chain 'R' and resid 196 through 238 removed outlier: 3.785A pdb=" N SER R 204 " --> pdb=" O ALA R 200 " (cutoff:3.500A) removed outlier: 5.285A pdb=" N VAL R 210 " --> pdb=" O VAL R 206 " (cutoff:3.500A) Proline residue: R 211 - end of helix removed outlier: 3.560A pdb=" N ARG R 221 " --> pdb=" O PHE R 217 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LYS R 235 " --> pdb=" O GLN R 231 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N SER R 236 " --> pdb=" O LYS R 232 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLU R 237 " --> pdb=" O ILE R 233 " (cutoff:3.500A) Processing helix chain 'R' and resid 269 through 299 removed outlier: 3.705A pdb=" N PHE R 282 " --> pdb=" O ILE R 278 " (cutoff:3.500A) Proline residue: R 288 - end of helix removed outlier: 4.082A pdb=" N ILE R 294 " --> pdb=" O PHE R 290 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N VAL R 297 " --> pdb=" O ASN R 293 " (cutoff:3.500A) Processing helix chain 'R' and resid 304 through 318 removed outlier: 3.813A pdb=" N ASN R 318 " --> pdb=" O ILE R 314 " (cutoff:3.500A) Processing helix chain 'R' and resid 321 through 327 Processing helix chain 'R' and resid 329 through 339 Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 214 removed outlier: 4.519A pdb=" N VAL A 224 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N GLY A 47 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 9.629A pdb=" N ALA A 243 " --> pdb=" O THR A 40 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 8.174A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 8.885A pdb=" N ALA A 249 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N ASN A 292 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N VAL A 248 " --> pdb=" O ASN A 292 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.646A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.905A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LEU B 70 " --> pdb=" O TRP B 82 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 7.095A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.312A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.798A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.423A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.659A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.887A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.649A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.976A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) 346 hydrogen bonds defined for protein. 1008 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: 0.89 Time building geometry restraints manager: 0.80 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: 1737 1.33 - 1.45: 1331 1.45 - 1.57: 3747 1.57 - 1.69: 5 1.69 - 1.81: 62 Bond restraints: 6882 Sorted by residual: bond pdb=" CA GLU R 237 " pdb=" C GLU R 237 " ideal model delta sigma weight residual 1.524 1.486 0.039 1.43e-02 4.89e+03 7.26e+00 bond pdb=" CAC G1I R 501 " pdb=" CAD G1I R 501 " ideal model delta sigma weight residual 1.397 1.449 -0.052 2.00e-02 2.50e+03 6.75e+00 bond pdb=" CA GLU R 237 " pdb=" CB GLU R 237 " ideal model delta sigma weight residual 1.531 1.496 0.035 1.34e-02 5.57e+03 6.71e+00 bond pdb=" N LYS R 235 " pdb=" CA LYS R 235 " ideal model delta sigma weight residual 1.459 1.429 0.030 1.21e-02 6.83e+03 6.27e+00 bond pdb=" CAI G1I R 501 " pdb=" CAJ G1I R 501 " ideal model delta sigma weight residual 1.523 1.570 -0.047 2.00e-02 2.50e+03 5.49e+00 ... (remaining 6877 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.84: 9274 1.84 - 3.68: 88 3.68 - 5.51: 23 5.51 - 7.35: 2 7.35 - 9.19: 1 Bond angle restraints: 9388 Sorted by residual: angle pdb=" N SER R 236 " pdb=" CA SER R 236 " pdb=" C SER R 236 " ideal model delta sigma weight residual 111.28 120.47 -9.19 1.09e+00 8.42e-01 7.11e+01 angle pdb=" N ASP R 234 " pdb=" CA ASP R 234 " pdb=" C ASP R 234 " ideal model delta sigma weight residual 111.82 117.66 -5.84 1.16e+00 7.43e-01 2.53e+01 angle pdb=" O ILE R 233 " pdb=" C ILE R 233 " pdb=" N ASP R 234 " ideal model delta sigma weight residual 121.87 117.29 4.58 9.70e-01 1.06e+00 2.23e+01 angle pdb=" CA ILE R 233 " pdb=" C ILE R 233 " pdb=" N ASP R 234 " ideal model delta sigma weight residual 117.15 121.88 -4.73 1.14e+00 7.69e-01 1.72e+01 angle pdb=" N SER R 236 " pdb=" CA SER R 236 " pdb=" CB SER R 236 " ideal model delta sigma weight residual 110.12 105.99 4.13 1.47e+00 4.63e-01 7.89e+00 ... (remaining 9383 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.07: 3895 28.07 - 56.14: 108 56.14 - 84.22: 9 84.22 - 112.29: 0 112.29 - 140.36: 3 Dihedral angle restraints: 4015 sinusoidal: 1417 harmonic: 2598 Sorted by residual: dihedral pdb=" C8 GTP A 401 " pdb=" C1' GTP A 401 " pdb=" N9 GTP A 401 " pdb=" O4' GTP A 401 " ideal model delta sinusoidal sigma weight residual 104.59 -35.77 140.36 1 2.00e+01 2.50e-03 4.25e+01 dihedral pdb=" O3A GTP A 401 " pdb=" O3B GTP A 401 " pdb=" PB GTP A 401 " pdb=" PG GTP A 401 " ideal model delta sinusoidal sigma weight residual 303.79 175.06 128.74 1 2.00e+01 2.50e-03 3.90e+01 dihedral pdb=" C5' GTP A 401 " pdb=" O5' GTP A 401 " pdb=" PA GTP A 401 " pdb=" O3A GTP A 401 " ideal model delta sinusoidal sigma weight residual 69.27 -57.70 126.97 1 2.00e+01 2.50e-03 3.84e+01 ... (remaining 4012 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 797 0.041 - 0.082: 244 0.082 - 0.123: 61 0.123 - 0.164: 3 0.164 - 0.205: 1 Chirality restraints: 1106 Sorted by residual: chirality pdb=" CA SER R 236 " pdb=" N SER R 236 " pdb=" C SER R 236 " pdb=" CB SER R 236 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.21 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" CAJ G1I R 501 " pdb=" CAF G1I R 501 " pdb=" CAI G1I R 501 " pdb=" OAM G1I R 501 " both_signs ideal model delta sigma weight residual False 2.40 2.55 -0.15 2.00e-01 2.50e+01 5.66e-01 chirality pdb=" CA ILE A 244 " pdb=" N ILE A 244 " pdb=" C ILE A 244 " pdb=" CB ILE A 244 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.92e-01 ... (remaining 1103 not shown) Planarity restraints: 1177 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE R 205 " 0.008 2.00e-02 2.50e+03 1.60e-02 2.57e+00 pdb=" C ILE R 205 " -0.028 2.00e-02 2.50e+03 pdb=" O ILE R 205 " 0.010 2.00e-02 2.50e+03 pdb=" N VAL R 206 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP A 331 " 0.022 5.00e-02 4.00e+02 3.38e-02 1.82e+00 pdb=" N PRO A 332 " -0.058 5.00e-02 4.00e+02 pdb=" CA PRO A 332 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 332 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR R 281 " -0.007 2.00e-02 2.50e+03 1.34e-02 1.79e+00 pdb=" C THR R 281 " 0.023 2.00e-02 2.50e+03 pdb=" O THR R 281 " -0.009 2.00e-02 2.50e+03 pdb=" N PHE R 282 " -0.008 2.00e-02 2.50e+03 ... (remaining 1174 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 510 2.74 - 3.28: 6307 3.28 - 3.82: 10683 3.82 - 4.36: 12368 4.36 - 4.90: 22591 Nonbonded interactions: 52459 Sorted by model distance: nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 2.201 3.040 nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.236 3.040 nonbonded pdb=" OD1 ASP R 113 " pdb=" OH TYR R 316 " model vdw 2.279 3.040 nonbonded pdb=" OD2 ASP R 113 " pdb=" OAM G1I R 501 " model vdw 2.309 3.040 nonbonded pdb=" O TYR R 132 " pdb=" OG1 THR R 136 " model vdw 2.309 3.040 ... (remaining 52454 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.180 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.480 Find NCS groups from input model: 0.030 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:6.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 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 : 0.003 0.052 6883 Z= 0.157 Angle : 0.500 9.190 9390 Z= 0.287 Chirality : 0.041 0.205 1106 Planarity : 0.003 0.034 1177 Dihedral : 13.528 140.362 2324 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 2.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % 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: 0.72 (0.28), residues: 873 helix: 1.44 (0.27), residues: 381 sheet: 0.47 (0.41), residues: 165 loop : -0.60 (0.32), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 239 TYR 0.008 0.001 TYR A 339 PHE 0.014 0.001 PHE B 234 TRP 0.006 0.001 TRP B 99 HIS 0.005 0.001 HIS B 183 Details of bonding type rmsd covalent geometry : bond 0.00286 ( 6882) covalent geometry : angle 0.50008 ( 9388) SS BOND : bond 0.00160 ( 1) SS BOND : angle 0.68669 ( 2) hydrogen bonds : bond 0.20994 ( 346) hydrogen bonds : angle 6.23167 ( 1008) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 98 time to evaluate : 0.277 Fit side-chains REVERT: A 386 MET cc_start: 0.8572 (ttm) cc_final: 0.8269 (ttp) outliers start: 0 outliers final: 0 residues processed: 98 average time/residue: 0.5977 time to fit residues: 61.4131 Evaluate side-chains 81 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 81 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 49 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 0.5980 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 chunk 45 optimal weight: 0.0670 chunk 74 optimal weight: 0.8980 overall best weight: 0.6518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS R 51 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.119731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.094544 restraints weight = 8767.416| |-----------------------------------------------------------------------------| r_work (start): 0.2997 rms_B_bonded: 1.84 r_work: 0.2878 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2749 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.1118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 6883 Z= 0.117 Angle : 0.488 5.542 9390 Z= 0.262 Chirality : 0.041 0.131 1106 Planarity : 0.003 0.029 1177 Dihedral : 8.595 140.285 979 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 1.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 1.20 % Allowed : 7.36 % Favored : 91.44 % 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: 1.05 (0.28), residues: 873 helix: 1.77 (0.27), residues: 391 sheet: 0.55 (0.39), residues: 171 loop : -0.56 (0.34), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 219 TYR 0.008 0.001 TYR A 339 PHE 0.012 0.001 PHE A 212 TRP 0.006 0.001 TRP B 99 HIS 0.004 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00243 ( 6882) covalent geometry : angle 0.48735 ( 9388) SS BOND : bond 0.00222 ( 1) SS BOND : angle 1.01635 ( 2) hydrogen bonds : bond 0.05109 ( 346) hydrogen bonds : angle 4.48059 ( 1008) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 95 time to evaluate : 0.245 Fit side-chains REVERT: A 221 MET cc_start: 0.8303 (ttp) cc_final: 0.7996 (ttp) REVERT: R 188 GLU cc_start: 0.7542 (mm-30) cc_final: 0.7310 (mm-30) REVERT: R 231 GLN cc_start: 0.8289 (tm-30) cc_final: 0.8002 (tm-30) REVERT: R 239 ARG cc_start: 0.8376 (OUTLIER) cc_final: 0.8065 (ptt180) outliers start: 8 outliers final: 0 residues processed: 97 average time/residue: 0.6620 time to fit residues: 67.2206 Evaluate side-chains 86 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 85 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 239 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 45 optimal weight: 0.7980 chunk 84 optimal weight: 0.6980 chunk 59 optimal weight: 0.3980 chunk 24 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 chunk 37 optimal weight: 0.7980 chunk 12 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 8 optimal weight: 0.5980 chunk 85 optimal weight: 0.5980 chunk 77 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 51 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.120560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.095384 restraints weight = 8721.803| |-----------------------------------------------------------------------------| r_work (start): 0.3000 rms_B_bonded: 1.84 r_work: 0.2883 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2753 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 moved from start: 0.1353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 6883 Z= 0.105 Angle : 0.458 5.431 9390 Z= 0.245 Chirality : 0.040 0.131 1106 Planarity : 0.003 0.029 1177 Dihedral : 8.241 139.128 979 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 1.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 0.60 % Allowed : 10.96 % Favored : 88.44 % 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: 1.31 (0.29), residues: 873 helix: 2.03 (0.27), residues: 390 sheet: 0.68 (0.40), residues: 171 loop : -0.50 (0.34), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 219 TYR 0.008 0.001 TYR A 339 PHE 0.012 0.001 PHE A 212 TRP 0.006 0.001 TRP B 297 HIS 0.004 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00222 ( 6882) covalent geometry : angle 0.45809 ( 9388) SS BOND : bond 0.00210 ( 1) SS BOND : angle 0.91777 ( 2) hydrogen bonds : bond 0.04521 ( 346) hydrogen bonds : angle 4.15814 ( 1008) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 87 time to evaluate : 0.265 Fit side-chains REVERT: B 303 ASP cc_start: 0.8501 (p0) cc_final: 0.8169 (p0) REVERT: R 79 ASP cc_start: 0.8384 (m-30) cc_final: 0.8075 (m-30) REVERT: R 231 GLN cc_start: 0.8097 (tm-30) cc_final: 0.7856 (tm-30) outliers start: 4 outliers final: 2 residues processed: 90 average time/residue: 0.6320 time to fit residues: 59.7202 Evaluate side-chains 82 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 80 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 300 LYS Chi-restraints excluded: chain B residue 61 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- 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: 53.2374 > 50: distance: 87 - 194: 8.431 distance: 90 - 191: 7.237 distance: 101 - 183: 9.748 distance: 123 - 129: 25.723 distance: 129 - 130: 31.826 distance: 130 - 131: 17.607 distance: 130 - 133: 28.890 distance: 131 - 132: 11.138 distance: 131 - 134: 9.669 distance: 134 - 135: 3.729 distance: 135 - 136: 19.828 distance: 135 - 138: 10.478 distance: 136 - 137: 9.631 distance: 136 - 142: 8.346 distance: 138 - 139: 6.709 distance: 139 - 140: 19.602 distance: 139 - 141: 26.026 distance: 142 - 143: 7.128 distance: 143 - 144: 9.572 distance: 143 - 146: 5.783 distance: 144 - 145: 19.291 distance: 144 - 151: 5.881 distance: 146 - 147: 13.579 distance: 147 - 148: 15.057 distance: 148 - 149: 24.186 distance: 149 - 150: 17.780 distance: 151 - 152: 3.921 distance: 152 - 153: 3.342 distance: 152 - 155: 7.082 distance: 153 - 154: 10.092 distance: 153 - 156: 5.925 distance: 156 - 157: 12.780 distance: 157 - 158: 9.866 distance: 157 - 160: 16.560 distance: 158 - 159: 30.787 distance: 158 - 164: 12.684 distance: 160 - 161: 16.202 distance: 161 - 162: 4.237 distance: 161 - 163: 19.819 distance: 164 - 165: 9.110 distance: 165 - 166: 9.305 distance: 165 - 168: 18.994 distance: 166 - 167: 11.858 distance: 166 - 175: 12.073 distance: 168 - 169: 18.560 distance: 169 - 170: 21.082 distance: 171 - 172: 7.176 distance: 172 - 173: 12.503 distance: 172 - 174: 9.970 distance: 175 - 176: 9.875 distance: 176 - 177: 8.601 distance: 176 - 179: 11.619 distance: 177 - 178: 7.831 distance: 177 - 180: 6.447 distance: 180 - 181: 7.094 distance: 181 - 182: 12.758 distance: 182 - 183: 13.376 distance: 182 - 184: 3.387 distance: 184 - 185: 7.010 distance: 185 - 186: 12.136 distance: 185 - 188: 21.918 distance: 186 - 187: 3.710 distance: 186 - 191: 13.439 distance: 188 - 189: 31.656 distance: 188 - 190: 12.765 distance: 191 - 192: 9.484 distance: 192 - 193: 4.868 distance: 192 - 195: 5.318 distance: 193 - 194: 7.377 distance: 193 - 199: 5.455 distance: 195 - 196: 16.419 distance: 196 - 197: 23.555 distance: 196 - 198: 18.886