Starting phenix.real_space_refine on Sat Aug 23 13:43:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7kch_22808/08_2025/7kch_22808.cif Found real_map, /net/cci-nas-00/data/ceres_data/7kch_22808/08_2025/7kch_22808.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.33 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7kch_22808/08_2025/7kch_22808.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7kch_22808/08_2025/7kch_22808.map" model { file = "/net/cci-nas-00/data/ceres_data/7kch_22808/08_2025/7kch_22808.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7kch_22808/08_2025/7kch_22808.cif" } resolution = 4.33 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= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 3 5.21 5 S 63 5.16 5 C 7597 2.51 5 N 2174 2.21 5 O 2405 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 48 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: 12248 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 3365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 680, 3365 Classifications: {'peptide': 680} Incomplete info: {'truncation_to_alanine': 592} Link IDs: {'PTRANS': 21, 'TRANS': 658} Chain breaks: 8 Unresolved chain link angles: 21 Unresolved non-hydrogen bonds: 2164 Unresolved non-hydrogen angles: 2757 Unresolved non-hydrogen dihedrals: 1796 Unresolved non-hydrogen chiralities: 187 Planarities with less than four sites: {'TRP:plan': 4, 'GLU:plan': 52, 'ASP:plan': 36, 'ARG:plan': 33, 'ASN:plan1': 34, 'TYR:plan': 20, 'HIS:plan': 19, 'PHE:plan': 39, 'GLN:plan1': 34} Unresolved non-hydrogen planarities: 1224 Chain: "B" Number of atoms: 2933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 2933 Classifications: {'peptide': 375} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 355} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Restraints were copied for chains: C, G Time building chain proxies: 2.37, per 1000 atoms: 0.19 Number of scatterers: 12248 At special positions: 0 Unit cell: (123.848, 144.672, 140.288, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 63 16.00 P 6 15.00 Mg 3 11.99 O 2405 8.00 N 2174 7.00 C 7597 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: 0.84 Conformation dependent library (CDL) restraints added in 450.6 milliseconds Enol-peptide restraints added in 1.2 microseconds 3562 Ramachandran restraints generated. 1781 Oldfield, 0 Emsley, 1781 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3372 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 22 sheets defined 48.2% alpha, 12.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.49 Creating SS restraints... Processing helix chain 'G' and resid 78 through 92 removed outlier: 3.537A pdb=" N MET G 82 " --> pdb=" O ASN G 78 " (cutoff:3.500A) Processing helix chain 'G' and resid 97 through 101 removed outlier: 3.793A pdb=" N HIS G 101 " --> pdb=" O PRO G 98 " (cutoff:3.500A) Processing helix chain 'G' and resid 112 through 128 removed outlier: 3.700A pdb=" N ARG G 116 " --> pdb=" O PRO G 112 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N MET G 123 " --> pdb=" O MET G 119 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N PHE G 124 " --> pdb=" O THR G 120 " (cutoff:3.500A) Processing helix chain 'G' and resid 139 through 146 removed outlier: 4.023A pdb=" N TYR G 143 " --> pdb=" O VAL G 139 " (cutoff:3.500A) Processing helix chain 'G' and resid 181 through 197 removed outlier: 3.638A pdb=" N THR G 194 " --> pdb=" O MET G 190 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N GLU G 195 " --> pdb=" O LYS G 191 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N ARG G 196 " --> pdb=" O ILE G 192 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLY G 197 " --> pdb=" O LEU G 193 " (cutoff:3.500A) Processing helix chain 'G' and resid 202 through 204 No H-bonds generated for 'chain 'G' and resid 202 through 204' Processing helix chain 'G' and resid 205 through 216 Processing helix chain 'G' and resid 224 through 230 Processing helix chain 'G' and resid 233 through 237 removed outlier: 4.607A pdb=" N LEU G 236 " --> pdb=" O SER G 233 " (cutoff:3.500A) Processing helix chain 'G' and resid 251 through 255 removed outlier: 3.814A pdb=" N ARG G 254 " --> pdb=" O GLY G 251 " (cutoff:3.500A) Processing helix chain 'G' and resid 258 through 263 removed outlier: 3.541A pdb=" N LEU G 261 " --> pdb=" O PRO G 258 " (cutoff:3.500A) Processing helix chain 'G' and resid 273 through 284 removed outlier: 3.551A pdb=" N LYS G 284 " --> pdb=" O ASN G 280 " (cutoff:3.500A) Processing helix chain 'G' and resid 290 through 296 removed outlier: 3.754A pdb=" N ALA G 295 " --> pdb=" O LYS G 291 " (cutoff:3.500A) Processing helix chain 'G' and resid 301 through 305 removed outlier: 3.858A pdb=" N MET G 305 " --> pdb=" O GLY G 302 " (cutoff:3.500A) Processing helix chain 'G' and resid 308 through 321 Processing helix chain 'G' and resid 334 through 336 No H-bonds generated for 'chain 'G' and resid 334 through 336' Processing helix chain 'G' and resid 337 through 349 removed outlier: 3.830A pdb=" N ALA G 347 " --> pdb=" O GLY G 343 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N SER G 348 " --> pdb=" O SER G 344 " (cutoff:3.500A) Processing helix chain 'G' and resid 359 through 366 Processing helix chain 'G' and resid 368 through 373 removed outlier: 3.735A pdb=" N ARG G 372 " --> pdb=" O SER G 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 92 Processing helix chain 'A' and resid 117 through 127 Processing helix chain 'A' and resid 136 through 149 Processing helix chain 'A' and resid 165 through 182 Processing helix chain 'A' and resid 191 through 207 Proline residue: A 200 - end of helix Processing helix chain 'A' and resid 243 through 248 removed outlier: 3.875A pdb=" N THR A 248 " --> pdb=" O SER A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 265 Processing helix chain 'A' and resid 268 through 276 removed outlier: 3.586A pdb=" N GLU A 273 " --> pdb=" O PRO A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 314 Processing helix chain 'A' and resid 316 through 335 Processing helix chain 'A' and resid 344 through 348 removed outlier: 3.615A pdb=" N GLU A 347 " --> pdb=" O ASP A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 365 Processing helix chain 'A' and resid 367 through 377 Processing helix chain 'A' and resid 393 through 425 removed outlier: 3.597A pdb=" N ASP A 399 " --> pdb=" O SER A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 481 Processing helix chain 'A' and resid 491 through 501 Processing helix chain 'A' and resid 506 through 517 removed outlier: 3.717A pdb=" N LEU A 517 " --> pdb=" O GLU A 513 " (cutoff:3.500A) Processing helix chain 'A' and resid 521 through 532 Processing helix chain 'A' and resid 564 through 569 Processing helix chain 'A' and resid 574 through 583 removed outlier: 3.588A pdb=" N GLN A 578 " --> pdb=" O VAL A 574 " (cutoff:3.500A) Processing helix chain 'A' and resid 586 through 593 Processing helix chain 'A' and resid 615 through 632 Processing helix chain 'A' and resid 654 through 665 Processing helix chain 'A' and resid 666 through 677 removed outlier: 3.668A pdb=" N GLY A 677 " --> pdb=" O ILE A 673 " (cutoff:3.500A) Processing helix chain 'A' and resid 684 through 695 Processing helix chain 'A' and resid 710 through 718 Processing helix chain 'A' and resid 735 through 748 Processing helix chain 'B' and resid 78 through 92 removed outlier: 3.537A pdb=" N MET B 82 " --> pdb=" O ASN B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 97 through 101 removed outlier: 3.793A pdb=" N HIS B 101 " --> pdb=" O PRO B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 128 removed outlier: 3.700A pdb=" N ARG B 116 " --> pdb=" O PRO B 112 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N MET B 123 " --> pdb=" O MET B 119 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N PHE B 124 " --> pdb=" O THR B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 146 removed outlier: 4.023A pdb=" N TYR B 143 " --> pdb=" O VAL B 139 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 197 removed outlier: 3.637A pdb=" N THR B 194 " --> pdb=" O MET B 190 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N GLU B 195 " --> pdb=" O LYS B 191 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N ARG B 196 " --> pdb=" O ILE B 192 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLY B 197 " --> pdb=" O LEU B 193 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 204 No H-bonds generated for 'chain 'B' and resid 202 through 204' Processing helix chain 'B' and resid 205 through 216 Processing helix chain 'B' and resid 224 through 230 Processing helix chain 'B' and resid 233 through 237 removed outlier: 4.608A pdb=" N LEU B 236 " --> pdb=" O SER B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 255 removed outlier: 3.814A pdb=" N ARG B 254 " --> pdb=" O GLY B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 263 removed outlier: 3.541A pdb=" N LEU B 261 " --> pdb=" O PRO B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 284 removed outlier: 3.551A pdb=" N LYS B 284 " --> pdb=" O ASN B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 290 through 296 removed outlier: 3.754A pdb=" N ALA B 295 " --> pdb=" O LYS B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 305 removed outlier: 3.858A pdb=" N MET B 305 " --> pdb=" O GLY B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 321 Processing helix chain 'B' and resid 334 through 336 No H-bonds generated for 'chain 'B' and resid 334 through 336' Processing helix chain 'B' and resid 337 through 349 removed outlier: 3.829A pdb=" N ALA B 347 " --> pdb=" O GLY B 343 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N SER B 348 " --> pdb=" O SER B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 366 Processing helix chain 'B' and resid 368 through 373 removed outlier: 3.735A pdb=" N ARG B 372 " --> pdb=" O SER B 368 " (cutoff:3.500A) Processing helix chain 'C' and resid 78 through 92 removed outlier: 3.537A pdb=" N MET C 82 " --> pdb=" O ASN C 78 " (cutoff:3.500A) Processing helix chain 'C' and resid 97 through 101 removed outlier: 3.792A pdb=" N HIS C 101 " --> pdb=" O PRO C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 128 removed outlier: 3.701A pdb=" N ARG C 116 " --> pdb=" O PRO C 112 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N MET C 123 " --> pdb=" O MET C 119 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N PHE C 124 " --> pdb=" O THR C 120 " (cutoff:3.500A) Processing helix chain 'C' and resid 139 through 146 removed outlier: 4.023A pdb=" N TYR C 143 " --> pdb=" O VAL C 139 " (cutoff:3.500A) Processing helix chain 'C' and resid 181 through 197 removed outlier: 3.638A pdb=" N THR C 194 " --> pdb=" O MET C 190 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N GLU C 195 " --> pdb=" O LYS C 191 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N ARG C 196 " --> pdb=" O ILE C 192 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLY C 197 " --> pdb=" O LEU C 193 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 204 No H-bonds generated for 'chain 'C' and resid 202 through 204' Processing helix chain 'C' and resid 205 through 216 Processing helix chain 'C' and resid 224 through 230 Processing helix chain 'C' and resid 233 through 237 removed outlier: 4.607A pdb=" N LEU C 236 " --> pdb=" O SER C 233 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 255 removed outlier: 3.814A pdb=" N ARG C 254 " --> pdb=" O GLY C 251 " (cutoff:3.500A) Processing helix chain 'C' and resid 258 through 263 removed outlier: 3.541A pdb=" N LEU C 261 " --> pdb=" O PRO C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 273 through 284 removed outlier: 3.551A pdb=" N LYS C 284 " --> pdb=" O ASN C 280 " (cutoff:3.500A) Processing helix chain 'C' and resid 290 through 296 removed outlier: 3.755A pdb=" N ALA C 295 " --> pdb=" O LYS C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 305 removed outlier: 3.858A pdb=" N MET C 305 " --> pdb=" O GLY C 302 " (cutoff:3.500A) Processing helix chain 'C' and resid 308 through 321 Processing helix chain 'C' and resid 334 through 336 No H-bonds generated for 'chain 'C' and resid 334 through 336' Processing helix chain 'C' and resid 337 through 349 removed outlier: 3.829A pdb=" N ALA C 347 " --> pdb=" O GLY C 343 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N SER C 348 " --> pdb=" O SER C 344 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 366 Processing helix chain 'C' and resid 368 through 373 removed outlier: 3.736A pdb=" N ARG C 372 " --> pdb=" O SER C 368 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'G' and resid 29 through 32 removed outlier: 6.952A pdb=" N LEU G 8 " --> pdb=" O LEU G 104 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'G' and resid 53 through 54 removed outlier: 3.603A pdb=" N ARG G 37 " --> pdb=" O THR G 66 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'G' and resid 71 through 72 Processing sheet with id=AA4, first strand: chain 'G' and resid 169 through 170 Processing sheet with id=AA5, first strand: chain 'G' and resid 169 through 170 removed outlier: 3.533A pdb=" N ASP G 154 " --> pdb=" O HIS G 161 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N VAL G 163 " --> pdb=" O VAL G 152 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N ILE G 151 " --> pdb=" O VAL G 298 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N SER G 300 " --> pdb=" O ILE G 151 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N LEU G 153 " --> pdb=" O SER G 300 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N MET G 299 " --> pdb=" O ILE G 330 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'G' and resid 238 through 241 removed outlier: 3.693A pdb=" N LYS G 238 " --> pdb=" O ILE G 250 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 103 through 106 removed outlier: 7.033A pdb=" N LEU A 103 " --> pdb=" O ARG A 640 " (cutoff:3.500A) removed outlier: 7.969A pdb=" N VAL A 642 " --> pdb=" O LEU A 103 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ALA A 105 " --> pdb=" O VAL A 642 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N GLN A 154 " --> pdb=" O GLY A 435 " (cutoff:3.500A) removed outlier: 8.466A pdb=" N LEU A 437 " --> pdb=" O GLN A 154 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N ILE A 156 " --> pdb=" O LEU A 437 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N VAL A 432 " --> pdb=" O PHE A 227 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N GLU A 224 " --> pdb=" O ALA A 235 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N ALA A 235 " --> pdb=" O GLU A 224 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N GLN A 226 " --> pdb=" O SER A 233 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 381 through 382 removed outlier: 3.665A pdb=" N LYS A 381 " --> pdb=" O ILE A 388 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 539 through 541 Processing sheet with id=AB1, first strand: chain 'A' and resid 680 through 683 Processing sheet with id=AB2, first strand: chain 'B' and resid 29 through 32 removed outlier: 6.953A pdb=" N LEU B 8 " --> pdb=" O LEU B 104 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 53 through 54 removed outlier: 3.603A pdb=" N ARG B 37 " --> pdb=" O THR B 66 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 71 through 72 Processing sheet with id=AB5, first strand: chain 'B' and resid 169 through 170 Processing sheet with id=AB6, first strand: chain 'B' and resid 169 through 170 removed outlier: 3.533A pdb=" N ASP B 154 " --> pdb=" O HIS B 161 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N VAL B 163 " --> pdb=" O VAL B 152 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N ILE B 151 " --> pdb=" O VAL B 298 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N SER B 300 " --> pdb=" O ILE B 151 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N LEU B 153 " --> pdb=" O SER B 300 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N MET B 299 " --> pdb=" O ILE B 330 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 238 through 241 removed outlier: 3.692A pdb=" N LYS B 238 " --> pdb=" O ILE B 250 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 29 through 32 removed outlier: 6.952A pdb=" N LEU C 8 " --> pdb=" O LEU C 104 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 53 through 54 removed outlier: 3.603A pdb=" N ARG C 37 " --> pdb=" O THR C 66 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 71 through 72 Processing sheet with id=AC2, first strand: chain 'C' and resid 169 through 170 Processing sheet with id=AC3, first strand: chain 'C' and resid 169 through 170 removed outlier: 3.532A pdb=" N ASP C 154 " --> pdb=" O HIS C 161 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N VAL C 163 " --> pdb=" O VAL C 152 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N ILE C 151 " --> pdb=" O VAL C 298 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N SER C 300 " --> pdb=" O ILE C 151 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N LEU C 153 " --> pdb=" O SER C 300 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N MET C 299 " --> pdb=" O ILE C 330 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 238 through 241 removed outlier: 3.693A pdb=" N LYS C 238 " --> pdb=" O ILE C 250 " (cutoff:3.500A) 623 hydrogen bonds defined for protein. 1701 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: 1.71 Time building geometry restraints manager: 1.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 3964 1.33 - 1.45: 1731 1.45 - 1.57: 6616 1.57 - 1.68: 9 1.68 - 1.80: 111 Bond restraints: 12431 Sorted by residual: bond pdb=" C GLY C 150 " pdb=" N ILE C 151 " ideal model delta sigma weight residual 1.333 1.292 0.040 1.20e-02 6.94e+03 1.13e+01 bond pdb=" C GLY G 150 " pdb=" N ILE G 151 " ideal model delta sigma weight residual 1.333 1.293 0.040 1.20e-02 6.94e+03 1.12e+01 bond pdb=" C GLY B 150 " pdb=" N ILE B 151 " ideal model delta sigma weight residual 1.333 1.293 0.039 1.20e-02 6.94e+03 1.08e+01 bond pdb=" C VAL B 163 " pdb=" N PRO B 164 " ideal model delta sigma weight residual 1.331 1.293 0.038 1.28e-02 6.10e+03 9.01e+00 bond pdb=" C VAL G 163 " pdb=" N PRO G 164 " ideal model delta sigma weight residual 1.331 1.293 0.038 1.28e-02 6.10e+03 8.80e+00 ... (remaining 12426 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.42: 16259 2.42 - 4.85: 652 4.85 - 7.27: 55 7.27 - 9.70: 9 9.70 - 12.12: 3 Bond angle restraints: 16978 Sorted by residual: angle pdb=" C LEU C 94 " pdb=" N ARG C 95 " pdb=" CA ARG C 95 " ideal model delta sigma weight residual 121.54 129.47 -7.93 1.91e+00 2.74e-01 1.72e+01 angle pdb=" C LEU B 94 " pdb=" N ARG B 95 " pdb=" CA ARG B 95 " ideal model delta sigma weight residual 121.54 129.45 -7.91 1.91e+00 2.74e-01 1.72e+01 angle pdb=" C LEU G 94 " pdb=" N ARG G 95 " pdb=" CA ARG G 95 " ideal model delta sigma weight residual 121.54 129.45 -7.91 1.91e+00 2.74e-01 1.71e+01 angle pdb=" C ASN C 162 " pdb=" N VAL C 163 " pdb=" CA VAL C 163 " ideal model delta sigma weight residual 123.33 119.79 3.54 8.70e-01 1.32e+00 1.65e+01 angle pdb=" C ASN B 162 " pdb=" N VAL B 163 " pdb=" CA VAL B 163 " ideal model delta sigma weight residual 123.33 119.82 3.51 8.70e-01 1.32e+00 1.63e+01 ... (remaining 16973 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.14: 7241 34.14 - 68.29: 168 68.29 - 102.43: 3 102.43 - 136.57: 9 136.57 - 170.72: 6 Dihedral angle restraints: 7427 sinusoidal: 2214 harmonic: 5213 Sorted by residual: dihedral pdb=" C2' ADP C 401 " pdb=" C1' ADP C 401 " pdb=" N9 ADP C 401 " pdb=" C4 ADP C 401 " ideal model delta sinusoidal sigma weight residual 91.55 -97.73 -170.72 1 2.00e+01 2.50e-03 4.77e+01 dihedral pdb=" C2' ADP G 401 " pdb=" C1' ADP G 401 " pdb=" N9 ADP G 401 " pdb=" C4 ADP G 401 " ideal model delta sinusoidal sigma weight residual 91.55 -97.75 -170.70 1 2.00e+01 2.50e-03 4.77e+01 dihedral pdb=" C2' ADP B 401 " pdb=" C1' ADP B 401 " pdb=" N9 ADP B 401 " pdb=" C4 ADP B 401 " ideal model delta sinusoidal sigma weight residual 91.55 -97.79 -170.66 1 2.00e+01 2.50e-03 4.77e+01 ... (remaining 7424 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 1243 0.048 - 0.095: 571 0.095 - 0.143: 161 0.143 - 0.191: 26 0.191 - 0.238: 9 Chirality restraints: 2010 Sorted by residual: chirality pdb=" CB ILE B 34 " pdb=" CA ILE B 34 " pdb=" CG1 ILE B 34 " pdb=" CG2 ILE B 34 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.24 2.00e-01 2.50e+01 1.42e+00 chirality pdb=" CB ILE G 34 " pdb=" CA ILE G 34 " pdb=" CG1 ILE G 34 " pdb=" CG2 ILE G 34 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.24 2.00e-01 2.50e+01 1.41e+00 chirality pdb=" CB ILE C 34 " pdb=" CA ILE C 34 " pdb=" CG1 ILE C 34 " pdb=" CG2 ILE C 34 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.23 2.00e-01 2.50e+01 1.38e+00 ... (remaining 2007 not shown) Planarity restraints: 2252 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CYS B 257 " -0.053 5.00e-02 4.00e+02 7.91e-02 1.00e+01 pdb=" N PRO B 258 " 0.137 5.00e-02 4.00e+02 pdb=" CA PRO B 258 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO B 258 " -0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS G 257 " 0.053 5.00e-02 4.00e+02 7.90e-02 9.99e+00 pdb=" N PRO G 258 " -0.137 5.00e-02 4.00e+02 pdb=" CA PRO G 258 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO G 258 " 0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS C 257 " 0.053 5.00e-02 4.00e+02 7.90e-02 9.98e+00 pdb=" N PRO C 258 " -0.137 5.00e-02 4.00e+02 pdb=" CA PRO C 258 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO C 258 " 0.045 5.00e-02 4.00e+02 ... (remaining 2249 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 1318 2.72 - 3.26: 12209 3.26 - 3.81: 20335 3.81 - 4.35: 21634 4.35 - 4.90: 36872 Nonbonded interactions: 92368 Sorted by model distance: nonbonded pdb=" O ASN B 297 " pdb=" OD1 ASN B 297 " model vdw 2.175 3.040 nonbonded pdb=" O ASN G 297 " pdb=" OD1 ASN G 297 " model vdw 2.176 3.040 nonbonded pdb=" O ASN C 297 " pdb=" OD1 ASN C 297 " model vdw 2.176 3.040 nonbonded pdb=" CB MET G 47 " pdb=" NH2 ARG C 147 " model vdw 2.215 3.520 nonbonded pdb=" O SER C 155 " pdb=" OG1 THR C 303 " model vdw 2.241 3.040 ... (remaining 92363 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 'B' selection = chain 'C' selection = chain 'G' } 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: 11.710 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: 0.170 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 10.310 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.010 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: 0.010 Load rotamer database and sin/cos tables:0.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5244 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 : 0.011 0.063 12431 Z= 0.554 Angle : 1.074 12.124 16978 Z= 0.619 Chirality : 0.057 0.238 2010 Planarity : 0.008 0.079 2252 Dihedral : 16.548 170.718 4055 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 19.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.50 % Favored : 89.50 % Rotamer: Outliers : 4.72 % Allowed : 16.35 % Favored : 78.93 % 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: -4.19 (0.16), residues: 1781 helix: -2.75 (0.12), residues: 761 sheet: -1.81 (0.31), residues: 257 loop : -3.06 (0.20), residues: 763 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 196 TYR 0.008 0.002 TYR B 279 PHE 0.029 0.003 PHE B 255 TRP 0.020 0.004 TRP G 79 HIS 0.016 0.004 HIS C 275 Details of bonding type rmsd covalent geometry : bond 0.01142 (12431) covalent geometry : angle 1.07387 (16978) hydrogen bonds : bond 0.20495 ( 617) hydrogen bonds : angle 8.36831 ( 1701) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3562 Ramachandran restraints generated. 1781 Oldfield, 0 Emsley, 1781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3562 Ramachandran restraints generated. 1781 Oldfield, 0 Emsley, 1781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 351 time to evaluate : 0.361 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: G 41 GLN cc_start: 0.6624 (tt0) cc_final: 0.5893 (pm20) REVERT: G 122 ILE cc_start: 0.7662 (mt) cc_final: 0.7175 (mt) REVERT: G 167 GLU cc_start: 0.8320 (OUTLIER) cc_final: 0.6905 (tp30) REVERT: G 179 ASP cc_start: 0.6417 (m-30) cc_final: 0.6035 (p0) REVERT: B 176 MET cc_start: 0.4989 (mmm) cc_final: 0.4674 (tpp) REVERT: C 10 CYS cc_start: 0.6038 (p) cc_final: 0.5742 (p) REVERT: C 81 ASP cc_start: 0.7331 (m-30) cc_final: 0.6863 (m-30) REVERT: C 121 GLN cc_start: 0.8182 (tm-30) cc_final: 0.7901 (tm-30) REVERT: C 140 LEU cc_start: 0.7725 (mp) cc_final: 0.7410 (mp) outliers start: 45 outliers final: 12 residues processed: 380 average time/residue: 0.0879 time to fit residues: 48.9954 Evaluate side-chains 231 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 218 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 98 optimal weight: 8.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 40.0000 chunk 77 optimal weight: 50.0000 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 10.0000 chunk 149 optimal weight: 0.8980 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 49 GLN G 101 HIS ** G 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 173 HIS G 353 GLN B 78 ASN B 101 HIS B 280 ASN B 353 GLN C 49 GLN C 101 HIS ** C 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 173 HIS C 246 GLN C 353 GLN C 371 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.070938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.056314 restraints weight = 63004.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.057679 restraints weight = 37387.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.058654 restraints weight = 25146.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.059349 restraints weight = 18546.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.059754 restraints weight = 14540.846| |-----------------------------------------------------------------------------| r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6545 moved from start: 0.5358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.090 12431 Z= 0.222 Angle : 0.804 14.599 16978 Z= 0.409 Chirality : 0.050 0.228 2010 Planarity : 0.006 0.083 2252 Dihedral : 12.847 175.157 1931 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 0.31 % Allowed : 4.19 % Favored : 95.49 % 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: -2.11 (0.18), residues: 1781 helix: -0.41 (0.17), residues: 767 sheet: -1.68 (0.31), residues: 262 loop : -2.31 (0.21), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.002 ARG G 210 TYR 0.030 0.003 TYR B 198 PHE 0.022 0.003 PHE G 255 TRP 0.027 0.003 TRP B 79 HIS 0.011 0.002 HIS G 161 Details of bonding type rmsd covalent geometry : bond 0.00486 (12431) covalent geometry : angle 0.80409 (16978) hydrogen bonds : bond 0.04018 ( 617) hydrogen bonds : angle 5.32846 ( 1701) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3562 Ramachandran restraints generated. 1781 Oldfield, 0 Emsley, 1781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3562 Ramachandran restraints generated. 1781 Oldfield, 0 Emsley, 1781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 243 time to evaluate : 0.333 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 179 ASP cc_start: 0.7038 (m-30) cc_final: 0.6704 (p0) REVERT: G 305 MET cc_start: 0.6495 (mmp) cc_final: 0.6211 (mmm) REVERT: G 352 PHE cc_start: 0.7417 (m-80) cc_final: 0.7041 (m-80) REVERT: B 82 MET cc_start: 0.6217 (ppp) cc_final: 0.5815 (ppp) REVERT: B 123 MET cc_start: 0.8538 (pmm) cc_final: 0.7081 (mmt) REVERT: B 267 ILE cc_start: 0.5821 (tp) cc_final: 0.5061 (tp) REVERT: B 341 ILE cc_start: 0.8673 (mt) cc_final: 0.8386 (mm) REVERT: C 107 GLU cc_start: 0.3628 (mt-10) cc_final: 0.3220 (mt-10) REVERT: C 118 LYS cc_start: 0.8809 (mmmt) cc_final: 0.8584 (mtmt) REVERT: C 325 MET cc_start: 0.6378 (mmm) cc_final: 0.6126 (mmm) REVERT: C 359 LYS cc_start: 0.8645 (tptm) cc_final: 0.8435 (tptt) outliers start: 3 outliers final: 1 residues processed: 245 average time/residue: 0.0772 time to fit residues: 28.6851 Evaluate side-chains 184 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 183 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/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: 65.7881 > 50: distance: 107 - 123: 23.983 distance: 118 - 123: 21.069 distance: 123 - 124: 5.387 distance: 124 - 125: 28.136 distance: 124 - 127: 40.998 distance: 125 - 126: 31.859 distance: 125 - 131: 28.748 distance: 127 - 128: 38.279 distance: 127 - 129: 36.725 distance: 128 - 130: 28.661 distance: 131 - 132: 30.741 distance: 132 - 133: 16.021 distance: 133 - 134: 15.934 distance: 133 - 135: 37.408 distance: 135 - 136: 12.305 distance: 136 - 137: 24.397 distance: 136 - 139: 33.599 distance: 137 - 138: 20.519 distance: 137 - 143: 20.038 distance: 138 - 163: 23.307 distance: 139 - 140: 10.981 distance: 140 - 141: 18.424 distance: 140 - 142: 17.411 distance: 143 - 144: 11.303 distance: 144 - 145: 10.956 distance: 144 - 147: 13.160 distance: 145 - 146: 20.331 distance: 145 - 152: 24.196 distance: 147 - 148: 12.444 distance: 148 - 149: 9.975 distance: 149 - 150: 6.666 distance: 149 - 151: 5.624 distance: 152 - 153: 58.643 distance: 153 - 154: 41.303 distance: 153 - 156: 42.976 distance: 154 - 155: 13.261 distance: 154 - 163: 50.984 distance: 156 - 157: 28.174 distance: 157 - 158: 16.331 distance: 158 - 159: 4.567 distance: 163 - 164: 22.841 distance: 164 - 165: 33.413 distance: 164 - 167: 36.773 distance: 165 - 166: 18.102 distance: 165 - 174: 52.646 distance: 167 - 168: 14.282 distance: 168 - 169: 10.161 distance: 168 - 170: 11.759 distance: 169 - 171: 7.073 distance: 170 - 172: 13.796 distance: 171 - 173: 8.539 distance: 172 - 173: 7.847 distance: 174 - 175: 34.661 distance: 175 - 176: 42.940 distance: 175 - 178: 5.161 distance: 176 - 177: 37.369 distance: 176 - 185: 19.425 distance: 178 - 179: 6.793 distance: 179 - 180: 14.064 distance: 180 - 181: 24.807 distance: 181 - 182: 3.566 distance: 182 - 183: 3.920 distance: 182 - 184: 3.190 distance: 185 - 186: 14.902 distance: 186 - 187: 25.549 distance: 186 - 189: 55.400 distance: 187 - 188: 46.160 distance: 187 - 191: 32.029 distance: 189 - 190: 26.605 distance: 191 - 192: 39.752 distance: 191 - 197: 30.434 distance: 192 - 193: 13.866 distance: 192 - 195: 50.650 distance: 193 - 194: 16.527 distance: 193 - 198: 26.015 distance: 195 - 196: 21.405 distance: 196 - 197: 20.304 distance: 198 - 199: 24.438 distance: 199 - 200: 10.932 distance: 199 - 202: 19.082 distance: 200 - 201: 14.061 distance: 200 - 207: 7.169 distance: 201 - 221: 15.509 distance: 202 - 203: 19.363 distance: 203 - 204: 11.986 distance: 204 - 205: 17.479 distance: 204 - 206: 3.913