Starting phenix.real_space_refine on Sat Jun 14 21:51:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7z7h_14532/06_2025/7z7h_14532.cif Found real_map, /net/cci-nas-00/data/ceres_data/7z7h_14532/06_2025/7z7h_14532.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7z7h_14532/06_2025/7z7h_14532.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7z7h_14532/06_2025/7z7h_14532.map" model { file = "/net/cci-nas-00/data/ceres_data/7z7h_14532/06_2025/7z7h_14532.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7z7h_14532/06_2025/7z7h_14532.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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 12 5.49 5 Mg 5 5.21 5 S 109 5.16 5 C 10165 2.51 5 N 2720 2.21 5 O 3100 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 164 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 16111 Number of models: 1 Model: "" Number of chains: 12 Chain: "D" Number of atoms: 2900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2900 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "F" Number of atoms: 1427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1427 Classifications: {'peptide': 181} Link IDs: {'PTRANS': 12, 'TRANS': 168} Chain: "B" Number of atoms: 2900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2900 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 2900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2900 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 2900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2900 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 2900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2900 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 63 Unusual residues: {' MG': 1, 'ADP': 1, 'APR': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'NCA': 1} Classifications: {'undetermined': 1} 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} Chain: "E" 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} Chain: "C" 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} Chain: "A" 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} Time building chain proxies: 9.95, per 1000 atoms: 0.62 Number of scatterers: 16111 At special positions: 0 Unit cell: (124.2, 88.2, 197.1, 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 109 16.00 P 12 15.00 Mg 5 11.99 O 3100 8.00 N 2720 7.00 C 10165 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 4.14 Conformation dependent library (CDL) restraints added in 2.0 seconds 4018 Ramachandran restraints generated. 2009 Oldfield, 0 Emsley, 2009 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3774 Finding SS restraints... Secondary structure from input PDB file: 106 helices and 31 sheets defined 51.2% alpha, 16.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.46 Creating SS restraints... Processing helix chain 'D' and resid 55 through 61 removed outlier: 4.087A pdb=" N GLN D 59 " --> pdb=" O GLY D 55 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N SER D 60 " --> pdb=" O ASP D 56 " (cutoff:3.500A) Processing helix chain 'D' and resid 78 through 93 removed outlier: 3.550A pdb=" N TRP D 86 " --> pdb=" O MET D 82 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N TYR D 91 " --> pdb=" O HIS D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 101 Processing helix chain 'D' and resid 113 through 126 Processing helix chain 'D' and resid 137 through 146 removed outlier: 3.522A pdb=" N LEU D 142 " --> pdb=" O ALA D 138 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N TYR D 143 " --> pdb=" O VAL D 139 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ALA D 144 " --> pdb=" O LEU D 140 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N SER D 145 " --> pdb=" O SER D 141 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 175 Processing helix chain 'D' and resid 181 through 197 removed outlier: 3.503A pdb=" N LYS D 191 " --> pdb=" O ASP D 187 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ARG D 196 " --> pdb=" O ILE D 192 " (cutoff:3.500A) Processing helix chain 'D' and resid 202 through 217 removed outlier: 3.618A pdb=" N ILE D 208 " --> pdb=" O ALA D 204 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL D 209 " --> pdb=" O GLU D 205 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ARG D 210 " --> pdb=" O ARG D 206 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ASP D 211 " --> pdb=" O GLU D 207 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ILE D 212 " --> pdb=" O ILE D 208 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N CYS D 217 " --> pdb=" O LYS D 213 " (cutoff:3.500A) Processing helix chain 'D' and resid 222 through 233 removed outlier: 3.533A pdb=" N SER D 232 " --> pdb=" O ALA D 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 234 through 237 Processing helix chain 'D' and resid 252 through 263 removed outlier: 3.675A pdb=" N CYS D 257 " --> pdb=" O GLU D 253 " (cutoff:3.500A) Proline residue: D 258 - end of helix removed outlier: 4.306A pdb=" N LEU D 261 " --> pdb=" O CYS D 257 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N PHE D 262 " --> pdb=" O PRO D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 264 through 267 Processing helix chain 'D' and resid 273 through 284 Processing helix chain 'D' and resid 288 through 296 removed outlier: 4.592A pdb=" N ASP D 292 " --> pdb=" O ASP D 288 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N TYR D 294 " --> pdb=" O ARG D 290 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ALA D 295 " --> pdb=" O LYS D 291 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ASN D 296 " --> pdb=" O ASP D 292 " (cutoff:3.500A) Processing helix chain 'D' and resid 301 through 306 removed outlier: 3.802A pdb=" N TYR D 306 " --> pdb=" O THR D 303 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 321 Processing helix chain 'D' and resid 334 through 349 removed outlier: 4.368A pdb=" N VAL D 339 " --> pdb=" O ARG D 335 " (cutoff:3.500A) removed outlier: 5.013A pdb=" N TRP D 340 " --> pdb=" O LYS D 336 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N GLY D 343 " --> pdb=" O VAL D 339 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU D 349 " --> pdb=" O ILE D 345 " (cutoff:3.500A) Processing helix chain 'D' and resid 351 through 356 removed outlier: 3.699A pdb=" N MET D 355 " --> pdb=" O THR D 351 " (cutoff:3.500A) Processing helix chain 'D' and resid 359 through 366 Processing helix chain 'D' and resid 367 through 373 removed outlier: 4.074A pdb=" N HIS D 371 " --> pdb=" O PRO D 367 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ARG D 372 " --> pdb=" O SER D 368 " (cutoff:3.500A) Processing helix chain 'F' and resid 118 through 126 Processing helix chain 'F' and resid 137 through 148 removed outlier: 3.954A pdb=" N PHE F 148 " --> pdb=" O PHE F 144 " (cutoff:3.500A) Processing helix chain 'F' and resid 158 through 168 Processing helix chain 'F' and resid 172 through 184 removed outlier: 4.488A pdb=" N ASP F 176 " --> pdb=" O PRO F 172 " (cutoff:3.500A) Processing helix chain 'F' and resid 247 through 251 removed outlier: 3.935A pdb=" N THR F 250 " --> pdb=" O GLN F 247 " (cutoff:3.500A) Processing helix chain 'F' and resid 273 through 275 No H-bonds generated for 'chain 'F' and resid 273 through 275' Processing helix chain 'B' and resid 55 through 61 removed outlier: 3.563A pdb=" N GLN B 59 " --> pdb=" O GLY B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 93 Processing helix chain 'B' and resid 97 through 101 Processing helix chain 'B' and resid 112 through 128 removed outlier: 4.297A pdb=" N ARG B 116 " --> pdb=" O PRO B 112 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N PHE B 127 " --> pdb=" O MET B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 144 removed outlier: 3.727A pdb=" N ALA B 144 " --> pdb=" O LEU B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 175 Processing helix chain 'B' and resid 181 through 197 removed outlier: 3.703A pdb=" N ARG B 196 " --> pdb=" O ILE B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 217 removed outlier: 3.664A pdb=" N ILE B 208 " --> pdb=" O ALA B 204 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N CYS B 217 " --> pdb=" O LYS B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 233 removed outlier: 3.582A pdb=" N SER B 232 " --> pdb=" O ALA B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 234 through 237 Processing helix chain 'B' and resid 252 through 263 Proline residue: B 258 - end of helix removed outlier: 4.461A pdb=" N LEU B 261 " --> pdb=" O CYS B 257 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N PHE B 262 " --> pdb=" O PRO B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 264 through 267 Processing helix chain 'B' and resid 273 through 284 Processing helix chain 'B' and resid 288 through 296 removed outlier: 4.288A pdb=" N ASP B 292 " --> pdb=" O ASP B 288 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ASN B 296 " --> pdb=" O ASP B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 306 removed outlier: 3.757A pdb=" N TYR B 306 " --> pdb=" O THR B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 321 Processing helix chain 'B' and resid 334 through 349 removed outlier: 3.550A pdb=" N SER B 338 " --> pdb=" O GLU B 334 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N VAL B 339 " --> pdb=" O ARG B 335 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N TRP B 340 " --> pdb=" O LYS B 336 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU B 349 " --> pdb=" O ILE B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 351 through 356 Processing helix chain 'B' and resid 359 through 366 Processing helix chain 'B' and resid 367 through 373 removed outlier: 3.680A pdb=" N HIS B 371 " --> pdb=" O PRO B 367 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 61 Processing helix chain 'E' and resid 78 through 93 Processing helix chain 'E' and resid 97 through 101 Processing helix chain 'E' and resid 113 through 128 Processing helix chain 'E' and resid 137 through 144 removed outlier: 3.549A pdb=" N ALA E 144 " --> pdb=" O LEU E 140 " (cutoff:3.500A) Processing helix chain 'E' and resid 172 through 175 removed outlier: 3.517A pdb=" N ILE E 175 " --> pdb=" O PRO E 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 172 through 175' Processing helix chain 'E' and resid 181 through 197 Processing helix chain 'E' and resid 201 through 217 removed outlier: 4.205A pdb=" N GLU E 205 " --> pdb=" O VAL E 201 " (cutoff:3.500A) Processing helix chain 'E' and resid 222 through 233 removed outlier: 3.648A pdb=" N SER E 232 " --> pdb=" O ALA E 228 " (cutoff:3.500A) Processing helix chain 'E' and resid 234 through 237 Processing helix chain 'E' and resid 252 through 260 removed outlier: 3.785A pdb=" N CYS E 257 " --> pdb=" O GLU E 253 " (cutoff:3.500A) Proline residue: E 258 - end of helix Processing helix chain 'E' and resid 261 through 268 Proline residue: E 264 - end of helix Processing helix chain 'E' and resid 273 through 284 Processing helix chain 'E' and resid 288 through 296 removed outlier: 4.478A pdb=" N ASP E 292 " --> pdb=" O ASP E 288 " (cutoff:3.500A) Processing helix chain 'E' and resid 301 through 306 Processing helix chain 'E' and resid 308 through 321 Processing helix chain 'E' and resid 334 through 349 removed outlier: 4.339A pdb=" N VAL E 339 " --> pdb=" O ARG E 335 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N TRP E 340 " --> pdb=" O LYS E 336 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU E 349 " --> pdb=" O ILE E 345 " (cutoff:3.500A) Processing helix chain 'E' and resid 351 through 356 removed outlier: 3.795A pdb=" N MET E 355 " --> pdb=" O THR E 351 " (cutoff:3.500A) Processing helix chain 'E' and resid 359 through 366 Processing helix chain 'E' and resid 367 through 373 removed outlier: 3.600A pdb=" N HIS E 371 " --> pdb=" O PRO E 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 61 Processing helix chain 'C' and resid 78 through 93 Processing helix chain 'C' and resid 97 through 101 Processing helix chain 'C' and resid 113 through 128 Processing helix chain 'C' and resid 137 through 144 removed outlier: 3.516A pdb=" N ALA C 144 " --> pdb=" O LEU C 140 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 175 removed outlier: 3.504A pdb=" N ILE C 175 " --> pdb=" O PRO C 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 172 through 175' Processing helix chain 'C' and resid 181 through 197 Processing helix chain 'C' and resid 202 through 217 removed outlier: 3.700A pdb=" N ILE C 208 " --> pdb=" O ALA C 204 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 233 removed outlier: 3.512A pdb=" N SER C 232 " --> pdb=" O ALA C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 234 through 237 Processing helix chain 'C' and resid 252 through 257 Processing helix chain 'C' and resid 258 through 263 removed outlier: 4.142A pdb=" N PHE C 262 " --> pdb=" O PRO C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 264 through 267 Processing helix chain 'C' and resid 273 through 284 Processing helix chain 'C' and resid 288 through 296 removed outlier: 4.375A pdb=" N ASP C 292 " --> pdb=" O ASP C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 306 removed outlier: 3.626A pdb=" N TYR C 306 " --> pdb=" O THR C 303 " (cutoff:3.500A) Processing helix chain 'C' and resid 308 through 321 Processing helix chain 'C' and resid 337 through 349 removed outlier: 3.536A pdb=" N GLY C 343 " --> pdb=" O VAL C 339 " (cutoff:3.500A) Processing helix chain 'C' and resid 351 through 356 removed outlier: 3.637A pdb=" N MET C 355 " --> pdb=" O THR C 351 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 366 Processing helix chain 'C' and resid 367 through 373 removed outlier: 3.601A pdb=" N HIS C 371 " --> pdb=" O PRO C 367 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LYS C 373 " --> pdb=" O ILE C 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 61 Processing helix chain 'A' and resid 78 through 92 Processing helix chain 'A' and resid 97 through 101 Processing helix chain 'A' and resid 113 through 128 Processing helix chain 'A' and resid 137 through 144 removed outlier: 3.560A pdb=" N ALA A 144 " --> pdb=" O LEU A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 175 removed outlier: 3.745A pdb=" N ILE A 175 " --> pdb=" O PRO A 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 172 through 175' Processing helix chain 'A' and resid 181 through 197 removed outlier: 3.611A pdb=" N ARG A 196 " --> pdb=" O ILE A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 217 removed outlier: 3.620A pdb=" N ILE A 208 " --> pdb=" O ALA A 204 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N CYS A 217 " --> pdb=" O LYS A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 233 removed outlier: 3.706A pdb=" N SER A 232 " --> pdb=" O ALA A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 260 Proline residue: A 258 - end of helix Processing helix chain 'A' and resid 261 through 268 Proline residue: A 264 - end of helix Processing helix chain 'A' and resid 273 through 284 removed outlier: 3.770A pdb=" N LYS A 284 " --> pdb=" O ASN A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 296 removed outlier: 3.590A pdb=" N ASN A 296 " --> pdb=" O ASP A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 306 removed outlier: 3.512A pdb=" N TYR A 306 " --> pdb=" O THR A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 321 Processing helix chain 'A' and resid 337 through 349 removed outlier: 3.628A pdb=" N LEU A 349 " --> pdb=" O ILE A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 356 removed outlier: 3.823A pdb=" N MET A 355 " --> pdb=" O THR A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 366 Processing helix chain 'A' and resid 367 through 373 removed outlier: 3.623A pdb=" N LYS A 373 " --> pdb=" O ILE A 369 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 29 through 32 removed outlier: 3.520A pdb=" N ALA D 29 " --> pdb=" O ALA D 19 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N THR D 106 " --> pdb=" O CYS D 10 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N MET D 132 " --> pdb=" O ILE D 357 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ILE D 357 " --> pdb=" O MET D 132 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 53 through 54 removed outlier: 3.578A pdb=" N VAL D 35 " --> pdb=" O LYS D 68 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 71 through 72 Processing sheet with id=AA4, first strand: chain 'D' and resid 169 through 170 Processing sheet with id=AA5, first strand: chain 'D' and resid 169 through 170 removed outlier: 3.530A pdb=" N VAL D 163 " --> pdb=" O VAL D 152 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ILE D 165 " --> pdb=" O GLY D 150 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 238 through 241 Processing sheet with id=AA7, first strand: chain 'F' and resid 226 through 228 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 226 through 228 current: chain 'F' and resid 192 through 195 removed outlier: 3.611A pdb=" N SER F 265 " --> pdb=" O HIS F 258 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N LEU F 209 " --> pdb=" O HIS F 280 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 29 through 32 removed outlier: 3.888A pdb=" N ALA B 29 " --> pdb=" O ALA B 19 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ALA B 19 " --> pdb=" O ALA B 29 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N PHE B 31 " --> pdb=" O VAL B 17 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N VAL B 17 " --> pdb=" O PHE B 31 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N THR B 106 " --> pdb=" O CYS B 10 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 53 through 54 removed outlier: 3.537A pdb=" N THR B 66 " --> pdb=" O ARG B 37 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 71 through 72 Processing sheet with id=AB2, first strand: chain 'B' and resid 169 through 170 removed outlier: 3.560A pdb=" N MET B 176 " --> pdb=" O ASN B 162 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 169 through 170 Processing sheet with id=AB4, first strand: chain 'B' and resid 238 through 241 Processing sheet with id=AB5, first strand: chain 'E' and resid 29 through 32 removed outlier: 3.601A pdb=" N ALA E 29 " --> pdb=" O ALA E 19 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA E 19 " --> pdb=" O ALA E 29 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N PHE E 31 " --> pdb=" O VAL E 17 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N THR E 106 " --> pdb=" O CYS E 10 " (cutoff:3.500A) removed outlier: 5.769A pdb=" N THR E 103 " --> pdb=" O TYR E 133 " (cutoff:3.500A) removed outlier: 7.431A pdb=" N ALA E 135 " --> pdb=" O THR E 103 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N LEU E 105 " --> pdb=" O ALA E 135 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 53 through 54 Processing sheet with id=AB7, first strand: chain 'E' and resid 71 through 72 Processing sheet with id=AB8, first strand: chain 'E' and resid 169 through 170 Processing sheet with id=AB9, first strand: chain 'E' and resid 169 through 170 removed outlier: 7.504A pdb=" N VAL E 298 " --> pdb=" O THR E 149 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N ILE E 151 " --> pdb=" O VAL E 298 " (cutoff:3.500A) removed outlier: 7.935A pdb=" N SER E 300 " --> pdb=" O ILE E 151 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N LEU E 153 " --> pdb=" O SER E 300 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 238 through 241 Processing sheet with id=AC2, first strand: chain 'C' and resid 29 through 32 removed outlier: 3.882A pdb=" N ALA C 29 " --> pdb=" O ALA C 19 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N LEU C 8 " --> pdb=" O LEU C 104 " (cutoff:3.500A) removed outlier: 8.608A pdb=" N THR C 106 " --> pdb=" O LEU C 8 " (cutoff:3.500A) removed outlier: 8.590A pdb=" N CYS C 10 " --> pdb=" O THR C 106 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N THR C 103 " --> pdb=" O TYR C 133 " (cutoff:3.500A) removed outlier: 7.830A pdb=" N ALA C 135 " --> pdb=" O THR C 103 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N LEU C 105 " --> pdb=" O ALA C 135 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 53 through 54 removed outlier: 3.723A pdb=" N ARG C 37 " --> pdb=" O THR C 66 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N THR C 66 " --> pdb=" O ARG C 37 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 71 through 72 Processing sheet with id=AC5, first strand: chain 'C' and resid 169 through 170 Processing sheet with id=AC6, first strand: chain 'C' and resid 169 through 170 removed outlier: 6.342A pdb=" N ILE C 151 " --> pdb=" O VAL C 298 " (cutoff:3.500A) removed outlier: 7.967A pdb=" N SER C 300 " --> pdb=" O ILE C 151 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N LEU C 153 " --> pdb=" O SER C 300 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 238 through 241 Processing sheet with id=AC8, first strand: chain 'A' and resid 29 through 32 removed outlier: 4.045A pdb=" N ALA A 29 " --> pdb=" O ALA A 19 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA A 19 " --> pdb=" O ALA A 29 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N PHE A 31 " --> pdb=" O VAL A 17 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N THR A 106 " --> pdb=" O CYS A 10 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N THR A 103 " --> pdb=" O TYR A 133 " (cutoff:3.500A) removed outlier: 7.400A pdb=" N ALA A 135 " --> pdb=" O THR A 103 " (cutoff:3.500A) removed outlier: 5.779A pdb=" N LEU A 105 " --> pdb=" O ALA A 135 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'A' and resid 53 through 54 removed outlier: 3.593A pdb=" N ARG A 37 " --> pdb=" O THR A 66 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N THR A 66 " --> pdb=" O ARG A 37 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'A' and resid 71 through 72 Processing sheet with id=AD2, first strand: chain 'A' and resid 169 through 170 Processing sheet with id=AD3, first strand: chain 'A' and resid 169 through 170 removed outlier: 7.790A pdb=" N VAL A 298 " --> pdb=" O THR A 149 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N ILE A 151 " --> pdb=" O VAL A 298 " (cutoff:3.500A) removed outlier: 8.156A pdb=" N SER A 300 " --> pdb=" O ILE A 151 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N LEU A 153 " --> pdb=" O SER A 300 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N ASN A 297 " --> pdb=" O ILE A 330 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'A' and resid 238 through 241 731 hydrogen bonds defined for protein. 1938 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: 6.14 Time building geometry restraints manager: 4.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5200 1.34 - 1.46: 3174 1.46 - 1.58: 7876 1.58 - 1.69: 20 1.69 - 1.81: 196 Bond restraints: 16466 Sorted by residual: bond pdb=" C1' APR D 403 " pdb=" O4' APR D 403 " ideal model delta sigma weight residual 1.393 1.639 -0.246 2.00e-02 2.50e+03 1.52e+02 bond pdb=" C4' APR D 403 " pdb=" O4' APR D 403 " ideal model delta sigma weight residual 1.430 1.632 -0.202 2.00e-02 2.50e+03 1.02e+02 bond pdb=" C2 APR D 403 " pdb=" N1 APR D 403 " ideal model delta sigma weight residual 1.331 1.531 -0.200 2.00e-02 2.50e+03 1.00e+02 bond pdb=" C6 APR D 403 " pdb=" N1 APR D 403 " ideal model delta sigma weight residual 1.338 1.527 -0.189 2.00e-02 2.50e+03 8.93e+01 bond pdb=" C7 NCA F 300 " pdb=" N7 NCA F 300 " ideal model delta sigma weight residual 1.340 1.525 -0.185 2.00e-02 2.50e+03 8.57e+01 ... (remaining 16461 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.40: 21788 3.40 - 6.81: 508 6.81 - 10.21: 44 10.21 - 13.61: 6 13.61 - 17.02: 2 Bond angle restraints: 22348 Sorted by residual: angle pdb=" C1' APR D 403 " pdb=" O4' APR D 403 " pdb=" C4' APR D 403 " ideal model delta sigma weight residual 111.27 94.25 17.02 3.00e+00 1.11e-01 3.22e+01 angle pdb=" O1A APR D 403 " pdb=" PA APR D 403 " pdb=" O2A APR D 403 " ideal model delta sigma weight residual 121.71 107.08 14.63 3.00e+00 1.11e-01 2.38e+01 angle pdb=" C MET A 283 " pdb=" N LYS A 284 " pdb=" CA LYS A 284 " ideal model delta sigma weight residual 121.94 112.61 9.33 2.00e+00 2.50e-01 2.18e+01 angle pdb=" O1B APR D 403 " pdb=" PB APR D 403 " pdb=" O2B APR D 403 " ideal model delta sigma weight residual 122.24 108.72 13.52 3.00e+00 1.11e-01 2.03e+01 angle pdb=" N MET A 283 " pdb=" CA MET A 283 " pdb=" C MET A 283 " ideal model delta sigma weight residual 111.71 116.48 -4.77 1.15e+00 7.56e-01 1.72e+01 ... (remaining 22343 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.61: 9354 22.61 - 45.21: 491 45.21 - 67.82: 75 67.82 - 90.43: 15 90.43 - 113.03: 5 Dihedral angle restraints: 9940 sinusoidal: 4052 harmonic: 5888 Sorted by residual: dihedral pdb=" CA PHE F 126 " pdb=" C PHE F 126 " pdb=" N PRO F 127 " pdb=" CA PRO F 127 " ideal model delta harmonic sigma weight residual 180.00 150.64 29.36 0 5.00e+00 4.00e-02 3.45e+01 dihedral pdb=" C5' ADP D 401 " pdb=" O5' ADP D 401 " pdb=" PA ADP D 401 " pdb=" O2A ADP D 401 " ideal model delta sinusoidal sigma weight residual -60.00 53.04 -113.03 1 2.00e+01 2.50e-03 3.34e+01 dihedral pdb=" C5' ADP B 401 " pdb=" O5' ADP B 401 " pdb=" PA ADP B 401 " pdb=" O2A ADP B 401 " ideal model delta sinusoidal sigma weight residual -60.00 50.80 -110.79 1 2.00e+01 2.50e-03 3.25e+01 ... (remaining 9937 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 2035 0.082 - 0.164: 412 0.164 - 0.245: 33 0.245 - 0.327: 1 0.327 - 0.409: 3 Chirality restraints: 2484 Sorted by residual: chirality pdb=" C4' APR D 403 " pdb=" C3' APR D 403 " pdb=" C5' APR D 403 " pdb=" O4' APR D 403 " both_signs ideal model delta sigma weight residual False -2.54 -2.95 0.41 2.00e-01 2.50e+01 4.18e+00 chirality pdb=" C1' APR D 403 " pdb=" C2' APR D 403 " pdb=" N9 APR D 403 " pdb=" O4' APR D 403 " both_signs ideal model delta sigma weight residual False 2.40 2.78 -0.39 2.00e-01 2.50e+01 3.73e+00 chirality pdb=" C4D APR D 403 " pdb=" C3D APR D 403 " pdb=" C5D APR D 403 " pdb=" O4D APR D 403 " both_signs ideal model delta sigma weight residual False -2.49 -2.16 -0.33 2.00e-01 2.50e+01 2.70e+00 ... (remaining 2481 not shown) Planarity restraints: 2849 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG F 117 " 0.160 9.50e-02 1.11e+02 8.76e-02 3.46e+01 pdb=" NE ARG F 117 " -0.042 2.00e-02 2.50e+03 pdb=" CZ ARG F 117 " 0.095 2.00e-02 2.50e+03 pdb=" NH1 ARG F 117 " -0.034 2.00e-02 2.50e+03 pdb=" NH2 ARG F 117 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR B 89 " 0.018 2.00e-02 2.50e+03 3.51e-02 1.23e+01 pdb=" C THR B 89 " -0.061 2.00e-02 2.50e+03 pdb=" O THR B 89 " 0.023 2.00e-02 2.50e+03 pdb=" N PHE B 90 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 89 " 0.017 2.00e-02 2.50e+03 3.42e-02 1.17e+01 pdb=" C THR A 89 " -0.059 2.00e-02 2.50e+03 pdb=" O THR A 89 " 0.022 2.00e-02 2.50e+03 pdb=" N PHE A 90 " 0.020 2.00e-02 2.50e+03 ... (remaining 2846 not shown) Histogram of nonbonded interaction distances: 1.78 - 2.40: 88 2.40 - 3.03: 10541 3.03 - 3.65: 23992 3.65 - 4.28: 33818 4.28 - 4.90: 56215 Nonbonded interactions: 124654 Sorted by model distance: nonbonded pdb=" O1B ADP D 401 " pdb="MG MG D 402 " model vdw 1.777 2.170 nonbonded pdb=" O1B ADP B 401 " pdb="MG MG B 402 " model vdw 1.829 2.170 nonbonded pdb=" O1A ADP D 401 " pdb="MG MG D 402 " model vdw 1.853 2.170 nonbonded pdb=" O3A ADP B 401 " pdb="MG MG B 402 " model vdw 1.873 2.170 nonbonded pdb=" O1B ADP A 401 " pdb="MG MG A 402 " model vdw 1.964 2.170 ... (remaining 124649 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 'C' selection = (chain 'D' and (resid 5 through 375 or resid 401 through 402)) selection = chain 'E' } 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: 2.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.750 Check model and map are aligned: 0.130 Set scattering table: 0.170 Process input model: 39.170 Find NCS groups from input model: 0.690 Set up NCS constraints: 0.090 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:3.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 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 : 0.013 0.868 16468 Z= 0.843 Angle : 1.248 17.017 22348 Z= 0.687 Chirality : 0.064 0.409 2484 Planarity : 0.007 0.088 2849 Dihedral : 14.273 113.033 6166 Min Nonbonded Distance : 1.777 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.17), residues: 2009 helix: -0.49 (0.17), residues: 617 sheet: 0.72 (0.24), residues: 440 loop : -0.14 (0.20), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.004 TRP E 356 HIS 0.019 0.003 HIS D 371 PHE 0.032 0.004 PHE D 31 TYR 0.033 0.006 TYR A 294 ARG 0.097 0.011 ARG F 117 Details of bonding type rmsd hydrogen bonds : bond 0.22843 ( 721) hydrogen bonds : angle 8.47394 ( 1938) covalent geometry : bond 0.01063 (16466) covalent geometry : angle 1.24834 (22348) Misc. bond : bond 0.61451 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4018 Ramachandran restraints generated. 2009 Oldfield, 0 Emsley, 2009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4018 Ramachandran restraints generated. 2009 Oldfield, 0 Emsley, 2009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 261 time to evaluate : 1.972 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: D 123 MET cc_start: 0.8850 (mmp) cc_final: 0.8555 (tpp) REVERT: F 183 TYR cc_start: 0.8305 (m-80) cc_final: 0.7876 (m-80) REVERT: F 212 ILE cc_start: 0.8540 (mt) cc_final: 0.8326 (pt) REVERT: F 282 ARG cc_start: 0.7291 (ptt-90) cc_final: 0.7077 (mpp-170) REVERT: B 34 ILE cc_start: 0.9248 (mt) cc_final: 0.8901 (tp) REVERT: B 153 LEU cc_start: 0.8834 (tp) cc_final: 0.8492 (tt) REVERT: E 65 LEU cc_start: 0.7066 (mt) cc_final: 0.6708 (mt) REVERT: E 78 ASN cc_start: 0.7159 (t0) cc_final: 0.6898 (t0) REVERT: E 356 TRP cc_start: 0.7091 (m100) cc_final: 0.6534 (m100) REVERT: C 9 VAL cc_start: 0.9438 (t) cc_final: 0.9232 (m) REVERT: C 155 SER cc_start: 0.8644 (t) cc_final: 0.8379 (m) REVERT: A 123 MET cc_start: 0.8228 (mmp) cc_final: 0.7963 (mmt) outliers start: 0 outliers final: 0 residues processed: 261 average time/residue: 0.2832 time to fit residues: 109.3953 Evaluate side-chains 152 residues out of total 1726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 152 time to evaluate : 1.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 171 optimal weight: 8.9990 chunk 153 optimal weight: 0.4980 chunk 85 optimal weight: 0.6980 chunk 52 optimal weight: 0.9980 chunk 103 optimal weight: 9.9990 chunk 82 optimal weight: 1.9990 chunk 159 optimal weight: 0.9990 chunk 61 optimal weight: 3.9990 chunk 96 optimal weight: 8.9990 chunk 118 optimal weight: 0.9990 chunk 184 optimal weight: 6.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 111 ASN D 252 ASN B 111 ASN B 115 ASN B 162 ASN B 252 ASN E 59 GLN E 111 ASN E 162 ASN C 59 GLN ** C 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 162 ASN A 12 ASN A 59 GLN ** A 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 252 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.073678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.064015 restraints weight = 84117.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.065710 restraints weight = 47400.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.066884 restraints weight = 30941.867| |-----------------------------------------------------------------------------| r_work (final): 0.3557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 moved from start: 0.2766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 16468 Z= 0.149 Angle : 0.755 9.075 22348 Z= 0.387 Chirality : 0.047 0.267 2484 Planarity : 0.005 0.039 2849 Dihedral : 8.444 88.064 2321 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.56 % Allowed : 8.11 % Favored : 90.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.19), residues: 2009 helix: 0.40 (0.18), residues: 743 sheet: 1.01 (0.25), residues: 387 loop : 0.81 (0.22), residues: 879 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D 79 HIS 0.006 0.001 HIS D 371 PHE 0.024 0.002 PHE E 90 TYR 0.019 0.002 TYR E 306 ARG 0.008 0.001 ARG F 117 Details of bonding type rmsd hydrogen bonds : bond 0.04725 ( 721) hydrogen bonds : angle 5.93016 ( 1938) covalent geometry : bond 0.00317 (16466) covalent geometry : angle 0.75493 (22348) Misc. bond : bond 0.00528 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4018 Ramachandran restraints generated. 2009 Oldfield, 0 Emsley, 2009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4018 Ramachandran restraints generated. 2009 Oldfield, 0 Emsley, 2009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 190 time to evaluate : 1.902 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: F 107 LYS cc_start: 0.8370 (OUTLIER) cc_final: 0.8018 (ptpp) REVERT: F 183 TYR cc_start: 0.8141 (m-80) cc_final: 0.7811 (m-80) REVERT: F 215 ASP cc_start: 0.8690 (p0) cc_final: 0.8316 (t70) REVERT: B 34 ILE cc_start: 0.9310 (mt) cc_final: 0.9098 (tp) REVERT: B 325 MET cc_start: 0.8111 (tpp) cc_final: 0.7439 (mmp) REVERT: B 355 MET cc_start: 0.7263 (mmp) cc_final: 0.6852 (mmm) REVERT: E 44 MET cc_start: -0.0864 (mmt) cc_final: -0.1148 (mpp) REVERT: E 47 MET cc_start: 0.3931 (tmm) cc_final: 0.3105 (tpt) REVERT: E 65 LEU cc_start: 0.6821 (mt) cc_final: 0.6446 (mt) REVERT: E 78 ASN cc_start: 0.6088 (t0) cc_final: 0.5641 (t0) REVERT: C 65 LEU cc_start: 0.7742 (OUTLIER) cc_final: 0.7263 (mt) REVERT: C 269 MET cc_start: 0.8200 (tpp) cc_final: 0.7729 (mtt) REVERT: C 283 MET cc_start: 0.7665 (mmp) cc_final: 0.7326 (mmm) REVERT: A 313 MET cc_start: 0.7604 (mmm) cc_final: 0.7026 (mmm) outliers start: 27 outliers final: 9 residues processed: 204 average time/residue: 0.2610 time to fit residues: 81.2881 Evaluate side-chains 144 residues out of total 1726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 133 time to evaluate : 1.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain F residue 107 LYS Chi-restraints excluded: chain F residue 149 ILE Chi-restraints excluded: chain F residue 174 LEU Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain A residue 47 MET Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 370 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 197 optimal weight: 0.6980 chunk 157 optimal weight: 7.9990 chunk 161 optimal weight: 10.0000 chunk 45 optimal weight: 4.9990 chunk 174 optimal weight: 0.8980 chunk 103 optimal weight: 5.9990 chunk 3 optimal weight: 9.9990 chunk 98 optimal weight: 1.9990 chunk 122 optimal weight: 3.9990 chunk 40 optimal weight: 8.9990 chunk 90 optimal weight: 10.0000 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 115 ASN F 103 ASN C 111 ASN A 40 HIS ** A 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 162 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.070707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.061000 restraints weight = 86692.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.062619 restraints weight = 49969.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.063740 restraints weight = 33261.953| |-----------------------------------------------------------------------------| r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.3417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 16468 Z= 0.164 Angle : 0.694 7.340 22348 Z= 0.350 Chirality : 0.045 0.245 2484 Planarity : 0.004 0.053 2849 Dihedral : 7.512 82.203 2321 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.56 % Allowed : 9.91 % Favored : 88.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.19), residues: 2009 helix: 0.45 (0.19), residues: 748 sheet: 1.08 (0.24), residues: 410 loop : 1.02 (0.23), residues: 851 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP E 356 HIS 0.008 0.001 HIS D 371 PHE 0.020 0.002 PHE B 223 TYR 0.014 0.001 TYR F 112 ARG 0.005 0.001 ARG C 196 Details of bonding type rmsd hydrogen bonds : bond 0.04490 ( 721) hydrogen bonds : angle 5.57039 ( 1938) covalent geometry : bond 0.00365 (16466) covalent geometry : angle 0.69362 (22348) Misc. bond : bond 0.00217 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4018 Ramachandran restraints generated. 2009 Oldfield, 0 Emsley, 2009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4018 Ramachandran restraints generated. 2009 Oldfield, 0 Emsley, 2009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 147 time to evaluate : 1.853 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 183 TYR cc_start: 0.8220 (m-80) cc_final: 0.7924 (m-80) REVERT: F 215 ASP cc_start: 0.8757 (p0) cc_final: 0.8335 (t70) REVERT: B 34 ILE cc_start: 0.9383 (mt) cc_final: 0.9162 (tp) REVERT: B 325 MET cc_start: 0.8164 (tpp) cc_final: 0.7484 (mmp) REVERT: B 355 MET cc_start: 0.7289 (mmp) cc_final: 0.6740 (mmm) REVERT: E 44 MET cc_start: -0.0347 (mmt) cc_final: -0.0686 (mpp) REVERT: E 78 ASN cc_start: 0.6323 (t0) cc_final: 0.5993 (t0) REVERT: E 294 TYR cc_start: 0.7220 (m-10) cc_final: 0.6915 (m-10) REVERT: E 325 MET cc_start: 0.6403 (tpp) cc_final: 0.5508 (ptm) REVERT: C 269 MET cc_start: 0.8437 (tpp) cc_final: 0.8013 (mtt) REVERT: C 283 MET cc_start: 0.7804 (mmp) cc_final: 0.7603 (mmp) REVERT: A 192 ILE cc_start: 0.8351 (pt) cc_final: 0.8145 (pt) outliers start: 27 outliers final: 14 residues processed: 165 average time/residue: 0.2526 time to fit residues: 65.3375 Evaluate side-chains 145 residues out of total 1726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 131 time to evaluate : 1.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 14 SER Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain F residue 137 ASP Chi-restraints excluded: chain F residue 149 ILE Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain E residue 370 VAL Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain A residue 33 SER Chi-restraints excluded: chain A residue 47 MET Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 370 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 98 optimal weight: 0.0270 chunk 136 optimal weight: 9.9990 chunk 31 optimal weight: 10.0000 chunk 97 optimal weight: 0.7980 chunk 154 optimal weight: 5.9990 chunk 149 optimal weight: 1.9990 chunk 59 optimal weight: 0.6980 chunk 68 optimal weight: 7.9990 chunk 100 optimal weight: 9.9990 chunk 33 optimal weight: 5.9990 chunk 188 optimal weight: 5.9990 overall best weight: 1.9042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 59 GLN C 12 ASN ** A 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.070629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.060935 restraints weight = 86032.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.062541 restraints weight = 49283.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.063675 restraints weight = 32621.629| |-----------------------------------------------------------------------------| r_work (final): 0.3477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.3915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 16468 Z= 0.131 Angle : 0.640 7.009 22348 Z= 0.320 Chirality : 0.044 0.193 2484 Planarity : 0.004 0.049 2849 Dihedral : 7.004 80.396 2321 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 1.51 % Allowed : 10.25 % Favored : 88.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.19), residues: 2009 helix: 0.55 (0.19), residues: 743 sheet: 1.11 (0.24), residues: 410 loop : 0.91 (0.23), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 79 HIS 0.008 0.001 HIS E 275 PHE 0.022 0.002 PHE A 352 TYR 0.011 0.001 TYR E 306 ARG 0.006 0.000 ARG C 196 Details of bonding type rmsd hydrogen bonds : bond 0.03892 ( 721) hydrogen bonds : angle 5.30342 ( 1938) covalent geometry : bond 0.00290 (16466) covalent geometry : angle 0.64012 (22348) Misc. bond : bond 0.00121 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4018 Ramachandran restraints generated. 2009 Oldfield, 0 Emsley, 2009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4018 Ramachandran restraints generated. 2009 Oldfield, 0 Emsley, 2009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 148 time to evaluate : 1.816 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 123 MET cc_start: 0.8782 (tpp) cc_final: 0.8514 (tpp) REVERT: F 105 GLN cc_start: 0.8833 (pm20) cc_final: 0.8598 (pm20) REVERT: F 183 TYR cc_start: 0.8225 (m-80) cc_final: 0.7448 (m-80) REVERT: F 215 ASP cc_start: 0.8651 (p0) cc_final: 0.8014 (t70) REVERT: B 34 ILE cc_start: 0.9381 (mt) cc_final: 0.9132 (tp) REVERT: B 227 MET cc_start: 0.8372 (tpp) cc_final: 0.8087 (mpp) REVERT: B 325 MET cc_start: 0.8011 (tpp) cc_final: 0.7495 (mmp) REVERT: B 355 MET cc_start: 0.7273 (mmp) cc_final: 0.6807 (mmm) REVERT: E 44 MET cc_start: -0.0544 (mmt) cc_final: -0.0812 (mpp) REVERT: E 78 ASN cc_start: 0.6287 (t0) cc_final: 0.5895 (t0) REVERT: E 294 TYR cc_start: 0.7295 (m-10) cc_final: 0.6966 (m-10) REVERT: E 325 MET cc_start: 0.6440 (OUTLIER) cc_final: 0.5569 (ptm) REVERT: C 269 MET cc_start: 0.8474 (tpp) cc_final: 0.8095 (mtt) REVERT: C 313 MET cc_start: 0.8897 (tpp) cc_final: 0.8597 (ttt) REVERT: A 123 MET cc_start: 0.8603 (mmt) cc_final: 0.8296 (tpp) REVERT: A 313 MET cc_start: 0.7558 (mmm) cc_final: 0.7154 (mmm) outliers start: 26 outliers final: 14 residues processed: 164 average time/residue: 0.2441 time to fit residues: 62.6235 Evaluate side-chains 145 residues out of total 1726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 130 time to evaluate : 1.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 14 SER Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain F residue 137 ASP Chi-restraints excluded: chain F residue 149 ILE Chi-restraints excluded: chain F residue 174 LEU Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 325 MET Chi-restraints excluded: chain E residue 370 VAL Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 317 ILE Chi-restraints excluded: chain A residue 370 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 61.7999 > 50: distance: 32 - 55: 3.139 distance: 36 - 64: 30.761 distance: 41 - 73: 25.166 distance: 50 - 55: 6.025 distance: 51 - 82: 17.972 distance: 55 - 56: 14.913 distance: 56 - 57: 26.605 distance: 56 - 59: 30.597 distance: 57 - 58: 36.094 distance: 57 - 64: 33.232 distance: 58 - 90: 40.173 distance: 59 - 60: 39.182 distance: 60 - 61: 44.788 distance: 61 - 62: 48.080 distance: 61 - 63: 30.491 distance: 64 - 65: 16.402 distance: 65 - 66: 31.559 distance: 65 - 68: 16.396 distance: 66 - 67: 53.698 distance: 66 - 73: 45.674 distance: 67 - 97: 28.731 distance: 68 - 69: 59.527 distance: 69 - 70: 42.422 distance: 70 - 71: 41.942 distance: 71 - 72: 40.673 distance: 73 - 74: 25.306 distance: 74 - 75: 20.764 distance: 74 - 77: 16.422 distance: 75 - 76: 40.459 distance: 75 - 82: 17.685 distance: 76 - 102: 15.690 distance: 77 - 78: 28.829 distance: 78 - 79: 33.981 distance: 79 - 80: 24.215 distance: 79 - 81: 20.199 distance: 82 - 83: 25.968 distance: 83 - 84: 21.334 distance: 83 - 86: 10.624 distance: 84 - 85: 6.091 distance: 84 - 90: 28.155 distance: 85 - 110: 14.564 distance: 86 - 87: 38.785 distance: 86 - 88: 30.142 distance: 87 - 89: 44.388 distance: 90 - 91: 22.589 distance: 91 - 92: 21.473 distance: 91 - 94: 16.976 distance: 92 - 93: 28.835 distance: 92 - 97: 20.450 distance: 94 - 95: 28.718 distance: 94 - 96: 16.546 distance: 97 - 98: 27.067 distance: 98 - 99: 43.431 distance: 98 - 101: 10.922 distance: 99 - 100: 21.341 distance: 99 - 102: 19.007 distance: 102 - 103: 25.712 distance: 103 - 104: 30.657 distance: 103 - 106: 46.240 distance: 104 - 105: 21.988 distance: 104 - 110: 23.686 distance: 106 - 107: 18.436 distance: 107 - 108: 41.955 distance: 107 - 109: 10.782 distance: 110 - 111: 41.229 distance: 111 - 112: 20.475 distance: 112 - 113: 31.111 distance: 112 - 115: 26.105 distance: 115 - 116: 26.239 distance: 115 - 121: 46.857 distance: 116 - 117: 33.102 distance: 116 - 119: 25.209 distance: 117 - 118: 13.964 distance: 117 - 122: 29.777 distance: 119 - 120: 19.408 distance: 120 - 121: 20.688 distance: 122 - 123: 10.757 distance: 123 - 124: 7.233 distance: 123 - 126: 26.283 distance: 124 - 125: 42.335 distance: 124 - 128: 30.921 distance: 126 - 127: 18.151