Starting phenix.real_space_refine on Sun Aug 24 14:15:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8thc_41253/08_2025/8thc_41253.cif Found real_map, /net/cci-nas-00/data/ceres_data/8thc_41253/08_2025/8thc_41253.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.67 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8thc_41253/08_2025/8thc_41253.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8thc_41253/08_2025/8thc_41253.map" model { file = "/net/cci-nas-00/data/ceres_data/8thc_41253/08_2025/8thc_41253.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8thc_41253/08_2025/8thc_41253.cif" } resolution = 3.67 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= 0.030 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 14 5.49 5 Mg 3 5.21 5 S 98 5.16 5 C 12925 2.51 5 N 3442 2.21 5 O 3948 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.02s 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: 20430 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 3897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 479, 3897 Classifications: {'peptide': 479} Link IDs: {'PTRANS': 21, 'TRANS': 457} Chain breaks: 4 Chain: "B" Number of atoms: 2495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2495 Classifications: {'peptide': 318} Link IDs: {'PTRANS': 9, 'TRANS': 308} Chain: "C" Number of atoms: 2571 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2571 Classifications: {'peptide': 325} Link IDs: {'PTRANS': 12, 'TRANS': 312} Chain: "D" Number of atoms: 2629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 2629 Classifications: {'peptide': 332} Link IDs: {'PTRANS': 12, 'TRANS': 319} Chain: "E" Number of atoms: 2675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2675 Classifications: {'peptide': 339} Link IDs: {'PTRANS': 14, 'TRANS': 324} Chain breaks: 1 Chain: "F" Number of atoms: 1995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 254, 1995 Classifications: {'peptide': 254} Link IDs: {'PTRANS': 8, 'TRANS': 245} Chain: "G" Number of atoms: 2011 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 2011 Classifications: {'peptide': 256} Link IDs: {'PTRANS': 8, 'TRANS': 247} Chain: "H" Number of atoms: 2003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 2003 Classifications: {'peptide': 255} Link IDs: {'PTRANS': 8, 'TRANS': 246} Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.88, per 1000 atoms: 0.19 Number of scatterers: 20430 At special positions: 0 Unit cell: (117.576, 122.544, 150.696, 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 98 16.00 P 14 15.00 Mg 3 11.99 O 3948 8.00 N 3442 7.00 C 12925 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.19 Conformation dependent library (CDL) restraints added in 826.0 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 5064 Ramachandran restraints generated. 2532 Oldfield, 0 Emsley, 2532 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4906 Finding SS restraints... Secondary structure from input PDB file: 109 helices and 17 sheets defined 50.4% alpha, 13.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.72 Creating SS restraints... Processing helix chain 'A' and resid 203 through 208 Processing helix chain 'A' and resid 209 through 211 No H-bonds generated for 'chain 'A' and resid 209 through 211' Processing helix chain 'A' and resid 240 through 245 Processing helix chain 'A' and resid 256 through 276 removed outlier: 3.906A pdb=" N LYS A 276 " --> pdb=" O HIS A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 356 removed outlier: 3.561A pdb=" N GLN A 348 " --> pdb=" O LYS A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 387 removed outlier: 6.090A pdb=" N ASP A 379 " --> pdb=" O LYS A 375 " (cutoff:3.500A) removed outlier: 5.778A pdb=" N ILE A 380 " --> pdb=" O ASP A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 418 through 429 Processing helix chain 'A' and resid 440 through 444 removed outlier: 3.808A pdb=" N LEU A 443 " --> pdb=" O ASP A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 455 Processing helix chain 'A' and resid 465 through 481 removed outlier: 3.503A pdb=" N VAL A 469 " --> pdb=" O SER A 465 " (cutoff:3.500A) Processing helix chain 'A' and resid 485 through 496 removed outlier: 3.556A pdb=" N LEU A 489 " --> pdb=" O CYS A 485 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 510 Processing helix chain 'A' and resid 535 through 557 removed outlier: 3.801A pdb=" N ILE A 539 " --> pdb=" O SER A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 581 removed outlier: 3.585A pdb=" N ASP A 581 " --> pdb=" O ASN A 577 " (cutoff:3.500A) Processing helix chain 'A' and resid 585 through 592 Processing helix chain 'A' and resid 616 through 627 removed outlier: 3.537A pdb=" N HIS A 620 " --> pdb=" O ASN A 616 " (cutoff:3.500A) Processing helix chain 'A' and resid 629 through 639 removed outlier: 3.965A pdb=" N ARG A 633 " --> pdb=" O TYR A 629 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N HIS A 637 " --> pdb=" O ARG A 633 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N LEU A 639 " --> pdb=" O ALA A 635 " (cutoff:3.500A) Processing helix chain 'A' and resid 645 through 661 Processing helix chain 'A' and resid 700 through 708 removed outlier: 4.044A pdb=" N LEU A 706 " --> pdb=" O GLU A 702 " (cutoff:3.500A) Processing helix chain 'A' and resid 709 through 716 Processing helix chain 'A' and resid 716 through 733 Processing helix chain 'A' and resid 773 through 781 Processing helix chain 'B' and resid 10 through 15 Processing helix chain 'B' and resid 26 through 40 Processing helix chain 'B' and resid 55 through 68 Processing helix chain 'B' and resid 70 through 74 Processing helix chain 'B' and resid 85 through 99 removed outlier: 4.130A pdb=" N ILE B 93 " --> pdb=" O VAL B 89 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N LYS B 94 " --> pdb=" O ARG B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 119 Processing helix chain 'B' and resid 120 through 134 removed outlier: 4.432A pdb=" N ARG B 129 " --> pdb=" O GLN B 125 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N THR B 130 " --> pdb=" O ALA B 126 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 150 removed outlier: 3.685A pdb=" N LYS B 149 " --> pdb=" O GLN B 146 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ILE B 150 " --> pdb=" O SER B 147 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 146 through 150' Processing helix chain 'B' and resid 151 through 157 Processing helix chain 'B' and resid 167 through 183 removed outlier: 3.949A pdb=" N VAL B 171 " --> pdb=" O SER B 167 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 199 removed outlier: 3.711A pdb=" N GLU B 199 " --> pdb=" O ILE B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 201 through 217 removed outlier: 3.572A pdb=" N GLY B 217 " --> pdb=" O VAL B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 220 through 226 Processing helix chain 'B' and resid 232 through 242 Processing helix chain 'B' and resid 244 through 255 Processing helix chain 'B' and resid 262 through 277 Processing helix chain 'B' and resid 281 through 302 removed outlier: 3.514A pdb=" N GLY B 302 " --> pdb=" O ARG B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 322 removed outlier: 3.628A pdb=" N LEU B 309 " --> pdb=" O THR B 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 14 through 19 Processing helix chain 'C' and resid 23 through 27 removed outlier: 3.574A pdb=" N VAL C 27 " --> pdb=" O LEU C 24 " (cutoff:3.500A) Processing helix chain 'C' and resid 31 through 44 Processing helix chain 'C' and resid 58 through 72 Processing helix chain 'C' and resid 74 through 78 Processing helix chain 'C' and resid 89 through 102 Processing helix chain 'C' and resid 118 through 122 removed outlier: 4.000A pdb=" N ALA C 121 " --> pdb=" O GLU C 118 " (cutoff:3.500A) Processing helix chain 'C' and resid 123 through 137 Processing helix chain 'C' and resid 149 through 153 removed outlier: 3.683A pdb=" N LYS C 152 " --> pdb=" O TYR C 149 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LEU C 153 " --> pdb=" O ALA C 150 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 149 through 153' Processing helix chain 'C' and resid 154 through 159 Processing helix chain 'C' and resid 170 through 186 removed outlier: 3.613A pdb=" N VAL C 183 " --> pdb=" O ALA C 179 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N HIS C 184 " --> pdb=" O ASN C 180 " (cutoff:3.500A) Processing helix chain 'C' and resid 190 through 202 removed outlier: 4.136A pdb=" N ASN C 202 " --> pdb=" O ILE C 198 " (cutoff:3.500A) Processing helix chain 'C' and resid 204 through 219 Processing helix chain 'C' and resid 228 through 237 removed outlier: 3.515A pdb=" N ILE C 232 " --> pdb=" O SER C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 240 through 254 Processing helix chain 'C' and resid 255 through 271 Processing helix chain 'C' and resid 273 through 288 removed outlier: 3.683A pdb=" N ASP C 287 " --> pdb=" O LYS C 283 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N TYR C 288 " --> pdb=" O ILE C 284 " (cutoff:3.500A) Processing helix chain 'C' and resid 292 through 313 removed outlier: 4.113A pdb=" N ARG C 296 " --> pdb=" O ASN C 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 315 through 334 removed outlier: 3.861A pdb=" N GLN C 319 " --> pdb=" O ASN C 315 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLU C 334 " --> pdb=" O SER C 330 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 31 Processing helix chain 'D' and resid 42 through 55 removed outlier: 4.021A pdb=" N VAL D 48 " --> pdb=" O HIS D 44 " (cutoff:3.500A) Processing helix chain 'D' and resid 71 through 83 Processing helix chain 'D' and resid 87 through 92 Processing helix chain 'D' and resid 105 through 116 Processing helix chain 'D' and resid 153 through 159 Processing helix chain 'D' and resid 193 through 208 Processing helix chain 'D' and resid 215 through 225 removed outlier: 3.531A pdb=" N ARG D 219 " --> pdb=" O GLY D 215 " (cutoff:3.500A) Processing helix chain 'D' and resid 227 through 246 Processing helix chain 'D' and resid 252 through 261 removed outlier: 3.751A pdb=" N VAL D 256 " --> pdb=" O THR D 252 " (cutoff:3.500A) Processing helix chain 'D' and resid 264 through 278 Processing helix chain 'D' and resid 279 through 291 Processing helix chain 'D' and resid 296 through 311 removed outlier: 3.538A pdb=" N VAL D 300 " --> pdb=" O SER D 296 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N THR D 310 " --> pdb=" O GLU D 306 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ASN D 311 " --> pdb=" O TYR D 307 " (cutoff:3.500A) Processing helix chain 'D' and resid 315 through 335 removed outlier: 3.671A pdb=" N TRP D 324 " --> pdb=" O ASN D 320 " (cutoff:3.500A) Processing helix chain 'D' and resid 338 through 353 Processing helix chain 'E' and resid 3 through 8 Processing helix chain 'E' and resid 19 through 32 removed outlier: 3.909A pdb=" N GLN E 32 " --> pdb=" O SER E 28 " (cutoff:3.500A) Processing helix chain 'E' and resid 48 through 61 Processing helix chain 'E' and resid 62 through 67 removed outlier: 3.643A pdb=" N TYR E 66 " --> pdb=" O PRO E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 97 through 105 removed outlier: 3.778A pdb=" N ASP E 100 " --> pdb=" O THR E 97 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLY E 102 " --> pdb=" O SER E 99 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N ASN E 103 " --> pdb=" O ASP E 100 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N ASN E 104 " --> pdb=" O MET E 101 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ASP E 105 " --> pdb=" O GLY E 102 " (cutoff:3.500A) Processing helix chain 'E' and resid 106 through 119 removed outlier: 3.729A pdb=" N MET E 119 " --> pdb=" O GLU E 115 " (cutoff:3.500A) Processing helix chain 'E' and resid 143 through 146 Processing helix chain 'E' and resid 147 through 161 Processing helix chain 'E' and resid 178 through 184 Processing helix chain 'E' and resid 194 through 210 Processing helix chain 'E' and resid 216 through 226 Processing helix chain 'E' and resid 229 through 245 Processing helix chain 'E' and resid 257 through 273 Processing helix chain 'E' and resid 275 through 292 Processing helix chain 'E' and resid 295 through 308 Processing helix chain 'E' and resid 314 through 334 Processing helix chain 'E' and resid 337 through 353 removed outlier: 3.983A pdb=" N HIS E 341 " --> pdb=" O LYS E 337 " (cutoff:3.500A) Processing helix chain 'F' and resid 8 through 19 removed outlier: 3.797A pdb=" N PHE F 12 " --> pdb=" O GLU F 8 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N PHE F 19 " --> pdb=" O ILE F 15 " (cutoff:3.500A) Processing helix chain 'F' and resid 72 through 80 Processing helix chain 'F' and resid 141 through 155 removed outlier: 3.805A pdb=" N GLN F 153 " --> pdb=" O ARG F 149 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N LEU F 154 " --> pdb=" O ASP F 150 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N SER F 155 " --> pdb=" O LEU F 151 " (cutoff:3.500A) Processing helix chain 'F' and resid 163 through 166 Processing helix chain 'F' and resid 209 through 216 Processing helix chain 'F' and resid 217 through 221 removed outlier: 4.354A pdb=" N SER F 220 " --> pdb=" O LYS F 217 " (cutoff:3.500A) Processing helix chain 'G' and resid 9 through 23 removed outlier: 3.902A pdb=" N LYS G 13 " --> pdb=" O ALA G 9 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N GLY G 18 " --> pdb=" O ARG G 14 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N PHE G 19 " --> pdb=" O ILE G 15 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N ASP G 21 " --> pdb=" O ASP G 17 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N CYS G 22 " --> pdb=" O GLY G 18 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N VAL G 23 " --> pdb=" O PHE G 19 " (cutoff:3.500A) Processing helix chain 'G' and resid 53 through 57 removed outlier: 3.683A pdb=" N ALA G 56 " --> pdb=" O GLY G 53 " (cutoff:3.500A) Processing helix chain 'G' and resid 72 through 80 Processing helix chain 'G' and resid 141 through 153 removed outlier: 3.979A pdb=" N GLN G 153 " --> pdb=" O ARG G 149 " (cutoff:3.500A) Processing helix chain 'G' and resid 190 through 194 Processing helix chain 'G' and resid 209 through 218 removed outlier: 4.223A pdb=" N GLY G 218 " --> pdb=" O ASP G 214 " (cutoff:3.500A) Processing helix chain 'G' and resid 219 through 221 No H-bonds generated for 'chain 'G' and resid 219 through 221' Processing helix chain 'H' and resid 9 through 18 removed outlier: 3.745A pdb=" N LYS H 13 " --> pdb=" O ALA H 9 " (cutoff:3.500A) Processing helix chain 'H' and resid 72 through 80 Processing helix chain 'H' and resid 141 through 153 removed outlier: 4.230A pdb=" N GLN H 153 " --> pdb=" O ARG H 149 " (cutoff:3.500A) Processing helix chain 'H' and resid 190 through 194 Processing helix chain 'H' and resid 209 through 217 Processing sheet with id=AA1, first strand: chain 'A' and resid 227 through 228 removed outlier: 4.439A pdb=" N VAL A 227 " --> pdb=" O GLU A 483 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N GLU A 483 " --> pdb=" O VAL A 227 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 337 through 338 removed outlier: 6.718A pdb=" N HIS A 337 " --> pdb=" O THR A 461 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 361 through 366 Processing sheet with id=AA4, first strand: chain 'A' and resid 600 through 601 removed outlier: 6.471A pdb=" N LEU E 94 " --> pdb=" O ILE E 139 " (cutoff:3.500A) removed outlier: 7.709A pdb=" N ASN E 141 " --> pdb=" O LEU E 94 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N ILE E 96 " --> pdb=" O ASN E 141 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N LYS E 136 " --> pdb=" O ARG E 166 " (cutoff:3.500A) removed outlier: 7.860A pdb=" N ILE E 168 " --> pdb=" O LYS E 136 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N VAL E 138 " --> pdb=" O ILE E 168 " (cutoff:3.500A) removed outlier: 7.432A pdb=" N VAL E 170 " --> pdb=" O VAL E 138 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N ILE E 140 " --> pdb=" O VAL E 170 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N LEU E 39 " --> pdb=" O MET E 169 " (cutoff:3.500A) removed outlier: 7.774A pdb=" N CYS E 171 " --> pdb=" O LEU E 39 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N LEU E 41 " --> pdb=" O CYS E 171 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU E 40 " --> pdb=" O LEU E 186 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 75 through 77 removed outlier: 6.094A pdb=" N LYS B 109 " --> pdb=" O ARG B 139 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N ALA B 141 " --> pdb=" O LYS B 109 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N VAL B 111 " --> pdb=" O ALA B 141 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N ALA B 143 " --> pdb=" O VAL B 111 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N LEU B 113 " --> pdb=" O ALA B 143 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N MET B 45 " --> pdb=" O PHE B 140 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE B 46 " --> pdb=" O ALA B 159 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 49 through 52 removed outlier: 6.064A pdb=" N LEU C 50 " --> pdb=" O PHE C 164 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'C' and resid 79 through 83 removed outlier: 4.161A pdb=" N LEU C 80 " --> pdb=" O LEU C 113 " (cutoff:3.500A) removed outlier: 5.805A pdb=" N LYS C 112 " --> pdb=" O ARG C 142 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 63 through 64 removed outlier: 3.983A pdb=" N TYR D 64 " --> pdb=" O PHE D 187 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'D' and resid 135 through 140 removed outlier: 5.716A pdb=" N LYS D 135 " --> pdb=" O ARG D 165 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N CYS D 167 " --> pdb=" O LYS D 135 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N ILE D 137 " --> pdb=" O CYS D 167 " (cutoff:3.500A) removed outlier: 7.620A pdb=" N ILE D 169 " --> pdb=" O ILE D 137 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N LEU D 139 " --> pdb=" O ILE D 169 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'F' and resid 57 through 60 removed outlier: 6.715A pdb=" N LYS F 5 " --> pdb=" O GLN F 58 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N TYR F 60 " --> pdb=" O GLU F 3 " (cutoff:3.500A) removed outlier: 7.444A pdb=" N GLU F 3 " --> pdb=" O TYR F 60 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N LEU F 88 " --> pdb=" O PHE F 6 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 66 through 71 removed outlier: 3.984A pdb=" N VAL F 26 " --> pdb=" O MET F 70 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N LEU F 25 " --> pdb=" O VAL F 40 " (cutoff:3.500A) removed outlier: 5.771A pdb=" N VAL F 40 " --> pdb=" O LEU F 25 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N ASN F 27 " --> pdb=" O GLN F 38 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLN F 38 " --> pdb=" O ASN F 27 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N ASP F 240 " --> pdb=" O ARG F 224 " (cutoff:3.500A) removed outlier: 5.886A pdb=" N ARG F 224 " --> pdb=" O ASP F 240 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 179 through 182 Processing sheet with id=AB4, first strand: chain 'G' and resid 60 through 61 removed outlier: 3.714A pdb=" N ARG G 61 " --> pdb=" O GLU G 3 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLU G 3 " --> pdb=" O ARG G 61 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 66 through 71 removed outlier: 3.613A pdb=" N VAL G 26 " --> pdb=" O MET G 70 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N LEU G 25 " --> pdb=" O VAL G 40 " (cutoff:3.500A) removed outlier: 5.791A pdb=" N VAL G 40 " --> pdb=" O LEU G 25 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N ASN G 27 " --> pdb=" O GLN G 38 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N GLN G 38 " --> pdb=" O ASN G 27 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ASP G 240 " --> pdb=" O ARG G 224 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N ARG G 224 " --> pdb=" O ASP G 240 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU G 137 " --> pdb=" O ILE G 227 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LEU G 229 " --> pdb=" O SER G 135 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LYS G 196 " --> pdb=" O SER G 138 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 206 through 208 removed outlier: 5.904A pdb=" N SER G 157 " --> pdb=" O ASP G 172 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N ASP G 172 " --> pdb=" O SER G 157 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ILE H 111 " --> pdb=" O ILE G 181 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N LEU H 88 " --> pdb=" O PHE H 6 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ALA H 92 " --> pdb=" O LEU H 2 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N GLU H 3 " --> pdb=" O TYR H 60 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N TYR H 60 " --> pdb=" O GLU H 3 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N LYS H 5 " --> pdb=" O GLN H 58 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 68 through 71 removed outlier: 5.505A pdb=" N LEU H 25 " --> pdb=" O VAL H 40 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N VAL H 40 " --> pdb=" O LEU H 25 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N ASP H 240 " --> pdb=" O ARG H 224 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N ARG H 224 " --> pdb=" O ASP H 240 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 177 through 182 removed outlier: 3.522A pdb=" N VAL H 180 " --> pdb=" O PHE H 169 " (cutoff:3.500A) removed outlier: 5.059A pdb=" N ASP H 172 " --> pdb=" O SER H 157 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N SER H 157 " --> pdb=" O ASP H 172 " (cutoff:3.500A) 1035 hydrogen bonds defined for protein. 2988 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.71 Time building geometry restraints manager: 1.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.36: 6761 1.36 - 1.51: 5018 1.51 - 1.65: 8826 1.65 - 1.80: 77 1.80 - 1.95: 75 Bond restraints: 20757 Sorted by residual: bond pdb=" N VAL H 225 " pdb=" CA VAL H 225 " ideal model delta sigma weight residual 1.458 1.495 -0.036 1.17e-02 7.31e+03 9.57e+00 bond pdb=" N ILE A 255 " pdb=" CA ILE A 255 " ideal model delta sigma weight residual 1.457 1.492 -0.034 1.14e-02 7.69e+03 9.08e+00 bond pdb=" N LEU G 88 " pdb=" CA LEU G 88 " ideal model delta sigma weight residual 1.454 1.489 -0.034 1.15e-02 7.56e+03 8.92e+00 bond pdb=" N ILE F 128 " pdb=" CA ILE F 128 " ideal model delta sigma weight residual 1.459 1.496 -0.037 1.25e-02 6.40e+03 8.82e+00 bond pdb=" N THR G 87 " pdb=" CA THR G 87 " ideal model delta sigma weight residual 1.454 1.487 -0.033 1.15e-02 7.56e+03 8.27e+00 ... (remaining 20752 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.87: 27429 1.87 - 3.75: 539 3.75 - 5.62: 89 5.62 - 7.50: 18 7.50 - 9.37: 8 Bond angle restraints: 28083 Sorted by residual: angle pdb=" N GLU F 129 " pdb=" CA GLU F 129 " pdb=" C GLU F 129 " ideal model delta sigma weight residual 113.18 107.24 5.94 1.21e+00 6.83e-01 2.41e+01 angle pdb=" CA LEU F 131 " pdb=" C LEU F 131 " pdb=" O LEU F 131 " ideal model delta sigma weight residual 121.58 117.13 4.45 1.16e+00 7.43e-01 1.47e+01 angle pdb=" CB ARG G 80 " pdb=" CG ARG G 80 " pdb=" CD ARG G 80 " ideal model delta sigma weight residual 111.30 119.81 -8.51 2.30e+00 1.89e-01 1.37e+01 angle pdb=" CA MET C 78 " pdb=" CB MET C 78 " pdb=" CG MET C 78 " ideal model delta sigma weight residual 114.10 121.50 -7.40 2.00e+00 2.50e-01 1.37e+01 angle pdb=" CA LEU G 88 " pdb=" C LEU G 88 " pdb=" O LEU G 88 " ideal model delta sigma weight residual 121.66 117.63 4.03 1.22e+00 6.72e-01 1.09e+01 ... (remaining 28078 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.01: 12010 24.01 - 48.01: 689 48.01 - 72.02: 102 72.02 - 96.03: 13 96.03 - 120.03: 1 Dihedral angle restraints: 12815 sinusoidal: 5300 harmonic: 7515 Sorted by residual: dihedral pdb=" O1B ADP E 401 " pdb=" O3A ADP E 401 " pdb=" PB ADP E 401 " pdb=" PA ADP E 401 " ideal model delta sinusoidal sigma weight residual 300.00 179.97 120.03 1 2.00e+01 2.50e-03 3.60e+01 dihedral pdb=" CA MET C 78 " pdb=" C MET C 78 " pdb=" N VAL C 79 " pdb=" CA VAL C 79 " ideal model delta harmonic sigma weight residual 180.00 160.13 19.87 0 5.00e+00 4.00e-02 1.58e+01 dihedral pdb=" CA MET A 334 " pdb=" C MET A 334 " pdb=" N ILE A 335 " pdb=" CA ILE A 335 " ideal model delta harmonic sigma weight residual 180.00 160.27 19.73 0 5.00e+00 4.00e-02 1.56e+01 ... (remaining 12812 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 2836 0.059 - 0.119: 405 0.119 - 0.178: 46 0.178 - 0.237: 6 0.237 - 0.297: 3 Chirality restraints: 3296 Sorted by residual: chirality pdb=" CB ILE C 106 " pdb=" CA ILE C 106 " pdb=" CG1 ILE C 106 " pdb=" CG2 ILE C 106 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.30 2.00e-01 2.50e+01 2.20e+00 chirality pdb=" CB ILE G 128 " pdb=" CA ILE G 128 " pdb=" CG1 ILE G 128 " pdb=" CG2 ILE G 128 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.27 2.00e-01 2.50e+01 1.81e+00 chirality pdb=" CB ILE A 219 " pdb=" CA ILE A 219 " pdb=" CG1 ILE A 219 " pdb=" CG2 ILE A 219 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.25 2.00e-01 2.50e+01 1.51e+00 ... (remaining 3293 not shown) Planarity restraints: 3557 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG H 224 " 0.253 9.50e-02 1.11e+02 1.13e-01 7.92e+00 pdb=" NE ARG H 224 " -0.016 2.00e-02 2.50e+03 pdb=" CZ ARG H 224 " 0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG H 224 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG H 224 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C HIS F 190 " 0.046 5.00e-02 4.00e+02 6.98e-02 7.79e+00 pdb=" N PRO F 191 " -0.121 5.00e-02 4.00e+02 pdb=" CA PRO F 191 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO F 191 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR E 97 " 0.045 5.00e-02 4.00e+02 6.84e-02 7.49e+00 pdb=" N PRO E 98 " -0.118 5.00e-02 4.00e+02 pdb=" CA PRO E 98 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO E 98 " 0.038 5.00e-02 4.00e+02 ... (remaining 3554 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 406 2.69 - 3.25: 20090 3.25 - 3.80: 32085 3.80 - 4.35: 41577 4.35 - 4.90: 68369 Nonbonded interactions: 162527 Sorted by model distance: nonbonded pdb=" OG1 THR C 60 " pdb="MG MG C 402 " model vdw 2.142 2.170 nonbonded pdb=" O2B AGS D 401 " pdb="MG MG D 402 " model vdw 2.163 2.170 nonbonded pdb=" OG1 THR B 56 " pdb="MG MG B 402 " model vdw 2.179 2.170 nonbonded pdb=" OH TYR C 71 " pdb=" O PHE C 111 " model vdw 2.244 3.040 nonbonded pdb=" OG SER E 99 " pdb=" OE2 GLU E 142 " model vdw 2.262 3.040 ... (remaining 162522 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 'F' selection = (chain 'G' and resid 1 through 254) selection = (chain 'H' and resid 1 through 254) } 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: 6.270 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: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.030 Process input model: 16.360 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 20757 Z= 0.169 Angle : 0.641 9.372 28083 Z= 0.343 Chirality : 0.044 0.297 3296 Planarity : 0.005 0.113 3557 Dihedral : 14.452 120.031 7909 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 0.09 % Allowed : 0.52 % Favored : 99.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.34 (0.17), residues: 2532 helix: 1.13 (0.15), residues: 1152 sheet: 0.38 (0.25), residues: 486 loop : -1.00 (0.19), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 69 TYR 0.015 0.001 TYR H 133 PHE 0.028 0.001 PHE E 305 TRP 0.036 0.002 TRP A 780 HIS 0.011 0.001 HIS D 340 Details of bonding type rmsd covalent geometry : bond 0.00281 (20757) covalent geometry : angle 0.64128 (28083) hydrogen bonds : bond 0.18600 ( 1035) hydrogen bonds : angle 6.69558 ( 2988) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5064 Ramachandran restraints generated. 2532 Oldfield, 0 Emsley, 2532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5064 Ramachandran restraints generated. 2532 Oldfield, 0 Emsley, 2532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 2307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 367 time to evaluate : 0.824 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 504 LEU cc_start: 0.8648 (mm) cc_final: 0.8403 (mm) REVERT: B 73 ASP cc_start: 0.8028 (p0) cc_final: 0.7772 (p0) REVERT: C 212 LEU cc_start: 0.9416 (mm) cc_final: 0.9157 (mm) REVERT: C 276 ASP cc_start: 0.7101 (m-30) cc_final: 0.6856 (m-30) REVERT: D 145 MET cc_start: 0.2913 (mmm) cc_final: 0.2654 (tpt) REVERT: E 174 MET cc_start: 0.8072 (ppp) cc_final: 0.7819 (tmm) REVERT: F 125 PHE cc_start: 0.5475 (m-80) cc_final: 0.5265 (p90) REVERT: F 126 LEU cc_start: 0.1063 (OUTLIER) cc_final: 0.0501 (tp) REVERT: F 239 PHE cc_start: 0.2416 (m-10) cc_final: 0.2197 (m-10) REVERT: G 1 MET cc_start: 0.2991 (tmm) cc_final: 0.2624 (tpt) REVERT: G 14 ARG cc_start: 0.7128 (ptm-80) cc_final: 0.6715 (ptm-80) REVERT: G 70 MET cc_start: 0.5866 (pmm) cc_final: 0.5516 (pmm) REVERT: G 120 ASP cc_start: 0.5891 (t0) cc_final: 0.4874 (p0) REVERT: G 249 PHE cc_start: 0.8334 (m-10) cc_final: 0.7997 (m-80) outliers start: 2 outliers final: 0 residues processed: 368 average time/residue: 0.1300 time to fit residues: 78.2149 Evaluate side-chains 268 residues out of total 2307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 267 time to evaluate : 0.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 126 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 71.5612 > 50: distance: 13 - 63: 34.243 distance: 16 - 60: 30.254 distance: 29 - 48: 34.262 distance: 32 - 45: 12.391 distance: 41 - 45: 16.336 distance: 45 - 46: 38.676 distance: 46 - 47: 42.626 distance: 46 - 49: 49.763 distance: 47 - 48: 38.845 distance: 47 - 52: 40.638 distance: 49 - 50: 24.898 distance: 49 - 51: 36.135 distance: 52 - 53: 39.720 distance: 53 - 54: 34.507 distance: 53 - 56: 26.801 distance: 54 - 55: 54.336 distance: 54 - 60: 39.996 distance: 56 - 57: 12.898 distance: 56 - 58: 5.426 distance: 57 - 59: 6.440 distance: 60 - 61: 5.126 distance: 61 - 62: 41.060 distance: 62 - 63: 11.854 distance: 62 - 68: 34.455 distance: 64 - 66: 12.302 distance: 68 - 69: 44.137 distance: 69 - 70: 35.145 distance: 69 - 72: 36.491 distance: 70 - 71: 52.321 distance: 70 - 77: 6.418 distance: 72 - 73: 38.959 distance: 73 - 74: 61.486 distance: 74 - 75: 25.691 distance: 75 - 76: 22.750 distance: 77 - 78: 43.486 distance: 77 - 83: 39.857 distance: 78 - 79: 32.207 distance: 78 - 81: 38.120 distance: 79 - 80: 25.770 distance: 81 - 82: 26.036 distance: 82 - 83: 42.490 distance: 84 - 85: 36.204 distance: 85 - 86: 27.714 distance: 85 - 88: 9.865 distance: 86 - 87: 12.906 distance: 86 - 95: 20.880 distance: 88 - 89: 13.862 distance: 89 - 90: 6.404 distance: 89 - 91: 25.259 distance: 90 - 92: 21.716 distance: 91 - 93: 29.252 distance: 92 - 94: 37.044 distance: 93 - 94: 9.100 distance: 95 - 96: 5.979 distance: 96 - 97: 24.531 distance: 96 - 99: 27.837 distance: 97 - 98: 19.552 distance: 97 - 102: 38.854 distance: 99 - 100: 16.659 distance: 99 - 101: 18.460 distance: 102 - 103: 32.389 distance: 103 - 104: 5.491 distance: 103 - 106: 30.818 distance: 104 - 105: 4.589 distance: 104 - 110: 53.275 distance: 107 - 108: 39.639 distance: 107 - 109: 38.720 distance: 110 - 111: 10.332 distance: 111 - 112: 47.062 distance: 111 - 114: 29.858 distance: 112 - 113: 4.860 distance: 112 - 118: 27.741 distance: 115 - 116: 7.291 distance: 116 - 117: 40.822 distance: 118 - 119: 25.010 distance: 119 - 120: 54.774 distance: 119 - 122: 27.041 distance: 120 - 121: 12.357 distance: 120 - 127: 24.740 distance: 122 - 123: 10.370 distance: 123 - 124: 7.557 distance: 124 - 125: 8.361