Starting phenix.real_space_refine on Sun May 3 00:32:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9n1q_48821/05_2026/9n1q_48821.cif Found real_map, /net/cci-nas-00/data/ceres_data/9n1q_48821/05_2026/9n1q_48821.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9n1q_48821/05_2026/9n1q_48821.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9n1q_48821/05_2026/9n1q_48821.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9n1q_48821/05_2026/9n1q_48821.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9n1q_48821/05_2026/9n1q_48821.map" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.087 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: 4 Type Number sf(0) Gaussians S 55 5.16 5 C 5928 2.51 5 N 1643 2.21 5 O 1713 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9339 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1899 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1899 Classifications: {'peptide': 229} Link IDs: {'PTRANS': 6, 'TRANS': 222} Chain breaks: 2 Chain: "B" Number of atoms: 2606 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2606 Classifications: {'peptide': 339} Link IDs: {'PTRANS': 5, 'TRANS': 333} Chain: "G" Number of atoms: 429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 429 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 4, 'TRANS': 51} Chain: "N" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 973 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 5, 'TRANS': 122} Chain: "P" Number of atoms: 249 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 249 Classifications: {'peptide': 30} Link IDs: {'TRANS': 29} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'AIB:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "R" Number of atoms: 3180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 393, 3180 Classifications: {'peptide': 393} Link IDs: {'PTRANS': 15, 'TRANS': 377} Chain breaks: 1 Chain: "R" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Time building chain proxies: 2.22, per 1000 atoms: 0.24 Number of scatterers: 9339 At special positions: 0 Unit cell: (81.1164, 102.277, 176.34, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 55 16.00 O 1713 8.00 N 1643 7.00 C 5928 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 Simple disulfide: pdb=" SG CYS R 43 " - pdb=" SG CYS R 67 " distance=2.04 Simple disulfide: pdb=" SG CYS R 58 " - pdb=" SG CYS R 100 " distance=2.03 Simple disulfide: pdb=" SG CYS R 81 " - pdb=" SG CYS R 121 " distance=2.03 Simple disulfide: pdb=" SG CYS R 224 " - pdb=" SG CYS R 294 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.95 Conformation dependent library (CDL) restraints added in 327.1 milliseconds 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2198 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 12 sheets defined 40.7% alpha, 17.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'A' and resid 9 through 38 removed outlier: 3.503A pdb=" N ARG A 13 " --> pdb=" O THR A 9 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N GLU A 15 " --> pdb=" O ASP A 11 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ALA A 22 " --> pdb=" O ALA A 18 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LYS A 32 " --> pdb=" O LYS A 28 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLN A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ARG A 38 " --> pdb=" O LYS A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 58 removed outlier: 4.426A pdb=" N VAL A 57 " --> pdb=" O LYS A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 278 removed outlier: 3.530A pdb=" N ASN A 278 " --> pdb=" O ASP A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 303 removed outlier: 3.841A pdb=" N GLU A 299 " --> pdb=" O ASP A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 312 Processing helix chain 'A' and resid 313 through 317 Processing helix chain 'A' and resid 333 through 350 removed outlier: 3.692A pdb=" N ALA A 337 " --> pdb=" O ARG A 333 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N TYR A 339 " --> pdb=" O THR A 335 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ARG A 342 " --> pdb=" O LYS A 338 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 removed outlier: 3.774A pdb=" N TYR A 391 " --> pdb=" O HIS A 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 26 removed outlier: 3.655A pdb=" N GLU B 12 " --> pdb=" O ARG B 8 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLN B 13 " --> pdb=" O GLN B 9 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU B 14 " --> pdb=" O GLU B 10 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.738A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 300 through 302 No H-bonds generated for 'chain 'B' and resid 300 through 302' Processing helix chain 'G' and resid 8 through 21 removed outlier: 3.794A pdb=" N LEU G 15 " --> pdb=" O GLN G 11 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N VAL G 16 " --> pdb=" O ALA G 12 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N GLU G 17 " --> pdb=" O ARG G 13 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLN G 18 " --> pdb=" O LYS G 14 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.899A pdb=" N LEU G 37 " --> pdb=" O ALA G 33 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N MET G 38 " --> pdb=" O ALA G 34 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 48 removed outlier: 3.843A pdb=" N ASP G 48 " --> pdb=" O ALA G 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 45 through 48' Processing helix chain 'N' and resid 61 through 65 removed outlier: 3.609A pdb=" N LYS N 65 " --> pdb=" O GLY N 62 " (cutoff:3.500A) Processing helix chain 'N' and resid 87 through 91 Processing helix chain 'P' and resid 2 through 29 removed outlier: 3.702A pdb=" N LYS P 12 " --> pdb=" O SER P 8 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ASP P 15 " --> pdb=" O SER P 11 " (cutoff:3.500A) Processing helix chain 'R' and resid 27 through 49 removed outlier: 3.544A pdb=" N LEU R 38 " --> pdb=" O GLU R 34 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N HIS R 44 " --> pdb=" O GLY R 40 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N HIS R 45 " --> pdb=" O ASP R 41 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LEU R 49 " --> pdb=" O HIS R 45 " (cutoff:3.500A) Processing helix chain 'R' and resid 87 through 92 removed outlier: 3.954A pdb=" N GLN R 92 " --> pdb=" O HIS R 89 " (cutoff:3.500A) Processing helix chain 'R' and resid 124 through 165 removed outlier: 3.597A pdb=" N ILE R 128 " --> pdb=" O ASP R 124 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N VAL R 147 " --> pdb=" O VAL R 143 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLY R 148 " --> pdb=" O MET R 144 " (cutoff:3.500A) Processing helix chain 'R' and resid 171 through 202 removed outlier: 3.525A pdb=" N TYR R 202 " --> pdb=" O LEU R 198 " (cutoff:3.500A) Processing helix chain 'R' and resid 208 through 216 Processing helix chain 'R' and resid 217 through 254 removed outlier: 3.621A pdb=" N VAL R 221 " --> pdb=" O SER R 217 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N GLY R 223 " --> pdb=" O GLY R 219 " (cutoff:3.500A) removed outlier: 5.217A pdb=" N CYS R 224 " --> pdb=" O ALA R 220 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N VAL R 226 " --> pdb=" O ALA R 222 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N ALA R 227 " --> pdb=" O GLY R 223 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ASN R 238 " --> pdb=" O GLY R 234 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLY R 246 " --> pdb=" O LEU R 242 " (cutoff:3.500A) Processing helix chain 'R' and resid 263 through 272 Processing helix chain 'R' and resid 275 through 287 Proline residue: R 281 - end of helix Processing helix chain 'R' and resid 308 through 336 removed outlier: 3.790A pdb=" N ARG R 336 " --> pdb=" O LYS R 332 " (cutoff:3.500A) Processing helix chain 'R' and resid 346 through 359 removed outlier: 3.572A pdb=" N ILE R 355 " --> pdb=" O THR R 351 " (cutoff:3.500A) Proline residue: R 356 - end of helix Processing helix chain 'R' and resid 375 through 400 removed outlier: 3.513A pdb=" N SER R 379 " --> pdb=" O GLY R 375 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N GLY R 393 " --> pdb=" O SER R 389 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N LEU R 394 " --> pdb=" O SER R 390 " (cutoff:3.500A) Processing helix chain 'R' and resid 404 through 422 removed outlier: 3.608A pdb=" N LEU R 411 " --> pdb=" O VAL R 407 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ARG R 413 " --> pdb=" O SER R 409 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 209 through 214 removed outlier: 6.567A pdb=" N HIS A 41 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N PHE A 222 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N LEU A 43 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 9.237A pdb=" N ALA A 243 " --> pdb=" O THR A 40 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N ASN A 292 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N VAL A 248 " --> pdb=" O ASN A 292 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 49 through 51 removed outlier: 3.515A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 62 removed outlier: 3.655A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.656A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.692A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.762A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.656A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 4.084A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7 removed outlier: 3.899A pdb=" N SER N 21 " --> pdb=" O SER N 7 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N SER N 71 " --> pdb=" O TYR N 80 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'N' and resid 10 through 12 removed outlier: 7.102A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'R' and resid 61 through 62 removed outlier: 3.939A pdb=" N THR R 61 " --> pdb=" O TRP R 68 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'R' and resid 76 through 80 removed outlier: 3.564A pdb=" N LYS R 98 " --> pdb=" O ALA R 77 " (cutoff:3.500A) 414 hydrogen bonds defined for protein. 1182 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.47 Time building geometry restraints manager: 1.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1993 1.33 - 1.45: 2287 1.45 - 1.57: 5191 1.57 - 1.69: 0 1.69 - 1.82: 75 Bond restraints: 9546 Sorted by residual: bond pdb=" C LEU P 26 " pdb=" N LEU P 27 " ideal model delta sigma weight residual 1.334 1.288 0.046 1.46e-02 4.69e+03 9.94e+00 bond pdb=" N LYS N 87 " pdb=" CA LYS N 87 " ideal model delta sigma weight residual 1.453 1.479 -0.026 8.30e-03 1.45e+04 9.83e+00 bond pdb=" N VAL R 398 " pdb=" CA VAL R 398 " ideal model delta sigma weight residual 1.459 1.497 -0.038 1.21e-02 6.83e+03 9.65e+00 bond pdb=" C ALA N 101 " pdb=" N PRO N 102 " ideal model delta sigma weight residual 1.329 1.366 -0.037 1.20e-02 6.94e+03 9.43e+00 bond pdb=" N ILE B 18 " pdb=" CA ILE B 18 " ideal model delta sigma weight residual 1.461 1.496 -0.036 1.19e-02 7.06e+03 9.02e+00 ... (remaining 9541 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.28: 11918 1.28 - 2.57: 753 2.57 - 3.85: 209 3.85 - 5.13: 41 5.13 - 6.42: 7 Bond angle restraints: 12928 Sorted by residual: angle pdb=" CA ASP B 228 " pdb=" C ASP B 228 " pdb=" O ASP B 228 " ideal model delta sigma weight residual 121.87 117.38 4.49 1.16e+00 7.43e-01 1.50e+01 angle pdb=" CA ASP R 195 " pdb=" C ASP R 195 " pdb=" O ASP R 195 " ideal model delta sigma weight residual 120.92 116.66 4.26 1.12e+00 7.97e-01 1.45e+01 angle pdb=" CA PHE N 108 " pdb=" CB PHE N 108 " pdb=" CG PHE N 108 " ideal model delta sigma weight residual 113.80 117.60 -3.80 1.00e+00 1.00e+00 1.44e+01 angle pdb=" N PRO N 102 " pdb=" CA PRO N 102 " pdb=" C PRO N 102 " ideal model delta sigma weight residual 111.57 117.04 -5.47 1.52e+00 4.33e-01 1.30e+01 angle pdb=" CA ASP R 195 " pdb=" CB ASP R 195 " pdb=" CG ASP R 195 " ideal model delta sigma weight residual 112.60 116.19 -3.59 1.00e+00 1.00e+00 1.29e+01 ... (remaining 12923 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.48: 5109 17.48 - 34.96: 436 34.96 - 52.44: 89 52.44 - 69.92: 13 69.92 - 87.40: 9 Dihedral angle restraints: 5656 sinusoidal: 2254 harmonic: 3402 Sorted by residual: dihedral pdb=" CB CYS R 43 " pdb=" SG CYS R 43 " pdb=" SG CYS R 67 " pdb=" CB CYS R 67 " ideal model delta sinusoidal sigma weight residual -86.00 -173.40 87.40 1 1.00e+01 1.00e-02 9.16e+01 dihedral pdb=" CB CYS R 58 " pdb=" SG CYS R 58 " pdb=" SG CYS R 100 " pdb=" CB CYS R 100 " ideal model delta sinusoidal sigma weight residual -86.00 -126.40 40.40 1 1.00e+01 1.00e-02 2.29e+01 dihedral pdb=" CB CYS R 224 " pdb=" SG CYS R 224 " pdb=" SG CYS R 294 " pdb=" CB CYS R 294 " ideal model delta sinusoidal sigma weight residual 93.00 124.33 -31.33 1 1.00e+01 1.00e-02 1.40e+01 ... (remaining 5653 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 1199 0.063 - 0.126: 183 0.126 - 0.189: 32 0.189 - 0.251: 4 0.251 - 0.314: 2 Chirality restraints: 1420 Sorted by residual: chirality pdb=" CA LEU P 27 " pdb=" N LEU P 27 " pdb=" C LEU P 27 " pdb=" CB LEU P 27 " both_signs ideal model delta sigma weight residual False 2.51 2.82 -0.31 2.00e-01 2.50e+01 2.47e+00 chirality pdb=" CA LYS N 87 " pdb=" N LYS N 87 " pdb=" C LYS N 87 " pdb=" CB LYS N 87 " both_signs ideal model delta sigma weight residual False 2.51 2.78 -0.27 2.00e-01 2.50e+01 1.83e+00 chirality pdb=" CA GLU B 226 " pdb=" N GLU B 226 " pdb=" C GLU B 226 " pdb=" CB GLU B 226 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.19e+00 ... (remaining 1417 not shown) Planarity restraints: 1653 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA R 397 " -0.015 2.00e-02 2.50e+03 2.91e-02 8.48e+00 pdb=" C ALA R 397 " 0.050 2.00e-02 2.50e+03 pdb=" O ALA R 397 " -0.019 2.00e-02 2.50e+03 pdb=" N VAL R 398 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 219 " -0.011 2.00e-02 2.50e+03 2.11e-02 4.43e+00 pdb=" C PHE A 219 " 0.036 2.00e-02 2.50e+03 pdb=" O PHE A 219 " -0.014 2.00e-02 2.50e+03 pdb=" N HIS A 220 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE N 108 " -0.009 2.00e-02 2.50e+03 1.83e-02 3.36e+00 pdb=" C PHE N 108 " 0.032 2.00e-02 2.50e+03 pdb=" O PHE N 108 " -0.012 2.00e-02 2.50e+03 pdb=" N ASP N 109 " -0.011 2.00e-02 2.50e+03 ... (remaining 1650 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 2182 2.79 - 3.32: 8463 3.32 - 3.85: 14271 3.85 - 4.37: 16913 4.37 - 4.90: 29590 Nonbonded interactions: 71419 Sorted by model distance: nonbonded pdb=" OD1 ASP R 63 " pdb=" N LYS R 64 " model vdw 2.265 3.120 nonbonded pdb=" OG SER B 74 " pdb=" OD1 ASP B 76 " model vdw 2.275 3.040 nonbonded pdb=" O TYR A 318 " pdb=" NH1 ARG A 336 " model vdw 2.282 3.120 nonbonded pdb=" O GLY A 355 " pdb=" NH1 ARG A 389 " model vdw 2.288 3.120 nonbonded pdb=" OD2 ASP A 343 " pdb=" NH2 ARG A 347 " model vdw 2.298 3.120 ... (remaining 71414 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.540 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: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 9.630 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 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 : 0.005 0.046 9552 Z= 0.336 Angle : 0.756 6.417 12940 Z= 0.499 Chirality : 0.050 0.314 1420 Planarity : 0.004 0.037 1653 Dihedral : 13.688 86.939 3440 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % 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 are not related in a simple way. whole: -1.16 (0.24), residues: 1155 helix: -0.25 (0.24), residues: 436 sheet: -0.89 (0.34), residues: 222 loop : -1.03 (0.27), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG R 108 TYR 0.012 0.001 TYR P 10 PHE 0.023 0.002 PHE B 222 TRP 0.017 0.002 TRP R 106 HIS 0.009 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00511 ( 9546) covalent geometry : angle 0.75610 (12928) SS BOND : bond 0.00390 ( 6) SS BOND : angle 0.94436 ( 12) hydrogen bonds : bond 0.28976 ( 414) hydrogen bonds : angle 8.01221 ( 1182) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 130 time to evaluate : 0.381 Fit side-chains revert: symmetry clash REVERT: R 68 TRP cc_start: 0.6261 (m-90) cc_final: 0.5529 (m-10) REVERT: R 344 LYS cc_start: 0.6489 (mmtm) cc_final: 0.5667 (mppt) outliers start: 0 outliers final: 0 residues processed: 130 average time/residue: 0.5886 time to fit residues: 81.8295 Evaluate side-chains 85 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 85 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 108 optimal weight: 0.9980 chunk 49 optimal weight: 0.9980 chunk 97 optimal weight: 3.9990 chunk 113 optimal weight: 5.9990 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 7.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 6 GLN B 110 ASN N 31 ASN R 122 GLN R 374 GLN R 392 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.185310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.135222 restraints weight = 10538.047| |-----------------------------------------------------------------------------| r_work (start): 0.3689 rms_B_bonded: 2.48 r_work: 0.3554 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.3421 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.1768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9552 Z= 0.139 Angle : 0.569 9.520 12940 Z= 0.301 Chirality : 0.041 0.152 1420 Planarity : 0.004 0.034 1653 Dihedral : 4.308 34.356 1280 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 0.90 % Allowed : 10.48 % Favored : 88.62 % 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 are not related in a simple way. whole: -0.24 (0.24), residues: 1155 helix: 1.13 (0.25), residues: 447 sheet: -0.72 (0.31), residues: 249 loop : -1.06 (0.28), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG R 94 TYR 0.032 0.001 TYR R 145 PHE 0.025 0.002 PHE R 384 TRP 0.012 0.001 TRP N 47 HIS 0.009 0.001 HIS R 45 Details of bonding type rmsd covalent geometry : bond 0.00284 ( 9546) covalent geometry : angle 0.56827 (12928) SS BOND : bond 0.00442 ( 6) SS BOND : angle 1.12567 ( 12) hydrogen bonds : bond 0.06495 ( 414) hydrogen bonds : angle 4.71179 ( 1182) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 104 time to evaluate : 0.354 Fit side-chains REVERT: A 209 GLU cc_start: 0.8408 (pt0) cc_final: 0.8007 (tt0) REVERT: B 45 MET cc_start: 0.8502 (mtt) cc_final: 0.8266 (mtt) REVERT: R 43 CYS cc_start: 0.6094 (OUTLIER) cc_final: 0.5065 (m) REVERT: R 66 SER cc_start: 0.7895 (p) cc_final: 0.7271 (t) REVERT: R 195 ASP cc_start: 0.7604 (t0) cc_final: 0.7386 (t0) REVERT: R 344 LYS cc_start: 0.6089 (mmtm) cc_final: 0.5110 (mppt) REVERT: R 419 ARG cc_start: 0.5190 (mmt90) cc_final: 0.4721 (ptm-80) outliers start: 9 outliers final: 1 residues processed: 110 average time/residue: 0.5926 time to fit residues: 69.7507 Evaluate side-chains 84 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 82 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain R residue 43 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 25 optimal weight: 10.0000 chunk 91 optimal weight: 0.9980 chunk 97 optimal weight: 0.6980 chunk 18 optimal weight: 5.9990 chunk 29 optimal weight: 2.9990 chunk 60 optimal weight: 4.9990 chunk 78 optimal weight: 20.0000 chunk 52 optimal weight: 4.9990 chunk 38 optimal weight: 0.9990 chunk 45 optimal weight: 3.9990 chunk 20 optimal weight: 0.8980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 31 ASN ** R 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 374 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.182589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.132845 restraints weight = 10574.832| |-----------------------------------------------------------------------------| r_work (start): 0.3662 rms_B_bonded: 2.47 r_work: 0.3524 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3384 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.2153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9552 Z= 0.142 Angle : 0.541 10.479 12940 Z= 0.285 Chirality : 0.041 0.146 1420 Planarity : 0.004 0.036 1653 Dihedral : 4.233 27.953 1280 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 1.90 % Allowed : 13.47 % Favored : 84.63 % 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 are not related in a simple way. whole: -0.02 (0.24), residues: 1155 helix: 1.45 (0.25), residues: 452 sheet: -0.63 (0.31), residues: 246 loop : -1.09 (0.28), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 134 TYR 0.028 0.001 TYR R 145 PHE 0.024 0.002 PHE N 108 TRP 0.013 0.001 TRP N 47 HIS 0.007 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00318 ( 9546) covalent geometry : angle 0.53994 (12928) SS BOND : bond 0.00349 ( 6) SS BOND : angle 1.11937 ( 12) hydrogen bonds : bond 0.05888 ( 414) hydrogen bonds : angle 4.36874 ( 1182) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 92 time to evaluate : 0.272 Fit side-chains REVERT: A 209 GLU cc_start: 0.8282 (pt0) cc_final: 0.7933 (mp0) REVERT: B 59 TYR cc_start: 0.8584 (OUTLIER) cc_final: 0.8138 (t80) REVERT: R 37 LYS cc_start: 0.7789 (OUTLIER) cc_final: 0.7342 (mttp) REVERT: R 43 CYS cc_start: 0.6033 (OUTLIER) cc_final: 0.5036 (m) REVERT: R 344 LYS cc_start: 0.6139 (mmtm) cc_final: 0.5205 (mppt) REVERT: R 345 PHE cc_start: 0.7291 (t80) cc_final: 0.6743 (m-80) REVERT: R 419 ARG cc_start: 0.5374 (mmt90) cc_final: 0.4870 (ptm-80) outliers start: 19 outliers final: 6 residues processed: 104 average time/residue: 0.5747 time to fit residues: 63.9678 Evaluate side-chains 95 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 86 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain R residue 37 LYS Chi-restraints excluded: chain R residue 43 CYS Chi-restraints excluded: chain R residue 134 VAL Chi-restraints excluded: chain R residue 323 VAL Chi-restraints excluded: chain R residue 398 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/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-2.1rc2-6044/lib/python3.9/site-packages/iotbx/cli_parser.py", line 995, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/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-2.1rc2-6044/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-2.1rc2-6044/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-2.1rc2-6044/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-2.1rc2-6044/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-2.1rc2-6044/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-2.1rc2-6044/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-2.1rc2-6044/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-2.1rc2-6044/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-2.1rc2-6044/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-2.1rc2-6044/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-2.1rc2-6044/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-2.1rc2-6044/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-2.1rc2-6044/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-2.1rc2-6044/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-2.1rc2-6044/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1590, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1493, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1374, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 60.0301 > 50: distance: 17 - 24: 5.753 distance: 18 - 48: 23.838 distance: 24 - 25: 17.296 distance: 25 - 26: 18.108 distance: 25 - 28: 9.619 distance: 26 - 27: 14.285 distance: 26 - 32: 19.141 distance: 28 - 29: 21.501 distance: 29 - 30: 12.202 distance: 29 - 31: 8.235 distance: 33 - 34: 18.127 distance: 33 - 36: 14.213 distance: 34 - 35: 5.942 distance: 34 - 40: 9.958 distance: 35 - 62: 21.071 distance: 36 - 37: 9.239 distance: 37 - 38: 28.506 distance: 37 - 39: 19.045 distance: 40 - 41: 4.857 distance: 41 - 42: 5.220 distance: 41 - 44: 7.841 distance: 42 - 43: 15.302 distance: 42 - 48: 5.851 distance: 43 - 71: 30.045 distance: 44 - 45: 25.200 distance: 45 - 46: 11.650 distance: 45 - 47: 11.485 distance: 48 - 49: 28.618 distance: 49 - 50: 13.169 distance: 49 - 52: 35.341 distance: 50 - 51: 8.847 distance: 50 - 53: 14.997 distance: 51 - 78: 36.400 distance: 53 - 54: 13.251 distance: 54 - 55: 27.494 distance: 54 - 57: 33.025 distance: 55 - 56: 8.297 distance: 55 - 62: 13.985 distance: 56 - 86: 45.771 distance: 57 - 58: 16.154 distance: 58 - 59: 24.527 distance: 59 - 60: 30.299 distance: 59 - 61: 15.752 distance: 62 - 63: 26.263 distance: 63 - 64: 28.630 distance: 63 - 66: 18.618 distance: 64 - 65: 7.626 distance: 64 - 71: 15.389 distance: 66 - 67: 46.581 distance: 67 - 68: 26.676 distance: 68 - 69: 11.759 distance: 69 - 70: 13.814 distance: 71 - 72: 10.521 distance: 72 - 73: 13.267 distance: 72 - 75: 9.386 distance: 73 - 74: 20.121 distance: 73 - 78: 29.872 distance: 75 - 76: 25.531 distance: 75 - 77: 20.415 distance: 78 - 79: 11.964 distance: 79 - 80: 37.634 distance: 79 - 82: 9.115 distance: 80 - 81: 30.112 distance: 80 - 86: 25.594 distance: 82 - 83: 12.714 distance: 83 - 84: 21.524 distance: 83 - 85: 15.791 distance: 86 - 87: 12.882 distance: 87 - 88: 37.586 distance: 87 - 90: 8.067 distance: 88 - 89: 42.175 distance: 88 - 91: 37.311 distance: 91 - 92: 5.319 distance: 92 - 93: 43.079 distance: 93 - 94: 20.019 distance: 93 - 95: 18.374