Starting phenix.real_space_refine on Fri Aug 22 23:38:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8kic_37257/08_2025/8kic_37257.cif Found real_map, /net/cci-nas-00/data/ceres_data/8kic_37257/08_2025/8kic_37257.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8kic_37257/08_2025/8kic_37257.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8kic_37257/08_2025/8kic_37257.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8kic_37257/08_2025/8kic_37257.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8kic_37257/08_2025/8kic_37257.map" } resolution = 2.5 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= 0.010 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 17 5.16 5 C 5374 2.51 5 N 1515 2.21 5 O 1683 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8589 Number of models: 1 Model: "" Number of chains: 9 Chain: "D" Number of atoms: 632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 632 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 3, 'TRANS': 83} Chain breaks: 1 Chain: "E" Number of atoms: 656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 656 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 3, 'TRANS': 86} Chain: "F" Number of atoms: 667 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 667 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 3, 'TRANS': 87} Chain: "C" Number of atoms: 2178 Number of conformers: 1 Conformer: "" Number of residues, atoms: 300, 2178 Classifications: {'peptide': 300} Link IDs: {'PTRANS': 12, 'TRANS': 287} Chain breaks: 1 Chain: "A" Number of atoms: 2178 Number of conformers: 1 Conformer: "" Number of residues, atoms: 300, 2178 Classifications: {'peptide': 300} Link IDs: {'PTRANS': 12, 'TRANS': 287} Chain breaks: 1 Chain: "B" Number of atoms: 2178 Number of conformers: 1 Conformer: "" Number of residues, atoms: 300, 2178 Classifications: {'peptide': 300} Link IDs: {'PTRANS': 12, 'TRANS': 287} Chain breaks: 1 Chain: "G" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 40 Classifications: {'peptide': 8} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'UNK:plan-1': 8} Unresolved non-hydrogen planarities: 8 Chain: "H" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 25 Classifications: {'peptide': 5} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'TRANS': 4} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'UNK:plan-1': 5} Unresolved non-hydrogen planarities: 5 Chain: "I" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 35 Classifications: {'peptide': 7} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'TRANS': 6} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'UNK:plan-1': 7} Unresolved non-hydrogen planarities: 7 Time building chain proxies: 2.53, per 1000 atoms: 0.29 Number of scatterers: 8589 At special positions: 0 Unit cell: (89.04, 125.504, 122.96, 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 17 16.00 O 1683 8.00 N 1515 7.00 C 5374 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.60 Conformation dependent library (CDL) restraints added in 599.7 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2094 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 20 sheets defined 21.8% alpha, 36.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.42 Creating SS restraints... Processing helix chain 'D' and resid 372 through 376 Processing helix chain 'D' and resid 401 through 407 Processing helix chain 'D' and resid 424 through 433 Processing helix chain 'E' and resid 372 through 376 Processing helix chain 'E' and resid 401 through 407 Processing helix chain 'E' and resid 424 through 433 Processing helix chain 'F' and resid 372 through 376 Processing helix chain 'F' and resid 401 through 407 Processing helix chain 'F' and resid 424 through 433 Processing helix chain 'C' and resid 42 through 50 removed outlier: 4.200A pdb=" N LYS C 48 " --> pdb=" O PRO C 44 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N VAL C 49 " --> pdb=" O MET C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 158 through 162 removed outlier: 3.513A pdb=" N LEU C 162 " --> pdb=" O SER C 159 " (cutoff:3.500A) Processing helix chain 'C' and resid 173 through 177 removed outlier: 3.658A pdb=" N GLY C 176 " --> pdb=" O ASN C 173 " (cutoff:3.500A) Processing helix chain 'C' and resid 248 through 262 Processing helix chain 'C' and resid 277 through 285 Processing helix chain 'C' and resid 301 through 307 Processing helix chain 'C' and resid 324 through 335 removed outlier: 3.808A pdb=" N LEU C 328 " --> pdb=" O SER C 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 50 removed outlier: 4.467A pdb=" N LYS A 48 " --> pdb=" O PRO A 44 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N VAL A 49 " --> pdb=" O MET A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 112 Processing helix chain 'A' and resid 158 through 162 removed outlier: 3.607A pdb=" N LEU A 162 " --> pdb=" O SER A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 177 removed outlier: 3.592A pdb=" N GLY A 176 " --> pdb=" O ASN A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 261 Processing helix chain 'A' and resid 277 through 282 Processing helix chain 'A' and resid 301 through 307 Processing helix chain 'A' and resid 324 through 335 removed outlier: 3.611A pdb=" N LEU A 328 " --> pdb=" O SER A 324 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 50 removed outlier: 4.233A pdb=" N LYS B 48 " --> pdb=" O PRO B 44 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VAL B 49 " --> pdb=" O MET B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 112 removed outlier: 3.835A pdb=" N ILE B 111 " --> pdb=" O ASN B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 158 through 162 removed outlier: 3.541A pdb=" N LYS B 161 " --> pdb=" O ASP B 158 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU B 162 " --> pdb=" O SER B 159 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 158 through 162' Processing helix chain 'B' and resid 173 through 177 removed outlier: 3.731A pdb=" N GLY B 176 " --> pdb=" O ASN B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 261 Processing helix chain 'B' and resid 279 through 284 Processing helix chain 'B' and resid 301 through 307 Processing helix chain 'B' and resid 324 through 335 removed outlier: 3.741A pdb=" N LEU B 328 " --> pdb=" O SER B 324 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 366 through 367 Processing sheet with id=AA2, first strand: chain 'D' and resid 382 through 384 Processing sheet with id=AA3, first strand: chain 'E' and resid 366 through 367 removed outlier: 3.716A pdb=" N LEU E 380 " --> pdb=" O ALA E 366 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLU E 396 " --> pdb=" O THR E 379 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 382 through 384 Processing sheet with id=AA5, first strand: chain 'E' and resid 439 through 440 removed outlier: 3.865A pdb=" N ILE E 439 " --> pdb=" O MET E 454 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 378 through 384 removed outlier: 6.387A pdb=" N THR F 379 " --> pdb=" O ASP F 395 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 53 through 60 removed outlier: 7.938A pdb=" N SER C 93 " --> pdb=" O ASN C 107 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N ASN C 107 " --> pdb=" O SER C 93 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N TYR C 103 " --> pdb=" O ILE C 97 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N ILE C 140 " --> pdb=" O SER C 134 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N SER C 134 " --> pdb=" O ILE C 140 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N LEU C 142 " --> pdb=" O ILE C 132 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N ILE C 117 " --> pdb=" O ALA C 129 " (cutoff:3.500A) removed outlier: 8.616A pdb=" N LEU C 131 " --> pdb=" O GLN C 115 " (cutoff:3.500A) removed outlier: 11.399A pdb=" N GLN C 115 " --> pdb=" O LEU C 131 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N GLU C 59 " --> pdb=" O GLN C 115 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N ILE C 117 " --> pdb=" O ARG C 57 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N ARG C 57 " --> pdb=" O ILE C 117 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N ILE C 119 " --> pdb=" O SER C 55 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N SER C 55 " --> pdb=" O ILE C 119 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 155 through 156 removed outlier: 7.263A pdb=" N ALA C 155 " --> pdb=" O LEU C 225 " (cutoff:3.500A) removed outlier: 8.149A pdb=" N GLY C 227 " --> pdb=" O ALA C 155 " (cutoff:3.500A) removed outlier: 5.814A pdb=" N ASN C 229 " --> pdb=" O ILE C 246 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N ILE C 246 " --> pdb=" O ASN C 229 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA C 231 " --> pdb=" O PHE C 244 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N GLN C 204 " --> pdb=" O LEU C 189 " (cutoff:3.500A) removed outlier: 5.753A pdb=" N LEU C 189 " --> pdb=" O GLN C 204 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N LEU C 218 " --> pdb=" O ILE C 226 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 271 through 275 removed outlier: 6.597A pdb=" N THR C 274 " --> pdb=" O VAL C 294 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N VAL C 294 " --> pdb=" O THR C 274 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 271 through 275 removed outlier: 6.597A pdb=" N THR C 274 " --> pdb=" O VAL C 294 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N VAL C 294 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N GLY C 344 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N LEU C 317 " --> pdb=" O LYS C 342 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N LYS C 342 " --> pdb=" O LEU C 317 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 53 through 60 removed outlier: 7.809A pdb=" N SER A 93 " --> pdb=" O ASN A 107 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N ASN A 107 " --> pdb=" O SER A 93 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N TYR A 103 " --> pdb=" O ILE A 97 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N ILE A 140 " --> pdb=" O SER A 134 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N SER A 134 " --> pdb=" O ILE A 140 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N LEU A 142 " --> pdb=" O ILE A 132 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N ILE A 117 " --> pdb=" O ALA A 129 " (cutoff:3.500A) removed outlier: 8.623A pdb=" N LEU A 131 " --> pdb=" O GLN A 115 " (cutoff:3.500A) removed outlier: 11.749A pdb=" N GLN A 115 " --> pdb=" O LEU A 131 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N GLU A 59 " --> pdb=" O GLN A 115 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N ILE A 117 " --> pdb=" O ARG A 57 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ARG A 57 " --> pdb=" O ILE A 117 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N ILE A 119 " --> pdb=" O SER A 55 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N SER A 55 " --> pdb=" O ILE A 119 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 30 through 31 removed outlier: 3.752A pdb=" N ILE A 232 " --> pdb=" O UNK G 30 " (cutoff:3.500A) removed outlier: 5.797A pdb=" N ASN A 229 " --> pdb=" O ILE A 246 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N ILE A 246 " --> pdb=" O ASN A 229 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N GLN A 204 " --> pdb=" O LEU A 189 " (cutoff:3.500A) removed outlier: 5.736A pdb=" N LEU A 189 " --> pdb=" O GLN A 204 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N LEU A 218 " --> pdb=" O ILE A 226 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 267 through 268 removed outlier: 3.646A pdb=" N LEU A 268 " --> pdb=" O ASP A 359 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 271 through 275 removed outlier: 6.818A pdb=" N LYS A 272 " --> pdb=" O SER A 295 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 271 through 275 removed outlier: 6.818A pdb=" N LYS A 272 " --> pdb=" O SER A 295 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N GLY A 344 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N LEU A 317 " --> pdb=" O LYS A 342 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N LYS A 342 " --> pdb=" O LEU A 317 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 53 through 60 removed outlier: 6.525A pdb=" N TYR B 103 " --> pdb=" O ILE B 97 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N ILE B 140 " --> pdb=" O SER B 134 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N SER B 134 " --> pdb=" O ILE B 140 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N LEU B 142 " --> pdb=" O ILE B 132 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N ILE B 117 " --> pdb=" O ALA B 129 " (cutoff:3.500A) removed outlier: 8.837A pdb=" N LEU B 131 " --> pdb=" O GLN B 115 " (cutoff:3.500A) removed outlier: 11.671A pdb=" N GLN B 115 " --> pdb=" O LEU B 131 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 167 through 172 removed outlier: 5.345A pdb=" N PHE B 202 " --> pdb=" O GLY B 190 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N PHE B 244 " --> pdb=" O THR B 230 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N LEU B 218 " --> pdb=" O ILE B 226 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 267 through 268 removed outlier: 3.588A pdb=" N ASP B 359 " --> pdb=" O LEU B 268 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 271 through 275 removed outlier: 6.693A pdb=" N THR B 274 " --> pdb=" O VAL B 294 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N VAL B 294 " --> pdb=" O THR B 274 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 271 through 275 removed outlier: 6.693A pdb=" N THR B 274 " --> pdb=" O VAL B 294 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N VAL B 294 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N GLY B 344 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N LEU B 317 " --> pdb=" O LYS B 342 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N LYS B 342 " --> pdb=" O LEU B 317 " (cutoff:3.500A) 334 hydrogen bonds defined for protein. 870 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: 1.45 Time building geometry restraints manager: 0.86 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: 1945 1.33 - 1.45: 1487 1.45 - 1.57: 5197 1.57 - 1.69: 0 1.69 - 1.81: 34 Bond restraints: 8663 Sorted by residual: bond pdb=" N ILE B 232 " pdb=" CA ILE B 232 " ideal model delta sigma weight residual 1.458 1.500 -0.042 1.08e-02 8.57e+03 1.52e+01 bond pdb=" N ILE D 443 " pdb=" CA ILE D 443 " ideal model delta sigma weight residual 1.459 1.507 -0.048 1.25e-02 6.40e+03 1.49e+01 bond pdb=" N ILE F 443 " pdb=" CA ILE F 443 " ideal model delta sigma weight residual 1.459 1.506 -0.047 1.25e-02 6.40e+03 1.43e+01 bond pdb=" N VAL F 444 " pdb=" CA VAL F 444 " ideal model delta sigma weight residual 1.459 1.497 -0.038 1.25e-02 6.40e+03 9.31e+00 bond pdb=" N ILE E 443 " pdb=" CA ILE E 443 " ideal model delta sigma weight residual 1.459 1.497 -0.038 1.25e-02 6.40e+03 9.25e+00 ... (remaining 8658 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.14: 11574 3.14 - 6.28: 110 6.28 - 9.42: 8 9.42 - 12.56: 1 12.56 - 15.70: 3 Bond angle restraints: 11696 Sorted by residual: angle pdb=" C ILE D 438 " pdb=" N ILE D 439 " pdb=" CA ILE D 439 " ideal model delta sigma weight residual 122.93 115.75 7.18 1.31e+00 5.83e-01 3.00e+01 angle pdb=" N UNK G 29 " pdb=" CA UNK G 29 " pdb=" C UNK G 29 " ideal model delta sigma weight residual 110.74 95.04 15.70 3.00e+00 1.11e-01 2.74e+01 angle pdb=" N UNK G 30 " pdb=" CA UNK G 30 " pdb=" C UNK G 30 " ideal model delta sigma weight residual 110.74 97.52 13.22 3.00e+00 1.11e-01 1.94e+01 angle pdb=" CA LEU B 233 " pdb=" C LEU B 233 " pdb=" O LEU B 233 " ideal model delta sigma weight residual 120.70 115.99 4.71 1.08e+00 8.57e-01 1.90e+01 angle pdb=" N UNK G 33 " pdb=" CA UNK G 33 " pdb=" C UNK G 33 " ideal model delta sigma weight residual 110.74 123.52 -12.78 3.00e+00 1.11e-01 1.82e+01 ... (remaining 11691 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.54: 4579 17.54 - 35.07: 504 35.07 - 52.61: 161 52.61 - 70.14: 48 70.14 - 87.68: 15 Dihedral angle restraints: 5307 sinusoidal: 2032 harmonic: 3275 Sorted by residual: dihedral pdb=" CA UNK G 33 " pdb=" C UNK G 33 " pdb=" N UNK G 34 " pdb=" CA UNK G 34 " ideal model delta harmonic sigma weight residual -180.00 -155.02 -24.98 0 5.00e+00 4.00e-02 2.50e+01 dihedral pdb=" CD ARG D 445 " pdb=" NE ARG D 445 " pdb=" CZ ARG D 445 " pdb=" NH1 ARG D 445 " ideal model delta sinusoidal sigma weight residual 0.00 36.07 -36.07 1 1.00e+01 1.00e-02 1.84e+01 dihedral pdb=" CA ASN A 201 " pdb=" C ASN A 201 " pdb=" N PHE A 202 " pdb=" CA PHE A 202 " ideal model delta harmonic sigma weight residual 180.00 -159.60 -20.40 0 5.00e+00 4.00e-02 1.66e+01 ... (remaining 5304 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.095: 1280 0.095 - 0.189: 127 0.189 - 0.284: 4 0.284 - 0.378: 2 0.378 - 0.473: 1 Chirality restraints: 1414 Sorted by residual: chirality pdb=" CA UNK G 33 " pdb=" N UNK G 33 " pdb=" C UNK G 33 " pdb=" CB UNK G 33 " both_signs ideal model delta sigma weight residual False 2.52 2.05 0.47 2.00e-01 2.50e+01 5.58e+00 chirality pdb=" CB ILE B 111 " pdb=" CA ILE B 111 " pdb=" CG1 ILE B 111 " pdb=" CG2 ILE B 111 " both_signs ideal model delta sigma weight residual False 2.64 2.33 0.31 2.00e-01 2.50e+01 2.45e+00 chirality pdb=" CB VAL D 444 " pdb=" CA VAL D 444 " pdb=" CG1 VAL D 444 " pdb=" CG2 VAL D 444 " both_signs ideal model delta sigma weight residual False -2.63 -2.33 -0.30 2.00e-01 2.50e+01 2.31e+00 ... (remaining 1411 not shown) Planarity restraints: 1539 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG D 445 " 0.638 9.50e-02 1.11e+02 2.86e-01 4.99e+01 pdb=" NE ARG D 445 " -0.038 2.00e-02 2.50e+03 pdb=" CZ ARG D 445 " -0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG D 445 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG D 445 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU B 336 " 0.065 5.00e-02 4.00e+02 9.75e-02 1.52e+01 pdb=" N PRO B 337 " -0.169 5.00e-02 4.00e+02 pdb=" CA PRO B 337 " 0.050 5.00e-02 4.00e+02 pdb=" CD PRO B 337 " 0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE E 443 " -0.013 2.00e-02 2.50e+03 2.56e-02 6.55e+00 pdb=" C ILE E 443 " 0.044 2.00e-02 2.50e+03 pdb=" O ILE E 443 " -0.017 2.00e-02 2.50e+03 pdb=" N VAL E 444 " -0.015 2.00e-02 2.50e+03 ... (remaining 1536 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 334 2.72 - 3.26: 7630 3.26 - 3.81: 12822 3.81 - 4.35: 16367 4.35 - 4.90: 28390 Nonbonded interactions: 65543 Sorted by model distance: nonbonded pdb=" NZ LYS C 116 " pdb=" OD1 ASP C 128 " model vdw 2.171 3.120 nonbonded pdb=" OE2 GLU C 275 " pdb=" OG SER C 324 " model vdw 2.185 3.040 nonbonded pdb=" OG SER C 149 " pdb=" NZ LYS C 150 " model vdw 2.273 3.120 nonbonded pdb=" O GLY B 198 " pdb=" NH1 ARG B 329 " model vdw 2.298 3.120 nonbonded pdb=" OE1 GLU A 275 " pdb=" OG SER A 324 " model vdw 2.310 3.040 ... (remaining 65538 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' } ncs_group { reference = chain 'D' selection = (chain 'E' and (resid 365 through 449 or resid 451 through 452)) selection = (chain 'F' and (resid 365 through 449 or resid 451 through 452)) } ncs_group { reference = (chain 'G' and resid 29 through 35) selection = chain 'I' } 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: 5.950 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: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 10.260 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.030 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:6.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7150 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 0.074 8663 Z= 0.262 Angle : 0.816 15.696 11696 Z= 0.464 Chirality : 0.054 0.473 1414 Planarity : 0.010 0.286 1539 Dihedral : 17.673 87.678 3213 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.44 % Allowed : 2.26 % Favored : 97.30 % Rotamer: Outliers : 3.54 % Allowed : 23.56 % Favored : 72.90 % 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: -0.24 (0.24), residues: 1148 helix: 0.21 (0.38), residues: 195 sheet: 0.27 (0.28), residues: 324 loop : -0.44 (0.24), residues: 629 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 419 TYR 0.008 0.002 TYR E 451 PHE 0.013 0.002 PHE C 127 HIS 0.005 0.002 HIS C 109 Details of bonding type rmsd covalent geometry : bond 0.00486 ( 8663) covalent geometry : angle 0.81555 (11696) hydrogen bonds : bond 0.17100 ( 321) hydrogen bonds : angle 7.10359 ( 870) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 103 time to evaluate : 0.346 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 32 outliers final: 15 residues processed: 128 average time/residue: 0.5154 time to fit residues: 70.5971 Evaluate side-chains 76 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 61 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 443 ILE Chi-restraints excluded: chain E residue 452 LEU Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 118 SER Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 275 GLU Chi-restraints excluded: chain C residue 334 THR Chi-restraints excluded: chain A residue 118 SER Chi-restraints excluded: chain A residue 149 SER Chi-restraints excluded: chain A residue 303 SER Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain B residue 100 SER Chi-restraints excluded: chain B residue 334 THR Chi-restraints excluded: chain B residue 339 THR 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: 55.6266 > 50: distance: 70 - 143: 12.927 distance: 73 - 140: 12.768 distance: 80 - 124: 10.821 distance: 106 - 113: 4.362 distance: 113 - 114: 8.674 distance: 114 - 117: 5.840 distance: 115 - 116: 6.028 distance: 115 - 121: 3.066 distance: 117 - 118: 12.452 distance: 118 - 119: 12.222 distance: 118 - 120: 4.393 distance: 121 - 122: 3.392 distance: 122 - 123: 5.487 distance: 122 - 125: 4.345 distance: 125 - 126: 3.745 distance: 126 - 127: 6.851 distance: 126 - 128: 9.368 distance: 129 - 131: 4.234 distance: 130 - 131: 11.107 distance: 132 - 256: 10.754 distance: 133 - 134: 6.354 distance: 133 - 136: 3.915 distance: 134 - 135: 4.548 distance: 135 - 253: 14.287 distance: 136 - 137: 6.174 distance: 136 - 138: 6.191 distance: 137 - 139: 9.468 distance: 140 - 141: 3.484 distance: 141 - 142: 3.767 distance: 141 - 144: 4.623 distance: 142 - 149: 3.726 distance: 145 - 146: 7.674 distance: 146 - 147: 6.185 distance: 146 - 148: 7.691 distance: 149 - 150: 4.548 distance: 149 - 243: 13.981 distance: 150 - 151: 11.376 distance: 150 - 153: 10.540 distance: 151 - 152: 9.032 distance: 151 - 156: 5.848 distance: 152 - 240: 10.734 distance: 153 - 155: 5.440 distance: 156 - 157: 3.124 distance: 157 - 158: 5.854 distance: 157 - 160: 8.640 distance: 158 - 159: 9.170 distance: 158 - 164: 5.957 distance: 160 - 161: 10.614 distance: 161 - 162: 5.606 distance: 161 - 163: 4.134 distance: 164 - 165: 5.513 distance: 165 - 166: 9.009 distance: 165 - 168: 9.424 distance: 166 - 167: 15.981 distance: 166 - 169: 8.499 distance: 169 - 170: 4.309 distance: 170 - 173: 9.242 distance: 171 - 175: 3.938 distance: 173 - 174: 15.880 distance: 175 - 176: 14.308 distance: 176 - 177: 21.793 distance: 176 - 179: 24.830 distance: 177 - 178: 15.360 distance: 177 - 183: 6.762 distance: 179 - 180: 9.982 distance: 179 - 181: 32.023 distance: 180 - 182: 3.983 distance: 183 - 184: 8.775 distance: 184 - 185: 8.331 distance: 184 - 187: 7.953 distance: 185 - 186: 4.789 distance: 187 - 188: 17.100 distance: 188 - 189: 15.761 distance: 188 - 190: 12.054