Starting phenix.real_space_refine on Sat Aug 23 03:53:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/3j9s_6272/08_2025/3j9s_6272.cif Found real_map, /net/cci-nas-00/data/ceres_data/3j9s_6272/08_2025/3j9s_6272.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/3j9s_6272/08_2025/3j9s_6272.map" default_real_map = "/net/cci-nas-00/data/ceres_data/3j9s_6272/08_2025/3j9s_6272.map" model { file = "/net/cci-nas-00/data/ceres_data/3j9s_6272/08_2025/3j9s_6272.cif" } default_model = "/net/cci-nas-00/data/ceres_data/3j9s_6272/08_2025/3j9s_6272.cif" } resolution = 2.6 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 ------------------------------------------------------------------------------- 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= 0.007 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: 7 Type Number sf(0) Gaussians Ca 6 9.91 5 Zn 3 6.06 5 S 45 5.16 5 Cl 3 4.86 5 C 6012 2.51 5 N 1638 2.21 5 O 2106 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 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: 9813 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 398, 3162 Unusual residues: {'ACE': 1} Classifications: {'peptide': 397, 'undetermined': 1} Modifications used: {'COO': 1} Link IDs: {'ACE_C-N': 1, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 376} Chain: "A" Number of atoms: 109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 109 Unusual residues: {' CA': 2, ' CL': 1, ' ZN': 1} Classifications: {'undetermined': 4, 'water': 105} Link IDs: {None: 108} Chain: "B" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 105 Classifications: {'water': 105} Link IDs: {None: 104} Chain: "C" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 105 Classifications: {'water': 105} Link IDs: {None: 104} Restraints were copied for chains: B, C Time building chain proxies: 1.96, per 1000 atoms: 0.20 Number of scatterers: 9813 At special positions: 0 Unit cell: (87.978, 84.909, 106.392, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 3 29.99 Ca 6 19.99 Cl 3 17.00 S 45 16.00 O 2106 8.00 N 1638 7.00 C 6012 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: 0.83 Conformation dependent library (CDL) restraints added in 276.6 milliseconds Enol-peptide restraints added in 476.8 nanoseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN C 501 " pdb="ZN ZN C 501 " - pdb=" NE2 HIS A 153 " pdb="ZN ZN C 501 " - pdb=" NE2 HIS B 153 " pdb="ZN ZN C 501 " - pdb=" NE2 HIS C 153 " 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2268 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 12 sheets defined 38.0% alpha, 30.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.24 Creating SS restraints... Processing helix chain 'A' and resid 1 through 18 Processing helix chain 'A' and resid 23 through 42 removed outlier: 3.932A pdb=" N VAL A 27 " --> pdb=" O LEU A 23 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N ASP A 29 " --> pdb=" O SER A 25 " (cutoff:3.500A) removed outlier: 5.556A pdb=" N LEU A 30 " --> pdb=" O ASN A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 101 removed outlier: 3.735A pdb=" N THR A 84 " --> pdb=" O THR A 80 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL A 101 " --> pdb=" O MET A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 120 Processing helix chain 'A' and resid 122 through 128 removed outlier: 3.867A pdb=" N ARG A 126 " --> pdb=" O LYS A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 144 Processing helix chain 'A' and resid 201 through 203 No H-bonds generated for 'chain 'A' and resid 201 through 203' Processing helix chain 'A' and resid 301 through 308 removed outlier: 3.636A pdb=" N LEU A 307 " --> pdb=" O ALA A 303 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N PHE A 308 " --> pdb=" O VAL A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 341 through 353 Processing helix chain 'A' and resid 362 through 365 Processing helix chain 'A' and resid 366 through 373 Processing helix chain 'A' and resid 375 through 396 removed outlier: 3.994A pdb=" N LEU A 395 " --> pdb=" O ILE A 391 " (cutoff:3.500A) Processing helix chain 'B' and resid 1 through 18 Processing helix chain 'B' and resid 23 through 42 removed outlier: 3.932A pdb=" N VAL B 27 " --> pdb=" O LEU B 23 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N ASP B 29 " --> pdb=" O SER B 25 " (cutoff:3.500A) removed outlier: 5.555A pdb=" N LEU B 30 " --> pdb=" O ASN B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 101 removed outlier: 3.736A pdb=" N THR B 84 " --> pdb=" O THR B 80 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VAL B 101 " --> pdb=" O MET B 97 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 120 Processing helix chain 'B' and resid 122 through 128 removed outlier: 3.867A pdb=" N ARG B 126 " --> pdb=" O LYS B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 133 through 144 Processing helix chain 'B' and resid 201 through 203 No H-bonds generated for 'chain 'B' and resid 201 through 203' Processing helix chain 'B' and resid 301 through 308 removed outlier: 3.637A pdb=" N LEU B 307 " --> pdb=" O ALA B 303 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N PHE B 308 " --> pdb=" O VAL B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 341 through 353 Processing helix chain 'B' and resid 362 through 365 Processing helix chain 'B' and resid 366 through 373 Processing helix chain 'B' and resid 375 through 396 removed outlier: 3.994A pdb=" N LEU B 395 " --> pdb=" O ILE B 391 " (cutoff:3.500A) Processing helix chain 'C' and resid 1 through 18 Processing helix chain 'C' and resid 23 through 42 removed outlier: 3.932A pdb=" N VAL C 27 " --> pdb=" O LEU C 23 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N ASP C 29 " --> pdb=" O SER C 25 " (cutoff:3.500A) removed outlier: 5.555A pdb=" N LEU C 30 " --> pdb=" O ASN C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 74 through 101 removed outlier: 3.735A pdb=" N THR C 84 " --> pdb=" O THR C 80 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL C 101 " --> pdb=" O MET C 97 " (cutoff:3.500A) Processing helix chain 'C' and resid 113 through 120 Processing helix chain 'C' and resid 122 through 128 removed outlier: 3.866A pdb=" N ARG C 126 " --> pdb=" O LYS C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 133 through 144 Processing helix chain 'C' and resid 201 through 203 No H-bonds generated for 'chain 'C' and resid 201 through 203' Processing helix chain 'C' and resid 301 through 308 removed outlier: 3.637A pdb=" N LEU C 307 " --> pdb=" O ALA C 303 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N PHE C 308 " --> pdb=" O VAL C 304 " (cutoff:3.500A) Processing helix chain 'C' and resid 341 through 353 Processing helix chain 'C' and resid 362 through 365 Processing helix chain 'C' and resid 366 through 373 Processing helix chain 'C' and resid 375 through 396 removed outlier: 3.994A pdb=" N LEU C 395 " --> pdb=" O ILE C 391 " (cutoff:3.500A) Processing sheet with id=1, first strand: chain 'A' and resid 45 through 48 Processing sheet with id=2, first strand: chain 'A' and resid 150 through 153 Processing sheet with id=3, first strand: chain 'A' and resid 158 through 168 removed outlier: 5.658A pdb=" N GLY A 185 " --> pdb=" O PRO A 159 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N MET A 177 " --> pdb=" O ASN A 167 " (cutoff:3.500A) removed outlier: 5.627A pdb=" N LEU A 324 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N LEU A 226 " --> pdb=" O LEU A 324 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N ILE A 326 " --> pdb=" O THR A 224 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N THR A 224 " --> pdb=" O ILE A 326 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N VAL A 330 " --> pdb=" O THR A 220 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N THR A 220 " --> pdb=" O VAL A 330 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N ASP A 286 " --> pdb=" O LEU A 214 " (cutoff:3.500A) removed outlier: 11.805A pdb=" N ARG A 216 " --> pdb=" O ASN A 284 " (cutoff:3.500A) removed outlier: 10.296A pdb=" N ASN A 284 " --> pdb=" O ARG A 216 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N LEU A 218 " --> pdb=" O ALA A 282 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N ALA A 282 " --> pdb=" O LEU A 218 " (cutoff:3.500A) removed outlier: 9.135A pdb=" N THR A 220 " --> pdb=" O ILE A 280 " (cutoff:3.500A) removed outlier: 10.030A pdb=" N ILE A 280 " --> pdb=" O THR A 220 " (cutoff:3.500A) removed outlier: 9.703A pdb=" N THR A 222 " --> pdb=" O GLY A 278 " (cutoff:3.500A) removed outlier: 10.859A pdb=" N GLY A 278 " --> pdb=" O THR A 222 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N LEU A 264 " --> pdb=" O ASP A 286 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N ILE A 288 " --> pdb=" O GLU A 262 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N GLU A 262 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N LEU A 290 " --> pdb=" O GLU A 260 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N GLU A 260 " --> pdb=" O LEU A 290 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N PHE A 292 " --> pdb=" O ASN A 258 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N ASN A 258 " --> pdb=" O PHE A 292 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N VAL A 259 " --> pdb=" O GLN A 274 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N GLN A 274 " --> pdb=" O VAL A 259 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N ILE A 261 " --> pdb=" O THR A 272 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N THR A 272 " --> pdb=" O ILE A 261 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N PHE A 263 " --> pdb=" O ILE A 270 " (cutoff:3.500A) Processing sheet with id=4, first strand: chain 'A' and resid 236 through 239 Processing sheet with id=5, first strand: chain 'B' and resid 45 through 48 Processing sheet with id=6, first strand: chain 'B' and resid 150 through 153 Processing sheet with id=7, first strand: chain 'B' and resid 158 through 168 removed outlier: 5.658A pdb=" N GLY B 185 " --> pdb=" O PRO B 159 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N MET B 177 " --> pdb=" O ASN B 167 " (cutoff:3.500A) removed outlier: 5.627A pdb=" N LEU B 324 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N LEU B 226 " --> pdb=" O LEU B 324 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N ILE B 326 " --> pdb=" O THR B 224 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N THR B 224 " --> pdb=" O ILE B 326 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N VAL B 330 " --> pdb=" O THR B 220 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N THR B 220 " --> pdb=" O VAL B 330 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N ASP B 286 " --> pdb=" O LEU B 214 " (cutoff:3.500A) removed outlier: 11.805A pdb=" N ARG B 216 " --> pdb=" O ASN B 284 " (cutoff:3.500A) removed outlier: 10.295A pdb=" N ASN B 284 " --> pdb=" O ARG B 216 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N LEU B 218 " --> pdb=" O ALA B 282 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N ALA B 282 " --> pdb=" O LEU B 218 " (cutoff:3.500A) removed outlier: 9.135A pdb=" N THR B 220 " --> pdb=" O ILE B 280 " (cutoff:3.500A) removed outlier: 10.029A pdb=" N ILE B 280 " --> pdb=" O THR B 220 " (cutoff:3.500A) removed outlier: 9.703A pdb=" N THR B 222 " --> pdb=" O GLY B 278 " (cutoff:3.500A) removed outlier: 10.859A pdb=" N GLY B 278 " --> pdb=" O THR B 222 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N LEU B 264 " --> pdb=" O ASP B 286 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N ILE B 288 " --> pdb=" O GLU B 262 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N GLU B 262 " --> pdb=" O ILE B 288 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N LEU B 290 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N GLU B 260 " --> pdb=" O LEU B 290 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N PHE B 292 " --> pdb=" O ASN B 258 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N ASN B 258 " --> pdb=" O PHE B 292 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N VAL B 259 " --> pdb=" O GLN B 274 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N GLN B 274 " --> pdb=" O VAL B 259 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N ILE B 261 " --> pdb=" O THR B 272 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N THR B 272 " --> pdb=" O ILE B 261 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N PHE B 263 " --> pdb=" O ILE B 270 " (cutoff:3.500A) Processing sheet with id=8, first strand: chain 'B' and resid 236 through 239 Processing sheet with id=9, first strand: chain 'C' and resid 45 through 48 Processing sheet with id=10, first strand: chain 'C' and resid 150 through 153 Processing sheet with id=11, first strand: chain 'C' and resid 158 through 168 removed outlier: 5.658A pdb=" N GLY C 185 " --> pdb=" O PRO C 159 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N MET C 177 " --> pdb=" O ASN C 167 " (cutoff:3.500A) removed outlier: 5.628A pdb=" N LEU C 324 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N LEU C 226 " --> pdb=" O LEU C 324 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N ILE C 326 " --> pdb=" O THR C 224 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N THR C 224 " --> pdb=" O ILE C 326 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N VAL C 330 " --> pdb=" O THR C 220 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N THR C 220 " --> pdb=" O VAL C 330 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N ASP C 286 " --> pdb=" O LEU C 214 " (cutoff:3.500A) removed outlier: 11.805A pdb=" N ARG C 216 " --> pdb=" O ASN C 284 " (cutoff:3.500A) removed outlier: 10.295A pdb=" N ASN C 284 " --> pdb=" O ARG C 216 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N LEU C 218 " --> pdb=" O ALA C 282 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N ALA C 282 " --> pdb=" O LEU C 218 " (cutoff:3.500A) removed outlier: 9.135A pdb=" N THR C 220 " --> pdb=" O ILE C 280 " (cutoff:3.500A) removed outlier: 10.030A pdb=" N ILE C 280 " --> pdb=" O THR C 220 " (cutoff:3.500A) removed outlier: 9.703A pdb=" N THR C 222 " --> pdb=" O GLY C 278 " (cutoff:3.500A) removed outlier: 10.859A pdb=" N GLY C 278 " --> pdb=" O THR C 222 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N LEU C 264 " --> pdb=" O ASP C 286 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N ILE C 288 " --> pdb=" O GLU C 262 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N GLU C 262 " --> pdb=" O ILE C 288 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N LEU C 290 " --> pdb=" O GLU C 260 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N GLU C 260 " --> pdb=" O LEU C 290 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N PHE C 292 " --> pdb=" O ASN C 258 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N ASN C 258 " --> pdb=" O PHE C 292 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N VAL C 259 " --> pdb=" O GLN C 274 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N GLN C 274 " --> pdb=" O VAL C 259 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N ILE C 261 " --> pdb=" O THR C 272 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N THR C 272 " --> pdb=" O ILE C 261 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N PHE C 263 " --> pdb=" O ILE C 270 " (cutoff:3.500A) Processing sheet with id=12, first strand: chain 'C' and resid 236 through 239 441 hydrogen bonds defined for protein. 1251 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: 1.23 Time building geometry restraints manager: 1.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 1596 1.29 - 1.42: 2547 1.42 - 1.55: 5459 1.55 - 1.68: 13 1.68 - 1.81: 81 Bond restraints: 9696 Sorted by residual: bond pdb=" C ALA C 110 " pdb=" N PRO C 111 " ideal model delta sigma weight residual 1.333 1.408 -0.076 1.17e-02 7.31e+03 4.20e+01 bond pdb=" C ALA A 110 " pdb=" N PRO A 111 " ideal model delta sigma weight residual 1.333 1.408 -0.076 1.17e-02 7.31e+03 4.18e+01 bond pdb=" C ALA B 110 " pdb=" N PRO B 111 " ideal model delta sigma weight residual 1.333 1.408 -0.076 1.17e-02 7.31e+03 4.17e+01 bond pdb=" C PHE B 361 " pdb=" N PRO B 362 " ideal model delta sigma weight residual 1.335 1.406 -0.071 1.15e-02 7.56e+03 3.82e+01 bond pdb=" C PHE A 361 " pdb=" N PRO A 362 " ideal model delta sigma weight residual 1.335 1.406 -0.071 1.15e-02 7.56e+03 3.82e+01 ... (remaining 9691 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.47: 12516 3.47 - 6.95: 589 6.95 - 10.42: 65 10.42 - 13.90: 3 13.90 - 17.37: 27 Bond angle restraints: 13200 Sorted by residual: angle pdb=" C PHE C 361 " pdb=" N PRO C 362 " pdb=" CA PRO C 362 " ideal model delta sigma weight residual 119.66 113.23 6.43 7.20e-01 1.93e+00 7.98e+01 angle pdb=" C PHE A 361 " pdb=" N PRO A 362 " pdb=" CA PRO A 362 " ideal model delta sigma weight residual 119.66 113.23 6.43 7.20e-01 1.93e+00 7.98e+01 angle pdb=" C PHE B 361 " pdb=" N PRO B 362 " pdb=" CA PRO B 362 " ideal model delta sigma weight residual 119.66 113.29 6.37 7.20e-01 1.93e+00 7.82e+01 angle pdb=" N SER C 339 " pdb=" CA SER C 339 " pdb=" C SER C 339 " ideal model delta sigma weight residual 111.36 120.50 -9.14 1.09e+00 8.42e-01 7.03e+01 angle pdb=" N SER B 339 " pdb=" CA SER B 339 " pdb=" C SER B 339 " ideal model delta sigma weight residual 111.36 120.49 -9.13 1.09e+00 8.42e-01 7.02e+01 ... (remaining 13195 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 4970 17.94 - 35.87: 583 35.87 - 53.81: 198 53.81 - 71.75: 42 71.75 - 89.68: 21 Dihedral angle restraints: 5814 sinusoidal: 2325 harmonic: 3489 Sorted by residual: dihedral pdb=" CH3 ACE B 0 " pdb=" C ACE B 0 " pdb=" N MET B 1 " pdb=" CA MET B 1 " ideal model delta sinusoidal sigma weight residual -180.00 -160.61 -19.39 1 5.00e+00 4.00e-02 2.18e+01 dihedral pdb=" CH3 ACE C 0 " pdb=" C ACE C 0 " pdb=" N MET C 1 " pdb=" CA MET C 1 " ideal model delta sinusoidal sigma weight residual -180.00 -160.66 -19.34 1 5.00e+00 4.00e-02 2.17e+01 dihedral pdb=" CH3 ACE A 0 " pdb=" C ACE A 0 " pdb=" N MET A 1 " pdb=" CA MET A 1 " ideal model delta sinusoidal sigma weight residual -180.00 -160.68 -19.32 1 5.00e+00 4.00e-02 2.16e+01 ... (remaining 5811 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.089: 965 0.089 - 0.179: 349 0.179 - 0.268: 113 0.268 - 0.357: 37 0.357 - 0.447: 27 Chirality restraints: 1491 Sorted by residual: chirality pdb=" CA LYS B 17 " pdb=" N LYS B 17 " pdb=" C LYS B 17 " pdb=" CB LYS B 17 " both_signs ideal model delta sigma weight residual False 2.51 2.06 0.45 2.00e-01 2.50e+01 4.99e+00 chirality pdb=" CA LYS C 17 " pdb=" N LYS C 17 " pdb=" C LYS C 17 " pdb=" CB LYS C 17 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.93e+00 chirality pdb=" CA LYS A 17 " pdb=" N LYS A 17 " pdb=" C LYS A 17 " pdb=" CB LYS A 17 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.93e+00 ... (remaining 1488 not shown) Planarity restraints: 1740 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ACE B 0 " -0.031 2.00e-02 2.50e+03 1.01e-01 1.28e+02 pdb=" O ACE B 0 " -0.024 2.00e-02 2.50e+03 pdb=" CH3 ACE B 0 " 0.092 2.00e-02 2.50e+03 pdb=" N MET B 1 " -0.161 2.00e-02 2.50e+03 pdb=" CA MET B 1 " 0.124 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ACE C 0 " -0.030 2.00e-02 2.50e+03 1.01e-01 1.28e+02 pdb=" O ACE C 0 " -0.024 2.00e-02 2.50e+03 pdb=" CH3 ACE C 0 " 0.091 2.00e-02 2.50e+03 pdb=" N MET C 1 " -0.161 2.00e-02 2.50e+03 pdb=" CA MET C 1 " 0.124 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ACE A 0 " -0.030 2.00e-02 2.50e+03 1.01e-01 1.28e+02 pdb=" O ACE A 0 " -0.024 2.00e-02 2.50e+03 pdb=" CH3 ACE A 0 " 0.091 2.00e-02 2.50e+03 pdb=" N MET A 1 " -0.161 2.00e-02 2.50e+03 pdb=" CA MET A 1 " 0.124 2.00e-02 2.50e+03 ... (remaining 1737 not shown) Histogram of nonbonded interaction distances: 0.22 - 1.15: 9 1.15 - 2.09: 8 2.09 - 3.03: 6267 3.03 - 3.96: 26695 3.96 - 4.90: 54752 Warning: very small nonbonded interaction distances. Nonbonded interactions: 87731 Sorted by model distance: nonbonded pdb="CA CA A 503 " pdb="CA CA C 503 " model vdw 0.216 1.980 nonbonded pdb="CA CA B 503 " pdb="CA CA C 503 " model vdw 0.216 1.980 nonbonded pdb="CA CA A 503 " pdb="CA CA B 503 " model vdw 0.217 1.980 nonbonded pdb="CL CL B 502 " pdb="CL CL C 502 " model vdw 0.273 3.340 nonbonded pdb="CL CL A 502 " pdb="CL CL B 502 " model vdw 0.273 3.340 ... (remaining 87726 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } 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: 0.040 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: 0.150 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 9.260 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:7.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7175 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 : 0.021 0.358 9699 Z= 1.420 Angle : 1.798 17.372 13200 Z= 1.165 Chirality : 0.120 0.447 1491 Planarity : 0.009 0.101 1740 Dihedral : 18.550 89.683 3546 Min Nonbonded Distance : 0.216 Molprobity Statistics. All-atom Clashscore : 25.10 Ramachandran Plot: Outliers : 0.76 % Allowed : 1.27 % Favored : 97.97 % Rotamer: Outliers : 6.86 % Allowed : 17.71 % Favored : 75.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 1.97 (0.24), residues: 1185 helix: 2.81 (0.23), residues: 387 sheet: 1.93 (0.30), residues: 315 loop : -0.44 (0.26), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 168 TYR 0.022 0.005 TYR C 135 PHE 0.043 0.004 PHE A 129 TRP 0.015 0.003 TRP A 247 HIS 0.012 0.004 HIS A 316 Details of bonding type rmsd covalent geometry : bond 0.02029 ( 9696) covalent geometry : angle 1.79764 (13200) hydrogen bonds : bond 0.24496 ( 441) hydrogen bonds : angle 6.87298 ( 1251) metal coordination : bond 0.21303 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 245 time to evaluate : 0.394 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 PHE cc_start: 0.7766 (OUTLIER) cc_final: 0.7299 (p90) outliers start: 72 outliers final: 15 residues processed: 286 average time/residue: 0.6984 time to fit residues: 210.6330 Evaluate side-chains 144 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 128 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 PHE Chi-restraints excluded: chain A residue 134 GLU Chi-restraints excluded: chain A residue 170 GLN Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain B residue 129 PHE Chi-restraints excluded: chain B residue 134 GLU Chi-restraints excluded: chain B residue 205 THR Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 239 THR Chi-restraints excluded: chain B residue 382 LEU Chi-restraints excluded: chain C residue 129 PHE Chi-restraints excluded: chain C residue 134 GLU Chi-restraints excluded: chain C residue 214 LEU Chi-restraints excluded: chain C residue 239 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: 67.8668 > 50: distance: 19 - 23: 19.764 distance: 23 - 24: 27.309 distance: 24 - 25: 45.690 distance: 24 - 27: 67.867 distance: 25 - 26: 52.671 distance: 25 - 30: 51.159 distance: 27 - 28: 49.763 distance: 27 - 29: 47.476 distance: 30 - 31: 47.160 distance: 31 - 32: 42.527 distance: 31 - 34: 31.965 distance: 32 - 33: 49.322 distance: 32 - 39: 37.542 distance: 34 - 35: 12.796 distance: 35 - 36: 23.353 distance: 36 - 37: 21.705 distance: 36 - 38: 6.368 distance: 39 - 40: 14.013 distance: 40 - 41: 67.597 distance: 40 - 43: 52.657 distance: 41 - 42: 65.539 distance: 41 - 47: 46.179 distance: 43 - 44: 18.393 distance: 43 - 45: 45.792 distance: 44 - 46: 23.405 distance: 47 - 48: 39.481 distance: 48 - 49: 50.310 distance: 48 - 51: 38.156 distance: 49 - 50: 50.730 distance: 49 - 56: 33.140 distance: 51 - 52: 30.346 distance: 52 - 53: 20.212 distance: 53 - 54: 25.514 distance: 53 - 55: 30.613 distance: 56 - 57: 7.682 distance: 57 - 58: 33.572 distance: 57 - 60: 51.880 distance: 58 - 59: 58.036 distance: 58 - 67: 58.926 distance: 59 - 112: 26.492 distance: 60 - 61: 27.867 distance: 61 - 62: 7.544 distance: 61 - 63: 22.409 distance: 62 - 64: 14.149 distance: 63 - 65: 11.327 distance: 64 - 66: 19.584 distance: 65 - 66: 13.325 distance: 67 - 68: 32.537 distance: 68 - 69: 36.412 distance: 68 - 71: 23.514 distance: 69 - 70: 19.153 distance: 69 - 75: 29.563 distance: 70 - 169: 4.474 distance: 72 - 73: 4.193 distance: 72 - 74: 7.009 distance: 75 - 76: 37.707 distance: 76 - 77: 38.152 distance: 76 - 79: 26.003 distance: 77 - 78: 35.775 distance: 77 - 83: 32.238 distance: 79 - 80: 21.338 distance: 80 - 81: 37.354 distance: 80 - 82: 55.914 distance: 83 - 84: 26.398 distance: 84 - 85: 9.765 distance: 84 - 87: 4.637 distance: 85 - 86: 19.914 distance: 85 - 91: 7.676 distance: 87 - 88: 12.778 distance: 88 - 89: 17.427 distance: 88 - 90: 24.887 distance: 91 - 92: 19.726 distance: 92 - 93: 36.126 distance: 93 - 94: 27.970 distance: 93 - 95: 35.973 distance: 95 - 96: 18.953 distance: 96 - 97: 16.030 distance: 96 - 99: 12.910 distance: 97 - 98: 12.328 distance: 97 - 104: 7.089 distance: 99 - 100: 6.003 distance: 100 - 101: 4.832 distance: 101 - 102: 3.755 distance: 101 - 103: 10.503