Starting phenix.real_space_refine on Thu Jul 2 14:51:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7rxd_24729/07_2026/7rxd_24729.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rxd_24729/07_2026/7rxd_24729.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7rxd_24729/07_2026/7rxd_24729.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rxd_24729/07_2026/7rxd_24729.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7rxd_24729/07_2026/7rxd_24729.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rxd_24729/07_2026/7rxd_24729.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7rxd_24729/07_2026/7rxd_24729.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7rxd_24729/07_2026/7rxd_24729.cif" } resolution = 3.6 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 Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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 31 5.16 5 C 5749 2.51 5 N 1490 2.21 5 O 1737 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 23 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9007 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 3433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3433 Classifications: {'peptide': 439} Link IDs: {'PTRANS': 24, 'TRANS': 414} Chain breaks: 4 Chain: "H" Number of atoms: 1582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1582 Classifications: {'peptide': 207} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 192} Chain breaks: 2 Chain: "L" Number of atoms: 1588 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1588 Classifications: {'peptide': 204} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 194} Chain breaks: 2 Chain: "N" Number of atoms: 990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 990 Classifications: {'peptide': 125} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 121} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "R" Number of atoms: 1391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1391 Classifications: {'peptide': 173} Link IDs: {'PTRANS': 9, 'TRANS': 163} Chain breaks: 2 Chain: "A" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 23 Unusual residues: {'GLC': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 1.57, per 1000 atoms: 0.17 Number of scatterers: 9007 At special positions: 0 Unit cell: (118.72, 133.56, 111.3, 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 31 16.00 O 1737 8.00 N 1490 7.00 C 5749 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 150 " - pdb=" SG CYS H 206 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 94 " distance=2.04 Simple disulfide: pdb=" SG CYS L 139 " - pdb=" SG CYS L 199 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS R 379 " - pdb=" SG CYS R 432 " distance=2.05 Simple disulfide: pdb=" SG CYS R 480 " - pdb=" SG CYS R 488 " 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 Links applied ALPHA1-4 " GLC A 1 " - " GLC A 2 " Time building additional restraints: 0.71 Conformation dependent library (CDL) restraints added in 421.6 milliseconds 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2126 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 22 sheets defined 27.9% alpha, 33.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing helix chain 'B' and resid 17 through 28 Processing helix chain 'B' and resid 43 through 52 Proline residue: B 49 - end of helix Processing helix chain 'B' and resid 64 through 74 removed outlier: 4.055A pdb=" N PHE B 68 " --> pdb=" O ALA B 64 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLY B 69 " --> pdb=" O HIS B 65 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N GLY B 70 " --> pdb=" O ASP B 66 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 89 Processing helix chain 'B' and resid 91 through 98 removed outlier: 3.553A pdb=" N TRP B 95 " --> pdb=" O TYR B 91 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 141 removed outlier: 4.490A pdb=" N ALA B 135 " --> pdb=" O GLU B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 154 through 164 removed outlier: 3.923A pdb=" N THR B 158 " --> pdb=" O GLU B 154 " (cutoff:3.500A) Proline residue: B 160 - end of helix Processing helix chain 'B' and resid 182 through 185 removed outlier: 4.399A pdb=" N ASP B 185 " --> pdb=" O VAL B 182 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 182 through 185' Processing helix chain 'B' and resid 186 through 202 Processing helix chain 'B' and resid 210 through 220 Processing helix chain 'B' and resid 229 through 231 No H-bonds generated for 'chain 'B' and resid 229 through 231' Processing helix chain 'B' and resid 232 through 240 Processing helix chain 'B' and resid 273 through 284 Processing helix chain 'B' and resid 287 through 298 removed outlier: 3.640A pdb=" N ASP B 297 " --> pdb=" O ALA B 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 313 Processing helix chain 'B' and resid 315 through 328 Processing helix chain 'B' and resid 336 through 353 removed outlier: 3.913A pdb=" N PHE B 340 " --> pdb=" O GLN B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 357 through 370 removed outlier: 3.610A pdb=" N MET B 370 " --> pdb=" O GLN B 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 374 through 388 Processing helix chain 'B' and resid 391 through 406 Processing helix chain 'B' and resid 502 through 517 Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.568A pdb=" N PHE H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.798A pdb=" N THR H 91 " --> pdb=" O SER H 88 " (cutoff:3.500A) Processing helix chain 'L' and resid 85 through 89 Processing helix chain 'L' and resid 126 through 133 Processing helix chain 'L' and resid 188 through 194 removed outlier: 3.722A pdb=" N HIS L 194 " --> pdb=" O ASP L 190 " (cutoff:3.500A) Processing helix chain 'N' and resid 62 through 65 removed outlier: 3.531A pdb=" N LYS N 65 " --> pdb=" O ASP N 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 62 through 65' Processing helix chain 'N' and resid 87 through 91 Processing helix chain 'R' and resid 337 through 343 removed outlier: 3.748A pdb=" N VAL R 341 " --> pdb=" O PRO R 337 " (cutoff:3.500A) Processing helix chain 'R' and resid 365 through 370 Processing helix chain 'R' and resid 383 through 387 removed outlier: 3.798A pdb=" N LEU R 387 " --> pdb=" O PRO R 384 " (cutoff:3.500A) Processing helix chain 'R' and resid 405 through 410 removed outlier: 4.935A pdb=" N ARG R 408 " --> pdb=" O ASP R 405 " (cutoff:3.500A) Processing helix chain 'R' and resid 416 through 422 Processing helix chain 'R' and resid 438 through 443 Processing helix chain 'R' and resid 502 through 505 Processing sheet with id=AA1, first strand: chain 'B' and resid 37 through 39 removed outlier: 5.958A pdb=" N ILE B 10 " --> pdb=" O GLU B 39 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N VAL B 9 " --> pdb=" O ILE B 60 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N PHE B 62 " --> pdb=" O VAL B 9 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N TRP B 11 " --> pdb=" O PHE B 62 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N ALA B 265 " --> pdb=" O PRO B 108 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 37 through 39 removed outlier: 5.958A pdb=" N ILE B 10 " --> pdb=" O GLU B 39 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N VAL B 9 " --> pdb=" O ILE B 60 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N PHE B 62 " --> pdb=" O VAL B 9 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N TRP B 11 " --> pdb=" O PHE B 62 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 99 through 100 Processing sheet with id=AA4, first strand: chain 'B' and resid 225 through 228 Processing sheet with id=AA5, first strand: chain 'B' and resid 171 through 173 removed outlier: 4.055A pdb=" N LYS B 171 " --> pdb=" O ASP B 178 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 250 through 251 Processing sheet with id=AA7, first strand: chain 'B' and resid 522 through 526 Processing sheet with id=AA8, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AA9, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.770A pdb=" N GLY H 33 " --> pdb=" O ARG H 99 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N MET H 34 " --> pdb=" O TYR H 50 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N TYR H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ALA H 40 " --> pdb=" O GLY H 44 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 130 through 134 removed outlier: 4.043A pdb=" N GLY H 149 " --> pdb=" O LEU H 134 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N TYR H 186 " --> pdb=" O ASP H 154 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 130 through 134 removed outlier: 4.043A pdb=" N GLY H 149 " --> pdb=" O LEU H 134 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N TYR H 186 " --> pdb=" O ASP H 154 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AB4, first strand: chain 'L' and resid 10 through 14 removed outlier: 6.835A pdb=" N LEU L 11 " --> pdb=" O GLU L 110 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N LYS L 112 " --> pdb=" O LEU L 11 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N VAL L 13 " --> pdb=" O LYS L 112 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N LEU L 39 " --> pdb=" O TYR L 55 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N TYR L 55 " --> pdb=" O LEU L 39 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N TRP L 41 " --> pdb=" O LEU L 53 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 10 through 14 removed outlier: 6.835A pdb=" N LEU L 11 " --> pdb=" O GLU L 110 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N LYS L 112 " --> pdb=" O LEU L 11 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N VAL L 13 " --> pdb=" O LYS L 112 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'L' and resid 119 through 123 removed outlier: 5.682A pdb=" N TYR L 178 " --> pdb=" O ASN L 143 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'L' and resid 150 through 154 Processing sheet with id=AB8, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AB9, first strand: chain 'N' and resid 10 through 13 removed outlier: 6.299A pdb=" N GLY N 10 " --> pdb=" O THR N 118 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N SER N 120 " --> pdb=" O GLY N 10 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N VAL N 12 " --> pdb=" O SER N 120 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N LYS N 99 " --> pdb=" O ARG N 33 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ARG N 33 " --> pdb=" O LYS N 99 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N MET N 34 " --> pdb=" O ALA N 50 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N ALA N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'N' and resid 10 through 13 removed outlier: 6.299A pdb=" N GLY N 10 " --> pdb=" O THR N 118 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N SER N 120 " --> pdb=" O GLY N 10 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N VAL N 12 " --> pdb=" O SER N 120 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'R' and resid 354 through 358 removed outlier: 3.921A pdb=" N VAL R 395 " --> pdb=" O ILE R 358 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'R' and resid 452 through 454 Processing sheet with id=AC4, first strand: chain 'R' and resid 473 through 474 423 hydrogen bonds defined for protein. 1116 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: 1.94 Time building geometry restraints manager: 0.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 2864 1.35 - 1.48: 2471 1.48 - 1.61: 3844 1.61 - 1.74: 0 1.74 - 1.87: 47 Bond restraints: 9226 Sorted by residual: bond pdb=" CB CYS R 379 " pdb=" SG CYS R 379 " ideal model delta sigma weight residual 1.808 1.875 -0.067 3.30e-02 9.18e+02 4.09e+00 bond pdb=" CB VAL N 48 " pdb=" CG2 VAL N 48 " ideal model delta sigma weight residual 1.521 1.478 0.043 3.30e-02 9.18e+02 1.68e+00 bond pdb=" CB CYS R 432 " pdb=" SG CYS R 432 " ideal model delta sigma weight residual 1.808 1.768 0.040 3.30e-02 9.18e+02 1.48e+00 bond pdb=" C ILE B 133 " pdb=" N PRO B 134 " ideal model delta sigma weight residual 1.334 1.356 -0.022 2.34e-02 1.83e+03 9.00e-01 bond pdb=" C GLY R 431 " pdb=" N CYS R 432 " ideal model delta sigma weight residual 1.328 1.340 -0.012 1.35e-02 5.49e+03 8.27e-01 ... (remaining 9221 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.65: 12440 2.65 - 5.31: 82 5.31 - 7.96: 3 7.96 - 10.62: 0 10.62 - 13.27: 2 Bond angle restraints: 12527 Sorted by residual: angle pdb=" N CYS R 432 " pdb=" CA CYS R 432 " pdb=" C CYS R 432 " ideal model delta sigma weight residual 107.88 119.63 -11.75 1.41e+00 5.03e-01 6.95e+01 angle pdb=" CA CYS R 432 " pdb=" CB CYS R 432 " pdb=" SG CYS R 432 " ideal model delta sigma weight residual 114.40 127.67 -13.27 2.30e+00 1.89e-01 3.33e+01 angle pdb=" C GLY R 431 " pdb=" N CYS R 432 " pdb=" CA CYS R 432 " ideal model delta sigma weight residual 122.45 118.44 4.01 1.78e+00 3.16e-01 5.07e+00 angle pdb=" N GLU B 23 " pdb=" CA GLU B 23 " pdb=" CB GLU B 23 " ideal model delta sigma weight residual 110.16 113.37 -3.21 1.48e+00 4.57e-01 4.70e+00 angle pdb=" C GLU B 173 " pdb=" N ASN B 174 " pdb=" CA ASN B 174 " ideal model delta sigma weight residual 121.54 125.58 -4.04 1.91e+00 2.74e-01 4.47e+00 ... (remaining 12522 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 4945 17.94 - 35.87: 421 35.87 - 53.81: 73 53.81 - 71.75: 14 71.75 - 89.68: 11 Dihedral angle restraints: 5464 sinusoidal: 2137 harmonic: 3327 Sorted by residual: dihedral pdb=" CA GLU H 158 " pdb=" C GLU H 158 " pdb=" N PRO H 159 " pdb=" CA PRO H 159 " ideal model delta harmonic sigma weight residual 180.00 144.49 35.51 0 5.00e+00 4.00e-02 5.04e+01 dihedral pdb=" CB CYS R 379 " pdb=" SG CYS R 379 " pdb=" SG CYS R 432 " pdb=" CB CYS R 432 " ideal model delta sinusoidal sigma weight residual 93.00 34.17 58.83 1 1.00e+01 1.00e-02 4.63e+01 dihedral pdb=" CB CYS H 150 " pdb=" SG CYS H 150 " pdb=" SG CYS H 206 " pdb=" CB CYS H 206 " ideal model delta sinusoidal sigma weight residual 93.00 140.09 -47.09 1 1.00e+01 1.00e-02 3.06e+01 ... (remaining 5461 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.935: 1366 0.935 - 1.870: 0 1.870 - 2.806: 0 2.806 - 3.741: 0 3.741 - 4.676: 1 Chirality restraints: 1367 Sorted by residual: chirality pdb=" C1 GLC A 1 " pdb=" C2 GLC A 1 " pdb=" O1 GLC A 1 " pdb=" O5 GLC A 1 " both_signs ideal model delta sigma weight residual False 2.33 -2.34 4.68 2.00e-01 2.50e+01 5.47e+02 chirality pdb=" C1 GLC A 2 " pdb=" O4 GLC A 1 " pdb=" C2 GLC A 2 " pdb=" O5 GLC A 2 " both_signs ideal model delta sigma weight residual False 2.40 2.32 0.08 2.00e-02 2.50e+03 1.72e+01 chirality pdb=" CA CYS R 432 " pdb=" N CYS R 432 " pdb=" C CYS R 432 " pdb=" CB CYS R 432 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.79e+00 ... (remaining 1364 not shown) Planarity restraints: 1604 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU H 158 " 0.076 5.00e-02 4.00e+02 1.17e-01 2.19e+01 pdb=" N PRO H 159 " -0.203 5.00e-02 4.00e+02 pdb=" CA PRO H 159 " 0.063 5.00e-02 4.00e+02 pdb=" CD PRO H 159 " 0.063 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER R 383 " -0.053 5.00e-02 4.00e+02 8.02e-02 1.03e+01 pdb=" N PRO R 384 " 0.139 5.00e-02 4.00e+02 pdb=" CA PRO R 384 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO R 384 " -0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 123 " 0.050 5.00e-02 4.00e+02 7.68e-02 9.43e+00 pdb=" N PRO B 124 " -0.133 5.00e-02 4.00e+02 pdb=" CA PRO B 124 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO B 124 " 0.042 5.00e-02 4.00e+02 ... (remaining 1601 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 200 2.69 - 3.24: 8625 3.24 - 3.80: 14199 3.80 - 4.35: 18927 4.35 - 4.90: 31721 Nonbonded interactions: 73672 Sorted by model distance: nonbonded pdb=" OD1 ASP R 442 " pdb=" OH TYR R 451 " model vdw 2.138 3.040 nonbonded pdb=" O MET H 110 " pdb=" OH TYR L 42 " model vdw 2.140 3.040 nonbonded pdb=" ND2 ASN H 207 " pdb=" OD1 ASP H 218 " model vdw 2.145 3.120 nonbonded pdb=" OE1 GLN L 27 " pdb=" OG1 THR N 118 " model vdw 2.204 3.040 nonbonded pdb=" OD2 ASP R 398 " pdb=" OH TYR R 423 " model vdw 2.208 3.040 ... (remaining 73667 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.160 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: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.910 Find NCS groups from input model: 0.060 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: 0.010 Load rotamer database and sin/cos tables:1.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7494 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 9234 Z= 0.139 Angle : 0.573 13.271 12544 Z= 0.303 Chirality : 0.133 4.676 1367 Planarity : 0.005 0.117 1604 Dihedral : 13.877 89.685 3317 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 0.21 % Allowed : 0.21 % Favored : 99.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % Cis-general : 0.00 % Twisted Proline : 1.72 % 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: 0.47 (0.25), residues: 1118 helix: 0.60 (0.33), residues: 261 sheet: 0.60 (0.27), residues: 346 loop : 0.11 (0.29), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG N 38 TYR 0.015 0.001 TYR R 505 PHE 0.020 0.002 PHE B 259 TRP 0.016 0.001 TRP L 56 HIS 0.004 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.14 ( 9226) covalent geometry : angle 0.56424 / 0.30 (12527) SS BOND : bond 0.00845 / 0.42 ( 7) SS BOND : angle 1.87767 / 1.30 ( 14) hydrogen bonds : bond 0.13486 / 8.28 ( 401) hydrogen bonds : angle 6.96838 / 4.82 ( 1116) link_ALPHA1-4 : bond 0.02745 / 1.44 ( 1) link_ALPHA1-4 : angle 5.24159 / 2.78 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 142 time to evaluate : 0.365 Fit side-chains REVERT: B 327 LYS cc_start: 0.8157 (mttt) cc_final: 0.7643 (tptt) REVERT: B 405 HIS cc_start: 0.8620 (t-90) cc_final: 0.8062 (t-170) REVERT: B 485 LEU cc_start: 0.8913 (tp) cc_final: 0.8316 (tp) REVERT: H 6 GLU cc_start: 0.7247 (mp0) cc_final: 0.6941 (mp0) REVERT: H 153 LYS cc_start: 0.8456 (mmtt) cc_final: 0.8255 (mmtp) outliers start: 2 outliers final: 0 residues processed: 143 average time/residue: 0.0946 time to fit residues: 19.3253 Evaluate side-chains 111 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 111 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 108 optimal weight: 10.0000 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 6.9990 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 7.9990 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 4.9990 chunk 106 optimal weight: 0.8980 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 125 ASN B 204 HIS ** B 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 143 ASN ** R 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4304 r_free = 0.4304 target = 0.194480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.163050 restraints weight = 11775.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.159785 restraints weight = 11079.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.157491 restraints weight = 12011.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.158693 restraints weight = 9995.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.159248 restraints weight = 7295.111| |-----------------------------------------------------------------------------| r_work (final): 0.3941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.1033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 9234 Z= 0.196 Angle : 0.603 14.695 12544 Z= 0.314 Chirality : 0.043 0.170 1367 Planarity : 0.005 0.103 1604 Dihedral : 4.512 33.940 1250 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.24 % Allowed : 7.97 % Favored : 90.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % Cis-general : 0.00 % Twisted Proline : 1.72 % 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: 0.62 (0.25), residues: 1118 helix: 1.07 (0.32), residues: 263 sheet: 0.64 (0.27), residues: 344 loop : 0.03 (0.28), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG L 147 TYR 0.035 0.002 TYR R 505 PHE 0.023 0.002 PHE B 510 TRP 0.018 0.002 TRP N 47 HIS 0.003 0.001 HIS L 95 Details of bonding type rmsd/Z covalent geometry : bond 0.00464 / 0.20 ( 9226) covalent geometry : angle 0.59849 / 0.31 (12527) SS BOND : bond 0.00754 / 0.39 ( 7) SS BOND : angle 2.23476 / 1.55 ( 14) hydrogen bonds : bond 0.03514 / 2.22 ( 401) hydrogen bonds : angle 5.53453 / 3.89 ( 1116) link_ALPHA1-4 : bond 0.00200 / 0.11 ( 1) link_ALPHA1-4 : angle 1.80920 / 1.06 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 134 time to evaluate : 0.372 Fit side-chains REVERT: B 318 ILE cc_start: 0.8707 (mm) cc_final: 0.8373 (mp) REVERT: B 405 HIS cc_start: 0.8672 (t-90) cc_final: 0.8159 (t-170) REVERT: B 532 PHE cc_start: 0.7631 (m-80) cc_final: 0.7181 (m-80) REVERT: H 6 GLU cc_start: 0.7246 (mp0) cc_final: 0.6978 (mp0) REVERT: H 219 LYS cc_start: 0.7540 (tppt) cc_final: 0.7300 (tppt) REVERT: R 357 ARG cc_start: 0.6722 (ttp-170) cc_final: 0.6502 (ttp-170) outliers start: 12 outliers final: 10 residues processed: 139 average time/residue: 0.0929 time to fit residues: 18.4772 Evaluate side-chains 128 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 118 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain H residue 89 GLU Chi-restraints excluded: chain H residue 110 MET Chi-restraints excluded: chain L residue 3 MET Chi-restraints excluded: chain L residue 21 MET Chi-restraints excluded: chain R residue 392 PHE Chi-restraints excluded: chain R residue 401 VAL Chi-restraints excluded: chain R residue 432 CYS Chi-restraints excluded: chain R residue 478 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 28 optimal weight: 5.9990 chunk 35 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 75 optimal weight: 8.9990 chunk 61 optimal weight: 4.9990 chunk 57 optimal weight: 0.8980 chunk 11 optimal weight: 9.9990 chunk 82 optimal weight: 5.9990 chunk 111 optimal weight: 1.9990 chunk 45 optimal weight: 5.9990 chunk 89 optimal weight: 0.4980 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 101 ASN B 125 ASN B 204 HIS ** B 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 32 ASN ** R 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.190546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.160659 restraints weight = 11518.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.159694 restraints weight = 16571.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.162060 restraints weight = 15027.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.162282 restraints weight = 9117.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.163189 restraints weight = 7969.322| |-----------------------------------------------------------------------------| r_work (final): 0.4015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.1301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 9234 Z= 0.169 Angle : 0.567 13.752 12544 Z= 0.296 Chirality : 0.043 0.276 1367 Planarity : 0.005 0.093 1604 Dihedral : 4.442 32.308 1250 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 1.66 % Allowed : 12.32 % Favored : 86.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % Cis-general : 0.00 % Twisted Proline : 1.72 % 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: 0.63 (0.25), residues: 1118 helix: 1.16 (0.32), residues: 265 sheet: 0.56 (0.26), residues: 354 loop : 0.03 (0.29), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 147 TYR 0.027 0.001 TYR R 505 PHE 0.017 0.002 PHE R 374 TRP 0.020 0.001 TRP N 47 HIS 0.004 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00404 / 0.17 ( 9226) covalent geometry : angle 0.56201 / 0.29 (12527) SS BOND : bond 0.00873 / 0.47 ( 7) SS BOND : angle 2.14795 / 1.44 ( 14) hydrogen bonds : bond 0.03114 / 1.97 ( 401) hydrogen bonds : angle 5.28331 / 3.73 ( 1116) link_ALPHA1-4 : bond 0.00065 / 0.03 ( 1) link_ALPHA1-4 : angle 1.59323 / 0.86 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 132 time to evaluate : 0.248 Fit side-chains REVERT: B 405 HIS cc_start: 0.8652 (t-90) cc_final: 0.8177 (t-170) REVERT: H 219 LYS cc_start: 0.7590 (tppt) cc_final: 0.7372 (tppt) REVERT: L 87 GLU cc_start: 0.8195 (pp20) cc_final: 0.7946 (pp20) REVERT: R 357 ARG cc_start: 0.6908 (ttp-170) cc_final: 0.6556 (ttp-170) outliers start: 16 outliers final: 12 residues processed: 140 average time/residue: 0.0848 time to fit residues: 17.4463 Evaluate side-chains 133 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 121 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 110 MET Chi-restraints excluded: chain L residue 3 MET Chi-restraints excluded: chain L residue 21 MET Chi-restraints excluded: chain L residue 66 ASP Chi-restraints excluded: chain L residue 95 HIS Chi-restraints excluded: chain R residue 401 VAL Chi-restraints excluded: chain R residue 432 CYS Chi-restraints excluded: chain R residue 478 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/site-packages/iotbx/cli_parser.py", line 987, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( ^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1602, in energies_sites pair_proxies = self.pair_proxies( ^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1505, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1386, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 54.9108 > 50: distance: 27 - 97: 10.020 distance: 43 - 82: 21.068 distance: 46 - 79: 6.893 distance: 52 - 78: 3.639 distance: 71 - 73: 9.271 distance: 73 - 74: 3.470 distance: 73 - 225: 10.562 distance: 74 - 75: 10.183 distance: 74 - 77: 12.183 distance: 75 - 76: 12.932 distance: 75 - 79: 14.541 distance: 76 - 222: 15.420 distance: 77 - 78: 10.902 distance: 79 - 80: 11.750 distance: 80 - 81: 20.625 distance: 80 - 83: 4.355 distance: 81 - 82: 28.225 distance: 81 - 86: 20.878 distance: 83 - 84: 8.589 distance: 83 - 85: 3.793 distance: 86 - 87: 10.765 distance: 86 - 211: 5.970 distance: 87 - 88: 19.051 distance: 87 - 90: 6.922 distance: 88 - 89: 24.260 distance: 88 - 94: 18.653 distance: 89 - 208: 14.979 distance: 90 - 91: 6.287 distance: 90 - 92: 10.096 distance: 94 - 95: 6.533 distance: 95 - 98: 5.986 distance: 96 - 97: 8.521 distance: 96 - 99: 6.567 distance: 99 - 100: 8.569 distance: 99 - 193: 7.327 distance: 100 - 101: 5.529 distance: 100 - 103: 4.048 distance: 101 - 102: 18.416 distance: 101 - 113: 5.080 distance: 102 - 190: 12.025 distance: 103 - 104: 5.898 distance: 105 - 107: 3.507 distance: 106 - 108: 4.176 distance: 108 - 110: 3.338 distance: 111 - 112: 4.008 distance: 113 - 114: 8.862 distance: 114 - 115: 6.951 distance: 114 - 117: 14.600 distance: 115 - 116: 13.507 distance: 115 - 121: 7.891 distance: 117 - 118: 10.652 distance: 118 - 119: 15.357 distance: 118 - 120: 10.143 distance: 121 - 122: 9.561 distance: 122 - 123: 3.201 distance: 122 - 125: 3.428 distance: 123 - 124: 15.107 distance: 123 - 127: 3.889 distance: 124 - 151: 12.126 distance: 125 - 126: 10.102 distance: 127 - 128: 8.604 distance: 128 - 129: 15.515 distance: 128 - 131: 7.686 distance: 129 - 130: 11.368 distance: 129 - 135: 14.584 distance: 130 - 159: 3.425 distance: 131 - 132: 13.254 distance: 132 - 134: 5.347 distance: 135 - 136: 14.594 distance: 136 - 137: 13.748 distance: 136 - 139: 9.626 distance: 137 - 138: 14.780 distance: 137 - 143: 22.648 distance: 139 - 140: 16.650 distance: 140 - 141: 6.133 distance: 140 - 142: 3.367 distance: 143 - 144: 30.352 distance: 144 - 145: 24.704 distance: 144 - 147: 27.850 distance: 145 - 146: 25.303 distance: 145 - 151: 3.743 distance: 147 - 148: 25.919 distance: 148 - 149: 19.040 distance: 148 - 150: 14.137