Starting phenix.real_space_refine on Sat Aug 23 08:46:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8iy5_35814/08_2025/8iy5_35814.cif Found real_map, /net/cci-nas-00/data/ceres_data/8iy5_35814/08_2025/8iy5_35814.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8iy5_35814/08_2025/8iy5_35814.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8iy5_35814/08_2025/8iy5_35814.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8iy5_35814/08_2025/8iy5_35814.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8iy5_35814/08_2025/8iy5_35814.map" } resolution = 2.8 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= 0.501 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 2308 atoms to isotropic. 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 76 5.16 5 C 5847 2.51 5 N 1541 2.21 5 O 1712 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 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: 9176 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1764 Classifications: {'peptide': 219} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 216} Chain breaks: 2 Chain: "B" Number of atoms: 2583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2583 Classifications: {'peptide': 336} Link IDs: {'PTRANS': 5, 'TRANS': 330} Chain: "C" Number of atoms: 407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 407 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 4, 'TRANS': 48} Chain: "E" Number of atoms: 1783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1783 Classifications: {'peptide': 232} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Chain: "R" Number of atoms: 2468 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 316, 2465 Classifications: {'peptide': 316} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 13, 'TRANS': 302} Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 50 Planarities with less than four sites: {'ARG:plan': 3} Unresolved non-hydrogen planarities: 15 Conformer: "B" Number of residues, atoms: 316, 2465 Classifications: {'peptide': 316} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 13, 'TRANS': 302} Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 50 Planarities with less than four sites: {'ARG:plan': 3} Unresolved non-hydrogen planarities: 15 bond proxies already assigned to first conformer: 2521 Chain: "L" Number of atoms: 171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 171 Classifications: {'peptide': 21} Modifications used: {'COO': 1} Link IDs: {'TRANS': 20} Time building chain proxies: 2.26, per 1000 atoms: 0.25 Number of scatterers: 9176 At special positions: 0 Unit cell: (88.312, 124.334, 139.44, 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 76 16.00 O 1712 8.00 N 1541 7.00 C 5847 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS B 103 " - pdb=" SG CYS B 114 " distance=2.05 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 147 " - pdb=" SG CYS E 217 " distance=2.04 Simple disulfide: pdb=" SG CYS R 90 " - pdb=" SG CYS R 358 " distance=2.03 Simple disulfide: pdb=" SG CYS R 174 " - pdb=" SG CYS R 255 " distance=2.03 Simple disulfide: pdb=" SG CYS L 1 " - pdb=" SG CYS L 15 " distance=2.03 Simple disulfide: pdb=" SG CYS L 3 " - pdb=" SG CYS L 11 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.72 Conformation dependent library (CDL) restraints added in 314.7 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2208 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 13 sheets defined 36.5% alpha, 22.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.17 Creating SS restraints... Processing helix chain 'A' and resid 6 through 31 removed outlier: 3.908A pdb=" N ALA A 11 " --> pdb=" O ALA A 7 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LYS A 29 " --> pdb=" O GLU A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 216 removed outlier: 3.523A pdb=" N GLU A 216 " --> pdb=" O HIS A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 232 removed outlier: 4.572A pdb=" N TYR A 230 " --> pdb=" O LEU A 227 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N LEU A 232 " --> pdb=" O ASP A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 254 Processing helix chain 'A' and resid 277 through 281 removed outlier: 3.732A pdb=" N LYS A 280 " --> pdb=" O LYS A 277 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N SER A 281 " --> pdb=" O ILE A 278 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 277 through 281' Processing helix chain 'A' and resid 282 through 286 removed outlier: 3.892A pdb=" N ILE A 285 " --> pdb=" O PRO A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 311 Processing helix chain 'A' and resid 329 through 351 removed outlier: 3.758A pdb=" N GLN A 333 " --> pdb=" O THR A 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 6 through 26 Processing helix chain 'B' and resid 29 through 35 removed outlier: 3.606A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 12 through 22 Processing helix chain 'C' and resid 29 through 44 removed outlier: 4.353A pdb=" N ALA C 35 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N ASP C 36 " --> pdb=" O LYS C 32 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N LEU C 37 " --> pdb=" O ALA C 33 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 32 Processing helix chain 'E' and resid 53 through 56 removed outlier: 3.913A pdb=" N GLY E 56 " --> pdb=" O SER E 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 53 through 56' Processing helix chain 'E' and resid 208 through 212 removed outlier: 3.773A pdb=" N VAL E 212 " --> pdb=" O ALA E 209 " (cutoff:3.500A) Processing helix chain 'R' and resid 97 through 129 Processing helix chain 'R' and resid 134 through 165 Proline residue: R 156 - end of helix Processing helix chain 'R' and resid 171 through 205 Proline residue: R 178 - end of helix removed outlier: 3.694A pdb=" N VAL R 203 " --> pdb=" O ARG R 199 " (cutoff:3.500A) Processing helix chain 'R' and resid 214 through 233 removed outlier: 3.861A pdb=" N THR R 218 " --> pdb=" O VAL R 214 " (cutoff:3.500A) Processing helix chain 'R' and resid 235 through 239 Processing helix chain 'R' and resid 263 through 281 removed outlier: 5.992A pdb=" N ASP R 274 " --> pdb=" O LYS R 270 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N TRP R 275 " --> pdb=" O THR R 271 " (cutoff:3.500A) Processing helix chain 'R' and resid 282 through 301 Processing helix chain 'R' and resid 313 through 350 removed outlier: 3.666A pdb=" N GLN R 317 " --> pdb=" O ASP R 313 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N PHE R 332 " --> pdb=" O LEU R 328 " (cutoff:3.500A) Proline residue: R 338 - end of helix removed outlier: 3.678A pdb=" N TYR R 350 " --> pdb=" O LYS R 346 " (cutoff:3.500A) Processing helix chain 'R' and resid 357 through 390 removed outlier: 3.754A pdb=" N VAL R 366 " --> pdb=" O SER R 362 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N ASN R 382 " --> pdb=" O ASN R 378 " (cutoff:3.500A) Proline residue: R 383 - end of helix Processing helix chain 'R' and resid 390 through 403 Processing helix chain 'L' and resid 8 through 18 Processing sheet with id=AA1, first strand: chain 'A' and resid 186 through 191 removed outlier: 6.264A pdb=" N VAL A 34 " --> pdb=" O LYS A 197 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N PHE A 199 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N LEU A 36 " --> pdb=" O PHE A 199 " (cutoff:3.500A) removed outlier: 9.069A pdb=" N ALA A 220 " --> pdb=" O GLU A 33 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 7.867A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.786A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N LEU A 39 " --> pdb=" O CYS A 224 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.858A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 3.851A pdb=" N ALA B 113 " --> pdb=" O ALA B 104 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 153 removed outlier: 5.151A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N SER B 160 " --> pdb=" O CYS B 148 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N GLN B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N SER B 161 " --> pdb=" O THR B 165 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 7.009A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.655A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.643A pdb=" N CYS B 294 " --> pdb=" O LEU B 308 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.167A pdb=" N GLY E 10 " --> pdb=" O THR E 118 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLY E 44 " --> pdb=" O ALA E 40 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 128 through 130 Processing sheet with id=AB3, first strand: chain 'E' and resid 134 through 136 removed outlier: 6.188A pdb=" N VAL E 135 " --> pdb=" O GLU E 234 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N TRP E 164 " --> pdb=" O LEU E 176 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'R' and resid 240 through 247 445 hydrogen bonds defined for protein. 1268 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: 1.27 Time building geometry restraints manager: 0.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2948 1.34 - 1.46: 2274 1.46 - 1.59: 4041 1.59 - 1.71: 0 1.71 - 1.83: 104 Bond restraints: 9367 Sorted by residual: bond pdb=" CA ASP B 312 " pdb=" C ASP B 312 " ideal model delta sigma weight residual 1.523 1.545 -0.022 1.34e-02 5.57e+03 2.58e+00 bond pdb=" C VAL E 12 " pdb=" N GLN E 13 " ideal model delta sigma weight residual 1.330 1.352 -0.022 1.47e-02 4.63e+03 2.24e+00 bond pdb=" C CYS B 114 " pdb=" N GLY B 115 " ideal model delta sigma weight residual 1.326 1.340 -0.013 1.09e-02 8.42e+03 1.50e+00 bond pdb=" CB PRO A 288 " pdb=" CG PRO A 288 " ideal model delta sigma weight residual 1.492 1.552 -0.060 5.00e-02 4.00e+02 1.44e+00 bond pdb=" CA VAL R 177 " pdb=" CB VAL R 177 " ideal model delta sigma weight residual 1.539 1.533 0.006 5.40e-03 3.43e+04 1.16e+00 ... (remaining 9362 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.75: 12581 2.75 - 5.51: 98 5.51 - 8.26: 14 8.26 - 11.02: 0 11.02 - 13.77: 1 Bond angle restraints: 12694 Sorted by residual: angle pdb=" CA CYS B 103 " pdb=" CB CYS B 103 " pdb=" SG CYS B 103 " ideal model delta sigma weight residual 114.40 128.17 -13.77 2.30e+00 1.89e-01 3.59e+01 angle pdb=" N GLY R 239 " pdb=" CA GLY R 239 " pdb=" C GLY R 239 " ideal model delta sigma weight residual 112.49 119.59 -7.10 1.21e+00 6.83e-01 3.45e+01 angle pdb=" N GLY B 115 " pdb=" CA GLY B 115 " pdb=" C GLY B 115 " ideal model delta sigma weight residual 111.19 117.89 -6.70 1.45e+00 4.76e-01 2.14e+01 angle pdb=" CA CYS B 114 " pdb=" CB CYS B 114 " pdb=" SG CYS B 114 " ideal model delta sigma weight residual 114.40 122.61 -8.21 2.30e+00 1.89e-01 1.27e+01 angle pdb=" C HIS E 220 " pdb=" N LEU E 221 " pdb=" CA LEU E 221 " ideal model delta sigma weight residual 121.54 128.35 -6.81 1.91e+00 2.74e-01 1.27e+01 ... (remaining 12689 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.75: 5083 17.75 - 35.50: 422 35.50 - 53.25: 66 53.25 - 71.00: 7 71.00 - 88.74: 8 Dihedral angle restraints: 5586 sinusoidal: 2166 harmonic: 3420 Sorted by residual: dihedral pdb=" CB CYS R 90 " pdb=" SG CYS R 90 " pdb=" SG CYS R 358 " pdb=" CB CYS R 358 " ideal model delta sinusoidal sigma weight residual 93.00 42.81 50.19 1 1.00e+01 1.00e-02 3.45e+01 dihedral pdb=" CB CYS B 103 " pdb=" SG CYS B 103 " pdb=" SG CYS B 114 " pdb=" CB CYS B 114 " ideal model delta sinusoidal sigma weight residual -86.00 -36.60 -49.40 1 1.00e+01 1.00e-02 3.35e+01 dihedral pdb=" CA HIS E 220 " pdb=" C HIS E 220 " pdb=" N LEU E 221 " pdb=" CA LEU E 221 " ideal model delta harmonic sigma weight residual 180.00 155.63 24.37 0 5.00e+00 4.00e-02 2.37e+01 ... (remaining 5583 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 1139 0.049 - 0.098: 247 0.098 - 0.148: 61 0.148 - 0.197: 2 0.197 - 0.246: 1 Chirality restraints: 1450 Sorted by residual: chirality pdb=" CA CYS B 103 " pdb=" N CYS B 103 " pdb=" C CYS B 103 " pdb=" CB CYS B 103 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.51e+00 chirality pdb=" CA TYR E 178 " pdb=" N TYR E 178 " pdb=" C TYR E 178 " pdb=" CB TYR E 178 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.60e-01 chirality pdb=" CA ILE E 177 " pdb=" N ILE E 177 " pdb=" C ILE E 177 " pdb=" CB ILE E 177 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.48e-01 ... (remaining 1447 not shown) Planarity restraints: 1600 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU E 221 " 0.011 2.00e-02 2.50e+03 2.17e-02 4.73e+00 pdb=" C LEU E 221 " -0.038 2.00e-02 2.50e+03 pdb=" O LEU E 221 " 0.014 2.00e-02 2.50e+03 pdb=" N GLU E 222 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL C 54 " 0.028 5.00e-02 4.00e+02 4.30e-02 2.96e+00 pdb=" N PRO C 55 " -0.074 5.00e-02 4.00e+02 pdb=" CA PRO C 55 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO C 55 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 250 " -0.012 2.00e-02 2.50e+03 1.27e-02 2.82e+00 pdb=" CG PHE A 250 " 0.030 2.00e-02 2.50e+03 pdb=" CD1 PHE A 250 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 PHE A 250 " -0.008 2.00e-02 2.50e+03 pdb=" CE1 PHE A 250 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE A 250 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHE A 250 " 0.001 2.00e-02 2.50e+03 ... (remaining 1597 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 324 2.71 - 3.26: 9092 3.26 - 3.81: 14927 3.81 - 4.35: 18752 4.35 - 4.90: 31786 Nonbonded interactions: 74881 Sorted by model distance: nonbonded pdb=" O PHE E 32 " pdb=" NH2 ARG E 72 " model vdw 2.166 3.120 nonbonded pdb=" OD1 ASP A 350 " pdb=" ND2 ASN R 134 " model vdw 2.178 3.120 nonbonded pdb=" OD1 ASP B 290 " pdb=" NE ARG B 314 " model vdw 2.193 3.120 nonbonded pdb=" OG1 THR B 86 " pdb=" OD1 ASN B 88 " model vdw 2.223 3.040 nonbonded pdb=" OG SER R 342 " pdb=" OD1 ASP R 368 " model vdw 2.238 3.040 ... (remaining 74876 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=0.30 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: 0.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.000 Extract box with map and model: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 8.320 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 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:6.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5518 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 0.060 9374 Z= 0.147 Angle : 0.690 13.775 12708 Z= 0.398 Chirality : 0.044 0.246 1450 Planarity : 0.004 0.054 1600 Dihedral : 13.175 88.745 3357 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.88 % Favored : 95.86 % Rotamer: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.34 (0.25), residues: 1160 helix: 1.59 (0.27), residues: 381 sheet: -0.66 (0.30), residues: 290 loop : -1.40 (0.28), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 49 TYR 0.022 0.001 TYR E 178 PHE 0.030 0.002 PHE A 250 TRP 0.027 0.001 TRP B 332 HIS 0.004 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00290 ( 9367) covalent geometry : angle 0.68362 (12694) SS BOND : bond 0.00807 ( 7) SS BOND : angle 2.85949 ( 14) hydrogen bonds : bond 0.12519 ( 445) hydrogen bonds : angle 5.83658 ( 1268) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 163 time to evaluate : 0.300 Fit side-chains REVERT: B 76 ASP cc_start: 0.6166 (p0) cc_final: 0.5739 (p0) REVERT: C 38 MET cc_start: 0.5927 (mmm) cc_final: 0.5559 (mmt) outliers start: 0 outliers final: 0 residues processed: 163 average time/residue: 0.4249 time to fit residues: 74.9451 Evaluate side-chains 130 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 130 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 108 optimal weight: 0.5980 chunk 49 optimal weight: 0.8980 chunk 97 optimal weight: 10.0000 chunk 113 optimal weight: 4.9990 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 9.9990 chunk 33 optimal weight: 8.9990 chunk 65 optimal weight: 0.0020 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 0.9990 chunk 100 optimal weight: 9.9990 overall best weight: 1.2992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 ASN A 256 ASN A 333 GLN R 104 ASN R 373 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4667 r_free = 0.4667 target = 0.250752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.196106 restraints weight = 11726.096| |-----------------------------------------------------------------------------| r_work (start): 0.4190 rms_B_bonded: 2.52 r_work: 0.3995 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3995 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3990 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3990 r_free = 0.3990 target_work(ls_wunit_k1) = 0.176 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3990 r_free = 0.3990 target_work(ls_wunit_k1) = 0.176 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3990 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6296 moved from start: 0.1178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 9374 Z= 0.137 Angle : 0.629 9.066 12708 Z= 0.331 Chirality : 0.045 0.260 1450 Planarity : 0.004 0.046 1600 Dihedral : 4.967 27.889 1266 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.35 % Allowed : 4.06 % Favored : 95.60 % Rotamer: Outliers : 1.79 % Allowed : 10.63 % Favored : 87.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -0.18 (0.25), residues: 1160 helix: 1.55 (0.27), residues: 389 sheet: -0.52 (0.30), residues: 280 loop : -1.22 (0.29), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 49 TYR 0.016 0.001 TYR E 178 PHE 0.028 0.002 PHE R 112 TRP 0.015 0.001 TRP B 332 HIS 0.004 0.001 HIS B 62 Details of bonding type rmsd covalent geometry : bond 0.00301 ( 9367) covalent geometry : angle 0.62577 (12694) SS BOND : bond 0.00549 ( 7) SS BOND : angle 2.04245 ( 14) hydrogen bonds : bond 0.03709 ( 445) hydrogen bonds : angle 4.95086 ( 1268) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 144 time to evaluate : 0.315 Fit side-chains revert: symmetry clash REVERT: A 25 GLU cc_start: 0.7268 (tm-30) cc_final: 0.6839 (tt0) REVERT: A 314 LYS cc_start: 0.6281 (mptp) cc_final: 0.6015 (mptm) REVERT: A 333 GLN cc_start: 0.6346 (OUTLIER) cc_final: 0.6129 (mp10) REVERT: B 336 LEU cc_start: 0.8074 (OUTLIER) cc_final: 0.7196 (mt) REVERT: C 38 MET cc_start: 0.6060 (mmm) cc_final: 0.5310 (mmt) REVERT: R 126 ILE cc_start: 0.7251 (mm) cc_final: 0.6984 (mp) REVERT: R 363 PHE cc_start: 0.7252 (t80) cc_final: 0.6957 (t80) REVERT: L 7 MET cc_start: 0.1491 (pmm) cc_final: 0.0762 (pp-130) outliers start: 18 outliers final: 9 residues processed: 152 average time/residue: 0.4459 time to fit residues: 73.6063 Evaluate side-chains 138 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 127 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 333 GLN Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain R residue 325 VAL Chi-restraints excluded: chain R residue 373 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 39 optimal weight: 8.9990 chunk 25 optimal weight: 3.9990 chunk 64 optimal weight: 5.9990 chunk 45 optimal weight: 0.2980 chunk 91 optimal weight: 0.9990 chunk 114 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 chunk 54 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 110 optimal weight: 3.9990 chunk 98 optimal weight: 10.0000 overall best weight: 1.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 333 GLN E 220 HIS R 314 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4642 r_free = 0.4642 target = 0.247626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4293 r_free = 0.4293 target = 0.206192 restraints weight = 9952.330| |-----------------------------------------------------------------------------| r_work (start): 0.4569 rms_B_bonded: 2.66 r_work: 0.4277 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.4277 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3976 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3976 r_free = 0.3976 target_work(ls_wunit_k1) = 0.175 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3976 r_free = 0.3976 target_work(ls_wunit_k1) = 0.175 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3976 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6348 moved from start: 0.1520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9374 Z= 0.146 Angle : 0.622 9.003 12708 Z= 0.329 Chirality : 0.044 0.248 1450 Planarity : 0.004 0.043 1600 Dihedral : 5.020 28.696 1266 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.31 % Favored : 95.43 % Rotamer: Outliers : 2.18 % Allowed : 13.11 % Favored : 84.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -0.19 (0.25), residues: 1160 helix: 1.51 (0.26), residues: 389 sheet: -0.44 (0.30), residues: 274 loop : -1.24 (0.28), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 49 TYR 0.017 0.002 TYR E 178 PHE 0.025 0.002 PHE R 112 TRP 0.008 0.001 TRP B 339 HIS 0.005 0.001 HIS B 62 Details of bonding type rmsd covalent geometry : bond 0.00328 ( 9367) covalent geometry : angle 0.61822 (12694) SS BOND : bond 0.00751 ( 7) SS BOND : angle 2.21592 ( 14) hydrogen bonds : bond 0.03674 ( 445) hydrogen bonds : angle 4.84601 ( 1268) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 139 time to evaluate : 0.336 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 25 GLU cc_start: 0.7208 (tm-30) cc_final: 0.6842 (tt0) REVERT: A 248 LYS cc_start: 0.3964 (mmtm) cc_final: 0.3439 (mmmt) REVERT: A 314 LYS cc_start: 0.6441 (mptp) cc_final: 0.6158 (mptm) REVERT: E 208 GLU cc_start: 0.7178 (tm-30) cc_final: 0.6346 (pp20) REVERT: R 173 MET cc_start: 0.4742 (ppp) cc_final: 0.4407 (ptp) REVERT: R 256 LEU cc_start: 0.6442 (pt) cc_final: 0.6180 (pt) REVERT: R 363 PHE cc_start: 0.7230 (t80) cc_final: 0.6946 (t80) outliers start: 22 outliers final: 15 residues processed: 149 average time/residue: 0.4565 time to fit residues: 73.4457 Evaluate side-chains 143 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 128 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LYS Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 333 GLN Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 218 MET Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain R residue 325 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/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: 51.835 > 50: distance: 53 - 58: 10.002 distance: 58 - 59: 3.369 distance: 59 - 60: 5.631 distance: 59 - 62: 3.358 distance: 60 - 61: 5.056 distance: 60 - 66: 8.110 distance: 62 - 63: 7.140 distance: 62 - 64: 13.718 distance: 63 - 65: 8.347 distance: 66 - 190: 9.644 distance: 67 - 68: 10.174 distance: 67 - 70: 12.514 distance: 68 - 69: 4.723 distance: 68 - 74: 4.259 distance: 69 - 201: 14.059 distance: 70 - 71: 7.346 distance: 71 - 72: 5.470 distance: 71 - 73: 3.233 distance: 74 - 75: 3.414 distance: 75 - 76: 6.962 distance: 75 - 78: 4.851 distance: 76 - 77: 9.038 distance: 76 - 85: 5.249 distance: 78 - 79: 3.777 distance: 79 - 80: 3.442 distance: 79 - 81: 7.088 distance: 80 - 82: 7.101 distance: 81 - 83: 8.214 distance: 82 - 84: 8.336 distance: 83 - 84: 6.888 distance: 85 - 86: 4.066 distance: 85 - 204: 6.488 distance: 86 - 87: 9.794 distance: 86 - 89: 7.733 distance: 87 - 88: 7.576 distance: 87 - 93: 8.931 distance: 89 - 90: 14.468 distance: 90 - 91: 4.899 distance: 90 - 92: 12.150 distance: 93 - 94: 5.548 distance: 94 - 95: 15.445 distance: 94 - 97: 5.489 distance: 95 - 96: 23.680 distance: 95 - 101: 13.267 distance: 97 - 98: 11.335 distance: 98 - 99: 16.272 distance: 98 - 100: 7.488 distance: 101 - 102: 5.553 distance: 102 - 103: 19.221 distance: 102 - 105: 14.880 distance: 103 - 104: 11.463 distance: 103 - 110: 11.909 distance: 105 - 106: 9.484 distance: 106 - 107: 4.161 distance: 107 - 108: 4.084 distance: 108 - 109: 8.418 distance: 110 - 111: 10.775 distance: 111 - 112: 14.561 distance: 111 - 114: 3.059 distance: 112 - 113: 19.078 distance: 112 - 119: 11.493 distance: 114 - 115: 9.250 distance: 115 - 116: 12.679 distance: 116 - 117: 15.067 distance: 117 - 118: 13.234 distance: 119 - 120: 10.598 distance: 120 - 121: 9.511 distance: 120 - 123: 10.339 distance: 121 - 122: 11.332 distance: 121 - 127: 5.676 distance: 123 - 124: 11.982 distance: 124 - 125: 20.578 distance: 124 - 126: 26.580 distance: 127 - 128: 11.168 distance: 128 - 129: 7.250 distance: 128 - 131: 28.142 distance: 129 - 130: 20.639 distance: 129 - 135: 11.725 distance: 131 - 132: 16.876 distance: 132 - 133: 11.870 distance: 132 - 134: 22.056 distance: 135 - 136: 13.952 distance: 136 - 137: 8.672 distance: 136 - 139: 16.109 distance: 137 - 138: 19.130 distance: 137 - 146: 7.978 distance: 139 - 140: 11.079 distance: 140 - 141: 10.582 distance: 140 - 142: 10.211 distance: 141 - 143: 18.997 distance: 142 - 144: 15.507 distance: 143 - 145: 18.681 distance: 144 - 145: 13.285