Starting phenix.real_space_refine on Thu Jan 18 14:43:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f7x_28912/01_2024/8f7x_28912.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f7x_28912/01_2024/8f7x_28912.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.28 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f7x_28912/01_2024/8f7x_28912.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f7x_28912/01_2024/8f7x_28912.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f7x_28912/01_2024/8f7x_28912.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f7x_28912/01_2024/8f7x_28912.pdb" } resolution = 3.28 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.005 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 64 5.16 5 C 5653 2.51 5 N 1519 2.21 5 O 1666 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "R PHE 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 157": "NH1" <-> "NH2" Residue "R ARG 162": "NH1" <-> "NH2" Residue "R ARG 243": "NH1" <-> "NH2" Residue "R ARG 246": "NH1" <-> "NH2" Residue "R ARG 252": "NH1" <-> "NH2" Residue "R ARG 260": "NH1" <-> "NH2" Residue "R TYR 319": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 8": "NH1" <-> "NH2" Residue "P ARG 12": "NH1" <-> "NH2" Residue "A ARG 15": "NH1" <-> "NH2" Residue "A ARG 242": "NH1" <-> "NH2" Residue "A TYR 320": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 8": "NH1" <-> "NH2" Residue "B ARG 42": "NH1" <-> "NH2" Residue "B ARG 96": "NH1" <-> "NH2" Residue "B ARG 129": "NH1" <-> "NH2" Residue "B ARG 134": "NH1" <-> "NH2" Residue "B ARG 137": "NH1" <-> "NH2" Residue "B ASP 212": "OD1" <-> "OD2" Residue "B ARG 214": "NH1" <-> "NH2" Residue "B PHE 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 256": "NH1" <-> "NH2" Residue "B ARG 314": "NH1" <-> "NH2" Residue "E ARG 98": "NH1" <-> "NH2" Residue "E TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 161": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 8902 Number of models: 1 Model: "" Number of chains: 6 Chain: "R" Number of atoms: 2211 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2211 Classifications: {'peptide': 285} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 273} Chain: "P" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 105 Classifications: {'peptide': 14} Link IDs: {'TRANS': 13} Chain: "A" Number of atoms: 1782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1782 Classifications: {'peptide': 221} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 218} Chain breaks: 2 Chain: "B" Number of atoms: 2576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2576 Classifications: {'peptide': 335} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 329} Chain: "C" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 436 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 4, 'TRANS': 51} Chain: "E" Number of atoms: 1792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1792 Classifications: {'peptide': 234} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 223} Chain breaks: 1 Time building chain proxies: 5.25, per 1000 atoms: 0.59 Number of scatterers: 8902 At special positions: 0 Unit cell: (100.8, 111.72, 134.4, 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 64 16.00 O 1666 8.00 N 1519 7.00 C 5653 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS R 123 " - pdb=" SG CYS R 200 " distance=2.02 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.04 Simple disulfide: pdb=" SG CYS E 160 " - pdb=" SG CYS E 230 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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: 3.28 Conformation dependent library (CDL) restraints added in 1.8 seconds 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2128 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 14 sheets defined 38.2% alpha, 22.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.96 Creating SS restraints... Processing helix chain 'R' and resid 49 through 78 Processing helix chain 'R' and resid 84 through 102 Processing helix chain 'R' and resid 103 through 114 removed outlier: 3.501A pdb=" N THR R 109 " --> pdb=" O PRO R 105 " (cutoff:3.500A) Processing helix chain 'R' and resid 119 through 154 Processing helix chain 'R' and resid 157 through 162 removed outlier: 3.603A pdb=" N VAL R 161 " --> pdb=" O ARG R 157 " (cutoff:3.500A) Processing helix chain 'R' and resid 163 through 189 Proline residue: R 184 - end of helix Processing helix chain 'R' and resid 207 through 245 Proline residue: R 213 - end of helix removed outlier: 4.836A pdb=" N VAL R 226 " --> pdb=" O PHE R 222 " (cutoff:3.500A) Proline residue: R 227 - end of helix Processing helix chain 'R' and resid 251 through 288 Proline residue: R 278 - end of helix Processing helix chain 'R' and resid 294 through 320 removed outlier: 3.757A pdb=" N VAL R 298 " --> pdb=" O SER R 294 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ASN R 311 " --> pdb=" O LEU R 307 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N SER R 312 " --> pdb=" O GLY R 308 " (cutoff:3.500A) Proline residue: R 316 - end of helix Processing helix chain 'R' and resid 323 through 333 removed outlier: 3.620A pdb=" N PHE R 333 " --> pdb=" O CYS R 329 " (cutoff:3.500A) Processing helix chain 'P' and resid 6 through 14 Processing helix chain 'A' and resid 6 through 32 removed outlier: 3.822A pdb=" N ARG A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 44 No H-bonds generated for 'chain 'A' and resid 42 through 44' Processing helix chain 'A' and resid 45 through 54 removed outlier: 3.554A pdb=" N ILE A 49 " --> pdb=" O GLY A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 255 removed outlier: 3.792A pdb=" N LEU A 249 " --> pdb=" O GLU A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 281 Processing helix chain 'A' and resid 282 through 286 removed outlier: 4.333A pdb=" N ILE A 285 " --> pdb=" O PRO A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 310 removed outlier: 3.727A pdb=" N LEU A 310 " --> pdb=" O GLN A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 352 removed outlier: 3.749A pdb=" N ASN A 331 " --> pdb=" O THR A 327 " (cutoff:3.500A) Processing helix chain 'B' and resid 7 through 24 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'C' and resid 10 through 25 removed outlier: 3.503A pdb=" N ILE C 25 " --> pdb=" O MET C 21 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 44 removed outlier: 3.560A pdb=" N ALA C 33 " --> pdb=" O LYS C 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 32 removed outlier: 3.757A pdb=" N SER E 31 " --> pdb=" O ALA E 28 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N PHE E 32 " --> pdb=" O PHE E 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 28 through 32' Processing helix chain 'E' and resid 53 through 56 removed outlier: 4.133A 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 221 through 225 removed outlier: 3.720A pdb=" N VAL E 225 " --> pdb=" O ALA E 222 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'R' and resid 190 through 193 Processing sheet with id=AA2, first strand: chain 'A' and resid 185 through 190 removed outlier: 3.536A pdb=" N VAL A 185 " --> pdb=" O ASP A 200 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LEU A 37 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N CYS A 224 " --> pdb=" O LEU A 39 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 46 through 51 removed outlier: 3.548A pdb=" N ASN B 340 " --> pdb=" O ARG B 46 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.857A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.634A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.835A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.312A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.533A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N SER B 161 " --> pdb=" O THR B 165 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.552A pdb=" N ALA B 203 " --> pdb=" O SER B 207 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.880A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.360A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ARG B 251 " --> pdb=" O THR B 243 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N SER B 245 " --> pdb=" O THR B 249 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.879A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AB2, first strand: chain 'E' and resid 58 through 60 removed outlier: 6.545A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ARG E 98 " --> pdb=" O PHE E 110 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N PHE E 110 " --> pdb=" O ARG E 98 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 58 through 60 removed outlier: 6.545A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 142 through 143 Processing sheet with id=AB5, first strand: chain 'E' and resid 147 through 149 removed outlier: 6.401A pdb=" N VAL E 148 " --> pdb=" O GLU E 247 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLY E 226 " --> pdb=" O LEU E 246 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N LEU E 175 " --> pdb=" O TYR E 191 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N TYR E 191 " --> pdb=" O LEU E 175 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N TRP E 177 " --> pdb=" O LEU E 189 " (cutoff:3.500A) 460 hydrogen bonds defined for protein. 1314 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: 2.46 Time building geometry restraints manager: 3.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 2879 1.35 - 1.46: 2111 1.46 - 1.58: 3995 1.58 - 1.70: 0 1.70 - 1.82: 91 Bond restraints: 9076 Sorted by residual: bond pdb=" C THR R 277 " pdb=" N PRO R 278 " ideal model delta sigma weight residual 1.335 1.365 -0.029 1.36e-02 5.41e+03 4.59e+00 bond pdb=" C VAL R 183 " pdb=" N PRO R 184 " ideal model delta sigma weight residual 1.335 1.361 -0.026 1.36e-02 5.41e+03 3.61e+00 bond pdb=" C LEU R 104 " pdb=" N PRO R 105 " ideal model delta sigma weight residual 1.333 1.360 -0.027 1.44e-02 4.82e+03 3.56e+00 bond pdb=" CA THR R 277 " pdb=" C THR R 277 " ideal model delta sigma weight residual 1.521 1.542 -0.021 1.14e-02 7.69e+03 3.35e+00 bond pdb=" C TYR E 236 " pdb=" N PRO E 237 " ideal model delta sigma weight residual 1.334 1.375 -0.041 2.34e-02 1.83e+03 3.12e+00 ... (remaining 9071 not shown) Histogram of bond angle deviations from ideal: 99.27 - 106.24: 182 106.24 - 113.20: 4812 113.20 - 120.16: 3208 120.16 - 127.12: 3996 127.12 - 134.08: 90 Bond angle restraints: 12288 Sorted by residual: angle pdb=" N GLY R 182 " pdb=" CA GLY R 182 " pdb=" C GLY R 182 " ideal model delta sigma weight residual 112.83 120.42 -7.59 1.22e+00 6.72e-01 3.88e+01 angle pdb=" C VAL R 181 " pdb=" N GLY R 182 " pdb=" CA GLY R 182 " ideal model delta sigma weight residual 120.03 125.95 -5.92 1.12e+00 7.97e-01 2.79e+01 angle pdb=" C THR B 86 " pdb=" N THR B 87 " pdb=" CA THR B 87 " ideal model delta sigma weight residual 122.07 127.98 -5.91 1.43e+00 4.89e-01 1.71e+01 angle pdb=" C ARG E 192 " pdb=" N MET E 193 " pdb=" CA MET E 193 " ideal model delta sigma weight residual 122.61 128.93 -6.32 1.56e+00 4.11e-01 1.64e+01 angle pdb=" N GLY R 189 " pdb=" CA GLY R 189 " pdb=" C GLY R 189 " ideal model delta sigma weight residual 111.36 116.04 -4.68 1.17e+00 7.31e-01 1.60e+01 ... (remaining 12283 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.11: 5126 14.11 - 28.22: 223 28.22 - 42.33: 46 42.33 - 56.45: 5 56.45 - 70.56: 1 Dihedral angle restraints: 5401 sinusoidal: 2098 harmonic: 3303 Sorted by residual: dihedral pdb=" CA TRP B 82 " pdb=" C TRP B 82 " pdb=" N ASP B 83 " pdb=" CA ASP B 83 " ideal model delta harmonic sigma weight residual 180.00 161.64 18.36 0 5.00e+00 4.00e-02 1.35e+01 dihedral pdb=" CA TRP B 169 " pdb=" C TRP B 169 " pdb=" N ASP B 170 " pdb=" CA ASP B 170 " ideal model delta harmonic sigma weight residual 180.00 161.94 18.06 0 5.00e+00 4.00e-02 1.30e+01 dihedral pdb=" CA GLU E 235 " pdb=" C GLU E 235 " pdb=" N TYR E 236 " pdb=" CA TYR E 236 " ideal model delta harmonic sigma weight residual 180.00 -162.83 -17.17 0 5.00e+00 4.00e-02 1.18e+01 ... (remaining 5398 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 1081 0.056 - 0.112: 256 0.112 - 0.169: 57 0.169 - 0.225: 9 0.225 - 0.281: 2 Chirality restraints: 1405 Sorted by residual: chirality pdb=" CB ILE B 157 " pdb=" CA ILE B 157 " pdb=" CG1 ILE B 157 " pdb=" CG2 ILE B 157 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.28 2.00e-01 2.50e+01 1.98e+00 chirality pdb=" CB ILE A 184 " pdb=" CA ILE A 184 " pdb=" CG1 ILE A 184 " pdb=" CG2 ILE A 184 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.24 2.00e-01 2.50e+01 1.39e+00 chirality pdb=" CB THR E 91 " pdb=" CA THR E 91 " pdb=" OG1 THR E 91 " pdb=" CG2 THR E 91 " both_signs ideal model delta sigma weight residual False 2.55 2.34 0.21 2.00e-01 2.50e+01 1.15e+00 ... (remaining 1402 not shown) Planarity restraints: 1558 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE R 129 " -0.016 2.00e-02 2.50e+03 3.18e-02 1.01e+01 pdb=" C ILE R 129 " 0.055 2.00e-02 2.50e+03 pdb=" O ILE R 129 " -0.020 2.00e-02 2.50e+03 pdb=" N ASP R 130 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 82 " 0.020 2.00e-02 2.50e+03 1.39e-02 4.82e+00 pdb=" CG TRP B 82 " -0.037 2.00e-02 2.50e+03 pdb=" CD1 TRP B 82 " 0.011 2.00e-02 2.50e+03 pdb=" CD2 TRP B 82 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP B 82 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP B 82 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP B 82 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 82 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 82 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP B 82 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL C 54 " 0.035 5.00e-02 4.00e+02 5.24e-02 4.40e+00 pdb=" N PRO C 55 " -0.091 5.00e-02 4.00e+02 pdb=" CA PRO C 55 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO C 55 " 0.029 5.00e-02 4.00e+02 ... (remaining 1555 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 1882 2.80 - 3.32: 7899 3.32 - 3.85: 14056 3.85 - 4.37: 15829 4.37 - 4.90: 28745 Nonbonded interactions: 68411 Sorted by model distance: nonbonded pdb=" OG SER E 205 " pdb=" OG1 THR E 216 " model vdw 2.274 2.440 nonbonded pdb=" OG SER B 74 " pdb=" OD1 ASP B 76 " model vdw 2.321 2.440 nonbonded pdb=" O GLY B 224 " pdb=" NH1 ARG B 251 " model vdw 2.342 2.520 nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.344 2.440 nonbonded pdb=" O ILE E 139 " pdb=" OG1 THR E 239 " model vdw 2.347 2.440 ... (remaining 68406 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 1.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 3.970 Check model and map are aligned: 0.130 Set scattering table: 0.100 Process input model: 27.170 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.040 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:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7528 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 : 0.004 0.048 9076 Z= 0.275 Angle : 0.876 7.834 12288 Z= 0.514 Chirality : 0.053 0.281 1405 Planarity : 0.006 0.052 1558 Dihedral : 8.644 70.556 3264 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 0.10 % Allowed : 1.65 % Favored : 98.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.24), residues: 1127 helix: 2.33 (0.22), residues: 397 sheet: 0.05 (0.31), residues: 278 loop : -1.27 (0.27), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP B 82 HIS 0.006 0.001 HIS B 266 PHE 0.033 0.003 PHE A 354 TYR 0.024 0.002 TYR R 132 ARG 0.013 0.001 ARG B 150 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 248 time to evaluate : 1.075 Fit side-chains revert: symmetry clash REVERT: A 190 THR cc_start: 0.8556 (m) cc_final: 0.8302 (t) REVERT: B 138 GLU cc_start: 0.7765 (mt-10) cc_final: 0.7550 (mt-10) REVERT: B 212 ASP cc_start: 0.8038 (t70) cc_final: 0.7710 (t70) REVERT: E 219 ARG cc_start: 0.7919 (ttp-110) cc_final: 0.7485 (ttp-110) outliers start: 1 outliers final: 0 residues processed: 248 average time/residue: 0.2313 time to fit residues: 76.1809 Evaluate side-chains 142 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 142 time to evaluate : 0.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 5.9990 chunk 84 optimal weight: 4.9990 chunk 47 optimal weight: 0.5980 chunk 28 optimal weight: 6.9990 chunk 57 optimal weight: 0.8980 chunk 45 optimal weight: 8.9990 chunk 87 optimal weight: 0.0470 chunk 33 optimal weight: 6.9990 chunk 53 optimal weight: 7.9990 chunk 65 optimal weight: 4.9990 chunk 101 optimal weight: 5.9990 overall best weight: 2.3082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 79 HIS R 87 ASN ** R 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 133 ASN R 154 HIS A 195 HIS A 241 ASN ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 322 HIS B 259 GLN E 35 HIS E 39 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.3230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 9076 Z= 0.314 Angle : 0.627 7.750 12288 Z= 0.333 Chirality : 0.044 0.145 1405 Planarity : 0.005 0.044 1558 Dihedral : 4.273 22.202 1239 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 2.89 % Allowed : 9.28 % Favored : 87.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.24), residues: 1127 helix: 3.13 (0.23), residues: 395 sheet: 0.05 (0.30), residues: 288 loop : -1.17 (0.27), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 82 HIS 0.006 0.002 HIS B 54 PHE 0.019 0.002 PHE P 1 TYR 0.021 0.002 TYR B 85 ARG 0.006 0.001 ARG B 314 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 178 time to evaluate : 0.939 Fit side-chains revert: symmetry clash REVERT: A 36 LEU cc_start: 0.8889 (OUTLIER) cc_final: 0.8665 (pp) REVERT: A 190 THR cc_start: 0.8823 (m) cc_final: 0.8425 (t) REVERT: B 136 SER cc_start: 0.8770 (t) cc_final: 0.8538 (p) REVERT: B 333 ASP cc_start: 0.8607 (p0) cc_final: 0.8242 (p0) REVERT: E 39 GLN cc_start: 0.8193 (OUTLIER) cc_final: 0.7916 (tt0) REVERT: E 219 ARG cc_start: 0.8017 (ttp-110) cc_final: 0.7549 (ttp-110) outliers start: 28 outliers final: 16 residues processed: 198 average time/residue: 0.2320 time to fit residues: 61.6374 Evaluate side-chains 160 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 142 time to evaluate : 1.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 50 LEU Chi-restraints excluded: chain R residue 66 LEU Chi-restraints excluded: chain R residue 71 LEU Chi-restraints excluded: chain R residue 177 LEU Chi-restraints excluded: chain R residue 247 LEU Chi-restraints excluded: chain R residue 317 ILE Chi-restraints excluded: chain P residue 5 THR Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain C residue 41 CYS Chi-restraints excluded: chain E residue 39 GLN Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 156 VAL Chi-restraints excluded: chain E residue 207 SER Chi-restraints excluded: chain E residue 214 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 56 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 84 optimal weight: 7.9990 chunk 69 optimal weight: 4.9990 chunk 28 optimal weight: 9.9990 chunk 101 optimal weight: 8.9990 chunk 110 optimal weight: 3.9990 chunk 90 optimal weight: 4.9990 chunk 34 optimal weight: 5.9990 chunk 81 optimal weight: 5.9990 chunk 100 optimal weight: 2.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 241 ASN ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 175 GLN B 259 GLN E 39 GLN E 195 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.4608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.071 9076 Z= 0.462 Angle : 0.726 9.250 12288 Z= 0.381 Chirality : 0.047 0.161 1405 Planarity : 0.005 0.050 1558 Dihedral : 4.729 26.128 1239 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 4.02 % Allowed : 12.06 % Favored : 83.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.24), residues: 1127 helix: 2.50 (0.24), residues: 400 sheet: 0.11 (0.29), residues: 283 loop : -1.35 (0.26), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 82 HIS 0.008 0.003 HIS A 322 PHE 0.033 0.003 PHE E 108 TYR 0.031 0.003 TYR E 94 ARG 0.008 0.001 ARG B 314 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 154 time to evaluate : 0.918 Fit side-chains revert: symmetry clash REVERT: A 190 THR cc_start: 0.9045 (m) cc_final: 0.8746 (t) REVERT: C 46 LYS cc_start: 0.7989 (ttmm) cc_final: 0.7671 (tptp) REVERT: E 219 ARG cc_start: 0.8099 (ttp-110) cc_final: 0.7537 (ttp-110) outliers start: 39 outliers final: 26 residues processed: 181 average time/residue: 0.2506 time to fit residues: 59.7049 Evaluate side-chains 159 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 133 time to evaluate : 1.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 50 LEU Chi-restraints excluded: chain R residue 98 THR Chi-restraints excluded: chain R residue 100 VAL Chi-restraints excluded: chain R residue 147 ASP Chi-restraints excluded: chain R residue 177 LEU Chi-restraints excluded: chain R residue 193 VAL Chi-restraints excluded: chain R residue 247 LEU Chi-restraints excluded: chain R residue 266 LEU Chi-restraints excluded: chain R residue 267 VAL Chi-restraints excluded: chain R residue 271 VAL Chi-restraints excluded: chain R residue 317 ILE Chi-restraints excluded: chain R residue 329 CYS Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 41 CYS Chi-restraints excluded: chain E residue 156 VAL Chi-restraints excluded: chain E residue 198 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 69.1232 > 50: distance: 4 - 9: 30.093 distance: 9 - 10: 28.011 distance: 10 - 11: 27.435 distance: 10 - 13: 13.822 distance: 11 - 12: 26.153 distance: 11 - 14: 13.650 distance: 14 - 15: 19.279 distance: 15 - 16: 10.241 distance: 15 - 18: 19.422 distance: 16 - 17: 43.945 distance: 16 - 21: 4.494 distance: 18 - 19: 39.646 distance: 18 - 20: 41.828 distance: 21 - 22: 11.286 distance: 22 - 23: 39.060 distance: 22 - 25: 14.172 distance: 23 - 24: 12.265 distance: 23 - 27: 40.376 distance: 27 - 28: 9.716 distance: 28 - 29: 22.062 distance: 28 - 31: 41.776 distance: 29 - 30: 19.634 distance: 29 - 33: 19.721 distance: 31 - 32: 39.124 distance: 33 - 34: 41.858 distance: 34 - 35: 48.267 distance: 34 - 37: 5.648 distance: 35 - 36: 9.858 distance: 35 - 40: 23.330 distance: 37 - 38: 10.171 distance: 37 - 39: 32.528 distance: 40 - 41: 15.258 distance: 40 - 46: 26.028 distance: 41 - 42: 31.548 distance: 41 - 44: 40.295 distance: 42 - 43: 27.463 distance: 42 - 47: 28.134 distance: 44 - 45: 18.089 distance: 45 - 46: 16.255 distance: 47 - 48: 17.051 distance: 48 - 49: 31.807 distance: 48 - 51: 26.387 distance: 49 - 50: 39.472 distance: 49 - 54: 40.257 distance: 54 - 55: 39.736 distance: 55 - 58: 51.354 distance: 56 - 61: 29.306 distance: 58 - 59: 10.080 distance: 58 - 60: 43.528 distance: 61 - 62: 27.417 distance: 61 - 67: 41.445 distance: 62 - 63: 29.320 distance: 62 - 65: 26.758 distance: 63 - 64: 34.231 distance: 63 - 68: 19.363 distance: 65 - 66: 17.674 distance: 66 - 67: 28.836 distance: 68 - 69: 8.393 distance: 69 - 70: 52.271 distance: 70 - 72: 34.556