Starting phenix.real_space_refine on Wed May 14 16:05:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8f7q_28907/05_2025/8f7q_28907.cif Found real_map, /net/cci-nas-00/data/ceres_data/8f7q_28907/05_2025/8f7q_28907.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.22 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8f7q_28907/05_2025/8f7q_28907.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8f7q_28907/05_2025/8f7q_28907.map" model { file = "/net/cci-nas-00/data/ceres_data/8f7q_28907/05_2025/8f7q_28907.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8f7q_28907/05_2025/8f7q_28907.cif" } resolution = 3.22 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= 0.009 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 100 5.16 5 C 7797 2.51 5 N 1949 2.21 5 O 2148 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 11994 Number of models: 1 Model: "" Number of chains: 11 Chain: "R" Number of atoms: 2312 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2312 Classifications: {'peptide': 287} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 276} Chain: "P" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 162 Classifications: {'peptide': 21} Link IDs: {'PTRANS': 1, 'TRANS': 19} Chain: "A" Number of atoms: 1816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1816 Classifications: {'peptide': 225} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 222} Chain breaks: 1 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: 437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 437 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 4, 'TRANS': 51} Chain: "E" Number of atoms: 1788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1788 Classifications: {'peptide': 233} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 222} Chain breaks: 1 Chain: "M" Number of atoms: 2312 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2312 Classifications: {'peptide': 287} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 276} Chain: "Q" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 162 Classifications: {'peptide': 21} Link IDs: {'PTRANS': 1, 'TRANS': 19} Chain: "F" Number of atoms: 149 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 149 Classifications: {'peptide': 19} Modifications used: {'COO': 1} Link IDs: {'TRANS': 18} Chain: "R" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 140 Unusual residues: {'CLR': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "M" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 140 Unusual residues: {'CLR': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Time building chain proxies: 7.01, per 1000 atoms: 0.58 Number of scatterers: 11994 At special positions: 0 Unit cell: (111.384, 112.455, 152.082, 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 100 16.00 O 2148 8.00 N 1949 7.00 C 7797 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS R 142 " - pdb=" SG CYS R 219 " distance=2.03 Simple disulfide: pdb=" SG CYS E 160 " - pdb=" SG CYS E 230 " distance=2.04 Simple disulfide: pdb=" SG CYS M 142 " - pdb=" SG CYS M 219 " 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: 2.59 Conformation dependent library (CDL) restraints added in 1.5 seconds 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2802 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 15 sheets defined 49.3% alpha, 18.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.39 Creating SS restraints... Processing helix chain 'R' and resid 66 through 98 Processing helix chain 'R' and resid 103 through 122 Processing helix chain 'R' and resid 122 through 133 removed outlier: 3.743A pdb=" N GLN R 126 " --> pdb=" O THR R 122 " (cutoff:3.500A) Processing helix chain 'R' and resid 138 through 173 Processing helix chain 'R' and resid 173 through 181 removed outlier: 3.597A pdb=" N LEU R 178 " --> pdb=" O PRO R 174 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N ASP R 179 " --> pdb=" O VAL R 175 " (cutoff:3.500A) Processing helix chain 'R' and resid 182 through 207 removed outlier: 4.080A pdb=" N ILE R 200 " --> pdb=" O LEU R 196 " (cutoff:3.500A) Proline residue: R 203 - end of helix Processing helix chain 'R' and resid 226 through 264 removed outlier: 3.594A pdb=" N TRP R 230 " --> pdb=" O PRO R 226 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N MET R 245 " --> pdb=" O PHE R 241 " (cutoff:3.500A) Proline residue: R 246 - end of helix Processing helix chain 'R' and resid 270 through 308 Proline residue: R 297 - end of helix Processing helix chain 'R' and resid 313 through 339 removed outlier: 3.858A pdb=" N ASN R 330 " --> pdb=" O LEU R 326 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N SER R 331 " --> pdb=" O GLY R 327 " (cutoff:3.500A) Proline residue: R 335 - end of helix Processing helix chain 'R' and resid 342 through 352 Processing helix chain 'P' and resid 12 through 21 removed outlier: 3.677A pdb=" N THR P 16 " --> pdb=" O THR P 12 " (cutoff:3.500A) Processing helix chain 'A' and resid 6 through 33 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 55 Processing helix chain 'A' and resid 207 through 212 removed outlier: 4.211A pdb=" N TRP A 211 " --> pdb=" O GLU A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 217 removed outlier: 4.457A pdb=" N GLY A 217 " --> pdb=" O CYS A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 231 removed outlier: 3.795A pdb=" N ASP A 231 " --> pdb=" O SER A 228 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 228 through 231' Processing helix chain 'A' and resid 241 through 255 Processing helix chain 'A' and resid 270 through 281 Processing helix chain 'A' and resid 295 through 310 Processing helix chain 'A' and resid 327 through 352 removed outlier: 3.593A pdb=" N ASN A 331 " --> pdb=" O THR A 327 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N PHE A 334 " --> pdb=" O LYS A 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 7 through 26 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'C' and resid 11 through 24 Processing helix chain 'C' and resid 29 through 45 Processing helix chain 'E' and resid 28 through 32 Processing helix chain 'E' and resid 53 through 56 removed outlier: 4.256A 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 'M' and resid 67 through 98 Processing helix chain 'M' and resid 103 through 122 removed outlier: 3.909A pdb=" N THR M 122 " --> pdb=" O LEU M 118 " (cutoff:3.500A) Processing helix chain 'M' and resid 122 through 133 Processing helix chain 'M' and resid 138 through 173 removed outlier: 3.619A pdb=" N PHE M 154 " --> pdb=" O TYR M 150 " (cutoff:3.500A) Processing helix chain 'M' and resid 173 through 181 removed outlier: 3.795A pdb=" N ASP M 179 " --> pdb=" O VAL M 175 " (cutoff:3.500A) Processing helix chain 'M' and resid 182 through 207 removed outlier: 3.811A pdb=" N ILE M 200 " --> pdb=" O LEU M 196 " (cutoff:3.500A) Proline residue: M 203 - end of helix Processing helix chain 'M' and resid 226 through 264 removed outlier: 3.566A pdb=" N TRP M 230 " --> pdb=" O PRO M 226 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N MET M 245 " --> pdb=" O PHE M 241 " (cutoff:3.500A) Proline residue: M 246 - end of helix removed outlier: 3.652A pdb=" N SER M 263 " --> pdb=" O LEU M 259 " (cutoff:3.500A) Processing helix chain 'M' and resid 270 through 308 Proline residue: M 297 - end of helix Processing helix chain 'M' and resid 313 through 340 removed outlier: 3.874A pdb=" N SER M 331 " --> pdb=" O GLY M 327 " (cutoff:3.500A) Proline residue: M 335 - end of helix Processing helix chain 'M' and resid 342 through 352 Processing helix chain 'Q' and resid 12 through 21 removed outlier: 3.761A pdb=" N THR Q 16 " --> pdb=" O THR Q 12 " (cutoff:3.500A) Processing helix chain 'F' and resid 337 through 352 Processing sheet with id=AA1, first strand: chain 'R' and resid 208 through 213 Processing sheet with id=AA2, first strand: chain 'A' and resid 185 through 191 removed outlier: 3.742A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.817A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU A 268 " --> pdb=" O HIS A 322 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 46 through 51 removed outlier: 5.148A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.758A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.344A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.690A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 102 through 105 removed outlier: 3.611A pdb=" N CYS B 121 " --> pdb=" O LEU B 139 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.670A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.788A 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: 3.623A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.456A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ASP B 254 " --> pdb=" O GLN B 259 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.687A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ASN B 293 " --> pdb=" O TYR B 289 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ASP B 303 " --> pdb=" O ASP B 298 " (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 10 through 11 removed outlier: 3.736A pdb=" N GLY E 10 " --> pdb=" O THR E 116 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N THR E 118 " --> pdb=" O GLY E 10 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 10 through 11 removed outlier: 3.736A pdb=" N GLY E 10 " --> pdb=" O THR E 116 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N THR E 118 " --> pdb=" O GLY E 10 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N PHE E 110 " --> pdb=" O ARG E 98 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 147 through 149 removed outlier: 3.694A pdb=" N GLU E 247 " --> pdb=" O VAL E 148 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N LEU E 175 " --> pdb=" O TYR E 191 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N TYR E 191 " --> pdb=" O LEU E 175 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N TRP E 177 " --> pdb=" O LEU E 189 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 156 through 160 Processing sheet with id=AB6, first strand: chain 'M' and resid 208 through 213 703 hydrogen bonds defined for protein. 2034 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: 3.82 Time building geometry restraints manager: 3.11 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: 3659 1.34 - 1.46: 2776 1.46 - 1.58: 5694 1.58 - 1.70: 0 1.70 - 1.82: 149 Bond restraints: 12278 Sorted by residual: bond pdb=" C ASN R 334 " pdb=" N PRO R 335 " ideal model delta sigma weight residual 1.335 1.397 -0.062 1.30e-02 5.92e+03 2.24e+01 bond pdb=" C LEU M 202 " pdb=" N PRO M 203 " ideal model delta sigma weight residual 1.335 1.362 -0.027 1.28e-02 6.10e+03 4.50e+00 bond pdb=" C LEU R 202 " pdb=" N PRO R 203 " ideal model delta sigma weight residual 1.335 1.362 -0.027 1.36e-02 5.41e+03 3.85e+00 bond pdb=" C LEU R 123 " pdb=" N PRO R 124 " ideal model delta sigma weight residual 1.335 1.358 -0.024 1.28e-02 6.10e+03 3.49e+00 bond pdb=" C THR R 296 " pdb=" N PRO R 297 " ideal model delta sigma weight residual 1.336 1.358 -0.022 1.20e-02 6.94e+03 3.33e+00 ... (remaining 12273 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.81: 15867 1.81 - 3.62: 695 3.62 - 5.43: 108 5.43 - 7.24: 27 7.24 - 9.05: 6 Bond angle restraints: 16703 Sorted by residual: angle pdb=" C ARG E 192 " pdb=" N MET E 193 " pdb=" CA MET E 193 " ideal model delta sigma weight residual 125.02 131.81 -6.79 1.76e+00 3.23e-01 1.49e+01 angle pdb=" N LEU R 123 " pdb=" CA LEU R 123 " pdb=" C LEU R 123 " ideal model delta sigma weight residual 109.81 117.47 -7.66 2.21e+00 2.05e-01 1.20e+01 angle pdb=" C ASP B 163 " pdb=" N THR B 164 " pdb=" CA THR B 164 " ideal model delta sigma weight residual 124.82 130.67 -5.85 1.78e+00 3.16e-01 1.08e+01 angle pdb=" C GLY E 210 " pdb=" N THR E 211 " pdb=" CA THR E 211 " ideal model delta sigma weight residual 125.66 131.62 -5.96 1.85e+00 2.92e-01 1.04e+01 angle pdb=" C ASP B 333 " pdb=" N SER B 334 " pdb=" CA SER B 334 " ideal model delta sigma weight residual 124.82 130.46 -5.64 1.78e+00 3.16e-01 1.00e+01 ... (remaining 16698 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.13: 7365 14.13 - 28.27: 321 28.27 - 42.40: 55 42.40 - 56.53: 4 56.53 - 70.67: 3 Dihedral angle restraints: 7748 sinusoidal: 3414 harmonic: 4334 Sorted by residual: dihedral pdb=" CA LYS B 78 " pdb=" C LYS B 78 " pdb=" N LEU B 79 " pdb=" CA LEU B 79 " ideal model delta harmonic sigma weight residual 180.00 158.92 21.08 0 5.00e+00 4.00e-02 1.78e+01 dihedral pdb=" CA PHE E 32 " pdb=" C PHE E 32 " pdb=" N GLY E 33 " pdb=" CA GLY E 33 " ideal model delta harmonic sigma weight residual 180.00 161.19 18.81 0 5.00e+00 4.00e-02 1.42e+01 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 180.00 162.12 17.88 0 5.00e+00 4.00e-02 1.28e+01 ... (remaining 7745 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 1709 0.082 - 0.165: 192 0.165 - 0.247: 31 0.247 - 0.330: 10 0.330 - 0.412: 11 Chirality restraints: 1953 Sorted by residual: chirality pdb=" C14 CLR R 402 " pdb=" C13 CLR R 402 " pdb=" C15 CLR R 402 " pdb=" C8 CLR R 402 " both_signs ideal model delta sigma weight residual False -2.32 -2.73 0.41 2.00e-01 2.50e+01 4.25e+00 chirality pdb=" C14 CLR M 405 " pdb=" C13 CLR M 405 " pdb=" C15 CLR M 405 " pdb=" C8 CLR M 405 " both_signs ideal model delta sigma weight residual False -2.32 -2.73 0.41 2.00e-01 2.50e+01 4.20e+00 chirality pdb=" C14 CLR M 402 " pdb=" C13 CLR M 402 " pdb=" C15 CLR M 402 " pdb=" C8 CLR M 402 " both_signs ideal model delta sigma weight residual False -2.32 -2.72 0.40 2.00e-01 2.50e+01 3.98e+00 ... (remaining 1950 not shown) Planarity restraints: 2013 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL M 336 " 0.013 2.00e-02 2.50e+03 2.67e-02 7.12e+00 pdb=" C VAL M 336 " -0.046 2.00e-02 2.50e+03 pdb=" O VAL M 336 " 0.017 2.00e-02 2.50e+03 pdb=" N LEU M 337 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " 0.033 5.00e-02 4.00e+02 4.98e-02 3.97e+00 pdb=" N PRO B 236 " -0.086 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ARG E 219 " 0.009 2.00e-02 2.50e+03 1.91e-02 3.65e+00 pdb=" C ARG E 219 " -0.033 2.00e-02 2.50e+03 pdb=" O ARG E 219 " 0.013 2.00e-02 2.50e+03 pdb=" N LEU E 220 " 0.011 2.00e-02 2.50e+03 ... (remaining 2010 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 2268 2.79 - 3.32: 10934 3.32 - 3.84: 19401 3.84 - 4.37: 21736 4.37 - 4.90: 39457 Nonbonded interactions: 93796 Sorted by model distance: nonbonded pdb=" O ALA M 325 " pdb=" OG1 THR M 329 " model vdw 2.262 3.040 nonbonded pdb=" OG SER E 205 " pdb=" OG1 THR E 216 " model vdw 2.276 3.040 nonbonded pdb=" OE2 GLU B 260 " pdb=" OG1 THR B 263 " model vdw 2.314 3.040 nonbonded pdb=" O ILE M 292 " pdb=" OG1 THR M 296 " model vdw 2.360 3.040 nonbonded pdb=" O LYS A 35 " pdb=" OG1 THR A 219 " model vdw 2.360 3.040 ... (remaining 93791 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'M' selection = chain 'R' } ncs_group { reference = chain 'P' selection = chain 'Q' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.510 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: 0.410 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 28.240 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.050 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:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7429 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 0.063 12281 Z= 0.242 Angle : 0.868 9.050 16709 Z= 0.476 Chirality : 0.065 0.412 1953 Planarity : 0.006 0.050 2013 Dihedral : 8.264 70.668 4937 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % 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: 0.89 (0.20), residues: 1462 helix: 1.88 (0.17), residues: 668 sheet: 0.50 (0.30), residues: 283 loop : -1.10 (0.24), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP E 111 HIS 0.006 0.001 HIS E 35 PHE 0.032 0.002 PHE Q 18 TYR 0.028 0.002 TYR R 301 ARG 0.005 0.000 ARG B 68 Details of bonding type rmsd hydrogen bonds : bond 0.11550 ( 699) hydrogen bonds : angle 5.75920 ( 2034) SS BOND : bond 0.00623 ( 3) SS BOND : angle 1.94012 ( 6) covalent geometry : bond 0.00439 (12278) covalent geometry : angle 0.86774 (16703) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 230 time to evaluate : 1.250 Fit side-chains revert: symmetry clash REVERT: R 163 MET cc_start: 0.8330 (mtp) cc_final: 0.8119 (mtp) REVERT: E 159 SER cc_start: 0.8060 (t) cc_final: 0.7788 (p) REVERT: E 187 GLN cc_start: 0.8014 (pt0) cc_final: 0.7788 (pt0) REVERT: M 257 MET cc_start: 0.7689 (ttt) cc_final: 0.7365 (ttt) outliers start: 0 outliers final: 0 residues processed: 230 average time/residue: 0.2555 time to fit residues: 81.3921 Evaluate side-chains 149 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 149 time to evaluate : 1.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 121 optimal weight: 2.9990 chunk 109 optimal weight: 8.9990 chunk 60 optimal weight: 0.2980 chunk 37 optimal weight: 3.9990 chunk 73 optimal weight: 4.9990 chunk 58 optimal weight: 0.8980 chunk 112 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 84 optimal weight: 3.9990 chunk 130 optimal weight: 0.8980 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 111 ASN R 190 ASN B 35 ASN B 75 GLN B 91 HIS B 230 ASN B 237 ASN B 266 HIS E 180 GLN M 106 ASN M 330 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.170107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.132611 restraints weight = 12791.906| |-----------------------------------------------------------------------------| r_work (start): 0.3466 rms_B_bonded: 2.01 r_work: 0.3183 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3033 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.2293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.098 12281 Z= 0.164 Angle : 0.556 7.491 16709 Z= 0.293 Chirality : 0.041 0.152 1953 Planarity : 0.004 0.051 2013 Dihedral : 5.402 52.068 2256 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 1.62 % Allowed : 6.64 % Favored : 91.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % 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: 1.82 (0.21), residues: 1462 helix: 2.77 (0.18), residues: 689 sheet: 0.57 (0.29), residues: 294 loop : -0.76 (0.25), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 82 HIS 0.006 0.001 HIS E 233 PHE 0.014 0.001 PHE B 199 TYR 0.018 0.002 TYR R 301 ARG 0.007 0.000 ARG E 87 Details of bonding type rmsd hydrogen bonds : bond 0.04881 ( 699) hydrogen bonds : angle 4.64736 ( 2034) SS BOND : bond 0.00513 ( 3) SS BOND : angle 1.37937 ( 6) covalent geometry : bond 0.00389 (12278) covalent geometry : angle 0.55594 (16703) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 162 time to evaluate : 1.194 Fit side-chains revert: symmetry clash REVERT: R 74 MET cc_start: 0.7725 (mmm) cc_final: 0.7353 (mmm) REVERT: R 163 MET cc_start: 0.8838 (mtp) cc_final: 0.8575 (mtp) REVERT: A 315 ASP cc_start: 0.7603 (m-30) cc_final: 0.7220 (p0) REVERT: C 38 MET cc_start: 0.7373 (mmm) cc_final: 0.6690 (mmm) REVERT: E 106 SER cc_start: 0.8533 (t) cc_final: 0.8329 (p) REVERT: E 159 SER cc_start: 0.8386 (t) cc_final: 0.8088 (p) REVERT: M 341 LEU cc_start: 0.7596 (mm) cc_final: 0.7097 (tt) outliers start: 21 outliers final: 13 residues processed: 173 average time/residue: 0.2346 time to fit residues: 58.4992 Evaluate side-chains 147 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 134 time to evaluate : 1.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 180 GLN Chi-restraints excluded: chain E residue 198 SER Chi-restraints excluded: chain M residue 164 SER Chi-restraints excluded: chain M residue 200 ILE Chi-restraints excluded: chain M residue 332 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 115 optimal weight: 5.9990 chunk 139 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 132 optimal weight: 4.9990 chunk 99 optimal weight: 5.9990 chunk 140 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 96 optimal weight: 7.9990 chunk 34 optimal weight: 0.9980 chunk 133 optimal weight: 8.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 88 ASN B 239 ASN E 82 GLN E 180 GLN E 187 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.163486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.127421 restraints weight = 12956.466| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 2.01 r_work: 0.3076 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.3215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 12281 Z= 0.183 Angle : 0.564 7.710 16709 Z= 0.296 Chirality : 0.041 0.145 1953 Planarity : 0.004 0.044 2013 Dihedral : 5.693 57.771 2256 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 2.08 % Allowed : 8.49 % Favored : 89.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % 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: 1.79 (0.21), residues: 1462 helix: 2.86 (0.18), residues: 683 sheet: 0.48 (0.29), residues: 280 loop : -0.82 (0.25), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 82 HIS 0.007 0.001 HIS E 233 PHE 0.015 0.002 PHE E 240 TYR 0.021 0.002 TYR E 94 ARG 0.008 0.000 ARG E 87 Details of bonding type rmsd hydrogen bonds : bond 0.04956 ( 699) hydrogen bonds : angle 4.55357 ( 2034) SS BOND : bond 0.00617 ( 3) SS BOND : angle 1.39123 ( 6) covalent geometry : bond 0.00442 (12278) covalent geometry : angle 0.56343 (16703) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 136 time to evaluate : 1.193 Fit side-chains revert: symmetry clash REVERT: R 74 MET cc_start: 0.7490 (mmm) cc_final: 0.7216 (mmm) REVERT: R 147 SER cc_start: 0.8518 (t) cc_final: 0.8210 (m) REVERT: R 163 MET cc_start: 0.8771 (mtp) cc_final: 0.8513 (mtp) REVERT: R 227 THR cc_start: 0.8865 (m) cc_final: 0.8643 (p) REVERT: A 230 TYR cc_start: 0.7997 (p90) cc_final: 0.7729 (p90) REVERT: A 315 ASP cc_start: 0.7719 (m-30) cc_final: 0.7502 (p0) REVERT: E 159 SER cc_start: 0.8295 (t) cc_final: 0.8001 (p) REVERT: M 341 LEU cc_start: 0.7747 (mm) cc_final: 0.7295 (tt) outliers start: 27 outliers final: 15 residues processed: 156 average time/residue: 0.2250 time to fit residues: 51.4833 Evaluate side-chains 143 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 128 time to evaluate : 1.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 314 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 180 GLN Chi-restraints excluded: chain E residue 198 SER Chi-restraints excluded: chain M residue 164 SER Chi-restraints excluded: chain M residue 200 ILE Chi-restraints excluded: chain M residue 332 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-dev-5687/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-dev-5687/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-dev-5687/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-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-dev-5687/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-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-dev-5687/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-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 70.4584 > 50: distance: 119 - 243: 25.916 distance: 122 - 240: 27.695 distance: 168 - 173: 25.312 distance: 173 - 174: 46.575 distance: 174 - 175: 57.570 distance: 174 - 177: 43.338 distance: 175 - 176: 54.017 distance: 177 - 178: 41.920 distance: 178 - 179: 11.979 distance: 179 - 180: 16.456 distance: 179 - 181: 16.776 distance: 182 - 183: 25.922 distance: 183 - 184: 42.309 distance: 183 - 186: 48.782 distance: 184 - 185: 48.019 distance: 184 - 194: 47.221 distance: 186 - 187: 5.883 distance: 187 - 188: 40.119 distance: 187 - 189: 31.947 distance: 188 - 190: 15.554 distance: 190 - 192: 46.694 distance: 191 - 192: 22.339 distance: 192 - 193: 21.701 distance: 194 - 195: 22.403 distance: 194 - 200: 24.919 distance: 195 - 196: 36.088 distance: 195 - 198: 19.626 distance: 196 - 197: 43.641 distance: 196 - 201: 19.335 distance: 198 - 199: 13.839 distance: 199 - 200: 10.535 distance: 201 - 202: 21.353 distance: 202 - 203: 36.260 distance: 202 - 205: 22.528 distance: 203 - 204: 13.847 distance: 203 - 209: 14.611 distance: 205 - 206: 26.675 distance: 206 - 207: 17.071 distance: 206 - 208: 28.419 distance: 209 - 210: 47.067 distance: 210 - 211: 43.436 distance: 210 - 213: 12.641 distance: 211 - 212: 40.461 distance: 211 - 216: 40.262 distance: 213 - 214: 29.634 distance: 213 - 215: 27.968 distance: 216 - 217: 41.076 distance: 217 - 218: 28.859 distance: 217 - 220: 39.350 distance: 218 - 219: 51.267 distance: 218 - 227: 48.081 distance: 220 - 221: 14.860 distance: 221 - 222: 10.239 distance: 221 - 223: 26.778 distance: 222 - 224: 21.361 distance: 223 - 225: 27.104 distance: 224 - 226: 18.745 distance: 225 - 226: 20.655 distance: 227 - 228: 47.946 distance: 229 - 230: 32.106 distance: 229 - 231: 12.203 distance: 231 - 232: 44.463 distance: 232 - 233: 15.312 distance: 232 - 235: 24.506 distance: 233 - 234: 32.413 distance: 233 - 236: 31.011 distance: 236 - 237: 39.894 distance: 237 - 238: 25.322 distance: 238 - 239: 15.292 distance: 238 - 240: 33.097 distance: 240 - 241: 3.760 distance: 241 - 242: 42.832 distance: 241 - 244: 32.429 distance: 242 - 243: 24.038 distance: 242 - 247: 35.007 distance: 244 - 245: 17.049 distance: 244 - 246: 21.008