Starting phenix.real_space_refine on Thu Feb 13 22:42:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7x5v_33016/02_2025/7x5v_33016_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7x5v_33016/02_2025/7x5v_33016.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.83 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7x5v_33016/02_2025/7x5v_33016.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7x5v_33016/02_2025/7x5v_33016.map" model { file = "/net/cci-nas-00/data/ceres_data/7x5v_33016/02_2025/7x5v_33016_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7x5v_33016/02_2025/7x5v_33016_neut.cif" } resolution = 2.83 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= 0.006 sd= 0.109 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 56 5.16 5 C 6263 2.51 5 N 1510 2.21 5 O 1675 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 150 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 9504 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 2345 Classifications: {'peptide': 290} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 7, 'TRANS': 282} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TRP:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "B" Number of atoms: 2345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 2345 Classifications: {'peptide': 290} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 7, 'TRANS': 282} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TRP:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "C" Number of atoms: 2345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 2345 Classifications: {'peptide': 290} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 7, 'TRANS': 282} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TRP:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "D" Number of atoms: 2345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 2345 Classifications: {'peptide': 290} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 7, 'TRANS': 282} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TRP:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "E" Number of atoms: 124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 124 Classifications: {'peptide': 16} Link IDs: {'TRANS': 15} Time building chain proxies: 6.68, per 1000 atoms: 0.70 Number of scatterers: 9504 At special positions: 0 Unit cell: (107.12, 108.16, 91.52, 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 56 16.00 O 1675 8.00 N 1510 7.00 C 6263 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.86 Conformation dependent library (CDL) restraints added in 1.3 seconds 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2192 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 4 sheets defined 79.2% alpha, 2.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.81 Creating SS restraints... Processing helix chain 'A' and resid 72 through 81 removed outlier: 3.832A pdb=" N VAL A 76 " --> pdb=" O HIS A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 107 Processing helix chain 'A' and resid 114 through 140 removed outlier: 3.937A pdb=" N TRP A 118 " --> pdb=" O TYR A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 172 removed outlier: 3.998A pdb=" N GLY A 172 " --> pdb=" O GLU A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 191 removed outlier: 3.583A pdb=" N MET A 179 " --> pdb=" O PRO A 176 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N ALA A 180 " --> pdb=" O PRO A 177 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N LEU A 181 " --> pdb=" O SER A 178 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASN A 184 " --> pdb=" O LEU A 181 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ARG A 186 " --> pdb=" O ARG A 183 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ALA A 187 " --> pdb=" O ASN A 184 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ILE A 190 " --> pdb=" O ALA A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 197 removed outlier: 4.129A pdb=" N ARG A 196 " --> pdb=" O ARG A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 237 Proline residue: A 212 - end of helix removed outlier: 4.378A pdb=" N ASN A 216 " --> pdb=" O PRO A 212 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N ALA A 217 " --> pdb=" O GLY A 213 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N HIS A 237 " --> pdb=" O VAL A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 255 Processing helix chain 'A' and resid 258 through 265 removed outlier: 3.754A pdb=" N VAL A 262 " --> pdb=" O THR A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 289 Processing helix chain 'A' and resid 290 through 303 Processing helix chain 'A' and resid 311 through 319 removed outlier: 4.068A pdb=" N ALA A 315 " --> pdb=" O VAL A 311 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N SER A 319 " --> pdb=" O ALA A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 337 Processing helix chain 'A' and resid 338 through 358 Processing helix chain 'B' and resid 72 through 81 Processing helix chain 'B' and resid 82 through 107 Processing helix chain 'B' and resid 114 through 140 removed outlier: 3.937A pdb=" N TRP B 118 " --> pdb=" O TYR B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 172 removed outlier: 3.999A pdb=" N GLY B 172 " --> pdb=" O GLU B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 191 removed outlier: 3.584A pdb=" N MET B 179 " --> pdb=" O PRO B 176 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N ALA B 180 " --> pdb=" O PRO B 177 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N LEU B 181 " --> pdb=" O SER B 178 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ASN B 184 " --> pdb=" O LEU B 181 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ARG B 186 " --> pdb=" O ARG B 183 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ALA B 187 " --> pdb=" O ASN B 184 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ILE B 190 " --> pdb=" O ALA B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 192 through 197 removed outlier: 4.128A pdb=" N ARG B 196 " --> pdb=" O ARG B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 197 through 237 Proline residue: B 212 - end of helix removed outlier: 4.378A pdb=" N ASN B 216 " --> pdb=" O PRO B 212 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N ALA B 217 " --> pdb=" O GLY B 213 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N HIS B 237 " --> pdb=" O VAL B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 265 removed outlier: 3.753A pdb=" N VAL B 262 " --> pdb=" O THR B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 289 Processing helix chain 'B' and resid 290 through 303 Processing helix chain 'B' and resid 311 through 319 removed outlier: 4.067A pdb=" N ALA B 315 " --> pdb=" O VAL B 311 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N SER B 319 " --> pdb=" O ALA B 315 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 337 Processing helix chain 'B' and resid 338 through 358 Processing helix chain 'C' and resid 72 through 81 Processing helix chain 'C' and resid 82 through 107 Processing helix chain 'C' and resid 114 through 140 removed outlier: 3.938A pdb=" N TRP C 118 " --> pdb=" O TYR C 114 " (cutoff:3.500A) Processing helix chain 'C' and resid 148 through 172 removed outlier: 3.999A pdb=" N GLY C 172 " --> pdb=" O GLU C 168 " (cutoff:3.500A) Processing helix chain 'C' and resid 176 through 191 removed outlier: 3.584A pdb=" N MET C 179 " --> pdb=" O PRO C 176 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N ALA C 180 " --> pdb=" O PRO C 177 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N LEU C 181 " --> pdb=" O SER C 178 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASN C 184 " --> pdb=" O LEU C 181 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ARG C 186 " --> pdb=" O ARG C 183 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ALA C 187 " --> pdb=" O ASN C 184 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ILE C 190 " --> pdb=" O ALA C 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 192 through 197 removed outlier: 4.129A pdb=" N ARG C 196 " --> pdb=" O ARG C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 197 through 237 Proline residue: C 212 - end of helix removed outlier: 4.378A pdb=" N ASN C 216 " --> pdb=" O PRO C 212 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N ALA C 217 " --> pdb=" O GLY C 213 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N HIS C 237 " --> pdb=" O VAL C 233 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 255 Processing helix chain 'C' and resid 258 through 265 removed outlier: 3.753A pdb=" N VAL C 262 " --> pdb=" O THR C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 282 through 289 Processing helix chain 'C' and resid 290 through 303 Processing helix chain 'C' and resid 311 through 319 removed outlier: 4.068A pdb=" N ALA C 315 " --> pdb=" O VAL C 311 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N SER C 319 " --> pdb=" O ALA C 315 " (cutoff:3.500A) Processing helix chain 'C' and resid 323 through 337 Processing helix chain 'C' and resid 338 through 358 Processing helix chain 'D' and resid 72 through 81 removed outlier: 3.832A pdb=" N VAL D 76 " --> pdb=" O HIS D 72 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 107 Processing helix chain 'D' and resid 114 through 140 removed outlier: 3.937A pdb=" N TRP D 118 " --> pdb=" O TYR D 114 " (cutoff:3.500A) Processing helix chain 'D' and resid 148 through 172 removed outlier: 3.998A pdb=" N GLY D 172 " --> pdb=" O GLU D 168 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 191 removed outlier: 3.585A pdb=" N MET D 179 " --> pdb=" O PRO D 176 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N ALA D 180 " --> pdb=" O PRO D 177 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N LEU D 181 " --> pdb=" O SER D 178 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASN D 184 " --> pdb=" O LEU D 181 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ARG D 186 " --> pdb=" O ARG D 183 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ALA D 187 " --> pdb=" O ASN D 184 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ILE D 190 " --> pdb=" O ALA D 187 " (cutoff:3.500A) Processing helix chain 'D' and resid 192 through 197 removed outlier: 4.128A pdb=" N ARG D 196 " --> pdb=" O ARG D 192 " (cutoff:3.500A) Processing helix chain 'D' and resid 197 through 237 Proline residue: D 212 - end of helix removed outlier: 4.377A pdb=" N ASN D 216 " --> pdb=" O PRO D 212 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N ALA D 217 " --> pdb=" O GLY D 213 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N HIS D 237 " --> pdb=" O VAL D 233 " (cutoff:3.500A) Processing helix chain 'D' and resid 258 through 265 removed outlier: 3.752A pdb=" N VAL D 262 " --> pdb=" O THR D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 282 through 289 Processing helix chain 'D' and resid 290 through 303 Processing helix chain 'D' and resid 311 through 319 removed outlier: 4.068A pdb=" N ALA D 315 " --> pdb=" O VAL D 311 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N SER D 319 " --> pdb=" O ALA D 315 " (cutoff:3.500A) Processing helix chain 'D' and resid 323 through 337 Processing helix chain 'D' and resid 338 through 358 Processing helix chain 'E' and resid 3 through 17 Processing sheet with id=AA1, first strand: chain 'A' and resid 244 through 248 Processing sheet with id=AA2, first strand: chain 'B' and resid 244 through 248 Processing sheet with id=AA3, first strand: chain 'C' and resid 244 through 248 Processing sheet with id=AA4, first strand: chain 'D' and resid 244 through 248 653 hydrogen bonds defined for protein. 1887 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: 2.79 Time building geometry restraints manager: 3.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 1489 1.31 - 1.44: 2983 1.44 - 1.56: 5208 1.56 - 1.68: 0 1.68 - 1.81: 88 Bond restraints: 9768 Sorted by residual: bond pdb=" CA THR D 244 " pdb=" C THR D 244 " ideal model delta sigma weight residual 1.520 1.474 0.047 1.22e-02 6.72e+03 1.48e+01 bond pdb=" N THR D 244 " pdb=" CA THR D 244 " ideal model delta sigma weight residual 1.455 1.416 0.039 1.25e-02 6.40e+03 9.80e+00 bond pdb=" C ASN D 251 " pdb=" O ASN D 251 " ideal model delta sigma weight residual 1.236 1.202 0.035 1.15e-02 7.56e+03 9.14e+00 bond pdb=" C ASP D 250 " pdb=" O ASP D 250 " ideal model delta sigma weight residual 1.230 1.187 0.044 1.56e-02 4.11e+03 7.84e+00 bond pdb=" CA ASN D 251 " pdb=" C ASN D 251 " ideal model delta sigma weight residual 1.524 1.493 0.031 1.27e-02 6.20e+03 6.00e+00 ... (remaining 9763 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.80: 12686 1.80 - 3.61: 465 3.61 - 5.41: 93 5.41 - 7.21: 17 7.21 - 9.02: 14 Bond angle restraints: 13275 Sorted by residual: angle pdb=" N HIS A 320 " pdb=" CA HIS A 320 " pdb=" C HIS A 320 " ideal model delta sigma weight residual 111.07 119.39 -8.32 1.07e+00 8.73e-01 6.05e+01 angle pdb=" N ASP C 250 " pdb=" CA ASP C 250 " pdb=" C ASP C 250 " ideal model delta sigma weight residual 111.71 102.69 9.02 1.34e+00 5.57e-01 4.53e+01 angle pdb=" N ASN C 251 " pdb=" CA ASN C 251 " pdb=" C ASN C 251 " ideal model delta sigma weight residual 111.07 117.57 -6.50 1.07e+00 8.73e-01 3.69e+01 angle pdb=" N ASN C 249 " pdb=" CA ASN C 249 " pdb=" C ASN C 249 " ideal model delta sigma weight residual 110.53 118.35 -7.82 1.29e+00 6.01e-01 3.68e+01 angle pdb=" N ARG B 146 " pdb=" CA ARG B 146 " pdb=" C ARG B 146 " ideal model delta sigma weight residual 112.23 119.74 -7.51 1.26e+00 6.30e-01 3.55e+01 ... (remaining 13270 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.13: 4957 17.13 - 34.26: 471 34.26 - 51.39: 104 51.39 - 68.53: 21 68.53 - 85.66: 8 Dihedral angle restraints: 5561 sinusoidal: 2130 harmonic: 3431 Sorted by residual: dihedral pdb=" C VAL D 252 " pdb=" N VAL D 252 " pdb=" CA VAL D 252 " pdb=" CB VAL D 252 " ideal model delta harmonic sigma weight residual -122.00 -133.38 11.38 0 2.50e+00 1.60e-01 2.07e+01 dihedral pdb=" CA TYR A 281 " pdb=" C TYR A 281 " pdb=" N THR A 282 " pdb=" CA THR A 282 " ideal model delta harmonic sigma weight residual 180.00 159.78 20.22 0 5.00e+00 4.00e-02 1.64e+01 dihedral pdb=" CA TYR B 281 " pdb=" C TYR B 281 " pdb=" N THR B 282 " pdb=" CA THR B 282 " ideal model delta harmonic sigma weight residual 180.00 159.79 20.21 0 5.00e+00 4.00e-02 1.63e+01 ... (remaining 5558 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 1254 0.071 - 0.142: 171 0.142 - 0.213: 19 0.213 - 0.284: 8 0.284 - 0.355: 2 Chirality restraints: 1454 Sorted by residual: chirality pdb=" CA VAL D 252 " pdb=" N VAL D 252 " pdb=" C VAL D 252 " pdb=" CB VAL D 252 " both_signs ideal model delta sigma weight residual False 2.44 2.09 0.35 2.00e-01 2.50e+01 3.15e+00 chirality pdb=" CA TYR C 248 " pdb=" N TYR C 248 " pdb=" C TYR C 248 " pdb=" CB TYR C 248 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.17e+00 chirality pdb=" CA LYS C 198 " pdb=" N LYS C 198 " pdb=" C LYS C 198 " pdb=" CB LYS C 198 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.79e+00 ... (remaining 1451 not shown) Planarity restraints: 1665 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN A 338 " -0.015 2.00e-02 2.50e+03 3.07e-02 9.44e+00 pdb=" C GLN A 338 " 0.053 2.00e-02 2.50e+03 pdb=" O GLN A 338 " -0.020 2.00e-02 2.50e+03 pdb=" N ILE A 339 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN D 338 " 0.015 2.00e-02 2.50e+03 3.07e-02 9.44e+00 pdb=" C GLN D 338 " -0.053 2.00e-02 2.50e+03 pdb=" O GLN D 338 " 0.020 2.00e-02 2.50e+03 pdb=" N ILE D 339 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN B 338 " -0.015 2.00e-02 2.50e+03 3.06e-02 9.36e+00 pdb=" C GLN B 338 " 0.053 2.00e-02 2.50e+03 pdb=" O GLN B 338 " -0.020 2.00e-02 2.50e+03 pdb=" N ILE B 339 " -0.018 2.00e-02 2.50e+03 ... (remaining 1662 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.49: 63 2.49 - 3.09: 7388 3.09 - 3.70: 14755 3.70 - 4.30: 21910 4.30 - 4.90: 35938 Nonbonded interactions: 80054 Sorted by model distance: nonbonded pdb=" OG1 THR A 247 " pdb=" OE1 GLN A 271 " model vdw 1.891 3.040 nonbonded pdb=" O HIS A 237 " pdb=" NH2 ARG C 254 " model vdw 1.930 3.120 nonbonded pdb=" OD1 ASN A 249 " pdb=" NE2 GLN A 271 " model vdw 1.981 3.120 nonbonded pdb=" O LEU B 328 " pdb=" OG SER B 332 " model vdw 2.155 3.040 nonbonded pdb=" O LEU D 328 " pdb=" OG SER D 332 " model vdw 2.156 3.040 ... (remaining 80049 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 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.800 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: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 25.660 Find NCS groups from input model: 0.550 Set up NCS constraints: 0.060 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:15.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7427 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 : 0.007 0.072 9768 Z= 0.425 Angle : 0.867 9.017 13275 Z= 0.544 Chirality : 0.052 0.355 1454 Planarity : 0.005 0.043 1665 Dihedral : 14.746 85.658 3369 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 19.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 1.40 % Allowed : 15.43 % Favored : 83.17 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % 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: -2.31 (0.21), residues: 1166 helix: -1.18 (0.15), residues: 786 sheet: -1.34 (0.59), residues: 48 loop : -2.03 (0.33), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 106 HIS 0.005 0.002 HIS A 320 PHE 0.024 0.002 PHE D 144 TYR 0.014 0.002 TYR D 109 ARG 0.005 0.001 ARG C 254 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 238 time to evaluate : 1.043 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 271 GLN cc_start: 0.7861 (OUTLIER) cc_final: 0.7614 (pm20) REVERT: C 78 ASP cc_start: 0.7827 (m-30) cc_final: 0.7590 (m-30) REVERT: D 78 ASP cc_start: 0.7537 (m-30) cc_final: 0.7313 (m-30) REVERT: D 123 PHE cc_start: 0.6518 (t80) cc_final: 0.6189 (t80) REVERT: D 329 PHE cc_start: 0.7706 (t80) cc_final: 0.7498 (t80) outliers start: 14 outliers final: 11 residues processed: 251 average time/residue: 1.0763 time to fit residues: 291.4302 Evaluate side-chains 177 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 165 time to evaluate : 1.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 249 ASN Chi-restraints excluded: chain A residue 271 GLN Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 271 GLN Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 247 THR Chi-restraints excluded: chain D residue 214 VAL Chi-restraints excluded: chain D residue 222 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 98 optimal weight: 0.7980 chunk 88 optimal weight: 2.9990 chunk 49 optimal weight: 0.7980 chunk 30 optimal weight: 0.0980 chunk 59 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 91 optimal weight: 0.3980 chunk 35 optimal weight: 0.8980 chunk 55 optimal weight: 0.8980 chunk 68 optimal weight: 0.0980 chunk 106 optimal weight: 3.9990 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 73 GLN A 266 GLN B 115 GLN B 184 ASN B 201 ASN ** B 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 115 GLN C 320 HIS D 73 GLN D 136 ASN D 201 ASN D 266 GLN D 320 HIS E 7 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.189644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.141492 restraints weight = 9356.380| |-----------------------------------------------------------------------------| r_work (start): 0.3656 rms_B_bonded: 2.13 r_work: 0.3406 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3279 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 moved from start: 0.2241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9768 Z= 0.176 Angle : 0.561 6.272 13275 Z= 0.299 Chirality : 0.039 0.145 1454 Planarity : 0.004 0.024 1665 Dihedral : 5.723 59.596 1307 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 4.31 % Allowed : 19.14 % Favored : 76.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.20 (0.25), residues: 1166 helix: 0.67 (0.18), residues: 782 sheet: -0.52 (0.65), residues: 48 loop : -0.87 (0.39), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 145 HIS 0.003 0.001 HIS A 237 PHE 0.025 0.001 PHE A 144 TYR 0.014 0.001 TYR D 245 ARG 0.004 0.001 ARG B 196 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 188 time to evaluate : 1.108 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 MET cc_start: 0.8365 (mtm) cc_final: 0.8105 (mtm) REVERT: A 268 SER cc_start: 0.8498 (m) cc_final: 0.8235 (p) REVERT: B 133 LEU cc_start: 0.7842 (tp) cc_final: 0.7598 (tp) REVERT: B 143 CYS cc_start: 0.6211 (OUTLIER) cc_final: 0.5662 (t) REVERT: B 186 ARG cc_start: 0.7165 (OUTLIER) cc_final: 0.6933 (ptm160) REVERT: B 269 LEU cc_start: 0.7819 (OUTLIER) cc_final: 0.7594 (mt) REVERT: D 123 PHE cc_start: 0.6664 (t80) cc_final: 0.6182 (t80) REVERT: D 148 ASN cc_start: 0.8488 (t0) cc_final: 0.8048 (t0) REVERT: D 329 PHE cc_start: 0.7891 (t80) cc_final: 0.7690 (t80) REVERT: D 348 VAL cc_start: 0.8593 (p) cc_final: 0.8311 (m) REVERT: D 352 LYS cc_start: 0.8029 (tppt) cc_final: 0.7732 (mptt) outliers start: 43 outliers final: 15 residues processed: 218 average time/residue: 0.9257 time to fit residues: 220.3386 Evaluate side-chains 180 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 162 time to evaluate : 1.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 CYS Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain B residue 114 TYR Chi-restraints excluded: chain B residue 143 CYS Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 186 ARG Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain C residue 114 TYR Chi-restraints excluded: chain C residue 143 CYS Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 247 THR Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 114 TYR Chi-restraints excluded: chain D residue 115 GLN Chi-restraints excluded: chain D residue 143 CYS Chi-restraints excluded: chain D residue 222 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 43 optimal weight: 0.0010 chunk 14 optimal weight: 5.9990 chunk 60 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 chunk 21 optimal weight: 0.0070 chunk 57 optimal weight: 0.9990 chunk 45 optimal weight: 0.3980 chunk 29 optimal weight: 10.0000 chunk 47 optimal weight: 3.9990 chunk 63 optimal weight: 1.9990 chunk 56 optimal weight: 0.9980 overall best weight: 0.4804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN A 266 GLN B 266 GLN C 96 ASN C 115 GLN ** C 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 266 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.184111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.126634 restraints weight = 9601.777| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 1.85 r_work: 0.3386 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3261 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 moved from start: 0.2900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9768 Z= 0.167 Angle : 0.525 6.805 13275 Z= 0.276 Chirality : 0.038 0.156 1454 Planarity : 0.004 0.033 1665 Dihedral : 4.562 46.212 1294 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 3.51 % Allowed : 20.54 % Favored : 75.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.92 (0.26), residues: 1166 helix: 1.20 (0.18), residues: 778 sheet: -0.20 (0.68), residues: 48 loop : -0.50 (0.40), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 145 HIS 0.003 0.001 HIS D 320 PHE 0.023 0.001 PHE A 144 TYR 0.010 0.001 TYR D 245 ARG 0.006 0.001 ARG D 196 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 178 time to evaluate : 1.064 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 MET cc_start: 0.8306 (mtm) cc_final: 0.8047 (mtt) REVERT: A 133 LEU cc_start: 0.7357 (tp) cc_final: 0.7143 (OUTLIER) REVERT: A 268 SER cc_start: 0.8489 (m) cc_final: 0.8218 (p) REVERT: A 342 ILE cc_start: 0.8232 (mm) cc_final: 0.7982 (mt) REVERT: B 133 LEU cc_start: 0.7648 (tp) cc_final: 0.7377 (tp) REVERT: B 137 PHE cc_start: 0.8092 (m-10) cc_final: 0.7685 (m-80) REVERT: B 143 CYS cc_start: 0.5670 (OUTLIER) cc_final: 0.5200 (t) REVERT: B 175 MET cc_start: 0.6671 (OUTLIER) cc_final: 0.6416 (mtt) REVERT: B 186 ARG cc_start: 0.7178 (OUTLIER) cc_final: 0.6925 (ptm160) REVERT: C 96 ASN cc_start: 0.8145 (t0) cc_final: 0.7845 (t0) REVERT: C 105 GLU cc_start: 0.8115 (tm-30) cc_final: 0.7357 (tp30) REVERT: C 133 LEU cc_start: 0.7684 (tp) cc_final: 0.7425 (tp) REVERT: C 143 CYS cc_start: 0.5423 (OUTLIER) cc_final: 0.4422 (t) REVERT: C 242 ASP cc_start: 0.8310 (t0) cc_final: 0.7981 (t0) REVERT: C 266 GLN cc_start: 0.7614 (mt0) cc_final: 0.7342 (mm-40) REVERT: C 342 ILE cc_start: 0.8164 (mm) cc_final: 0.7849 (mt) REVERT: D 123 PHE cc_start: 0.6586 (t80) cc_final: 0.6170 (t80) REVERT: D 132 GLU cc_start: 0.8076 (tt0) cc_final: 0.7873 (tp30) REVERT: D 143 CYS cc_start: 0.5146 (OUTLIER) cc_final: 0.4153 (t) REVERT: D 148 ASN cc_start: 0.8651 (t0) cc_final: 0.8441 (m-40) REVERT: D 209 LYS cc_start: 0.8013 (mttp) cc_final: 0.7360 (mtmm) REVERT: D 271 GLN cc_start: 0.8152 (OUTLIER) cc_final: 0.7867 (pm20) REVERT: D 352 LYS cc_start: 0.7952 (tppt) cc_final: 0.7672 (mptt) outliers start: 35 outliers final: 10 residues processed: 201 average time/residue: 0.8948 time to fit residues: 197.3225 Evaluate side-chains 174 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 159 time to evaluate : 1.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 TYR Chi-restraints excluded: chain A residue 250 ASP Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain B residue 143 CYS Chi-restraints excluded: chain B residue 175 MET Chi-restraints excluded: chain B residue 186 ARG Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain C residue 114 TYR Chi-restraints excluded: chain C residue 143 CYS Chi-restraints excluded: chain C residue 247 THR Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain D residue 114 TYR Chi-restraints excluded: chain D residue 143 CYS Chi-restraints excluded: chain D residue 258 THR Chi-restraints excluded: chain D residue 271 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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-5592/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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-5592/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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-5592/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-5592/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-5592/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-5592/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-5592/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-5592/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-5592/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-5592/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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-5592/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-5592/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-5592/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-5592/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: 59.2749 > 50: distance: 10 - 27: 6.633 distance: 17 - 36: 11.481 distance: 21 - 41: 19.984 distance: 24 - 27: 4.754 distance: 25 - 49: 16.192 distance: 27 - 28: 3.267 distance: 28 - 29: 7.617 distance: 28 - 31: 3.255 distance: 29 - 30: 10.415 distance: 29 - 36: 7.583 distance: 31 - 32: 3.572 distance: 33 - 35: 3.333 distance: 36 - 37: 12.787 distance: 37 - 38: 9.052 distance: 37 - 40: 10.041 distance: 38 - 39: 11.836 distance: 38 - 41: 13.932 distance: 41 - 42: 11.340 distance: 42 - 43: 8.919 distance: 43 - 44: 22.958 distance: 43 - 49: 19.645 distance: 45 - 46: 16.907 distance: 45 - 47: 27.611 distance: 46 - 48: 15.216 distance: 49 - 50: 13.889 distance: 50 - 51: 19.508 distance: 51 - 52: 29.881 distance: 51 - 53: 6.222 distance: 53 - 54: 51.019 distance: 54 - 55: 21.981 distance: 55 - 56: 14.899 distance: 55 - 57: 25.508 distance: 57 - 58: 25.769 distance: 58 - 59: 27.511 distance: 58 - 61: 30.441 distance: 59 - 60: 15.551 distance: 59 - 65: 8.768 distance: 61 - 62: 27.995 distance: 62 - 63: 12.338 distance: 62 - 64: 18.011 distance: 65 - 66: 8.130 distance: 66 - 67: 14.619 distance: 66 - 69: 13.289 distance: 67 - 68: 4.918 distance: 67 - 76: 17.565 distance: 69 - 70: 5.423 distance: 70 - 71: 11.946 distance: 71 - 73: 20.047 distance: 72 - 74: 19.180 distance: 73 - 75: 6.774 distance: 74 - 75: 15.503 distance: 76 - 77: 11.454 distance: 77 - 78: 23.649 distance: 77 - 80: 12.843 distance: 78 - 79: 30.889 distance: 78 - 84: 12.350 distance: 80 - 81: 11.488 distance: 81 - 82: 18.419 distance: 82 - 83: 34.282 distance: 84 - 85: 18.280 distance: 84 - 90: 26.154 distance: 85 - 86: 5.527 distance: 85 - 88: 15.895 distance: 86 - 87: 3.945 distance: 86 - 91: 17.133 distance: 88 - 89: 15.139 distance: 89 - 90: 17.854 distance: 91 - 92: 8.993 distance: 91 - 97: 17.117 distance: 92 - 93: 9.692 distance: 92 - 95: 11.162 distance: 93 - 94: 19.065 distance: 93 - 98: 5.146 distance: 95 - 96: 17.106 distance: 96 - 97: 4.437