Starting phenix.real_space_refine on Mon Jul 6 00:25:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7pbq_13299/07_2026/7pbq_13299_neut_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7pbq_13299/07_2026/7pbq_13299.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7pbq_13299/07_2026/7pbq_13299.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7pbq_13299/07_2026/7pbq_13299.map" model { file = "/net/cci-nas-00/data/ceres_data/7pbq_13299/07_2026/7pbq_13299_neut_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7pbq_13299/07_2026/7pbq_13299_neut_trim.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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: 7 Type Number sf(0) Gaussians P 46 5.49 5 Mg 4 5.21 5 S 101 5.16 5 C 9900 2.51 5 N 2683 2.21 5 O 3150 1.98 5 H 15439 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 31323 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 4910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 312, 4910 Classifications: {'peptide': 312} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 297} Chain: "B" Number of atoms: 4910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 312, 4910 Classifications: {'peptide': 312} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 297} Chain: "C" Number of atoms: 4895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 4895 Classifications: {'peptide': 309} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 294} Chain breaks: 1 Chain: "D" Number of atoms: 4934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 4934 Classifications: {'peptide': 313} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 298} Chain: "E" Number of atoms: 4910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 312, 4910 Classifications: {'peptide': 312} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 297} Chain: "F" Number of atoms: 4910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 312, 4910 Classifications: {'peptide': 312} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 297} Chain: "G" Number of atoms: 719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 719 Classifications: {'peptide': 48} Modifications used: {'COO': 1, 'NH1NOTPRO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 45} Chain: "U" Number of atoms: 479 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 479 Classifications: {'DNA': 15} Link IDs: {'rna3p': 14} Chain: "V" Number of atoms: 474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 474 Classifications: {'DNA': 15} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 14} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.17, per 1000 atoms: 0.17 Number of scatterers: 31323 At special positions: 0 Unit cell: (125.35, 139.52, 109, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 101 16.00 P 46 15.00 Mg 4 11.99 O 3150 8.00 N 2683 7.00 C 9900 6.00 H 15439 1.00 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: 2.67 Conformation dependent library (CDL) restraints added in 818.3 milliseconds 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3526 Finding SS restraints... Secondary structure from input PDB file: 103 helices and 18 sheets defined 59.0% alpha, 10.9% beta 13 base pairs and 28 stacking pairs defined. Time for finding SS restraints: 5.39 Creating SS restraints... Processing helix chain 'A' and resid 31 through 49 removed outlier: 3.532A pdb=" N GLN A 37 " --> pdb=" O LYS A 33 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 77 removed outlier: 3.829A pdb=" N PHE A 70 " --> pdb=" O THR A 66 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 88 No H-bonds generated for 'chain 'A' and resid 86 through 88' Processing helix chain 'A' and resid 90 through 99 removed outlier: 3.549A pdb=" N LEU A 94 " --> pdb=" O LYS A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 115 Processing helix chain 'A' and resid 116 through 121 Processing helix chain 'A' and resid 122 through 130 removed outlier: 4.027A pdb=" N ALA A 126 " --> pdb=" O VAL A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 164 Processing helix chain 'A' and resid 165 through 170 Processing helix chain 'A' and resid 182 through 197 removed outlier: 3.544A pdb=" N GLU A 188 " --> pdb=" O PRO A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 213 removed outlier: 3.658A pdb=" N ARG A 212 " --> pdb=" O GLU A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 234 Processing helix chain 'A' and resid 240 through 251 removed outlier: 3.681A pdb=" N ASP A 245 " --> pdb=" O ASP A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 274 Processing helix chain 'A' and resid 279 through 287 Processing helix chain 'A' and resid 290 through 298 Processing helix chain 'A' and resid 298 through 305 removed outlier: 3.641A pdb=" N LEU A 302 " --> pdb=" O TYR A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 326 Processing helix chain 'B' and resid 31 through 49 removed outlier: 3.589A pdb=" N ILE B 40 " --> pdb=" O ASP B 36 " (cutoff:3.500A) Processing helix chain 'B' and resid 64 through 77 removed outlier: 3.571A pdb=" N PHE B 70 " --> pdb=" O THR B 66 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA B 73 " --> pdb=" O ALA B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 88 No H-bonds generated for 'chain 'B' and resid 86 through 88' Processing helix chain 'B' and resid 90 through 98 Processing helix chain 'B' and resid 112 through 115 Processing helix chain 'B' and resid 116 through 130 removed outlier: 4.439A pdb=" N VAL B 122 " --> pdb=" O ALA B 118 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LEU B 123 " --> pdb=" O VAL B 119 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N TYR B 124 " --> pdb=" O GLU B 120 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N SER B 125 " --> pdb=" O GLU B 121 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ALA B 126 " --> pdb=" O VAL B 122 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLU B 128 " --> pdb=" O TYR B 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 142 Processing helix chain 'B' and resid 160 through 164 Processing helix chain 'B' and resid 165 through 170 Processing helix chain 'B' and resid 182 through 197 Processing helix chain 'B' and resid 202 through 211 removed outlier: 3.501A pdb=" N LEU B 207 " --> pdb=" O PRO B 203 " (cutoff:3.500A) Processing helix chain 'B' and resid 216 through 232 Processing helix chain 'B' and resid 240 through 252 Processing helix chain 'B' and resid 259 through 272 Processing helix chain 'B' and resid 279 through 287 removed outlier: 3.575A pdb=" N ASN B 286 " --> pdb=" O THR B 282 " (cutoff:3.500A) Processing helix chain 'B' and resid 290 through 297 removed outlier: 3.671A pdb=" N ASP B 296 " --> pdb=" O GLU B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 305 removed outlier: 3.624A pdb=" N LEU B 302 " --> pdb=" O TYR B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 318 through 326 Processing helix chain 'C' and resid 31 through 49 removed outlier: 3.527A pdb=" N ILE C 40 " --> pdb=" O ASP C 36 " (cutoff:3.500A) Processing helix chain 'C' and resid 64 through 77 removed outlier: 3.625A pdb=" N PHE C 70 " --> pdb=" O THR C 66 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 99 removed outlier: 3.528A pdb=" N LEU C 94 " --> pdb=" O LYS C 90 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 115 Processing helix chain 'C' and resid 116 through 130 removed outlier: 3.582A pdb=" N VAL C 122 " --> pdb=" O ALA C 118 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N SER C 125 " --> pdb=" O GLU C 121 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ALA C 126 " --> pdb=" O VAL C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 160 through 164 Processing helix chain 'C' and resid 165 through 170 Processing helix chain 'C' and resid 182 through 197 removed outlier: 3.511A pdb=" N GLU C 188 " --> pdb=" O PRO C 184 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 213 removed outlier: 3.976A pdb=" N ARG C 212 " --> pdb=" O GLU C 208 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 235 Processing helix chain 'C' and resid 240 through 252 removed outlier: 3.785A pdb=" N ASP C 245 " --> pdb=" O ASP C 241 " (cutoff:3.500A) Processing helix chain 'C' and resid 259 through 273 Processing helix chain 'C' and resid 279 through 287 Processing helix chain 'C' and resid 290 through 298 Processing helix chain 'C' and resid 298 through 305 removed outlier: 3.820A pdb=" N LEU C 302 " --> pdb=" O TYR C 298 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 326 Processing helix chain 'D' and resid 31 through 47 removed outlier: 3.532A pdb=" N ILE D 40 " --> pdb=" O ASP D 36 " (cutoff:3.500A) Processing helix chain 'D' and resid 64 through 77 Processing helix chain 'D' and resid 86 through 88 No H-bonds generated for 'chain 'D' and resid 86 through 88' Processing helix chain 'D' and resid 90 through 100 removed outlier: 3.663A pdb=" N LEU D 94 " --> pdb=" O LYS D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 112 through 115 Processing helix chain 'D' and resid 116 through 129 removed outlier: 3.613A pdb=" N GLU D 121 " --> pdb=" O MET D 117 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N VAL D 122 " --> pdb=" O ALA D 118 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N TYR D 124 " --> pdb=" O GLU D 120 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N SER D 125 " --> pdb=" O GLU D 121 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ALA D 126 " --> pdb=" O VAL D 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 165 through 172 removed outlier: 3.606A pdb=" N ARG D 171 " --> pdb=" O PRO D 167 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N PHE D 172 " --> pdb=" O LEU D 168 " (cutoff:3.500A) Processing helix chain 'D' and resid 182 through 197 removed outlier: 4.201A pdb=" N GLU D 188 " --> pdb=" O PRO D 184 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLU D 195 " --> pdb=" O GLU D 191 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ILE D 196 " --> pdb=" O ARG D 192 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N PHE D 197 " --> pdb=" O THR D 193 " (cutoff:3.500A) Processing helix chain 'D' and resid 202 through 212 removed outlier: 3.809A pdb=" N ARG D 212 " --> pdb=" O GLU D 208 " (cutoff:3.500A) Processing helix chain 'D' and resid 216 through 232 Processing helix chain 'D' and resid 240 through 251 Processing helix chain 'D' and resid 259 through 274 Processing helix chain 'D' and resid 279 through 288 Processing helix chain 'D' and resid 290 through 297 Processing helix chain 'D' and resid 298 through 305 removed outlier: 3.594A pdb=" N LEU D 302 " --> pdb=" O TYR D 298 " (cutoff:3.500A) Processing helix chain 'D' and resid 318 through 326 Processing helix chain 'E' and resid 31 through 49 removed outlier: 3.649A pdb=" N ILE E 40 " --> pdb=" O ASP E 36 " (cutoff:3.500A) Processing helix chain 'E' and resid 64 through 77 Processing helix chain 'E' and resid 90 through 100 removed outlier: 3.559A pdb=" N LEU E 94 " --> pdb=" O LYS E 90 " (cutoff:3.500A) Processing helix chain 'E' and resid 112 through 115 removed outlier: 3.821A pdb=" N MET E 115 " --> pdb=" O ILE E 112 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 112 through 115' Processing helix chain 'E' and resid 116 through 130 removed outlier: 3.510A pdb=" N GLU E 121 " --> pdb=" O MET E 117 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N VAL E 122 " --> pdb=" O ALA E 118 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LEU E 123 " --> pdb=" O VAL E 119 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N SER E 125 " --> pdb=" O GLU E 121 " (cutoff:3.500A) Processing helix chain 'E' and resid 165 through 170 Processing helix chain 'E' and resid 182 through 197 Processing helix chain 'E' and resid 202 through 212 removed outlier: 3.741A pdb=" N LEU E 207 " --> pdb=" O PRO E 203 " (cutoff:3.500A) Processing helix chain 'E' and resid 216 through 235 removed outlier: 3.510A pdb=" N LYS E 225 " --> pdb=" O ASN E 221 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ARG E 226 " --> pdb=" O ARG E 222 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ASP E 229 " --> pdb=" O LYS E 225 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ILE E 233 " --> pdb=" O ASP E 229 " (cutoff:3.500A) Processing helix chain 'E' and resid 240 through 251 Processing helix chain 'E' and resid 259 through 274 removed outlier: 3.545A pdb=" N GLY E 274 " --> pdb=" O ILE E 270 " (cutoff:3.500A) Processing helix chain 'E' and resid 279 through 287 Processing helix chain 'E' and resid 290 through 298 Processing helix chain 'E' and resid 298 through 305 Processing helix chain 'E' and resid 318 through 326 Processing helix chain 'F' and resid 31 through 48 removed outlier: 3.601A pdb=" N ILE F 40 " --> pdb=" O ASP F 36 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ARG F 48 " --> pdb=" O ALA F 44 " (cutoff:3.500A) Processing helix chain 'F' and resid 64 through 77 Processing helix chain 'F' and resid 86 through 88 No H-bonds generated for 'chain 'F' and resid 86 through 88' Processing helix chain 'F' and resid 90 through 99 removed outlier: 3.795A pdb=" N LEU F 94 " --> pdb=" O LYS F 90 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA F 96 " --> pdb=" O GLY F 92 " (cutoff:3.500A) Processing helix chain 'F' and resid 112 through 115 Processing helix chain 'F' and resid 116 through 130 removed outlier: 4.280A pdb=" N VAL F 122 " --> pdb=" O ALA F 118 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N LEU F 123 " --> pdb=" O VAL F 119 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N TYR F 124 " --> pdb=" O GLU F 120 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N SER F 125 " --> pdb=" O GLU F 121 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ALA F 126 " --> pdb=" O VAL F 122 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLU F 128 " --> pdb=" O TYR F 124 " (cutoff:3.500A) Processing helix chain 'F' and resid 138 through 142 Processing helix chain 'F' and resid 165 through 170 Processing helix chain 'F' and resid 182 through 197 Processing helix chain 'F' and resid 202 through 213 removed outlier: 3.646A pdb=" N ARG F 212 " --> pdb=" O GLU F 208 " (cutoff:3.500A) Processing helix chain 'F' and resid 216 through 234 Processing helix chain 'F' and resid 240 through 251 Processing helix chain 'F' and resid 259 through 273 removed outlier: 3.711A pdb=" N TYR F 273 " --> pdb=" O MET F 269 " (cutoff:3.500A) Processing helix chain 'F' and resid 279 through 288 removed outlier: 3.649A pdb=" N VAL F 285 " --> pdb=" O GLY F 281 " (cutoff:3.500A) Processing helix chain 'F' and resid 290 through 297 removed outlier: 3.608A pdb=" N VAL F 294 " --> pdb=" O GLU F 290 " (cutoff:3.500A) Processing helix chain 'F' and resid 298 through 304 Processing helix chain 'F' and resid 318 through 326 Processing helix chain 'G' and resid 157 through 170 Processing helix chain 'G' and resid 173 through 183 Processing helix chain 'G' and resid 190 through 202 Processing sheet with id=AA1, first strand: chain 'A' and resid 80 through 84 removed outlier: 6.499A pdb=" N LYS A 81 " --> pdb=" O PHE A 108 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N ASP A 110 " --> pdb=" O LYS A 81 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N THR A 83 " --> pdb=" O ASP A 110 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N LEU A 107 " --> pdb=" O VAL A 155 " (cutoff:3.500A) removed outlier: 8.036A pdb=" N ALA A 157 " --> pdb=" O LEU A 107 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N ILE A 109 " --> pdb=" O ALA A 157 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N LEU A 56 " --> pdb=" O GLY A 176 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 131 through 137 Processing sheet with id=AA3, first strand: chain 'A' and resid 308 through 311 Processing sheet with id=AA4, first strand: chain 'B' and resid 80 through 84 removed outlier: 6.479A pdb=" N LYS B 81 " --> pdb=" O PHE B 108 " (cutoff:3.500A) removed outlier: 7.858A pdb=" N ASP B 110 " --> pdb=" O LYS B 81 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N THR B 83 " --> pdb=" O ASP B 110 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N LEU B 107 " --> pdb=" O VAL B 155 " (cutoff:3.500A) removed outlier: 8.002A pdb=" N ALA B 157 " --> pdb=" O LEU B 107 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N ILE B 109 " --> pdb=" O ALA B 157 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N LEU B 56 " --> pdb=" O GLY B 176 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 131 through 136 Processing sheet with id=AA6, first strand: chain 'B' and resid 308 through 311 Processing sheet with id=AA7, first strand: chain 'C' and resid 80 through 84 removed outlier: 6.311A pdb=" N LEU C 107 " --> pdb=" O VAL C 155 " (cutoff:3.500A) removed outlier: 8.014A pdb=" N ALA C 157 " --> pdb=" O LEU C 107 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N ILE C 109 " --> pdb=" O ALA C 157 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 131 through 136 Processing sheet with id=AA9, first strand: chain 'C' and resid 308 through 311 Processing sheet with id=AB1, first strand: chain 'D' and resid 80 through 84 removed outlier: 6.296A pdb=" N LYS D 81 " --> pdb=" O PHE D 108 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N ASP D 110 " --> pdb=" O LYS D 81 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N THR D 83 " --> pdb=" O ASP D 110 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N LEU D 107 " --> pdb=" O VAL D 155 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N ALA D 157 " --> pdb=" O LEU D 107 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ILE D 109 " --> pdb=" O ALA D 157 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N THR D 55 " --> pdb=" O GLY D 156 " (cutoff:3.500A) removed outlier: 8.128A pdb=" N THR D 158 " --> pdb=" O THR D 55 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N LEU D 57 " --> pdb=" O THR D 158 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 131 through 136 Processing sheet with id=AB3, first strand: chain 'D' and resid 308 through 311 Processing sheet with id=AB4, first strand: chain 'E' and resid 80 through 84 removed outlier: 6.460A pdb=" N LYS E 81 " --> pdb=" O PHE E 108 " (cutoff:3.500A) removed outlier: 7.809A pdb=" N ASP E 110 " --> pdb=" O LYS E 81 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N THR E 83 " --> pdb=" O ASP E 110 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N LEU E 107 " --> pdb=" O VAL E 155 " (cutoff:3.500A) removed outlier: 7.873A pdb=" N ALA E 157 " --> pdb=" O LEU E 107 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N ILE E 109 " --> pdb=" O ALA E 157 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 131 through 136 Processing sheet with id=AB6, first strand: chain 'E' and resid 308 through 311 Processing sheet with id=AB7, first strand: chain 'F' and resid 80 through 84 removed outlier: 6.214A pdb=" N LEU F 107 " --> pdb=" O VAL F 155 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N ALA F 157 " --> pdb=" O LEU F 107 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N ILE F 109 " --> pdb=" O ALA F 157 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 131 through 136 Processing sheet with id=AB9, first strand: chain 'F' and resid 308 through 310 760 hydrogen bonds defined for protein. 2190 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 30 hydrogen bonds 60 hydrogen bond angles 0 basepair planarities 13 basepair parallelities 28 stacking parallelities Total time for adding SS restraints: 6.99 Time building geometry restraints manager: 3.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.06: 15439 1.06 - 1.28: 2655 1.28 - 1.50: 6784 1.50 - 1.72: 6587 1.72 - 1.95: 198 Bond restraints: 31663 Sorted by residual: bond pdb=" O3B AGS B 401 " pdb=" PB AGS B 401 " ideal model delta sigma weight residual 1.673 1.572 0.101 2.00e-02 2.50e+03 2.54e+01 bond pdb=" N THR C 19 " pdb=" H1 THR C 19 " ideal model delta sigma weight residual 0.960 0.860 0.100 2.00e-02 2.50e+03 2.51e+01 bond pdb=" N SER G 156 " pdb=" H1 SER G 156 " ideal model delta sigma weight residual 0.960 0.860 0.100 2.00e-02 2.50e+03 2.51e+01 bond pdb=" N THR A 19 " pdb=" H1 THR A 19 " ideal model delta sigma weight residual 0.960 0.860 0.100 2.00e-02 2.50e+03 2.50e+01 bond pdb=" N THR B 19 " pdb=" H1 THR B 19 " ideal model delta sigma weight residual 0.960 0.860 0.100 2.00e-02 2.50e+03 2.50e+01 ... (remaining 31658 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.15: 56663 2.15 - 4.31: 573 4.31 - 6.46: 48 6.46 - 8.62: 15 8.62 - 10.77: 15 Bond angle restraints: 57314 Sorted by residual: angle pdb=" O4' DT V 7 " pdb=" C1' DT V 7 " pdb=" N1 DT V 7 " ideal model delta sigma weight residual 108.00 111.81 -3.81 7.00e-01 2.04e+00 2.96e+01 angle pdb=" C4' DA U 2 " pdb=" O4' DA U 2 " pdb=" C1' DA U 2 " ideal model delta sigma weight residual 110.10 105.06 5.04 1.00e+00 1.00e+00 2.54e+01 angle pdb=" O4' DA V 11 " pdb=" C1' DA V 11 " pdb=" N9 DA V 11 " ideal model delta sigma weight residual 108.00 110.85 -2.85 7.00e-01 2.04e+00 1.66e+01 angle pdb=" N3 DT V 3 " pdb=" C4 DT V 3 " pdb=" O4 DT V 3 " ideal model delta sigma weight residual 119.90 122.33 -2.43 6.00e-01 2.78e+00 1.64e+01 angle pdb=" O5' DA U 2 " pdb=" C5' DA U 2 " pdb=" C4' DA U 2 " ideal model delta sigma weight residual 109.40 112.59 -3.19 8.00e-01 1.56e+00 1.59e+01 ... (remaining 57309 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.66: 14159 32.66 - 65.32: 565 65.32 - 97.98: 36 97.98 - 130.64: 0 130.64 - 163.30: 2 Dihedral angle restraints: 14762 sinusoidal: 8493 harmonic: 6269 Sorted by residual: dihedral pdb=" O2A ADP F 600 " pdb=" O3A ADP F 600 " pdb=" PA ADP F 600 " pdb=" PB ADP F 600 " ideal model delta sinusoidal sigma weight residual -60.00 103.30 -163.30 1 2.00e+01 2.50e-03 4.70e+01 dihedral pdb=" O2A ADP E 600 " pdb=" O3A ADP E 600 " pdb=" PA ADP E 600 " pdb=" PB ADP E 600 " ideal model delta sinusoidal sigma weight residual -60.00 100.63 -160.63 1 2.00e+01 2.50e-03 4.66e+01 dihedral pdb=" C1' ADP E 600 " pdb=" C4' ADP E 600 " pdb=" O4' ADP E 600 " pdb=" C5' ADP E 600 " ideal model delta sinusoidal sigma weight residual -150.00 -92.23 -57.77 1 2.00e+01 2.50e-03 1.12e+01 ... (remaining 14759 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 2241 0.080 - 0.160: 236 0.160 - 0.240: 7 0.240 - 0.320: 3 0.320 - 0.400: 1 Chirality restraints: 2488 Sorted by residual: chirality pdb=" P DT V 4 " pdb=" OP1 DT V 4 " pdb=" OP2 DT V 4 " pdb=" O5' DT V 4 " both_signs ideal model delta sigma weight residual True 2.34 -2.74 -0.40 2.00e-01 2.50e+01 4.00e+00 chirality pdb=" C3' AGS A 401 " pdb=" C2' AGS A 401 " pdb=" C4' AGS A 401 " pdb=" O3' AGS A 401 " both_signs ideal model delta sigma weight residual False -2.37 -2.65 0.28 2.00e-01 2.50e+01 1.90e+00 chirality pdb=" C3' AGS C 401 " pdb=" C2' AGS C 401 " pdb=" C4' AGS C 401 " pdb=" O3' AGS C 401 " both_signs ideal model delta sigma weight residual False -2.37 -2.64 0.27 2.00e-01 2.50e+01 1.78e+00 ... (remaining 2485 not shown) Planarity restraints: 4586 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG E 160 " 0.392 9.50e-02 1.11e+02 1.39e-01 7.05e+01 pdb=" NE ARG E 160 " 0.025 2.00e-02 2.50e+03 pdb=" CZ ARG E 160 " -0.021 2.00e-02 2.50e+03 pdb=" NH1 ARG E 160 " -0.017 2.00e-02 2.50e+03 pdb=" NH2 ARG E 160 " -0.100 2.00e-02 2.50e+03 pdb="HH11 ARG E 160 " -0.001 2.00e-02 2.50e+03 pdb="HH12 ARG E 160 " 0.001 2.00e-02 2.50e+03 pdb="HH21 ARG E 160 " -0.006 2.00e-02 2.50e+03 pdb="HH22 ARG E 160 " 0.101 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 192 " -0.203 9.50e-02 1.11e+02 8.38e-02 5.92e+01 pdb=" NE ARG B 192 " -0.002 2.00e-02 2.50e+03 pdb=" CZ ARG B 192 " -0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG B 192 " -0.045 2.00e-02 2.50e+03 pdb=" NH2 ARG B 192 " 0.090 2.00e-02 2.50e+03 pdb="HH11 ARG B 192 " -0.001 2.00e-02 2.50e+03 pdb="HH12 ARG B 192 " 0.055 2.00e-02 2.50e+03 pdb="HH21 ARG B 192 " 0.005 2.00e-02 2.50e+03 pdb="HH22 ARG B 192 " -0.092 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 169 " -0.166 9.50e-02 1.11e+02 6.78e-02 3.80e+01 pdb=" NE ARG C 169 " -0.011 2.00e-02 2.50e+03 pdb=" CZ ARG C 169 " 0.010 2.00e-02 2.50e+03 pdb=" NH1 ARG C 169 " 0.080 2.00e-02 2.50e+03 pdb=" NH2 ARG C 169 " -0.029 2.00e-02 2.50e+03 pdb="HH11 ARG C 169 " 0.003 2.00e-02 2.50e+03 pdb="HH12 ARG C 169 " -0.075 2.00e-02 2.50e+03 pdb="HH21 ARG C 169 " -0.000 2.00e-02 2.50e+03 pdb="HH22 ARG C 169 " 0.030 2.00e-02 2.50e+03 ... (remaining 4583 not shown) Histogram of nonbonded interaction distances: 1.51 - 2.13: 654 2.13 - 2.75: 55143 2.75 - 3.36: 82517 3.36 - 3.98: 105528 3.98 - 4.60: 171716 Nonbonded interactions: 415558 Sorted by model distance: nonbonded pdb="HH22 ARG F 214 " pdb=" OD2 ASP F 262 " model vdw 1.510 2.450 nonbonded pdb=" O ALA B 138 " pdb=" HG1 THR B 141 " model vdw 1.568 2.450 nonbonded pdb=" HG1 THR F 66 " pdb=" O1B ADP F 600 " model vdw 1.570 2.450 nonbonded pdb=" OE1 GLU A 299 " pdb="HH11 ARG A 315 " model vdw 1.578 2.450 nonbonded pdb=" O ALA E 138 " pdb=" HG1 THR E 141 " model vdw 1.601 2.450 ... (remaining 415553 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' and (resid 19 through 136 or resid 141 through 330)) selection = (chain 'B' and (resid 19 through 136 or resid 141 through 330)) selection = (chain 'C' and resid 19 through 330) selection = (chain 'D' and (resid 19 through 136 or resid 141 through 330)) selection = (chain 'E' and (resid 19 through 136 or resid 141 through 330)) selection = (chain 'F' and (resid 19 through 136 or resid 141 through 330)) } 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: 4.290 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: 0.160 Extract box with map and model: 0.340 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 33.280 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 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 : 0.005 0.101 16224 Z= 0.276 Angle : 0.807 10.773 22098 Z= 0.464 Chirality : 0.048 0.400 2488 Planarity : 0.010 0.134 2739 Dihedral : 15.090 163.296 6350 Min Nonbonded Distance : 1.821 Molprobity Statistics. All-atom Clashscore : 1.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 0.19 % Allowed : 1.19 % Favored : 98.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.62 (0.18), residues: 1902 helix: -0.85 (0.14), residues: 1004 sheet: 0.63 (0.29), residues: 318 loop : 0.25 (0.25), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.025 0.003 ARG D 171 TYR 0.027 0.004 TYR D 327 PHE 0.023 0.003 PHE A 25 HIS 0.016 0.003 HIS F 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00517 / 0.28 (16224) covalent geometry : angle 0.80691 / 0.46 (22098) hydrogen bonds : bond 0.26322 / 17.35 ( 790) hydrogen bonds : angle 8.49758 / 6.17 ( 2250) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 482 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 479 time to evaluate : 0.660 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 ASN cc_start: 0.8548 (m-40) cc_final: 0.8196 (m-40) REVERT: B 110 ASP cc_start: 0.7843 (t0) cc_final: 0.7636 (t0) REVERT: B 325 MET cc_start: 0.8563 (mmm) cc_final: 0.8118 (mmp) REVERT: C 125 SER cc_start: 0.8513 (m) cc_final: 0.8224 (p) REVERT: C 178 MET cc_start: 0.9154 (mmt) cc_final: 0.8641 (mmt) REVERT: C 199 MET cc_start: 0.7646 (mmp) cc_final: 0.7390 (mmt) REVERT: C 297 MET cc_start: 0.9060 (ttt) cc_final: 0.8833 (ttm) REVERT: D 58 PHE cc_start: 0.7770 (m-80) cc_final: 0.7379 (m-80) REVERT: D 250 MET cc_start: 0.8433 (ttp) cc_final: 0.8207 (ttp) REVERT: D 269 MET cc_start: 0.8636 (mtp) cc_final: 0.8401 (mtm) REVERT: D 313 THR cc_start: 0.8252 (m) cc_final: 0.8023 (m) REVERT: E 105 ASP cc_start: 0.7654 (m-30) cc_final: 0.7415 (m-30) REVERT: E 111 GLU cc_start: 0.7776 (mt-10) cc_final: 0.7518 (mt-10) REVERT: E 163 MET cc_start: 0.7378 (mmp) cc_final: 0.7047 (mmp) REVERT: E 165 SER cc_start: 0.7385 (t) cc_final: 0.7131 (m) REVERT: E 204 GLU cc_start: 0.7969 (mm-30) cc_final: 0.7741 (mm-30) REVERT: E 243 ILE cc_start: 0.8848 (mm) cc_final: 0.8605 (mt) REVERT: F 117 MET cc_start: 0.7773 (tpt) cc_final: 0.7530 (tpt) REVERT: F 284 SER cc_start: 0.8901 (m) cc_final: 0.8553 (t) REVERT: F 292 GLU cc_start: 0.8000 (mt-10) cc_final: 0.7673 (mm-30) REVERT: F 296 ASP cc_start: 0.7881 (m-30) cc_final: 0.7680 (m-30) outliers start: 3 outliers final: 1 residues processed: 481 average time/residue: 0.3486 time to fit residues: 228.3088 Evaluate side-chains 328 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 327 time to evaluate : 0.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 286 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/iotbx/cli_parser.py", line 987, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( ^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( ^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( ^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( ^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1602, in energies_sites pair_proxies = self.pair_proxies( ^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1505, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1386, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 63.6705 > 50: distance: 175 - 298: 8.418 distance: 178 - 295: 9.836 distance: 212 - 267: 14.387 distance: 214 - 226: 12.994 distance: 215 - 264: 4.031 distance: 226 - 227: 22.490 distance: 226 - 237: 16.284 distance: 227 - 228: 19.371 distance: 227 - 230: 30.668 distance: 227 - 238: 25.118 distance: 228 - 229: 9.800 distance: 228 - 250: 6.043 distance: 230 - 231: 12.090 distance: 230 - 239: 14.664 distance: 230 - 240: 7.341 distance: 231 - 232: 15.186 distance: 231 - 241: 8.047 distance: 231 - 242: 25.968 distance: 232 - 233: 10.662 distance: 232 - 243: 11.901 distance: 232 - 244: 5.597 distance: 233 - 234: 35.981 distance: 233 - 245: 8.974 distance: 234 - 235: 32.187 distance: 234 - 236: 30.873 distance: 235 - 246: 7.263 distance: 235 - 247: 7.155 distance: 236 - 248: 17.917 distance: 236 - 249: 13.482 distance: 250 - 251: 7.385 distance: 250 - 257: 10.838 distance: 251 - 252: 7.048 distance: 251 - 254: 3.223 distance: 251 - 258: 12.042 distance: 252 - 253: 25.856 distance: 252 - 264: 9.274 distance: 254 - 255: 10.383 distance: 254 - 256: 10.755 distance: 254 - 259: 11.564 distance: 255 - 260: 18.956 distance: 256 - 261: 9.054 distance: 256 - 262: 13.611 distance: 256 - 263: 11.598 distance: 264 - 265: 7.548 distance: 264 - 268: 10.464 distance: 265 - 266: 18.478 distance: 265 - 270: 21.603 distance: 266 - 267: 10.069 distance: 266 - 271: 16.762 distance: 271 - 272: 16.132 distance: 271 - 282: 5.833 distance: 272 - 273: 30.310 distance: 272 - 275: 17.405 distance: 272 - 283: 20.735 distance: 273 - 274: 16.593 distance: 273 - 295: 21.533 distance: 275 - 276: 16.886 distance: 275 - 284: 6.891 distance: 275 - 285: 20.664 distance: 276 - 277: 42.431 distance: 276 - 286: 24.565 distance: 276 - 287: 28.032 distance: 277 - 278: 48.397 distance: 277 - 288: 27.486 distance: 277 - 289: 22.627 distance: 278 - 279: 63.670 distance: 278 - 290: 38.596 distance: 279 - 280: 43.625 distance: 279 - 281: 49.879 distance: 280 - 291: 17.880 distance: 280 - 292: 16.374 distance: 281 - 293: 11.336 distance: 281 - 294: 16.875 distance: 295 - 296: 6.090 distance: 295 - 302: 5.918 distance: 296 - 297: 24.985 distance: 296 - 299: 6.783 distance: 297 - 298: 28.017 distance: 297 - 311: 37.839 distance: 299 - 300: 8.987 distance: 299 - 301: 12.599 distance: 299 - 304: 17.601 distance: 300 - 305: 10.616 distance: 300 - 306: 8.694 distance: 300 - 307: 5.534 distance: 301 - 308: 6.380 distance: 301 - 309: 9.117 distance: 301 - 310: 16.423 distance: 311 - 312: 18.420 distance: 311 - 316: 33.135 distance: 312 - 313: 23.169 distance: 312 - 315: 4.052 distance: 312 - 317: 22.450 distance: 313 - 314: 28.294 distance: 313 - 321: 43.896 distance: 315 - 318: 15.047 distance: 315 - 319: 9.875 distance: 315 - 320: 9.361 distance: 321 - 322: 42.967 distance: 321 - 328: 35.708 distance: 322 - 323: 26.789 distance: 322 - 325: 35.022 distance: 322 - 329: 33.084 distance: 323 - 324: 25.049 distance: 323 - 335: 41.086 distance: 324 - 377: 5.936 distance: 325 - 326: 18.602 distance: 325 - 327: 16.516 distance: 325 - 330: 8.550 distance: 326 - 331: 29.422 distance: 327 - 332: 9.170 distance: 327 - 333: 11.131 distance: 327 - 334: 8.475 distance: 335 - 336: 14.267 distance: 335 - 340: 13.980 distance: 336 - 337: 27.523 distance: 336 - 339: 7.643 distance: 336 - 341: 14.998 distance: 337 - 338: 20.039 distance: 337 - 345: 41.378 distance: 338 - 393: 6.690 distance: 339 - 342: 15.678 distance: 339 - 343: 8.350 distance: 339 - 344: 7.003 distance: 345 - 346: 12.006 distance: 345 - 354: 19.519 distance: 346 - 347: 29.970 distance: 346 - 349: 21.813 distance: 346 - 355: 26.787 distance: 347 - 348: 18.902 distance: 347 - 367: 12.432 distance: 348 - 402: 9.708 distance: 349 - 350: 10.463 distance: 349 - 356: 6.564 distance: 349 - 357: 10.290 distance: 350 - 351: 3.093 distance: 350 - 358: 10.293 distance: 350 - 359: 4.142 distance: 351 - 360: 4.973 distance: 351 - 361: 5.475 distance: 352 - 353: 23.541 distance: 352 - 362: 4.087 distance: 353 - 364: 23.897 distance: 353 - 365: 22.563 distance: 353 - 366: 21.062 distance: 367 - 368: 21.847 distance: 367 - 372: 8.661 distance: 368 - 369: 24.355 distance: 368 - 371: 25.649 distance: 368 - 373: 19.723 distance: 369 - 370: 19.119 distance: 369 - 377: 9.648 distance: 370 - 412: 12.277 distance: 371 - 374: 35.439 distance: 371 - 375: 18.255 distance: 371 - 376: 15.911