Starting phenix.real_space_refine on Mon Sep 23 18:10:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8otd_17175/09_2024/8otd_17175.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8otd_17175/09_2024/8otd_17175.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8otd_17175/09_2024/8otd_17175.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8otd_17175/09_2024/8otd_17175.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8otd_17175/09_2024/8otd_17175.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8otd_17175/09_2024/8otd_17175.cif" } resolution = 2.6 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= 0.002 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: 4 Type Number sf(0) Gaussians S 28 5.16 5 C 2772 2.51 5 N 692 2.21 5 O 848 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 48 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 4340 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 1085 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1085 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 2, 'TRANS': 132} Restraints were copied for chains: C, B, D Time building chain proxies: 3.22, per 1000 atoms: 0.74 Number of scatterers: 4340 At special positions: 0 Unit cell: (100.528, 97.232, 37.08, 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 28 16.00 O 848 8.00 N 692 7.00 C 2772 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 214 " - pdb=" SG CYS A 253 " distance=2.07 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: 1.12 Conformation dependent library (CDL) restraints added in 578.7 milliseconds 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1040 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 11 sheets defined 0.0% alpha, 68.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.55 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'C' and resid 124 through 126 removed outlier: 6.034A pdb=" N TYR A 125 " --> pdb=" O ILE B 126 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N TYR B 125 " --> pdb=" O ILE D 126 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 129 through 130 removed outlier: 6.477A pdb=" N LYS A 129 " --> pdb=" O SER B 130 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N LYS B 129 " --> pdb=" O SER D 130 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 133 through 134 removed outlier: 6.868A pdb=" N VAL A 133 " --> pdb=" O SER C 134 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 140 through 153 removed outlier: 6.874A pdb=" N ILE C 146 " --> pdb=" O ASN A 145 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N THR A 147 " --> pdb=" O ILE C 146 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N ASN C 148 " --> pdb=" O THR A 147 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N THR A 149 " --> pdb=" O ASN C 148 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N LEU C 150 " --> pdb=" O THR A 149 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N ASN A 151 " --> pdb=" O LEU C 150 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N ILE C 152 " --> pdb=" O ASN A 151 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N THR A 153 " --> pdb=" O ILE C 152 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N ARG A 140 " --> pdb=" O THR B 141 " (cutoff:3.500A) removed outlier: 7.882A pdb=" N TYR B 143 " --> pdb=" O ARG A 140 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N ILE A 142 " --> pdb=" O TYR B 143 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N ASN B 145 " --> pdb=" O ILE A 142 " (cutoff:3.500A) removed outlier: 8.583A pdb=" N LEU A 144 " --> pdb=" O ASN B 145 " (cutoff:3.500A) removed outlier: 7.866A pdb=" N THR B 147 " --> pdb=" O LEU A 144 " (cutoff:3.500A) removed outlier: 9.204A pdb=" N ILE A 146 " --> pdb=" O THR B 147 " (cutoff:3.500A) removed outlier: 10.021A pdb=" N THR B 149 " --> pdb=" O ILE A 146 " (cutoff:3.500A) removed outlier: 9.017A pdb=" N ASN A 148 " --> pdb=" O THR B 149 " (cutoff:3.500A) removed outlier: 10.210A pdb=" N ASN B 151 " --> pdb=" O ASN A 148 " (cutoff:3.500A) removed outlier: 9.066A pdb=" N LEU A 150 " --> pdb=" O ASN B 151 " (cutoff:3.500A) removed outlier: 10.067A pdb=" N THR B 153 " --> pdb=" O LEU A 150 " (cutoff:3.500A) removed outlier: 9.314A pdb=" N ILE A 152 " --> pdb=" O THR B 153 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N ARG B 140 " --> pdb=" O THR D 141 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N TYR D 143 " --> pdb=" O ARG B 140 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N ILE B 142 " --> pdb=" O TYR D 143 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N ASN D 145 " --> pdb=" O ILE B 142 " (cutoff:3.500A) removed outlier: 8.582A pdb=" N LEU B 144 " --> pdb=" O ASN D 145 " (cutoff:3.500A) removed outlier: 7.866A pdb=" N THR D 147 " --> pdb=" O LEU B 144 " (cutoff:3.500A) removed outlier: 9.205A pdb=" N ILE B 146 " --> pdb=" O THR D 147 " (cutoff:3.500A) removed outlier: 10.021A pdb=" N THR D 149 " --> pdb=" O ILE B 146 " (cutoff:3.500A) removed outlier: 9.017A pdb=" N ASN B 148 " --> pdb=" O THR D 149 " (cutoff:3.500A) removed outlier: 10.209A pdb=" N ASN D 151 " --> pdb=" O ASN B 148 " (cutoff:3.500A) removed outlier: 9.066A pdb=" N LEU B 150 " --> pdb=" O ASN D 151 " (cutoff:3.500A) removed outlier: 10.067A pdb=" N THR D 153 " --> pdb=" O LEU B 150 " (cutoff:3.500A) removed outlier: 9.314A pdb=" N ILE B 152 " --> pdb=" O THR D 153 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 156 through 176 removed outlier: 6.751A pdb=" N VAL A 162 " --> pdb=" O GLU C 161 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N GLU C 163 " --> pdb=" O VAL A 162 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N ASN A 164 " --> pdb=" O GLU C 163 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N ILE C 165 " --> pdb=" O ASN A 164 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N THR A 166 " --> pdb=" O ILE C 165 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N TYR A 157 " --> pdb=" O TYR B 158 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N VAL B 160 " --> pdb=" O TYR A 157 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N SER A 159 " --> pdb=" O VAL B 160 " (cutoff:3.500A) removed outlier: 5.829A pdb=" N VAL B 162 " --> pdb=" O SER A 159 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N GLU A 161 " --> pdb=" O VAL B 162 " (cutoff:3.500A) removed outlier: 9.726A pdb=" N ASN B 164 " --> pdb=" O GLU A 161 " (cutoff:3.500A) removed outlier: 9.346A pdb=" N GLU A 163 " --> pdb=" O ASN B 164 " (cutoff:3.500A) removed outlier: 10.000A pdb=" N THR B 166 " --> pdb=" O GLU A 163 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N ILE A 165 " --> pdb=" O THR B 166 " (cutoff:3.500A) removed outlier: 8.460A pdb=" N GLN B 168 " --> pdb=" O ILE A 165 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ALA A 167 " --> pdb=" O GLN B 168 " (cutoff:3.500A) removed outlier: 8.365A pdb=" N GLN B 170 " --> pdb=" O ALA A 167 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N VAL A 169 " --> pdb=" O GLN B 170 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N SER B 172 " --> pdb=" O VAL A 169 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N PHE A 171 " --> pdb=" O SER B 172 " (cutoff:3.500A) removed outlier: 8.447A pdb=" N THR B 174 " --> pdb=" O PHE A 171 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N LYS A 173 " --> pdb=" O THR B 174 " (cutoff:3.500A) removed outlier: 8.200A pdb=" N ILE B 176 " --> pdb=" O LYS A 173 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N VAL A 175 " --> pdb=" O ILE B 176 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N TYR B 157 " --> pdb=" O TYR D 158 " (cutoff:3.500A) removed outlier: 7.444A pdb=" N VAL D 160 " --> pdb=" O TYR B 157 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N SER B 159 " --> pdb=" O VAL D 160 " (cutoff:3.500A) removed outlier: 5.829A pdb=" N VAL D 162 " --> pdb=" O SER B 159 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N GLU B 161 " --> pdb=" O VAL D 162 " (cutoff:3.500A) removed outlier: 9.726A pdb=" N ASN D 164 " --> pdb=" O GLU B 161 " (cutoff:3.500A) removed outlier: 9.346A pdb=" N GLU B 163 " --> pdb=" O ASN D 164 " (cutoff:3.500A) removed outlier: 10.000A pdb=" N THR D 166 " --> pdb=" O GLU B 163 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N ILE B 165 " --> pdb=" O THR D 166 " (cutoff:3.500A) removed outlier: 8.460A pdb=" N GLN D 168 " --> pdb=" O ILE B 165 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N ALA B 167 " --> pdb=" O GLN D 168 " (cutoff:3.500A) removed outlier: 8.365A pdb=" N GLN D 170 " --> pdb=" O ALA B 167 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N VAL B 169 " --> pdb=" O GLN D 170 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N SER D 172 " --> pdb=" O VAL B 169 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N PHE B 171 " --> pdb=" O SER D 172 " (cutoff:3.500A) removed outlier: 8.448A pdb=" N THR D 174 " --> pdb=" O PHE B 171 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N LYS B 173 " --> pdb=" O THR D 174 " (cutoff:3.500A) removed outlier: 8.200A pdb=" N ILE D 176 " --> pdb=" O LYS B 173 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N VAL B 175 " --> pdb=" O ILE D 176 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 180 through 187 removed outlier: 8.672A pdb=" N ARG A 180 " --> pdb=" O LEU C 181 " (cutoff:3.500A) removed outlier: 9.797A pdb=" N ASN C 183 " --> pdb=" O ARG A 180 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N ASN A 182 " --> pdb=" O ASN C 183 " (cutoff:3.500A) removed outlier: 8.384A pdb=" N SER C 185 " --> pdb=" O ASN A 182 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N ILE A 184 " --> pdb=" O SER C 185 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N ILE C 187 " --> pdb=" O ILE A 184 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N ILE A 186 " --> pdb=" O ILE C 187 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N LEU A 181 " --> pdb=" O ARG B 180 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N ASN B 182 " --> pdb=" O LEU A 181 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N ASN A 183 " --> pdb=" O ASN B 182 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N LEU B 181 " --> pdb=" O ARG D 180 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N ASN D 182 " --> pdb=" O LEU B 181 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N ASN B 183 " --> pdb=" O ASN D 182 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 192 through 198 removed outlier: 5.862A pdb=" N LYS A 193 " --> pdb=" O GLN C 194 " (cutoff:3.500A) removed outlier: 8.599A pdb=" N ASP C 196 " --> pdb=" O LYS A 193 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N ILE A 195 " --> pdb=" O ASP C 196 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N THR C 198 " --> pdb=" O ILE A 195 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N TYR A 197 " --> pdb=" O THR C 198 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N LYS B 193 " --> pdb=" O MET A 192 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N GLN A 194 " --> pdb=" O LYS B 193 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N LYS D 193 " --> pdb=" O MET B 192 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N GLN B 194 " --> pdb=" O LYS D 193 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 201 through 206 removed outlier: 6.552A pdb=" N THR A 201 " --> pdb=" O VAL C 202 " (cutoff:3.500A) removed outlier: 8.040A pdb=" N ALA C 204 " --> pdb=" O THR A 201 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N ILE A 203 " --> pdb=" O ALA C 204 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N GLU C 206 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N GLU A 205 " --> pdb=" O GLU C 206 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 209 through 219 removed outlier: 6.838A pdb=" N THR C 215 " --> pdb=" O CYS A 214 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N LEU A 216 " --> pdb=" O THR C 215 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N ILE C 217 " --> pdb=" O LEU A 216 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N SER A 218 " --> pdb=" O ILE C 217 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N ILE C 219 " --> pdb=" O SER A 218 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N TYR A 209 " --> pdb=" O MET B 210 " (cutoff:3.500A) removed outlier: 7.863A pdb=" N ASP B 212 " --> pdb=" O TYR A 209 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N TYR A 211 " --> pdb=" O ASP B 212 " (cutoff:3.500A) removed outlier: 8.049A pdb=" N CYS B 214 " --> pdb=" O TYR A 211 " (cutoff:3.500A) removed outlier: 8.472A pdb=" N PHE A 213 " --> pdb=" O CYS B 214 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N LEU B 216 " --> pdb=" O PHE A 213 " (cutoff:3.500A) removed outlier: 8.980A pdb=" N THR A 215 " --> pdb=" O LEU B 216 " (cutoff:3.500A) removed outlier: 9.711A pdb=" N SER B 218 " --> pdb=" O THR A 215 " (cutoff:3.500A) removed outlier: 8.824A pdb=" N ILE A 217 " --> pdb=" O SER B 218 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N TYR B 209 " --> pdb=" O MET D 210 " (cutoff:3.500A) removed outlier: 7.863A pdb=" N ASP D 212 " --> pdb=" O TYR B 209 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N TYR B 211 " --> pdb=" O ASP D 212 " (cutoff:3.500A) removed outlier: 8.049A pdb=" N CYS D 214 " --> pdb=" O TYR B 211 " (cutoff:3.500A) removed outlier: 8.472A pdb=" N PHE B 213 " --> pdb=" O CYS D 214 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N LEU D 216 " --> pdb=" O PHE B 213 " (cutoff:3.500A) removed outlier: 8.980A pdb=" N THR B 215 " --> pdb=" O LEU D 216 " (cutoff:3.500A) removed outlier: 9.711A pdb=" N SER D 218 " --> pdb=" O THR B 215 " (cutoff:3.500A) removed outlier: 8.824A pdb=" N ILE B 217 " --> pdb=" O SER D 218 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 222 through 230 removed outlier: 6.224A pdb=" N ASN A 223 " --> pdb=" O ILE C 224 " (cutoff:3.500A) removed outlier: 7.612A pdb=" N LEU C 226 " --> pdb=" O ASN A 223 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N VAL A 225 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 7.828A pdb=" N MET C 228 " --> pdb=" O VAL A 225 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N MET A 227 " --> pdb=" O MET C 228 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N VAL C 230 " --> pdb=" O MET A 227 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N GLN A 229 " --> pdb=" O VAL C 230 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N ASN B 223 " --> pdb=" O HIS A 222 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N VAL A 230 " --> pdb=" O GLN B 229 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N ASN D 223 " --> pdb=" O HIS B 222 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N VAL B 230 " --> pdb=" O GLN D 229 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 233 through 252 removed outlier: 6.672A pdb=" N THR A 233 " --> pdb=" O THR C 234 " (cutoff:3.500A) removed outlier: 8.188A pdb=" N TYR C 236 " --> pdb=" O THR A 233 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N THR A 235 " --> pdb=" O TYR C 236 " (cutoff:3.500A) removed outlier: 7.926A pdb=" N GLY C 238 " --> pdb=" O THR A 235 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N PHE A 237 " --> pdb=" O GLY C 238 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N SER C 240 " --> pdb=" O PHE A 237 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N HIS A 239 " --> pdb=" O SER C 240 " (cutoff:3.500A) removed outlier: 8.437A pdb=" N GLN C 242 " --> pdb=" O HIS A 239 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N GLU A 241 " --> pdb=" O GLN C 242 " (cutoff:3.500A) removed outlier: 8.202A pdb=" N SER C 244 " --> pdb=" O GLU A 241 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N ILE A 243 " --> pdb=" O SER C 244 " (cutoff:3.500A) removed outlier: 8.312A pdb=" N GLU C 246 " --> pdb=" O ILE A 243 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N GLN A 245 " --> pdb=" O GLU C 246 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N TYR C 248 " --> pdb=" O GLN A 245 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N ARG A 247 " --> pdb=" O TYR C 248 " (cutoff:3.500A) removed outlier: 7.993A pdb=" N TYR C 250 " --> pdb=" O ARG A 247 " (cutoff:3.500A) removed outlier: 8.753A pdb=" N GLN A 249 " --> pdb=" O TYR C 250 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N ASP C 252 " --> pdb=" O GLN A 249 " (cutoff:3.500A) removed outlier: 9.152A pdb=" N VAL A 251 " --> pdb=" O ASP C 252 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N VAL B 251 " --> pdb=" O TYR A 250 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N ASP A 252 " --> pdb=" O VAL B 251 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N VAL D 251 " --> pdb=" O TYR B 250 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N ASP B 252 " --> pdb=" O VAL D 251 " (cutoff:3.500A) 102 hydrogen bonds defined for protein. 306 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.19 Time building geometry restraints manager: 1.14 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: 1058 1.34 - 1.46: 1274 1.46 - 1.58: 2032 1.58 - 1.70: 0 1.70 - 1.82: 48 Bond restraints: 4412 Sorted by residual: bond pdb=" CG HIS B 239 " pdb=" CD2 HIS B 239 " ideal model delta sigma weight residual 1.354 1.327 0.027 1.10e-02 8.26e+03 6.20e+00 bond pdb=" CG HIS C 239 " pdb=" CD2 HIS C 239 " ideal model delta sigma weight residual 1.354 1.327 0.027 1.10e-02 8.26e+03 6.03e+00 bond pdb=" CG HIS D 239 " pdb=" CD2 HIS D 239 " ideal model delta sigma weight residual 1.354 1.327 0.027 1.10e-02 8.26e+03 5.97e+00 bond pdb=" CG HIS A 239 " pdb=" CD2 HIS A 239 " ideal model delta sigma weight residual 1.354 1.327 0.027 1.10e-02 8.26e+03 5.85e+00 bond pdb=" CA SER B 218 " pdb=" CB SER B 218 " ideal model delta sigma weight residual 1.530 1.497 0.034 1.50e-02 4.44e+03 5.06e+00 ... (remaining 4407 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.56: 4616 1.56 - 3.11: 1091 3.11 - 4.67: 213 4.67 - 6.22: 60 6.22 - 7.78: 16 Bond angle restraints: 5996 Sorted by residual: angle pdb=" C ASP B 136 " pdb=" CA ASP B 136 " pdb=" CB ASP B 136 " ideal model delta sigma weight residual 109.84 117.62 -7.78 1.63e+00 3.76e-01 2.28e+01 angle pdb=" C ASP A 136 " pdb=" CA ASP A 136 " pdb=" CB ASP A 136 " ideal model delta sigma weight residual 109.84 117.61 -7.77 1.63e+00 3.76e-01 2.27e+01 angle pdb=" C ASP D 136 " pdb=" CA ASP D 136 " pdb=" CB ASP D 136 " ideal model delta sigma weight residual 109.84 117.58 -7.74 1.63e+00 3.76e-01 2.26e+01 angle pdb=" C ASP C 136 " pdb=" CA ASP C 136 " pdb=" CB ASP C 136 " ideal model delta sigma weight residual 109.84 117.58 -7.74 1.63e+00 3.76e-01 2.25e+01 angle pdb=" N GLU D 246 " pdb=" CA GLU D 246 " pdb=" C GLU D 246 " ideal model delta sigma weight residual 108.76 116.05 -7.29 1.58e+00 4.01e-01 2.13e+01 ... (remaining 5991 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.88: 2253 14.88 - 29.77: 274 29.77 - 44.65: 60 44.65 - 59.54: 48 59.54 - 74.42: 16 Dihedral angle restraints: 2651 sinusoidal: 1027 harmonic: 1624 Sorted by residual: dihedral pdb=" CA THR C 231 " pdb=" C THR C 231 " pdb=" N VAL C 232 " pdb=" CA VAL C 232 " ideal model delta harmonic sigma weight residual 180.00 156.11 23.89 0 5.00e+00 4.00e-02 2.28e+01 dihedral pdb=" CA THR A 231 " pdb=" C THR A 231 " pdb=" N VAL A 232 " pdb=" CA VAL A 232 " ideal model delta harmonic sigma weight residual 180.00 156.13 23.87 0 5.00e+00 4.00e-02 2.28e+01 dihedral pdb=" CA THR D 231 " pdb=" C THR D 231 " pdb=" N VAL D 232 " pdb=" CA VAL D 232 " ideal model delta harmonic sigma weight residual 180.00 156.15 23.85 0 5.00e+00 4.00e-02 2.27e+01 ... (remaining 2648 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 338 0.066 - 0.133: 270 0.133 - 0.199: 93 0.199 - 0.265: 7 0.265 - 0.331: 12 Chirality restraints: 720 Sorted by residual: chirality pdb=" CA LYS B 124 " pdb=" N LYS B 124 " pdb=" C LYS B 124 " pdb=" CB LYS B 124 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.74e+00 chirality pdb=" CA LYS D 124 " pdb=" N LYS D 124 " pdb=" C LYS D 124 " pdb=" CB LYS D 124 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.74e+00 chirality pdb=" CA LYS A 124 " pdb=" N LYS A 124 " pdb=" C LYS A 124 " pdb=" CB LYS A 124 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.73e+00 ... (remaining 717 not shown) Planarity restraints: 744 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR C 248 " 0.073 2.00e-02 2.50e+03 3.84e-02 2.95e+01 pdb=" CG TYR C 248 " -0.067 2.00e-02 2.50e+03 pdb=" CD1 TYR C 248 " -0.022 2.00e-02 2.50e+03 pdb=" CD2 TYR C 248 " -0.029 2.00e-02 2.50e+03 pdb=" CE1 TYR C 248 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR C 248 " 0.009 2.00e-02 2.50e+03 pdb=" CZ TYR C 248 " 0.011 2.00e-02 2.50e+03 pdb=" OH TYR C 248 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 248 " 0.073 2.00e-02 2.50e+03 3.83e-02 2.94e+01 pdb=" CG TYR A 248 " -0.067 2.00e-02 2.50e+03 pdb=" CD1 TYR A 248 " -0.022 2.00e-02 2.50e+03 pdb=" CD2 TYR A 248 " -0.029 2.00e-02 2.50e+03 pdb=" CE1 TYR A 248 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR A 248 " 0.009 2.00e-02 2.50e+03 pdb=" CZ TYR A 248 " 0.011 2.00e-02 2.50e+03 pdb=" OH TYR A 248 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 248 " 0.073 2.00e-02 2.50e+03 3.82e-02 2.92e+01 pdb=" CG TYR B 248 " -0.067 2.00e-02 2.50e+03 pdb=" CD1 TYR B 248 " -0.022 2.00e-02 2.50e+03 pdb=" CD2 TYR B 248 " -0.029 2.00e-02 2.50e+03 pdb=" CE1 TYR B 248 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TYR B 248 " 0.009 2.00e-02 2.50e+03 pdb=" CZ TYR B 248 " 0.011 2.00e-02 2.50e+03 pdb=" OH TYR B 248 " 0.020 2.00e-02 2.50e+03 ... (remaining 741 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 36 2.64 - 3.20: 3671 3.20 - 3.77: 6768 3.77 - 4.33: 9572 4.33 - 4.90: 17364 Nonbonded interactions: 37411 Sorted by model distance: nonbonded pdb=" SG CYS B 214 " pdb=" SG CYS B 253 " model vdw 2.073 3.760 nonbonded pdb=" SG CYS D 214 " pdb=" SG CYS D 253 " model vdw 2.074 3.760 nonbonded pdb=" SG CYS C 214 " pdb=" SG CYS C 253 " model vdw 2.075 3.760 nonbonded pdb=" NZ LYS D 129 " pdb=" OD2 ASP D 136 " model vdw 2.478 3.120 nonbonded pdb=" NZ LYS A 129 " pdb=" OD2 ASP A 136 " model vdw 2.478 3.120 ... (remaining 37406 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.980 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: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 14.310 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.010 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:14.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 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 : 0.008 0.043 4412 Z= 0.533 Angle : 1.482 7.777 5996 Z= 0.940 Chirality : 0.099 0.331 720 Planarity : 0.015 0.168 744 Dihedral : 16.818 74.422 1608 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.27 % Favored : 91.73 % Rotamer: Outliers : 4.76 % Allowed : 5.56 % Favored : 89.68 % Cbeta Deviations : 0.77 % 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: -3.89 (0.27), residues: 532 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.96 (0.21), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.004 HIS C 239 PHE 0.017 0.006 PHE B 171 TYR 0.073 0.008 TYR C 248 ARG 0.026 0.005 ARG A 247 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 151 time to evaluate : 0.504 Fit side-chains REVERT: A 178 LYS cc_start: 0.8086 (pttt) cc_final: 0.7376 (tttt) REVERT: B 172 SER cc_start: 0.8563 (t) cc_final: 0.8212 (m) REVERT: B 178 LYS cc_start: 0.8070 (pttt) cc_final: 0.7326 (tttt) REVERT: B 207 MET cc_start: 0.8322 (mtt) cc_final: 0.8079 (mtm) REVERT: C 145 ASN cc_start: 0.7983 (m-40) cc_final: 0.7709 (m-40) REVERT: C 178 LYS cc_start: 0.8235 (pttt) cc_final: 0.7533 (tttt) REVERT: C 247 ARG cc_start: 0.8300 (ttp80) cc_final: 0.6725 (ttp80) REVERT: D 172 SER cc_start: 0.8571 (t) cc_final: 0.8214 (m) REVERT: D 178 LYS cc_start: 0.8213 (pttt) cc_final: 0.7463 (tttt) outliers start: 24 outliers final: 0 residues processed: 159 average time/residue: 1.0825 time to fit residues: 178.2772 Evaluate side-chains 104 residues out of total 504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 104 time to evaluate : 0.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 43 optimal weight: 3.9990 chunk 39 optimal weight: 4.9990 chunk 21 optimal weight: 7.9990 chunk 13 optimal weight: 2.9990 chunk 26 optimal weight: 0.0370 chunk 40 optimal weight: 2.9990 chunk 15 optimal weight: 10.0000 chunk 24 optimal weight: 5.9990 chunk 30 optimal weight: 2.9990 chunk 47 optimal weight: 7.9990 chunk 14 optimal weight: 1.9990 overall best weight: 2.2066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 GLN A 145 ASN A 151 ASN A 170 GLN A 182 ASN A 242 GLN B 145 ASN B 151 ASN B 156 ASN B 170 GLN B 182 ASN B 239 HIS B 242 GLN C 151 ASN C 170 GLN C 182 ASN C 242 GLN D 151 ASN D 170 GLN D 182 ASN D 239 HIS D 242 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.2767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 4412 Z= 0.245 Angle : 0.663 7.343 5996 Z= 0.367 Chirality : 0.053 0.143 720 Planarity : 0.003 0.029 744 Dihedral : 6.448 20.816 596 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 2.58 % Allowed : 17.06 % Favored : 80.36 % 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: -3.38 (0.30), residues: 532 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.57 (0.23), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.002 HIS C 239 PHE 0.011 0.002 PHE B 213 TYR 0.023 0.002 TYR C 143 ARG 0.002 0.000 ARG D 247 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 119 time to evaluate : 0.460 Fit side-chains REVERT: A 178 LYS cc_start: 0.7851 (pttt) cc_final: 0.7053 (ttmt) REVERT: A 207 MET cc_start: 0.8356 (mtp) cc_final: 0.8039 (mtt) REVERT: B 163 GLU cc_start: 0.8193 (mt-10) cc_final: 0.7973 (mp0) REVERT: B 178 LYS cc_start: 0.7858 (pttt) cc_final: 0.7070 (ttpt) REVERT: C 163 GLU cc_start: 0.8576 (mt-10) cc_final: 0.8368 (mp0) REVERT: C 178 LYS cc_start: 0.7993 (pttt) cc_final: 0.7129 (tttt) REVERT: C 207 MET cc_start: 0.8581 (mtp) cc_final: 0.8291 (mtt) REVERT: D 172 SER cc_start: 0.8628 (t) cc_final: 0.8272 (m) REVERT: D 178 LYS cc_start: 0.8036 (pttt) cc_final: 0.7348 (tttt) outliers start: 13 outliers final: 4 residues processed: 127 average time/residue: 1.2736 time to fit residues: 166.8667 Evaluate side-chains 103 residues out of total 504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 99 time to evaluate : 0.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 185 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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-5461/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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-5461/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-5461/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-5461/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-5461/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-5461/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-5461/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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-5461/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-5461/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 56.4597 > 50: distance: 134 - 140: 8.195 distance: 140 - 141: 9.048 distance: 141 - 142: 14.241 distance: 141 - 144: 8.751 distance: 142 - 143: 10.622 distance: 142 - 149: 15.294 distance: 144 - 145: 21.701 distance: 145 - 146: 19.764 distance: 146 - 147: 10.780 distance: 146 - 148: 10.436 distance: 149 - 150: 6.592 distance: 150 - 151: 25.900 distance: 150 - 153: 6.618 distance: 151 - 152: 20.176 distance: 151 - 156: 25.913 distance: 153 - 154: 10.269 distance: 153 - 155: 18.919 distance: 156 - 157: 12.736 distance: 157 - 158: 19.834 distance: 157 - 160: 23.451 distance: 158 - 159: 24.565 distance: 158 - 163: 13.574 distance: 160 - 161: 20.994 distance: 160 - 162: 16.108 distance: 163 - 164: 4.066 distance: 164 - 165: 14.456 distance: 164 - 167: 15.591 distance: 165 - 166: 3.090 distance: 165 - 170: 9.999 distance: 167 - 168: 26.998 distance: 167 - 169: 6.776 distance: 170 - 171: 6.937 distance: 171 - 172: 13.695 distance: 171 - 174: 11.128 distance: 172 - 173: 22.130 distance: 172 - 177: 25.769 distance: 174 - 175: 11.891 distance: 174 - 176: 17.162 distance: 177 - 178: 11.614 distance: 178 - 179: 14.748 distance: 178 - 181: 13.468 distance: 179 - 180: 8.735 distance: 179 - 184: 10.439 distance: 181 - 182: 13.897 distance: 181 - 183: 27.601 distance: 184 - 185: 15.810 distance: 185 - 186: 12.365 distance: 185 - 188: 13.431 distance: 186 - 187: 17.869 distance: 186 - 191: 21.756 distance: 188 - 189: 22.969 distance: 188 - 190: 16.647 distance: 191 - 192: 14.169 distance: 192 - 193: 37.832 distance: 192 - 195: 24.738 distance: 193 - 194: 6.393 distance: 193 - 203: 13.896 distance: 195 - 196: 18.194 distance: 196 - 197: 5.484 distance: 196 - 198: 23.050 distance: 197 - 199: 17.360 distance: 199 - 201: 7.245 distance: 200 - 201: 12.344 distance: 201 - 202: 15.443 distance: 203 - 204: 18.784 distance: 204 - 205: 11.107 distance: 204 - 207: 17.202 distance: 205 - 206: 6.951 distance: 205 - 214: 17.957 distance: 207 - 208: 27.880 distance: 208 - 209: 7.775 distance: 208 - 210: 31.292 distance: 209 - 211: 6.951 distance: 210 - 212: 8.625 distance: 211 - 213: 14.630 distance: 212 - 213: 24.472 distance: 214 - 215: 30.408 distance: 215 - 216: 20.081 distance: 216 - 217: 5.937 distance: 216 - 218: 6.823