Starting phenix.real_space_refine on Fri Aug 22 22:18:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wc4_37430/08_2025/8wc4_37430_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wc4_37430/08_2025/8wc4_37430.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/8wc4_37430/08_2025/8wc4_37430.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wc4_37430/08_2025/8wc4_37430.map" model { file = "/net/cci-nas-00/data/ceres_data/8wc4_37430/08_2025/8wc4_37430_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wc4_37430/08_2025/8wc4_37430_neut.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= 0.001 sd= 0.079 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: 5 Type Number sf(0) Gaussians Br 1 7.06 5 S 56 5.16 5 C 5369 2.51 5 N 1426 2.21 5 O 1542 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8394 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1844 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1844 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 5, 'TRANS': 227} Chain breaks: 2 Unresolved non-hydrogen bonds: 87 Unresolved non-hydrogen angles: 105 Unresolved non-hydrogen dihedrals: 69 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 5, 'GLN:plan1': 1, 'ARG:plan': 5, 'ASN:plan1': 1, 'GLU:plan': 5} Unresolved non-hydrogen planarities: 67 Chain: "B" Number of atoms: 2484 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2484 Classifications: {'peptide': 334} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 5, 'TRANS': 328} Chain breaks: 1 Unresolved non-hydrogen bonds: 87 Unresolved non-hydrogen angles: 104 Unresolved non-hydrogen dihedrals: 70 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 7, 'GLU:plan': 5, 'ASP:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 69 Chain: "R" Number of atoms: 2054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 273, 2054 Classifications: {'peptide': 273} Incomplete info: {'truncation_to_alanine': 40} Link IDs: {'PTRANS': 12, 'TRANS': 260} Chain breaks: 2 Unresolved non-hydrogen bonds: 130 Unresolved non-hydrogen angles: 158 Unresolved non-hydrogen dihedrals: 108 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'TYR:plan': 2, 'GLU:plan': 4, 'ARG:plan': 3, 'GLN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 55 Chain: "S" Number of atoms: 1622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1622 Classifications: {'peptide': 214} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 9, 'TRANS': 204} Chain breaks: 3 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 1, 'ASP:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "Y" Number of atoms: 380 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 380 Classifications: {'peptide': 56} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 4, 'TRANS': 51} Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 62 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'GLU:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 26 Chain: "R" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Unusual residues: {'VMT': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.08, per 1000 atoms: 0.25 Number of scatterers: 8394 At special positions: 0 Unit cell: (89.25, 118.15, 124.95, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Br 1 34.99 S 56 16.00 O 1542 8.00 N 1426 7.00 C 5369 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.04 Simple disulfide: pdb=" SG CYS S 159 " - pdb=" SG CYS S 229 " distance=2.04 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: 0.62 Conformation dependent library (CDL) restraints added in 364.5 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2086 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 13 sheets defined 38.3% alpha, 19.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.24 Creating SS restraints... Processing helix chain 'A' and resid 6 through 31 removed outlier: 3.680A pdb=" N LYS A 10 " --> pdb=" O SER A 6 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N ALA A 11 " --> pdb=" O ALA A 7 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ALA A 12 " --> pdb=" O GLU A 8 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 55 removed outlier: 3.539A pdb=" N ARG A 54 " --> pdb=" O VAL A 50 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ILE A 55 " --> pdb=" O LYS A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 216 removed outlier: 3.844A pdb=" N GLN A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N PHE A 215 " --> pdb=" O ILE A 212 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ASN A 216 " --> pdb=" O GLN A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 245 removed outlier: 3.676A pdb=" N ALA A 236 " --> pdb=" O ARG A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 271 removed outlier: 3.729A pdb=" N LEU A 264 " --> pdb=" O LYS A 260 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLY A 271 " --> pdb=" O LYS A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 278 Processing helix chain 'A' and resid 279 through 285 removed outlier: 3.596A pdb=" N TYR A 285 " --> pdb=" O PHE A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 317 Processing helix chain 'A' and resid 337 through 358 Processing helix chain 'B' and resid 7 through 24 Processing helix chain 'B' and resid 29 through 35 removed outlier: 3.639A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'R' and resid 25 through 49 removed outlier: 3.721A pdb=" N ILE R 42 " --> pdb=" O VAL R 38 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N VAL R 43 " --> pdb=" O GLY R 39 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ILE R 44 " --> pdb=" O ASN R 40 " (cutoff:3.500A) Processing helix chain 'R' and resid 57 through 85 removed outlier: 4.223A pdb=" N LEU R 61 " --> pdb=" O THR R 57 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N MET R 76 " --> pdb=" O GLY R 72 " (cutoff:3.500A) Proline residue: R 77 - end of helix Processing helix chain 'R' and resid 94 through 126 removed outlier: 3.731A pdb=" N ALA R 123 " --> pdb=" O ASP R 119 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N VAL R 124 " --> pdb=" O ARG R 120 " (cutoff:3.500A) Processing helix chain 'R' and resid 129 through 134 Processing helix chain 'R' and resid 135 through 160 removed outlier: 3.573A pdb=" N ILE R 139 " --> pdb=" O ASN R 135 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N LEU R 140 " --> pdb=" O ILE R 136 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N VAL R 141 " --> pdb=" O SER R 137 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N MET R 142 " --> pdb=" O THR R 138 " (cutoff:3.500A) Proline residue: R 150 - end of helix Processing helix chain 'R' and resid 167 through 175 Processing helix chain 'R' and resid 188 through 198 Processing helix chain 'R' and resid 198 through 226 removed outlier: 3.538A pdb=" N ILE R 223 " --> pdb=" O GLN R 219 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASN R 224 " --> pdb=" O ALA R 220 " (cutoff:3.500A) Processing helix chain 'R' and resid 245 through 275 removed outlier: 3.587A pdb=" N THR R 249 " --> pdb=" O LYS R 245 " (cutoff:3.500A) Proline residue: R 263 - end of helix Proline residue: R 272 - end of helix Processing helix chain 'R' and resid 279 through 302 removed outlier: 4.043A pdb=" N ASN R 283 " --> pdb=" O PRO R 279 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ASP R 284 " --> pdb=" O PRO R 280 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ALA R 285 " --> pdb=" O SER R 281 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N GLY R 290 " --> pdb=" O LEU R 286 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N TYR R 291 " --> pdb=" O TYR R 287 " (cutoff:3.500A) Proline residue: R 298 - end of helix Processing helix chain 'R' and resid 305 through 313 Processing helix chain 'S' and resid 28 through 32 removed outlier: 3.666A pdb=" N PHE S 32 " --> pdb=" O PHE S 29 " (cutoff:3.500A) Processing helix chain 'S' and resid 220 through 224 removed outlier: 3.903A pdb=" N VAL S 224 " --> pdb=" O ALA S 221 " (cutoff:3.500A) Processing helix chain 'Y' and resid 9 through 24 removed outlier: 3.654A pdb=" N ASN Y 24 " --> pdb=" O LYS Y 20 " (cutoff:3.500A) Processing helix chain 'Y' and resid 29 through 45 removed outlier: 3.604A pdb=" N ASP Y 36 " --> pdb=" O LYS Y 32 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N LEU Y 37 " --> pdb=" O ALA Y 33 " (cutoff:3.500A) Processing helix chain 'Y' and resid 46 through 48 No H-bonds generated for 'chain 'Y' and resid 46 through 48' Processing sheet with id=AA1, first strand: chain 'A' and resid 184 through 190 removed outlier: 3.541A pdb=" N PHE A 189 " --> pdb=" O PHE A 196 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N VAL A 201 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 9.846A pdb=" N ALA A 220 " --> pdb=" O THR A 33 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N ARG A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 8.369A pdb=" N ILE A 222 " --> pdb=" O ARG A 35 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.994A pdb=" N VAL A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N LEU A 39 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 8.941A pdb=" N ASP A 226 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N ILE A 221 " --> pdb=" O ILE A 255 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N PHE A 257 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N PHE A 223 " --> pdb=" O PHE A 257 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N ASN A 259 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N VAL A 225 " --> pdb=" O ASN A 259 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.728A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 4.042A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU B 70 " --> pdb=" O TRP B 82 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.902A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 153 removed outlier: 6.574A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.564A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.571A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ARG B 251 " --> pdb=" O THR B 243 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 275 through 278 removed outlier: 3.608A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'S' and resid 3 through 4 removed outlier: 3.693A pdb=" N GLN S 3 " --> pdb=" O SER S 25 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N SER S 25 " --> pdb=" O GLN S 3 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ARG S 18 " --> pdb=" O MET S 83 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'S' and resid 58 through 60 removed outlier: 6.658A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 140 through 142 removed outlier: 3.566A pdb=" N ARG S 160 " --> pdb=" O THR S 141 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 146 through 148 removed outlier: 6.445A pdb=" N VAL S 147 " --> pdb=" O GLU S 246 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N TYR S 227 " --> pdb=" O THR S 243 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N GLY S 225 " --> pdb=" O LEU S 245 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'S' and resid 194 through 195 removed outlier: 3.577A pdb=" N ILE S 189 " --> pdb=" O TRP S 176 " (cutoff:3.500A) 376 hydrogen bonds defined for protein. 1077 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: 1.06 Time building geometry restraints manager: 0.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.31: 1357 1.31 - 1.47: 3583 1.47 - 1.63: 3558 1.63 - 1.78: 7 1.78 - 1.94: 75 Bond restraints: 8580 Sorted by residual: bond pdb=" C PRO R 56 " pdb=" O PRO R 56 " ideal model delta sigma weight residual 1.238 1.158 0.080 1.24e-02 6.50e+03 4.16e+01 bond pdb=" C MET R 195 " pdb=" O MET R 195 " ideal model delta sigma weight residual 1.236 1.177 0.059 1.16e-02 7.43e+03 2.59e+01 bond pdb=" CA ASN A 231 " pdb=" C ASN A 231 " ideal model delta sigma weight residual 1.525 1.474 0.051 1.02e-02 9.61e+03 2.49e+01 bond pdb=" C ASP B 312 " pdb=" O ASP B 312 " ideal model delta sigma weight residual 1.236 1.167 0.069 1.38e-02 5.25e+03 2.46e+01 bond pdb=" CA PHE R 50 " pdb=" C PHE R 50 " ideal model delta sigma weight residual 1.524 1.490 0.034 7.00e-03 2.04e+04 2.41e+01 ... (remaining 8575 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.09: 11535 3.09 - 6.18: 112 6.18 - 9.27: 16 9.27 - 12.36: 2 12.36 - 15.44: 1 Bond angle restraints: 11666 Sorted by residual: angle pdb=" N GLN R 52 " pdb=" CA GLN R 52 " pdb=" C GLN R 52 " ideal model delta sigma weight residual 112.45 97.01 15.44 1.39e+00 5.18e-01 1.23e+02 angle pdb=" C ILE R 223 " pdb=" CA ILE R 223 " pdb=" CB ILE R 223 " ideal model delta sigma weight residual 111.70 102.14 9.56 1.28e+00 6.10e-01 5.58e+01 angle pdb=" N ALA R 311 " pdb=" CA ALA R 311 " pdb=" C ALA R 311 " ideal model delta sigma weight residual 112.90 103.86 9.04 1.31e+00 5.83e-01 4.76e+01 angle pdb=" C THR R 55 " pdb=" N PRO R 56 " pdb=" CA PRO R 56 " ideal model delta sigma weight residual 119.28 126.65 -7.37 1.10e+00 8.26e-01 4.49e+01 angle pdb=" N TYR R 305 " pdb=" CA TYR R 305 " pdb=" C TYR R 305 " ideal model delta sigma weight residual 109.72 117.84 -8.12 1.25e+00 6.40e-01 4.22e+01 ... (remaining 11661 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.03: 4569 16.03 - 32.05: 349 32.05 - 48.08: 75 48.08 - 64.11: 12 64.11 - 80.13: 14 Dihedral angle restraints: 5019 sinusoidal: 1794 harmonic: 3225 Sorted by residual: dihedral pdb=" N LYS R 51 " pdb=" C LYS R 51 " pdb=" CA LYS R 51 " pdb=" CB LYS R 51 " ideal model delta harmonic sigma weight residual 122.80 139.77 -16.97 0 2.50e+00 1.60e-01 4.61e+01 dihedral pdb=" C LYS R 51 " pdb=" N LYS R 51 " pdb=" CA LYS R 51 " pdb=" CB LYS R 51 " ideal model delta harmonic sigma weight residual -122.60 -136.57 13.97 0 2.50e+00 1.60e-01 3.12e+01 dihedral pdb=" C ILE R 45 " pdb=" N ILE R 45 " pdb=" CA ILE R 45 " pdb=" CB ILE R 45 " ideal model delta harmonic sigma weight residual -122.00 -134.17 12.17 0 2.50e+00 1.60e-01 2.37e+01 ... (remaining 5016 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.120: 1293 0.120 - 0.239: 39 0.239 - 0.359: 5 0.359 - 0.478: 3 0.478 - 0.598: 1 Chirality restraints: 1341 Sorted by residual: chirality pdb=" CA LYS R 51 " pdb=" N LYS R 51 " pdb=" C LYS R 51 " pdb=" CB LYS R 51 " both_signs ideal model delta sigma weight residual False 2.51 1.91 0.60 2.00e-01 2.50e+01 8.94e+00 chirality pdb=" CA PHE R 50 " pdb=" N PHE R 50 " pdb=" C PHE R 50 " pdb=" CB PHE R 50 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.80e+00 chirality pdb=" CB ILE R 45 " pdb=" CA ILE R 45 " pdb=" CG1 ILE R 45 " pdb=" CG2 ILE R 45 " both_signs ideal model delta sigma weight residual False 2.64 2.26 0.38 2.00e-01 2.50e+01 3.61e+00 ... (remaining 1338 not shown) Planarity restraints: 1474 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TRP R 88 " 0.022 2.00e-02 2.50e+03 4.57e-02 2.09e+01 pdb=" C TRP R 88 " -0.079 2.00e-02 2.50e+03 pdb=" O TRP R 88 " 0.030 2.00e-02 2.50e+03 pdb=" N TYR R 89 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE R 194 " -0.020 2.00e-02 2.50e+03 4.11e-02 1.69e+01 pdb=" C PHE R 194 " 0.071 2.00e-02 2.50e+03 pdb=" O PHE R 194 " -0.027 2.00e-02 2.50e+03 pdb=" N MET R 195 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR R 55 " 0.017 2.00e-02 2.50e+03 3.33e-02 1.11e+01 pdb=" C THR R 55 " -0.058 2.00e-02 2.50e+03 pdb=" O THR R 55 " 0.021 2.00e-02 2.50e+03 pdb=" N PRO R 56 " 0.019 2.00e-02 2.50e+03 ... (remaining 1471 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 1141 2.75 - 3.29: 7801 3.29 - 3.83: 12896 3.83 - 4.36: 14793 4.36 - 4.90: 27137 Nonbonded interactions: 63768 Sorted by model distance: nonbonded pdb=" ND2 ASN R 40 " pdb=" OD1 ASP R 68 " model vdw 2.216 3.120 nonbonded pdb=" O GLN S 39 " pdb=" OG1 THR S 116 " model vdw 2.237 3.040 nonbonded pdb=" OD1 ASP B 205 " pdb=" OG SER B 207 " model vdw 2.325 3.040 nonbonded pdb=" NH1 ARG B 49 " pdb=" O TYR B 85 " model vdw 2.333 3.120 nonbonded pdb=" ND1 HIS B 311 " pdb=" OG SER B 331 " model vdw 2.334 3.120 ... (remaining 63763 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 8.030 Find NCS groups from input model: 0.030 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: 0.000 Load rotamer database and sin/cos tables:1.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 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 : 0.006 0.080 8582 Z= 0.366 Angle : 0.808 15.445 11670 Z= 0.487 Chirality : 0.059 0.598 1341 Planarity : 0.005 0.047 1474 Dihedral : 13.024 80.132 2927 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 0.93 % Allowed : 1.28 % Favored : 97.79 % Cbeta Deviations : 0.19 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: -0.26 (0.26), residues: 1084 helix: 1.22 (0.27), residues: 377 sheet: 0.20 (0.33), residues: 256 loop : -1.62 (0.27), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 19 TYR 0.030 0.002 TYR A 230 PHE 0.018 0.002 PHE R 214 TRP 0.021 0.002 TRP B 339 HIS 0.012 0.002 HIS R 49 Details of bonding type rmsd covalent geometry : bond 0.00588 ( 8580) covalent geometry : angle 0.80814 (11666) SS BOND : bond 0.00686 ( 2) SS BOND : angle 1.48953 ( 4) hydrogen bonds : bond 0.20606 ( 376) hydrogen bonds : angle 6.69945 ( 1077) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 161 time to evaluate : 0.281 Fit side-chains REVERT: A 234 GLN cc_start: 0.8086 (tp-100) cc_final: 0.7431 (tp-100) REVERT: A 238 ASN cc_start: 0.8730 (m110) cc_final: 0.8403 (m110) REVERT: A 323 ARG cc_start: 0.8034 (mtp85) cc_final: 0.7818 (ttm110) REVERT: B 247 ASP cc_start: 0.7774 (t0) cc_final: 0.7573 (t0) REVERT: R 157 MET cc_start: 0.7804 (ttm) cc_final: 0.7443 (ttm) REVERT: R 224 ASN cc_start: 0.7546 (m-40) cc_final: 0.7288 (m110) REVERT: S 18 ARG cc_start: 0.8407 (tpp80) cc_final: 0.7818 (ttm170) outliers start: 8 outliers final: 5 residues processed: 167 average time/residue: 0.1074 time to fit residues: 23.8403 Evaluate side-chains 135 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 130 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 49 HIS Chi-restraints excluded: chain R residue 54 HIS Chi-restraints excluded: chain R residue 270 LEU Chi-restraints excluded: chain R residue 310 ARG Chi-restraints excluded: chain Y residue 28 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 108 optimal weight: 10.0000 chunk 49 optimal weight: 3.9990 chunk 97 optimal weight: 5.9990 chunk 53 optimal weight: 8.9990 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 9.9990 chunk 51 optimal weight: 2.9990 chunk 100 optimal weight: 9.9990 chunk 106 optimal weight: 0.0970 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 GLN A 204 GLN B 32 GLN R 52 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.146611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.112406 restraints weight = 10855.419| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 2.38 r_work: 0.3158 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3034 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8606 moved from start: 0.1192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8582 Z= 0.142 Angle : 0.594 9.814 11670 Z= 0.313 Chirality : 0.044 0.145 1341 Planarity : 0.004 0.044 1474 Dihedral : 5.845 58.996 1203 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.17 % Allowed : 7.23 % Favored : 91.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 0.17 (0.25), residues: 1084 helix: 1.86 (0.27), residues: 374 sheet: 0.30 (0.34), residues: 249 loop : -1.52 (0.26), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 49 TYR 0.039 0.002 TYR R 287 PHE 0.019 0.001 PHE A 189 TRP 0.018 0.001 TRP B 339 HIS 0.006 0.001 HIS R 62 Details of bonding type rmsd covalent geometry : bond 0.00317 ( 8580) covalent geometry : angle 0.59354 (11666) SS BOND : bond 0.00752 ( 2) SS BOND : angle 1.18139 ( 4) hydrogen bonds : bond 0.05906 ( 376) hydrogen bonds : angle 4.80629 ( 1077) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 141 time to evaluate : 0.243 Fit side-chains REVERT: A 24 GLN cc_start: 0.8123 (tt0) cc_final: 0.7830 (mt0) REVERT: A 204 GLN cc_start: 0.8510 (mm-40) cc_final: 0.8239 (mm110) REVERT: A 238 ASN cc_start: 0.8912 (m110) cc_final: 0.8675 (m110) REVERT: R 157 MET cc_start: 0.7918 (ttm) cc_final: 0.7461 (ttm) REVERT: R 270 LEU cc_start: 0.8039 (OUTLIER) cc_final: 0.7827 (mm) REVERT: S 18 ARG cc_start: 0.8559 (tpp80) cc_final: 0.8327 (tpp-160) REVERT: Y 48 ASP cc_start: 0.8676 (t0) cc_final: 0.8444 (t0) outliers start: 10 outliers final: 6 residues processed: 145 average time/residue: 0.0900 time to fit residues: 17.4716 Evaluate side-chains 133 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 126 time to evaluate : 0.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain R residue 49 HIS Chi-restraints excluded: chain R residue 54 HIS Chi-restraints excluded: chain R residue 62 HIS Chi-restraints excluded: chain R residue 125 CYS Chi-restraints excluded: chain R residue 149 LEU Chi-restraints excluded: chain R residue 270 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 81 optimal weight: 1.9990 chunk 51 optimal weight: 6.9990 chunk 9 optimal weight: 1.9990 chunk 88 optimal weight: 0.7980 chunk 99 optimal weight: 0.8980 chunk 62 optimal weight: 8.9990 chunk 79 optimal weight: 2.9990 chunk 40 optimal weight: 6.9990 chunk 75 optimal weight: 0.9990 chunk 44 optimal weight: 3.9990 chunk 100 optimal weight: 9.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 GLN A 261 GLN B 32 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.148176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.115274 restraints weight = 10685.094| |-----------------------------------------------------------------------------| r_work (start): 0.3376 rms_B_bonded: 2.33 r_work: 0.3138 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3008 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8622 moved from start: 0.1563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8582 Z= 0.135 Angle : 0.560 11.579 11670 Z= 0.292 Chirality : 0.043 0.153 1341 Planarity : 0.004 0.041 1474 Dihedral : 5.181 53.540 1197 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 1.52 % Allowed : 11.66 % Favored : 86.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 0.38 (0.26), residues: 1084 helix: 2.17 (0.27), residues: 374 sheet: 0.37 (0.33), residues: 264 loop : -1.57 (0.27), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 323 TYR 0.032 0.002 TYR R 287 PHE 0.016 0.001 PHE A 189 TRP 0.017 0.001 TRP B 339 HIS 0.009 0.001 HIS R 62 Details of bonding type rmsd covalent geometry : bond 0.00310 ( 8580) covalent geometry : angle 0.55970 (11666) SS BOND : bond 0.00727 ( 2) SS BOND : angle 1.08859 ( 4) hydrogen bonds : bond 0.05254 ( 376) hydrogen bonds : angle 4.46804 ( 1077) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 136 time to evaluate : 0.189 Fit side-chains REVERT: A 24 GLN cc_start: 0.8177 (tt0) cc_final: 0.7882 (mt0) REVERT: A 204 GLN cc_start: 0.8398 (mm-40) cc_final: 0.8163 (mm110) REVERT: A 238 ASN cc_start: 0.8907 (m110) cc_final: 0.8632 (m110) REVERT: B 75 GLN cc_start: 0.8478 (mm-40) cc_final: 0.8169 (tt0) REVERT: R 54 HIS cc_start: 0.6858 (m170) cc_final: 0.6644 (m170) REVERT: R 157 MET cc_start: 0.7941 (ttm) cc_final: 0.7490 (ttm) outliers start: 13 outliers final: 11 residues processed: 145 average time/residue: 0.0848 time to fit residues: 16.6558 Evaluate side-chains 135 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 124 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain R residue 53 LEU Chi-restraints excluded: chain R residue 62 HIS Chi-restraints excluded: chain R residue 100 SER Chi-restraints excluded: chain R residue 125 CYS Chi-restraints excluded: chain R residue 149 LEU Chi-restraints excluded: chain R residue 164 LEU Chi-restraints excluded: chain R residue 270 LEU Chi-restraints excluded: chain S residue 62 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/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-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/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-2.0-5787/lib/python3.9/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-2.0-5787/lib/python3.9/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-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/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-2.0-5787/lib/python3.9/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-2.0-5787/lib/python3.9/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-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/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-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/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-2.0-5787/lib/python3.9/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-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/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-2.0-5787/lib/python3.9/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-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 58.7506 > 50: distance: 97 - 155: 15.283 distance: 107 - 146: 26.449 distance: 110 - 143: 18.139 distance: 127 - 131: 28.098 distance: 131 - 132: 39.331 distance: 132 - 133: 20.363 distance: 132 - 135: 21.653 distance: 133 - 134: 36.844 distance: 133 - 136: 32.994 distance: 136 - 137: 17.148 distance: 136 - 228: 33.944 distance: 137 - 138: 21.987 distance: 137 - 140: 23.080 distance: 138 - 139: 36.782 distance: 138 - 143: 34.965 distance: 139 - 225: 26.274 distance: 143 - 144: 25.903 distance: 144 - 145: 17.822 distance: 144 - 147: 36.561 distance: 145 - 146: 22.580 distance: 145 - 148: 25.089 distance: 148 - 149: 26.523 distance: 148 - 214: 16.370 distance: 149 - 150: 34.652 distance: 149 - 152: 21.858 distance: 150 - 151: 26.162 distance: 150 - 155: 22.652 distance: 151 - 211: 28.850 distance: 152 - 153: 33.483 distance: 152 - 154: 5.746 distance: 155 - 156: 26.608 distance: 156 - 157: 39.428 distance: 157 - 158: 26.159 distance: 157 - 159: 20.805 distance: 159 - 160: 32.588 distance: 160 - 161: 16.200 distance: 160 - 163: 36.794 distance: 161 - 162: 15.892 distance: 161 - 165: 26.091 distance: 163 - 164: 40.536 distance: 165 - 166: 23.065 distance: 166 - 167: 13.701 distance: 166 - 169: 8.793 distance: 167 - 168: 18.708 distance: 167 - 179: 28.787 distance: 170 - 171: 3.790 distance: 170 - 172: 8.235 distance: 171 - 173: 17.643 distance: 172 - 174: 22.391 distance: 172 - 175: 12.791 distance: 173 - 174: 23.458 distance: 174 - 176: 26.290 distance: 175 - 177: 34.939 distance: 179 - 180: 17.349 distance: 180 - 181: 6.418 distance: 180 - 183: 16.909 distance: 181 - 182: 18.092 distance: 181 - 187: 3.892 distance: 183 - 184: 19.864 distance: 184 - 185: 17.042 distance: 184 - 186: 17.070 distance: 187 - 188: 18.439 distance: 188 - 189: 7.311 distance: 188 - 191: 33.552 distance: 189 - 190: 12.334 distance: 189 - 193: 17.584 distance: 191 - 192: 10.736 distance: 193 - 194: 47.595 distance: 194 - 195: 12.581 distance: 194 - 197: 13.868 distance: 195 - 196: 8.675 distance: 195 - 204: 28.458 distance: 197 - 198: 10.384 distance: 198 - 199: 23.560 distance: 198 - 200: 20.212 distance: 199 - 201: 16.747 distance: 201 - 203: 24.504 distance: 202 - 203: 28.889