Starting phenix.real_space_refine on Fri Jul 3 07:05:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7phh_13416/07_2026/7phh_13416.cif Found real_map, /net/cci-nas-00/data/ceres_data/7phh_13416/07_2026/7phh_13416.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7phh_13416/07_2026/7phh_13416.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7phh_13416/07_2026/7phh_13416.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7phh_13416/07_2026/7phh_13416.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7phh_13416/07_2026/7phh_13416.map" model { file = "/net/cci-nas-00/data/ceres_data/7phh_13416/07_2026/7phh_13416.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7phh_13416/07_2026/7phh_13416.cif" } resolution = 3.2 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= 0.010 sd= 0.082 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 K 4 8.98 5 Zn 4 6.06 5 P 8 5.49 5 S 68 5.16 5 C 8376 2.51 5 N 2092 2.21 5 O 2168 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s 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: 12720 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 396, 3101 Classifications: {'peptide': 396} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 22, 'TRANS': 373} Chain breaks: 3 Unresolved non-hydrogen bonds: 149 Unresolved non-hydrogen angles: 185 Unresolved non-hydrogen dihedrals: 127 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ARG:plan': 6, 'PHE:plan': 1, 'ASP:plan': 1, 'TYR:plan': 4, 'GLU:plan': 6, 'ASN:plan1': 3} Unresolved non-hydrogen planarities: 100 Chain: "C" Number of atoms: 3101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 396, 3101 Classifications: {'peptide': 396} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 22, 'TRANS': 373} Chain breaks: 3 Unresolved non-hydrogen bonds: 149 Unresolved non-hydrogen angles: 185 Unresolved non-hydrogen dihedrals: 127 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ARG:plan': 6, 'PHE:plan': 1, 'ASP:plan': 1, 'TYR:plan': 4, 'GLU:plan': 6, 'ASN:plan1': 3} Unresolved non-hydrogen planarities: 100 Chain: "B" Number of atoms: 3101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 396, 3101 Classifications: {'peptide': 396} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 22, 'TRANS': 373} Chain breaks: 3 Unresolved non-hydrogen bonds: 149 Unresolved non-hydrogen angles: 185 Unresolved non-hydrogen dihedrals: 127 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ARG:plan': 6, 'PHE:plan': 1, 'ASP:plan': 1, 'TYR:plan': 4, 'GLU:plan': 6, 'ASN:plan1': 3} Unresolved non-hydrogen planarities: 100 Chain: "D" Number of atoms: 3101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 396, 3101 Classifications: {'peptide': 396} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 22, 'TRANS': 373} Chain breaks: 3 Unresolved non-hydrogen bonds: 149 Unresolved non-hydrogen angles: 185 Unresolved non-hydrogen dihedrals: 127 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ARG:plan': 6, 'PHE:plan': 1, 'ASP:plan': 1, 'TYR:plan': 4, 'GLU:plan': 6, 'ASN:plan1': 3} Unresolved non-hydrogen planarities: 100 Chain: "A" Number of atoms: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 82 Unusual residues: {' K': 4, ' ZN': 1, 'PCF': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 23 Chain: "C" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 78 Unusual residues: {' ZN': 1, 'PCF': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 23 Chain: "B" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 78 Unusual residues: {' ZN': 1, 'PCF': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 23 Chain: "D" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 78 Unusual residues: {' ZN': 1, 'PCF': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 23 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 791 SG CYS A 104 50.120 68.370 76.120 1.00107.92 S ATOM 797 SG CYS A 105 50.638 65.305 77.854 1.00105.62 S ATOM 6824 SG CYS B 83 54.203 67.163 78.031 1.00103.76 S ATOM 3892 SG CYS C 104 79.236 60.937 76.084 1.00107.92 S ATOM 3898 SG CYS C 105 78.744 64.004 77.820 1.00105.62 S ATOM 9925 SG CYS D 83 75.152 62.201 78.008 1.00103.76 S ATOM 3723 SG CYS C 83 67.265 75.204 78.005 1.00103.76 S ATOM 6993 SG CYS B 104 68.379 79.245 76.123 1.00107.92 S ATOM 6999 SG CYS B 105 65.315 78.727 77.859 1.00105.62 S ATOM 622 SG CYS A 83 62.208 54.199 78.025 1.00103.76 S ATOM 10094 SG CYS D 104 60.978 50.121 76.072 1.00107.92 S ATOM 10100 SG CYS D 105 64.041 50.636 77.810 1.00105.62 S Time building chain proxies: 3.36, per 1000 atoms: 0.26 Number of scatterers: 12720 At special positions: 0 Unit cell: (130.2, 130.2, 120.96, 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) Zn 4 29.99 K 4 19.00 S 68 16.00 P 8 15.00 O 2168 8.00 N 2092 7.00 C 8376 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.18 Conformation dependent library (CDL) restraints added in 681.6 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 603 " pdb="ZN ZN A 603 " - pdb=" SG CYS B 83 " pdb="ZN ZN A 603 " - pdb=" SG CYS A 105 " pdb="ZN ZN A 603 " - pdb=" SG CYS A 104 " pdb="ZN ZN A 603 " - pdb=" ND1 HIS A 77 " pdb=" ZN B 601 " pdb="ZN ZN B 601 " - pdb=" SG CYS C 83 " pdb="ZN ZN B 601 " - pdb=" SG CYS B 105 " pdb="ZN ZN B 601 " - pdb=" SG CYS B 104 " pdb="ZN ZN B 601 " - pdb=" ND1 HIS B 77 " pdb=" ZN C 603 " pdb="ZN ZN C 603 " - pdb=" SG CYS D 83 " pdb="ZN ZN C 603 " - pdb=" SG CYS C 105 " pdb="ZN ZN C 603 " - pdb=" SG CYS C 104 " pdb="ZN ZN C 603 " - pdb=" ND1 HIS C 77 " pdb=" ZN D 601 " pdb="ZN ZN D 601 " - pdb=" SG CYS A 83 " pdb="ZN ZN D 601 " - pdb=" SG CYS D 105 " pdb="ZN ZN D 601 " - pdb=" SG CYS D 104 " pdb="ZN ZN D 601 " - pdb=" ND1 HIS D 77 " Number of angles added : 12 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3000 Finding SS restraints... Secondary structure from input PDB file: 80 helices and 4 sheets defined 68.4% alpha, 3.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.37 Creating SS restraints... Processing helix chain 'A' and resid 23 through 28 Processing helix chain 'A' and resid 32 through 39 Processing helix chain 'A' and resid 60 through 74 removed outlier: 3.755A pdb=" N PHE A 64 " --> pdb=" O HIS A 60 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N HIS A 66 " --> pdb=" O GLY A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 95 Processing helix chain 'A' and resid 102 through 106 removed outlier: 3.531A pdb=" N TRP A 106 " --> pdb=" O PRO A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 119 Processing helix chain 'A' and resid 172 through 178 Processing helix chain 'A' and resid 182 through 185 Processing helix chain 'A' and resid 186 through 211 removed outlier: 3.712A pdb=" N ARG A 190 " --> pdb=" O SER A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 266 removed outlier: 3.592A pdb=" N THR A 246 " --> pdb=" O GLU A 242 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N PHE A 266 " --> pdb=" O MET A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 276 Processing helix chain 'A' and resid 276 through 295 Proline residue: A 288 - end of helix removed outlier: 3.516A pdb=" N LEU A 291 " --> pdb=" O LEU A 287 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N GLU A 292 " --> pdb=" O PRO A 288 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N VAL A 293 " --> pdb=" O PHE A 289 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N GLY A 294 " --> pdb=" O TYR A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 315 removed outlier: 3.757A pdb=" N ASP A 305 " --> pdb=" O LYS A 301 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N VAL A 312 " --> pdb=" O GLY A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 319 Processing helix chain 'A' and resid 320 through 326 removed outlier: 4.028A pdb=" N LEU A 324 " --> pdb=" O ARG A 320 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 341 removed outlier: 3.747A pdb=" N ARG A 332 " --> pdb=" O PHE A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 341 through 367 Processing helix chain 'A' and resid 386 through 399 removed outlier: 3.700A pdb=" N GLY A 390 " --> pdb=" O ASN A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 410 through 430 Processing helix chain 'A' and resid 431 through 452 Processing helix chain 'C' and resid 23 through 28 Processing helix chain 'C' and resid 32 through 39 Processing helix chain 'C' and resid 60 through 74 removed outlier: 3.756A pdb=" N PHE C 64 " --> pdb=" O HIS C 60 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N HIS C 66 " --> pdb=" O GLY C 62 " (cutoff:3.500A) Processing helix chain 'C' and resid 83 through 95 Processing helix chain 'C' and resid 102 through 106 removed outlier: 3.530A pdb=" N TRP C 106 " --> pdb=" O PRO C 103 " (cutoff:3.500A) Processing helix chain 'C' and resid 111 through 119 Processing helix chain 'C' and resid 172 through 178 Processing helix chain 'C' and resid 182 through 185 Processing helix chain 'C' and resid 186 through 211 removed outlier: 3.713A pdb=" N ARG C 190 " --> pdb=" O SER C 186 " (cutoff:3.500A) Processing helix chain 'C' and resid 242 through 266 removed outlier: 3.592A pdb=" N THR C 246 " --> pdb=" O GLU C 242 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N PHE C 266 " --> pdb=" O MET C 262 " (cutoff:3.500A) Processing helix chain 'C' and resid 269 through 276 Processing helix chain 'C' and resid 276 through 295 Proline residue: C 288 - end of helix removed outlier: 3.517A pdb=" N LEU C 291 " --> pdb=" O LEU C 287 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N GLU C 292 " --> pdb=" O PRO C 288 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N VAL C 293 " --> pdb=" O PHE C 289 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N GLY C 294 " --> pdb=" O TYR C 290 " (cutoff:3.500A) Processing helix chain 'C' and resid 300 through 315 removed outlier: 3.757A pdb=" N ASP C 305 " --> pdb=" O LYS C 301 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N VAL C 312 " --> pdb=" O GLY C 308 " (cutoff:3.500A) Processing helix chain 'C' and resid 316 through 319 Processing helix chain 'C' and resid 320 through 326 removed outlier: 4.029A pdb=" N LEU C 324 " --> pdb=" O ARG C 320 " (cutoff:3.500A) Processing helix chain 'C' and resid 328 through 341 removed outlier: 3.746A pdb=" N ARG C 332 " --> pdb=" O PHE C 328 " (cutoff:3.500A) Processing helix chain 'C' and resid 341 through 367 Processing helix chain 'C' and resid 386 through 399 removed outlier: 3.700A pdb=" N GLY C 390 " --> pdb=" O ASN C 386 " (cutoff:3.500A) Processing helix chain 'C' and resid 410 through 430 Processing helix chain 'C' and resid 431 through 452 Processing helix chain 'B' and resid 23 through 28 Processing helix chain 'B' and resid 32 through 39 Processing helix chain 'B' and resid 60 through 74 removed outlier: 3.756A pdb=" N PHE B 64 " --> pdb=" O HIS B 60 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N HIS B 66 " --> pdb=" O GLY B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 95 Processing helix chain 'B' and resid 102 through 106 removed outlier: 3.530A pdb=" N TRP B 106 " --> pdb=" O PRO B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 119 Processing helix chain 'B' and resid 172 through 178 Processing helix chain 'B' and resid 182 through 185 Processing helix chain 'B' and resid 186 through 211 removed outlier: 3.712A pdb=" N ARG B 190 " --> pdb=" O SER B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 266 removed outlier: 3.591A pdb=" N THR B 246 " --> pdb=" O GLU B 242 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N PHE B 266 " --> pdb=" O MET B 262 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 276 Processing helix chain 'B' and resid 276 through 295 Proline residue: B 288 - end of helix removed outlier: 3.517A pdb=" N LEU B 291 " --> pdb=" O LEU B 287 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N GLU B 292 " --> pdb=" O PRO B 288 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N VAL B 293 " --> pdb=" O PHE B 289 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N GLY B 294 " --> pdb=" O TYR B 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 300 through 315 removed outlier: 3.758A pdb=" N ASP B 305 " --> pdb=" O LYS B 301 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N VAL B 312 " --> pdb=" O GLY B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 316 through 319 Processing helix chain 'B' and resid 320 through 326 removed outlier: 4.029A pdb=" N LEU B 324 " --> pdb=" O ARG B 320 " (cutoff:3.500A) Processing helix chain 'B' and resid 328 through 341 removed outlier: 3.748A pdb=" N ARG B 332 " --> pdb=" O PHE B 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 341 through 367 Processing helix chain 'B' and resid 386 through 399 removed outlier: 3.700A pdb=" N GLY B 390 " --> pdb=" O ASN B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 410 through 430 Processing helix chain 'B' and resid 431 through 452 Processing helix chain 'D' and resid 23 through 28 Processing helix chain 'D' and resid 32 through 39 Processing helix chain 'D' and resid 60 through 74 removed outlier: 3.756A pdb=" N PHE D 64 " --> pdb=" O HIS D 60 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N HIS D 66 " --> pdb=" O GLY D 62 " (cutoff:3.500A) Processing helix chain 'D' and resid 83 through 95 Processing helix chain 'D' and resid 102 through 106 removed outlier: 3.530A pdb=" N TRP D 106 " --> pdb=" O PRO D 103 " (cutoff:3.500A) Processing helix chain 'D' and resid 111 through 119 Processing helix chain 'D' and resid 172 through 178 Processing helix chain 'D' and resid 182 through 185 Processing helix chain 'D' and resid 186 through 211 removed outlier: 3.712A pdb=" N ARG D 190 " --> pdb=" O SER D 186 " (cutoff:3.500A) Processing helix chain 'D' and resid 242 through 266 removed outlier: 3.591A pdb=" N THR D 246 " --> pdb=" O GLU D 242 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N PHE D 266 " --> pdb=" O MET D 262 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 276 Processing helix chain 'D' and resid 276 through 295 Proline residue: D 288 - end of helix removed outlier: 3.517A pdb=" N LEU D 291 " --> pdb=" O LEU D 287 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N GLU D 292 " --> pdb=" O PRO D 288 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N VAL D 293 " --> pdb=" O PHE D 289 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N GLY D 294 " --> pdb=" O TYR D 290 " (cutoff:3.500A) Processing helix chain 'D' and resid 300 through 315 removed outlier: 3.757A pdb=" N ASP D 305 " --> pdb=" O LYS D 301 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N VAL D 312 " --> pdb=" O GLY D 308 " (cutoff:3.500A) Processing helix chain 'D' and resid 316 through 319 Processing helix chain 'D' and resid 320 through 326 removed outlier: 4.029A pdb=" N LEU D 324 " --> pdb=" O ARG D 320 " (cutoff:3.500A) Processing helix chain 'D' and resid 328 through 341 removed outlier: 3.747A pdb=" N ARG D 332 " --> pdb=" O PHE D 328 " (cutoff:3.500A) Processing helix chain 'D' and resid 341 through 367 Processing helix chain 'D' and resid 386 through 399 removed outlier: 3.700A pdb=" N GLY D 390 " --> pdb=" O ASN D 386 " (cutoff:3.500A) Processing helix chain 'D' and resid 410 through 430 Processing helix chain 'D' and resid 431 through 452 Processing sheet with id=AA1, first strand: chain 'A' and resid 17 through 22 removed outlier: 3.931A pdb=" N GLU A 54 " --> pdb=" O ASP A 49 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ASP A 49 " --> pdb=" O GLU A 54 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 17 through 22 removed outlier: 3.930A pdb=" N GLU C 54 " --> pdb=" O ASP C 49 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ASP C 49 " --> pdb=" O GLU C 54 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 17 through 22 removed outlier: 3.930A pdb=" N GLU B 54 " --> pdb=" O ASP B 49 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ASP B 49 " --> pdb=" O GLU B 54 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 17 through 22 removed outlier: 3.931A pdb=" N GLU D 54 " --> pdb=" O ASP D 49 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ASP D 49 " --> pdb=" O GLU D 54 " (cutoff:3.500A) 740 hydrogen bonds defined for protein. 2172 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: 1.97 Time building geometry restraints manager: 1.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1916 1.31 - 1.43: 3797 1.43 - 1.56: 7246 1.56 - 1.68: 21 1.68 - 1.81: 104 Bond restraints: 13084 Sorted by residual: bond pdb=" C21 PCF C 602 " pdb=" O21 PCF C 602 " ideal model delta sigma weight residual 1.334 1.428 -0.094 2.00e-02 2.50e+03 2.19e+01 bond pdb=" C21 PCF A 602 " pdb=" O21 PCF A 602 " ideal model delta sigma weight residual 1.334 1.427 -0.093 2.00e-02 2.50e+03 2.15e+01 bond pdb=" C21 PCF B 603 " pdb=" O21 PCF B 603 " ideal model delta sigma weight residual 1.334 1.427 -0.093 2.00e-02 2.50e+03 2.15e+01 bond pdb=" C21 PCF A 601 " pdb=" O21 PCF A 601 " ideal model delta sigma weight residual 1.334 1.427 -0.093 2.00e-02 2.50e+03 2.15e+01 bond pdb=" C21 PCF D 603 " pdb=" O21 PCF D 603 " ideal model delta sigma weight residual 1.334 1.426 -0.092 2.00e-02 2.50e+03 2.13e+01 ... (remaining 13079 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.04: 17521 3.04 - 6.08: 247 6.08 - 9.12: 32 9.12 - 12.16: 4 12.16 - 15.20: 8 Bond angle restraints: 17812 Sorted by residual: angle pdb=" O12 PCF D 602 " pdb=" P PCF D 602 " pdb=" O14 PCF D 602 " ideal model delta sigma weight residual 123.69 108.49 15.20 3.00e+00 1.11e-01 2.57e+01 angle pdb=" O12 PCF C 601 " pdb=" P PCF C 601 " pdb=" O14 PCF C 601 " ideal model delta sigma weight residual 123.69 108.51 15.18 3.00e+00 1.11e-01 2.56e+01 angle pdb=" O12 PCF A 601 " pdb=" P PCF A 601 " pdb=" O14 PCF A 601 " ideal model delta sigma weight residual 123.69 108.51 15.18 3.00e+00 1.11e-01 2.56e+01 angle pdb=" O12 PCF B 602 " pdb=" P PCF B 602 " pdb=" O14 PCF B 602 " ideal model delta sigma weight residual 123.69 108.55 15.14 3.00e+00 1.11e-01 2.55e+01 angle pdb=" O12 PCF A 602 " pdb=" P PCF A 602 " pdb=" O14 PCF A 602 " ideal model delta sigma weight residual 123.69 109.03 14.66 3.00e+00 1.11e-01 2.39e+01 ... (remaining 17807 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.22: 7368 31.22 - 62.43: 296 62.43 - 93.65: 24 93.65 - 124.87: 0 124.87 - 156.08: 8 Dihedral angle restraints: 7696 sinusoidal: 3072 harmonic: 4624 Sorted by residual: dihedral pdb=" O21 PCF B 602 " pdb=" C2 PCF B 602 " pdb=" C3 PCF B 602 " pdb=" O31 PCF B 602 " ideal model delta sinusoidal sigma weight residual 59.47 -96.61 156.08 1 3.00e+01 1.11e-03 2.04e+01 dihedral pdb=" O21 PCF D 602 " pdb=" C2 PCF D 602 " pdb=" C3 PCF D 602 " pdb=" O31 PCF D 602 " ideal model delta sinusoidal sigma weight residual 59.47 -96.61 156.08 1 3.00e+01 1.11e-03 2.04e+01 dihedral pdb=" O21 PCF C 601 " pdb=" C2 PCF C 601 " pdb=" C3 PCF C 601 " pdb=" O31 PCF C 601 " ideal model delta sinusoidal sigma weight residual 59.47 -96.58 156.05 1 3.00e+01 1.11e-03 2.04e+01 ... (remaining 7693 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 1500 0.054 - 0.107: 394 0.107 - 0.161: 62 0.161 - 0.215: 0 0.215 - 0.268: 4 Chirality restraints: 1960 Sorted by residual: chirality pdb=" C2 PCF A 602 " pdb=" C1 PCF A 602 " pdb=" C3 PCF A 602 " pdb=" O21 PCF A 602 " both_signs ideal model delta sigma weight residual False -2.60 -2.33 -0.27 2.00e-01 2.50e+01 1.80e+00 chirality pdb=" C2 PCF D 603 " pdb=" C1 PCF D 603 " pdb=" C3 PCF D 603 " pdb=" O21 PCF D 603 " both_signs ideal model delta sigma weight residual False -2.60 -2.33 -0.27 2.00e-01 2.50e+01 1.79e+00 chirality pdb=" C2 PCF B 603 " pdb=" C1 PCF B 603 " pdb=" C3 PCF B 603 " pdb=" O21 PCF B 603 " both_signs ideal model delta sigma weight residual False -2.60 -2.33 -0.27 2.00e-01 2.50e+01 1.78e+00 ... (remaining 1957 not shown) Planarity restraints: 2212 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO C 174 " -0.009 2.00e-02 2.50e+03 1.81e-02 3.28e+00 pdb=" C PRO C 174 " 0.031 2.00e-02 2.50e+03 pdb=" O PRO C 174 " -0.012 2.00e-02 2.50e+03 pdb=" N ARG C 175 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO A 174 " -0.009 2.00e-02 2.50e+03 1.78e-02 3.18e+00 pdb=" C PRO A 174 " 0.031 2.00e-02 2.50e+03 pdb=" O PRO A 174 " -0.011 2.00e-02 2.50e+03 pdb=" N ARG A 175 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO B 174 " -0.009 2.00e-02 2.50e+03 1.78e-02 3.16e+00 pdb=" C PRO B 174 " 0.031 2.00e-02 2.50e+03 pdb=" O PRO B 174 " -0.011 2.00e-02 2.50e+03 pdb=" N ARG B 175 " -0.010 2.00e-02 2.50e+03 ... (remaining 2209 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.66: 114 2.66 - 3.28: 14189 3.28 - 3.90: 24386 3.90 - 4.52: 32217 4.52 - 5.14: 51006 Nonbonded interactions: 121912 Sorted by model distance: nonbonded pdb=" OG1 THR B 32 " pdb=" OH TYR B 71 " model vdw 2.045 3.040 nonbonded pdb=" OG1 THR C 32 " pdb=" OH TYR C 71 " model vdw 2.045 3.040 nonbonded pdb=" OG1 THR A 32 " pdb=" OH TYR A 71 " model vdw 2.045 3.040 nonbonded pdb=" OG1 THR D 32 " pdb=" OH TYR D 71 " model vdw 2.045 3.040 nonbonded pdb=" O ASP C 182 " pdb=" OG SER C 185 " model vdw 2.189 3.040 ... (remaining 121907 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 7 through 464 or resid 602)) selection = (chain 'B' and (resid 7 through 464 or (resid 602 and (name N or name C1 or name \ C11 or name C12 or name C13 or name C14 or name C15 or name C2 or name C21 or n \ ame C22 or name C23 or name C24 or name C25 or name C26 or name C3 or name C31 o \ r name C32 or name C33 or name C34 or name C35 or name C36 or name C37 or name C \ 38 or name O11 or name O12 or name O13 or name O14 or name O21 or name O22 or na \ me O31 or name O32 or name P )))) selection = (chain 'C' and (resid 7 through 464 or resid 602)) selection = (chain 'D' and (resid 7 through 464 or (resid 602 and (name N or name C1 or name \ C11 or name C12 or name C13 or name C14 or name C15 or name C2 or name C21 or n \ ame C22 or name C23 or name C24 or name C25 or name C26 or name C3 or name C31 o \ r name C32 or name C33 or name C34 or name C35 or name C36 or name C37 or name C \ 38 or name O11 or name O12 or name O13 or name O14 or name O21 or name O22 or na \ me O31 or name O32 or name P )))) } 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: 3.820 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: 0.270 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 14.960 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.040 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:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7199 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 : 0.017 0.801 13100 Z= 0.490 Angle : 1.066 29.202 17824 Z= 0.445 Chirality : 0.048 0.268 1960 Planarity : 0.005 0.040 2212 Dihedral : 16.500 156.084 4696 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 0.96 % Allowed : 11.82 % Favored : 87.22 % 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 are not related in a simple way. whole: -0.87 (0.19), residues: 1552 helix: -0.31 (0.15), residues: 940 sheet: 0.91 (0.88), residues: 40 loop : -0.94 (0.23), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 33 TYR 0.013 0.002 TYR D 109 PHE 0.019 0.002 PHE D 384 TRP 0.019 0.003 TRP B 255 HIS 0.005 0.002 HIS B 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00826 / 0.37 (13084) covalent geometry : angle 0.91563 / 0.42 (17812) hydrogen bonds : bond 0.11572 / 7.88 ( 740) hydrogen bonds : angle 5.95278 / 4.29 ( 2172) metal coordination : bond 0.42809 / 28.02 ( 16) metal coordination : angle 21.03750 / 11.36 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 214 time to evaluate : 0.302 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 ARG cc_start: 0.7186 (ttm110) cc_final: 0.6657 (tmt170) REVERT: A 36 TRP cc_start: 0.6803 (m100) cc_final: 0.6263 (m100) REVERT: A 214 ARG cc_start: 0.7330 (ttm170) cc_final: 0.6962 (ttt180) REVERT: A 247 TYR cc_start: 0.5764 (m-80) cc_final: 0.5377 (m-10) REVERT: A 457 LYS cc_start: 0.6205 (tmtm) cc_final: 0.5912 (tptt) REVERT: A 458 LYS cc_start: 0.7267 (tttt) cc_final: 0.6594 (ttpt) REVERT: C 9 ARG cc_start: 0.7309 (ttm110) cc_final: 0.6837 (tmt170) REVERT: C 36 TRP cc_start: 0.6832 (m100) cc_final: 0.6516 (m100) REVERT: C 75 LYS cc_start: 0.8178 (mttp) cc_final: 0.7913 (mttp) REVERT: C 247 TYR cc_start: 0.6040 (m-80) cc_final: 0.5502 (m-10) REVERT: C 311 ARG cc_start: 0.5420 (mmm-85) cc_final: 0.5082 (mtp85) REVERT: C 458 LYS cc_start: 0.7091 (tttt) cc_final: 0.6779 (mtpt) REVERT: B 9 ARG cc_start: 0.7298 (ttm110) cc_final: 0.6703 (tmt170) REVERT: B 36 TRP cc_start: 0.6839 (m100) cc_final: 0.6276 (m100) REVERT: B 214 ARG cc_start: 0.7302 (ttm170) cc_final: 0.7032 (mtp85) REVERT: B 247 TYR cc_start: 0.5962 (m-80) cc_final: 0.5505 (m-10) REVERT: B 311 ARG cc_start: 0.5561 (mmm-85) cc_final: 0.5300 (mtm110) REVERT: B 457 LYS cc_start: 0.6217 (tmtm) cc_final: 0.5943 (tptt) REVERT: B 458 LYS cc_start: 0.7296 (tttt) cc_final: 0.6627 (ttpt) REVERT: D 9 ARG cc_start: 0.7308 (ttm110) cc_final: 0.6806 (tmt170) REVERT: D 36 TRP cc_start: 0.6701 (m100) cc_final: 0.6134 (m100) REVERT: D 214 ARG cc_start: 0.7287 (ttm170) cc_final: 0.7033 (mtp85) REVERT: D 247 TYR cc_start: 0.5737 (m-80) cc_final: 0.5418 (m-10) REVERT: D 311 ARG cc_start: 0.5724 (mmm-85) cc_final: 0.5485 (mtm110) REVERT: D 430 MET cc_start: 0.7513 (mmt) cc_final: 0.7265 (mmt) REVERT: D 458 LYS cc_start: 0.7283 (tttt) cc_final: 0.6633 (ttpt) outliers start: 12 outliers final: 4 residues processed: 222 average time/residue: 0.1480 time to fit residues: 44.1376 Evaluate side-chains 164 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 160 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 315 PHE Chi-restraints excluded: chain C residue 315 PHE Chi-restraints excluded: chain B residue 315 PHE Chi-restraints excluded: chain D residue 315 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 98 optimal weight: 6.9990 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 20.0000 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 20.0000 chunk 149 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 437 ASN ** B 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 437 ASN ** D 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 437 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.187592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.146653 restraints weight = 14762.832| |-----------------------------------------------------------------------------| r_work (start): 0.3880 rms_B_bonded: 1.60 r_work: 0.3438 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3438 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8638 moved from start: 0.1380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13100 Z= 0.151 Angle : 0.550 6.008 17824 Z= 0.278 Chirality : 0.040 0.136 1960 Planarity : 0.005 0.039 2212 Dihedral : 13.146 140.499 2048 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 0.80 % Allowed : 15.51 % Favored : 83.68 % 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 are not related in a simple way. whole: 0.96 (0.21), residues: 1552 helix: 1.13 (0.16), residues: 956 sheet: None (None), residues: 0 loop : -0.02 (0.24), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 33 TYR 0.009 0.001 TYR D 48 PHE 0.010 0.001 PHE C 289 TRP 0.015 0.001 TRP D 255 HIS 0.005 0.001 HIS C 327 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.15 (13084) covalent geometry : angle 0.54549 / 0.28 (17812) hydrogen bonds : bond 0.05861 / 4.05 ( 740) hydrogen bonds : angle 4.73141 / 3.34 ( 2172) metal coordination : bond 0.01898 / 1.23 ( 16) metal coordination : angle 2.73559 / 1.39 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 177 time to evaluate : 0.512 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 TRP cc_start: 0.7555 (m100) cc_final: 0.7177 (m100) REVERT: A 214 ARG cc_start: 0.7964 (ttm170) cc_final: 0.7755 (ttt180) REVERT: A 275 LYS cc_start: 0.5487 (tptp) cc_final: 0.5126 (tptp) REVERT: A 321 ILE cc_start: 0.8065 (tp) cc_final: 0.7845 (tp) REVERT: A 457 LYS cc_start: 0.6699 (tmtm) cc_final: 0.6281 (tptt) REVERT: A 458 LYS cc_start: 0.7797 (tttt) cc_final: 0.7594 (mtpt) REVERT: C 36 TRP cc_start: 0.7571 (m100) cc_final: 0.7118 (m100) REVERT: C 247 TYR cc_start: 0.6127 (m-80) cc_final: 0.5826 (m-10) REVERT: C 458 LYS cc_start: 0.7614 (tttt) cc_final: 0.7240 (mtpt) REVERT: B 36 TRP cc_start: 0.7611 (m100) cc_final: 0.7217 (m100) REVERT: B 214 ARG cc_start: 0.7875 (ttm170) cc_final: 0.7671 (ttt180) REVERT: B 247 TYR cc_start: 0.6079 (m-80) cc_final: 0.5812 (m-10) REVERT: B 275 LYS cc_start: 0.5467 (tptp) cc_final: 0.5193 (tptp) REVERT: B 321 ILE cc_start: 0.8143 (tp) cc_final: 0.7934 (tp) REVERT: B 457 LYS cc_start: 0.6731 (tmtm) cc_final: 0.6293 (tptt) REVERT: D 36 TRP cc_start: 0.7531 (m100) cc_final: 0.7126 (m100) REVERT: D 214 ARG cc_start: 0.7964 (ttm170) cc_final: 0.7741 (ttt180) REVERT: D 321 ILE cc_start: 0.8073 (tp) cc_final: 0.7849 (tp) REVERT: D 430 MET cc_start: 0.8320 (mmt) cc_final: 0.8095 (mmt) outliers start: 10 outliers final: 7 residues processed: 180 average time/residue: 0.1453 time to fit residues: 35.4143 Evaluate side-chains 167 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 160 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 315 PHE Chi-restraints excluded: chain A residue 349 ILE Chi-restraints excluded: chain C residue 315 PHE Chi-restraints excluded: chain B residue 315 PHE Chi-restraints excluded: chain B residue 349 ILE Chi-restraints excluded: chain D residue 315 PHE Chi-restraints excluded: chain D residue 349 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- 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: 70.3242 > 50: distance: 64 - 68: 27.985 distance: 68 - 69: 22.622 distance: 69 - 70: 35.048 distance: 69 - 72: 11.023 distance: 70 - 71: 40.639 distance: 70 - 76: 5.704 distance: 72 - 73: 47.324 distance: 73 - 75: 29.458 distance: 76 - 77: 31.917 distance: 77 - 78: 57.496 distance: 78 - 86: 55.801 distance: 80 - 81: 40.747 distance: 81 - 82: 29.495 distance: 82 - 84: 30.089 distance: 82 - 217: 28.785 distance: 87 - 88: 39.740 distance: 92 - 93: 40.201 distance: 92 - 98: 46.698 distance: 93 - 96: 41.124 distance: 94 - 99: 40.917 distance: 96 - 97: 41.588 distance: 97 - 98: 30.166 distance: 99 - 100: 7.562 distance: 100 - 101: 39.339 distance: 100 - 103: 41.257 distance: 101 - 102: 56.620 distance: 104 - 105: 41.715 distance: 105 - 106: 37.419 distance: 105 - 108: 10.328 distance: 106 - 107: 24.709 distance: 106 - 112: 42.658 distance: 108 - 109: 36.607 distance: 109 - 110: 35.792 distance: 109 - 111: 51.613 distance: 112 - 113: 17.294 distance: 113 - 114: 19.955 distance: 113 - 116: 20.846 distance: 114 - 115: 3.003 distance: 114 - 119: 57.527 distance: 116 - 117: 16.163 distance: 119 - 120: 18.456 distance: 120 - 121: 40.198 distance: 120 - 123: 40.992 distance: 122 - 143: 32.305 distance: 123 - 124: 38.855 distance: 124 - 216: 35.861 distance: 125 - 126: 34.403 distance: 126 - 127: 6.805 distance: 127 - 128: 36.548 distance: 128 - 155: 30.709 distance: 129 - 130: 12.480 distance: 130 - 131: 5.067 distance: 130 - 133: 8.847 distance: 131 - 132: 26.759 distance: 131 - 136: 32.270 distance: 132 - 163: 28.681 distance: 133 - 134: 7.531 distance: 134 - 135: 12.243