Starting phenix.real_space_refine on Sat Jul 4 13:11:51 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cl1_45658/07_2026/9cl1_45658.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cl1_45658/07_2026/9cl1_45658.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.89 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9cl1_45658/07_2026/9cl1_45658.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cl1_45658/07_2026/9cl1_45658.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9cl1_45658/07_2026/9cl1_45658.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cl1_45658/07_2026/9cl1_45658.map" } resolution = 2.89 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= 0.145 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 Cu 9 5.60 5 S 90 5.16 5 C 13614 2.51 5 N 3348 2.21 5 O 3711 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 51 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 20772 Number of models: 1 Model: "" Number of chains: 14 Chain: "Aa" Number of atoms: 3017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 382, 3017 Classifications: {'peptide': 382} Link IDs: {'PTRANS': 24, 'TRANS': 357} Chain: "Ca" Number of atoms: 1958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1958 Classifications: {'peptide': 238} Link IDs: {'PTRANS': 12, 'TRANS': 225} Chain: "Ba" Number of atoms: 1894 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1894 Classifications: {'peptide': 229} Link IDs: {'PTRANS': 10, 'TRANS': 218} Chain breaks: 1 Chain: "Aa" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' CU': 2} Chain breaks: 2 Chain: "Ba" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' CU': 1} Chain breaks: 1 Chain: "Aa" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 32 Classifications: {'water': 32} Link IDs: {None: 31} Chain: "Ca" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "Ba" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "Bb" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "Bc" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "Ab" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 32 Classifications: {'water': 32} Link IDs: {None: 31} Chain: "Ac" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 32 Classifications: {'water': 32} Link IDs: {None: 31} Chain: "Cb" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "Cc" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Restraints were copied for chains: Ab, Ac, Cb, Cc, Bb, Bc Time building chain proxies: 4.96, per 1000 atoms: 0.24 Number of scatterers: 20772 At special positions: 0 Unit cell: (109.038, 111.176, 120.797, 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) Cu 9 28.99 S 90 16.00 O 3711 8.00 N 3348 7.00 C 13614 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: 1.59 Conformation dependent library (CDL) restraints added in 836.5 milliseconds 5046 Ramachandran restraints generated. 2523 Oldfield, 0 Emsley, 2523 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4698 Finding SS restraints... Secondary structure from input PDB file: 102 helices and 24 sheets defined 55.7% alpha, 15.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.59 Creating SS restraints... Processing helix chain 'Aa' and resid 41 through 46 Processing helix chain 'Aa' and resid 162 through 166 Processing helix chain 'Aa' and resid 185 through 208 removed outlier: 3.866A pdb=" N TRPAa 206 " --> pdb=" O TRPAa 202 " (cutoff:3.500A) Processing helix chain 'Aa' and resid 211 through 221 removed outlier: 4.303A pdb=" N ARGAa 215 " --> pdb=" O ILEAa 211 " (cutoff:3.500A) Processing helix chain 'Aa' and resid 229 through 258 Processing helix chain 'Aa' and resid 337 through 339 No H-bonds generated for 'chain 'Aa' and resid 337 through 339' Processing helix chain 'Aa' and resid 369 through 374 Processing helix chain 'Aa' and resid 376 through 382 removed outlier: 3.661A pdb=" N ILEAa 379 " --> pdb=" O LEUAa 376 " (cutoff:3.500A) Processing helix chain 'Ca' and resid 20 through 58 removed outlier: 7.576A pdb=" N ASPCa 54 " --> pdb=" O LEUCa 50 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N TRPCa 55 " --> pdb=" O THRCa 51 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ASPCa 56 " --> pdb=" O METCa 52 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N TRPCa 58 " --> pdb=" O ASPCa 54 " (cutoff:3.500A) Processing helix chain 'Ca' and resid 65 through 75 Proline residue: Ca 72 - end of helix Processing helix chain 'Ca' and resid 76 through 89 removed outlier: 3.503A pdb=" N ALACa 81 " --> pdb=" O THRCa 77 " (cutoff:3.500A) Processing helix chain 'Ca' and resid 94 through 114 removed outlier: 3.858A pdb=" N CYSCa 99 " --> pdb=" O GLYCa 95 " (cutoff:3.500A) Processing helix chain 'Ca' and resid 122 through 127 Processing helix chain 'Ca' and resid 131 through 146 Processing helix chain 'Ca' and resid 147 through 162 removed outlier: 4.269A pdb=" N ALACa 156 " --> pdb=" O ALACa 152 " (cutoff:3.500A) Processing helix chain 'Ca' and resid 162 through 172 Proline residue: Ca 169 - end of helix Processing helix chain 'Ca' and resid 173 through 175 No H-bonds generated for 'chain 'Ca' and resid 173 through 175' Processing helix chain 'Ca' and resid 187 through 195 Processing helix chain 'Ca' and resid 201 through 205 removed outlier: 3.547A pdb=" N ILECa 204 " --> pdb=" O PROCa 201 " (cutoff:3.500A) Processing helix chain 'Ca' and resid 215 through 217 No H-bonds generated for 'chain 'Ca' and resid 215 through 217' Processing helix chain 'Ca' and resid 218 through 245 removed outlier: 3.540A pdb=" N VALCa 222 " --> pdb=" O ASPCa 218 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N PHECa 236 " --> pdb=" O ILECa 232 " (cutoff:3.500A) Processing helix chain 'Ba' and resid 47 through 76 removed outlier: 3.842A pdb=" N LEUBa 51 " --> pdb=" O ASPBa 47 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N TRPBa 74 " --> pdb=" O GLYBa 70 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N SERBa 75 " --> pdb=" O VALBa 71 " (cutoff:3.500A) Processing helix chain 'Ba' and resid 82 through 89 removed outlier: 3.578A pdb=" N GLUBa 86 " --> pdb=" O ALABa 82 " (cutoff:3.500A) Processing helix chain 'Ba' and resid 89 through 114 Processing helix chain 'Ba' and resid 123 through 150 Processing helix chain 'Ba' and resid 151 through 161 removed outlier: 3.547A pdb=" N GLNBa 161 " --> pdb=" O GLYBa 157 " (cutoff:3.500A) Processing helix chain 'Ba' and resid 170 through 177 Processing helix chain 'Ba' and resid 179 through 199 Processing helix chain 'Ba' and resid 201 through 205 removed outlier: 3.975A pdb=" N LYSBa 204 " --> pdb=" O PHEBa 201 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N GLYBa 205 " --> pdb=" O PHEBa 202 " (cutoff:3.500A) No H-bonds generated for 'chain 'Ba' and resid 201 through 205' Processing helix chain 'Ba' and resid 208 through 232 Proline residue: Ba 217 - end of helix removed outlier: 3.524A pdb=" N ILEBa 220 " --> pdb=" O GLYBa 216 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N LEUBa 221 " --> pdb=" O PROBa 217 " (cutoff:3.500A) Proline residue: Ba 222 - end of helix removed outlier: 4.877A pdb=" N GLYBa 225 " --> pdb=" O LEUBa 221 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N LEUBa 226 " --> pdb=" O PROBa 222 " (cutoff:3.500A) Processing helix chain 'Ba' and resid 242 through 244 No H-bonds generated for 'chain 'Ba' and resid 242 through 244' Processing helix chain 'Ba' and resid 245 through 254 removed outlier: 3.682A pdb=" N VALBa 249 " --> pdb=" O HISBa 245 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LEUBa 254 " --> pdb=" O ILEBa 250 " (cutoff:3.500A) Processing helix chain 'Ba' and resid 257 through 273 removed outlier: 3.629A pdb=" N THRBa 263 " --> pdb=" O METBa 259 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLYBa 272 " --> pdb=" O SERBa 268 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N GLYBa 273 " --> pdb=" O PHEBa 269 " (cutoff:3.500A) Processing helix chain 'Ba' and resid 273 through 279 Processing helix chain 'Bb' and resid 47 through 76 removed outlier: 3.841A pdb=" N LEUBb 51 " --> pdb=" O ASPBb 47 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N TRPBb 74 " --> pdb=" O GLYBb 70 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N SERBb 75 " --> pdb=" O VALBb 71 " (cutoff:3.500A) Processing helix chain 'Bb' and resid 82 through 89 removed outlier: 3.578A pdb=" N GLUBb 86 " --> pdb=" O ALABb 82 " (cutoff:3.500A) Processing helix chain 'Bb' and resid 89 through 114 Processing helix chain 'Bb' and resid 123 through 150 Processing helix chain 'Bb' and resid 151 through 161 removed outlier: 3.547A pdb=" N GLNBb 161 " --> pdb=" O GLYBb 157 " (cutoff:3.500A) Processing helix chain 'Bb' and resid 170 through 177 Processing helix chain 'Bb' and resid 179 through 199 Processing helix chain 'Bb' and resid 201 through 205 removed outlier: 3.975A pdb=" N LYSBb 204 " --> pdb=" O PHEBb 201 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N GLYBb 205 " --> pdb=" O PHEBb 202 " (cutoff:3.500A) No H-bonds generated for 'chain 'Bb' and resid 201 through 205' Processing helix chain 'Bb' and resid 208 through 232 Proline residue: Bb 217 - end of helix removed outlier: 3.524A pdb=" N ILEBb 220 " --> pdb=" O GLYBb 216 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N LEUBb 221 " --> pdb=" O PROBb 217 " (cutoff:3.500A) Proline residue: Bb 222 - end of helix removed outlier: 4.878A pdb=" N GLYBb 225 " --> pdb=" O LEUBb 221 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N LEUBb 226 " --> pdb=" O PROBb 222 " (cutoff:3.500A) Processing helix chain 'Bb' and resid 242 through 244 No H-bonds generated for 'chain 'Bb' and resid 242 through 244' Processing helix chain 'Bb' and resid 245 through 254 removed outlier: 3.683A pdb=" N VALBb 249 " --> pdb=" O HISBb 245 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LEUBb 254 " --> pdb=" O ILEBb 250 " (cutoff:3.500A) Processing helix chain 'Bb' and resid 257 through 273 removed outlier: 3.628A pdb=" N THRBb 263 " --> pdb=" O METBb 259 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLYBb 272 " --> pdb=" O SERBb 268 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N GLYBb 273 " --> pdb=" O PHEBb 269 " (cutoff:3.500A) Processing helix chain 'Bb' and resid 273 through 279 Processing helix chain 'Bc' and resid 47 through 76 removed outlier: 3.841A pdb=" N LEUBc 51 " --> pdb=" O ASPBc 47 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N TRPBc 74 " --> pdb=" O GLYBc 70 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N SERBc 75 " --> pdb=" O VALBc 71 " (cutoff:3.500A) Processing helix chain 'Bc' and resid 82 through 89 removed outlier: 3.578A pdb=" N GLUBc 86 " --> pdb=" O ALABc 82 " (cutoff:3.500A) Processing helix chain 'Bc' and resid 89 through 114 Processing helix chain 'Bc' and resid 123 through 150 Processing helix chain 'Bc' and resid 151 through 161 removed outlier: 3.548A pdb=" N GLNBc 161 " --> pdb=" O GLYBc 157 " (cutoff:3.500A) Processing helix chain 'Bc' and resid 170 through 177 Processing helix chain 'Bc' and resid 179 through 199 Processing helix chain 'Bc' and resid 201 through 205 removed outlier: 3.975A pdb=" N LYSBc 204 " --> pdb=" O PHEBc 201 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLYBc 205 " --> pdb=" O PHEBc 202 " (cutoff:3.500A) No H-bonds generated for 'chain 'Bc' and resid 201 through 205' Processing helix chain 'Bc' and resid 208 through 232 Proline residue: Bc 217 - end of helix removed outlier: 3.524A pdb=" N ILEBc 220 " --> pdb=" O GLYBc 216 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N LEUBc 221 " --> pdb=" O PROBc 217 " (cutoff:3.500A) Proline residue: Bc 222 - end of helix removed outlier: 4.877A pdb=" N GLYBc 225 " --> pdb=" O LEUBc 221 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N LEUBc 226 " --> pdb=" O PROBc 222 " (cutoff:3.500A) Processing helix chain 'Bc' and resid 242 through 244 No H-bonds generated for 'chain 'Bc' and resid 242 through 244' Processing helix chain 'Bc' and resid 245 through 254 removed outlier: 3.683A pdb=" N VALBc 249 " --> pdb=" O HISBc 245 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LEUBc 254 " --> pdb=" O ILEBc 250 " (cutoff:3.500A) Processing helix chain 'Bc' and resid 257 through 273 removed outlier: 3.628A pdb=" N THRBc 263 " --> pdb=" O METBc 259 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLYBc 272 " --> pdb=" O SERBc 268 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N GLYBc 273 " --> pdb=" O PHEBc 269 " (cutoff:3.500A) Processing helix chain 'Bc' and resid 273 through 279 Processing helix chain 'Ab' and resid 41 through 46 Processing helix chain 'Ab' and resid 162 through 166 Processing helix chain 'Ab' and resid 185 through 208 removed outlier: 3.867A pdb=" N TRPAb 206 " --> pdb=" O TRPAb 202 " (cutoff:3.500A) Processing helix chain 'Ab' and resid 211 through 221 removed outlier: 4.303A pdb=" N ARGAb 215 " --> pdb=" O ILEAb 211 " (cutoff:3.500A) Processing helix chain 'Ab' and resid 229 through 258 Processing helix chain 'Ab' and resid 337 through 339 No H-bonds generated for 'chain 'Ab' and resid 337 through 339' Processing helix chain 'Ab' and resid 369 through 374 Processing helix chain 'Ab' and resid 376 through 382 removed outlier: 3.661A pdb=" N ILEAb 379 " --> pdb=" O LEUAb 376 " (cutoff:3.500A) Processing helix chain 'Ac' and resid 41 through 46 Processing helix chain 'Ac' and resid 162 through 166 Processing helix chain 'Ac' and resid 185 through 208 removed outlier: 3.867A pdb=" N TRPAc 206 " --> pdb=" O TRPAc 202 " (cutoff:3.500A) Processing helix chain 'Ac' and resid 211 through 221 removed outlier: 4.303A pdb=" N ARGAc 215 " --> pdb=" O ILEAc 211 " (cutoff:3.500A) Processing helix chain 'Ac' and resid 229 through 258 Processing helix chain 'Ac' and resid 337 through 339 No H-bonds generated for 'chain 'Ac' and resid 337 through 339' Processing helix chain 'Ac' and resid 369 through 374 Processing helix chain 'Ac' and resid 376 through 382 removed outlier: 3.660A pdb=" N ILEAc 379 " --> pdb=" O LEUAc 376 " (cutoff:3.500A) Processing helix chain 'Cb' and resid 20 through 58 removed outlier: 7.575A pdb=" N ASPCb 54 " --> pdb=" O LEUCb 50 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N TRPCb 55 " --> pdb=" O THRCb 51 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ASPCb 56 " --> pdb=" O METCb 52 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N TRPCb 58 " --> pdb=" O ASPCb 54 " (cutoff:3.500A) Processing helix chain 'Cb' and resid 65 through 75 Proline residue: Cb 72 - end of helix Processing helix chain 'Cb' and resid 76 through 89 removed outlier: 3.503A pdb=" N ALACb 81 " --> pdb=" O THRCb 77 " (cutoff:3.500A) Processing helix chain 'Cb' and resid 94 through 114 removed outlier: 3.857A pdb=" N CYSCb 99 " --> pdb=" O GLYCb 95 " (cutoff:3.500A) Processing helix chain 'Cb' and resid 122 through 127 Processing helix chain 'Cb' and resid 131 through 146 Processing helix chain 'Cb' and resid 147 through 162 removed outlier: 4.268A pdb=" N ALACb 156 " --> pdb=" O ALACb 152 " (cutoff:3.500A) Processing helix chain 'Cb' and resid 162 through 172 Proline residue: Cb 169 - end of helix Processing helix chain 'Cb' and resid 173 through 175 No H-bonds generated for 'chain 'Cb' and resid 173 through 175' Processing helix chain 'Cb' and resid 187 through 195 Processing helix chain 'Cb' and resid 201 through 205 removed outlier: 3.546A pdb=" N ILECb 204 " --> pdb=" O PROCb 201 " (cutoff:3.500A) Processing helix chain 'Cb' and resid 215 through 217 No H-bonds generated for 'chain 'Cb' and resid 215 through 217' Processing helix chain 'Cb' and resid 218 through 245 removed outlier: 3.540A pdb=" N VALCb 222 " --> pdb=" O ASPCb 218 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N PHECb 236 " --> pdb=" O ILECb 232 " (cutoff:3.500A) Processing helix chain 'Cc' and resid 20 through 58 removed outlier: 7.576A pdb=" N ASPCc 54 " --> pdb=" O LEUCc 50 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N TRPCc 55 " --> pdb=" O THRCc 51 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ASPCc 56 " --> pdb=" O METCc 52 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N TRPCc 58 " --> pdb=" O ASPCc 54 " (cutoff:3.500A) Processing helix chain 'Cc' and resid 65 through 75 Proline residue: Cc 72 - end of helix Processing helix chain 'Cc' and resid 76 through 89 removed outlier: 3.502A pdb=" N ALACc 81 " --> pdb=" O THRCc 77 " (cutoff:3.500A) Processing helix chain 'Cc' and resid 94 through 114 removed outlier: 3.857A pdb=" N CYSCc 99 " --> pdb=" O GLYCc 95 " (cutoff:3.500A) Processing helix chain 'Cc' and resid 122 through 127 Processing helix chain 'Cc' and resid 131 through 146 Processing helix chain 'Cc' and resid 147 through 162 removed outlier: 4.269A pdb=" N ALACc 156 " --> pdb=" O ALACc 152 " (cutoff:3.500A) Processing helix chain 'Cc' and resid 162 through 172 Proline residue: Cc 169 - end of helix Processing helix chain 'Cc' and resid 173 through 175 No H-bonds generated for 'chain 'Cc' and resid 173 through 175' Processing helix chain 'Cc' and resid 187 through 195 Processing helix chain 'Cc' and resid 201 through 205 removed outlier: 3.546A pdb=" N ILECc 204 " --> pdb=" O PROCc 201 " (cutoff:3.500A) Processing helix chain 'Cc' and resid 215 through 217 No H-bonds generated for 'chain 'Cc' and resid 215 through 217' Processing helix chain 'Cc' and resid 218 through 245 removed outlier: 3.540A pdb=" N VALCc 222 " --> pdb=" O ASPCc 218 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N PHECc 236 " --> pdb=" O ILECc 232 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'Aa' and resid 50 through 54 removed outlier: 4.490A pdb=" N LEUAa 52 " --> pdb=" O LYSAa 68 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N LYSAa 68 " --> pdb=" O LEUAa 52 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N TRPAa 54 " --> pdb=" O GLUAa 66 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N GLUAa 66 " --> pdb=" O TRPAa 54 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N ASPAa 123 " --> pdb=" O ILEAa 105 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N ILEAa 105 " --> pdb=" O ASPAa 123 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ARGAa 125 " --> pdb=" O SERAa 103 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N SERAa 103 " --> pdb=" O ARGAa 125 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N VALAa 127 " --> pdb=" O LYSAa 101 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'Aa' and resid 58 through 60 removed outlier: 6.899A pdb=" N VALAa 59 " --> pdb=" O GLUAa 160 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N VALAa 144 " --> pdb=" O PROAa 149 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N ILEAa 151 " --> pdb=" O METAa 142 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N METAa 142 " --> pdb=" O ILEAa 151 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N THRAa 140 " --> pdb=" O PROAa 153 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'Aa' and resid 113 through 114 removed outlier: 6.746A pdb=" N SERAa 113 " --> pdb=" O METAa 269 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'Aa' and resid 169 through 171 Processing sheet with id=AA5, first strand: chain 'Aa' and resid 346 through 348 removed outlier: 7.903A pdb=" N ALAAa 297 " --> pdb=" O TYRAa 291 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N TYRAa 291 " --> pdb=" O ALAAa 297 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N ARGAa 299 " --> pdb=" O ALAAa 289 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N ALAAa 289 " --> pdb=" O ARGAa 299 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N LYSAa 301 " --> pdb=" O GLUAa 287 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'Aa' and resid 341 through 342 removed outlier: 5.199A pdb=" N LEUAa 314 " --> pdb=" O PHEAa 394 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N PHEAa 394 " --> pdb=" O LEUAa 314 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLUAa 316 " --> pdb=" O PHEAa 392 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'Ca' and resid 177 through 180 Processing sheet with id=AA8, first strand: chain 'Ca' and resid 250 through 251 Processing sheet with id=AA9, first strand: chain 'Ba' and resid 206 through 207 Processing sheet with id=AB1, first strand: chain 'Bc' and resid 206 through 207 Processing sheet with id=AB2, first strand: chain 'Ab' and resid 50 through 54 removed outlier: 4.490A pdb=" N LEUAb 52 " --> pdb=" O LYSAb 68 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N LYSAb 68 " --> pdb=" O LEUAb 52 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N TRPAb 54 " --> pdb=" O GLUAb 66 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N GLUAb 66 " --> pdb=" O TRPAb 54 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N ASPAb 123 " --> pdb=" O ILEAb 105 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N ILEAb 105 " --> pdb=" O ASPAb 123 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ARGAb 125 " --> pdb=" O SERAb 103 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N SERAb 103 " --> pdb=" O ARGAb 125 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N VALAb 127 " --> pdb=" O LYSAb 101 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'Ab' and resid 58 through 60 removed outlier: 6.899A pdb=" N VALAb 59 " --> pdb=" O GLUAb 160 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N VALAb 144 " --> pdb=" O PROAb 149 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N ILEAb 151 " --> pdb=" O METAb 142 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N METAb 142 " --> pdb=" O ILEAb 151 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N THRAb 140 " --> pdb=" O PROAb 153 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'Ab' and resid 113 through 114 removed outlier: 6.747A pdb=" N SERAb 113 " --> pdb=" O METAb 269 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'Ab' and resid 169 through 171 Processing sheet with id=AB6, first strand: chain 'Ab' and resid 346 through 348 removed outlier: 7.903A pdb=" N ALAAb 297 " --> pdb=" O TYRAb 291 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N TYRAb 291 " --> pdb=" O ALAAb 297 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N ARGAb 299 " --> pdb=" O ALAAb 289 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N ALAAb 289 " --> pdb=" O ARGAb 299 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N LYSAb 301 " --> pdb=" O GLUAb 287 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'Ab' and resid 341 through 342 removed outlier: 5.198A pdb=" N LEUAb 314 " --> pdb=" O PHEAb 394 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N PHEAb 394 " --> pdb=" O LEUAb 314 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLUAb 316 " --> pdb=" O PHEAb 392 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'Ac' and resid 50 through 54 removed outlier: 4.490A pdb=" N LEUAc 52 " --> pdb=" O LYSAc 68 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N LYSAc 68 " --> pdb=" O LEUAc 52 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N TRPAc 54 " --> pdb=" O GLUAc 66 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N GLUAc 66 " --> pdb=" O TRPAc 54 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N ASPAc 123 " --> pdb=" O ILEAc 105 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N ILEAc 105 " --> pdb=" O ASPAc 123 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N ARGAc 125 " --> pdb=" O SERAc 103 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N SERAc 103 " --> pdb=" O ARGAc 125 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N VALAc 127 " --> pdb=" O LYSAc 101 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'Ac' and resid 58 through 60 removed outlier: 6.899A pdb=" N VALAc 59 " --> pdb=" O GLUAc 160 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N VALAc 144 " --> pdb=" O PROAc 149 " (cutoff:3.500A) removed outlier: 5.281A pdb=" N ILEAc 151 " --> pdb=" O METAc 142 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N METAc 142 " --> pdb=" O ILEAc 151 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N THRAc 140 " --> pdb=" O PROAc 153 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'Ac' and resid 113 through 114 removed outlier: 6.747A pdb=" N SERAc 113 " --> pdb=" O METAc 269 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'Ac' and resid 169 through 171 Processing sheet with id=AC3, first strand: chain 'Ac' and resid 346 through 348 removed outlier: 7.902A pdb=" N ALAAc 297 " --> pdb=" O TYRAc 291 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N TYRAc 291 " --> pdb=" O ALAAc 297 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N ARGAc 299 " --> pdb=" O ALAAc 289 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N ALAAc 289 " --> pdb=" O ARGAc 299 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N LYSAc 301 " --> pdb=" O GLUAc 287 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'Ac' and resid 341 through 342 removed outlier: 5.199A pdb=" N LEUAc 314 " --> pdb=" O PHEAc 394 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N PHEAc 394 " --> pdb=" O LEUAc 314 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLUAc 316 " --> pdb=" O PHEAc 392 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'Cb' and resid 177 through 180 Processing sheet with id=AC6, first strand: chain 'Cc' and resid 177 through 180 1116 hydrogen bonds defined for protein. 3240 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: 3.42 Time building geometry restraints manager: 2.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 6267 1.34 - 1.46: 5377 1.46 - 1.58: 9485 1.58 - 1.69: 0 1.69 - 1.81: 174 Bond restraints: 21303 Sorted by residual: bond pdb=" CA SERAb 37 " pdb=" CB SERAb 37 " ideal model delta sigma weight residual 1.530 1.480 0.050 1.39e-02 5.18e+03 1.27e+01 bond pdb=" N LEUBb 221 " pdb=" CA LEUBb 221 " ideal model delta sigma weight residual 1.462 1.489 -0.027 7.70e-03 1.69e+04 1.26e+01 bond pdb=" CA SERAc 37 " pdb=" CB SERAc 37 " ideal model delta sigma weight residual 1.530 1.481 0.049 1.39e-02 5.18e+03 1.25e+01 bond pdb=" N LEUBa 221 " pdb=" CA LEUBa 221 " ideal model delta sigma weight residual 1.462 1.489 -0.027 7.70e-03 1.69e+04 1.23e+01 bond pdb=" CA SERAa 37 " pdb=" CB SERAa 37 " ideal model delta sigma weight residual 1.530 1.481 0.049 1.39e-02 5.18e+03 1.22e+01 ... (remaining 21298 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.40: 28547 3.40 - 6.79: 518 6.79 - 10.19: 17 10.19 - 13.59: 3 13.59 - 16.99: 3 Bond angle restraints: 29088 Sorted by residual: angle pdb=" C HISAa 139 " pdb=" CA HISAa 139 " pdb=" CB HISAa 139 " ideal model delta sigma weight residual 109.35 92.36 16.99 1.98e+00 2.55e-01 7.36e+01 angle pdb=" C HISAb 139 " pdb=" CA HISAb 139 " pdb=" CB HISAb 139 " ideal model delta sigma weight residual 109.35 92.38 16.97 1.98e+00 2.55e-01 7.34e+01 angle pdb=" C HISAc 139 " pdb=" CA HISAc 139 " pdb=" CB HISAc 139 " ideal model delta sigma weight residual 109.35 92.40 16.95 1.98e+00 2.55e-01 7.33e+01 angle pdb=" CA PHEAc 71 " pdb=" CB PHEAc 71 " pdb=" CG PHEAc 71 " ideal model delta sigma weight residual 113.80 121.20 -7.40 1.00e+00 1.00e+00 5.47e+01 angle pdb=" CA PHEAa 71 " pdb=" CB PHEAa 71 " pdb=" CG PHEAa 71 " ideal model delta sigma weight residual 113.80 121.17 -7.37 1.00e+00 1.00e+00 5.43e+01 ... (remaining 29083 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 10214 17.94 - 35.88: 1315 35.88 - 53.83: 417 53.83 - 71.77: 93 71.77 - 89.71: 24 Dihedral angle restraints: 12063 sinusoidal: 4704 harmonic: 7359 Sorted by residual: dihedral pdb=" CA VALAc 293 " pdb=" C VALAc 293 " pdb=" N PROAc 294 " pdb=" CA PROAc 294 " ideal model delta harmonic sigma weight residual 180.00 133.18 46.82 0 5.00e+00 4.00e-02 8.77e+01 dihedral pdb=" CA VALAa 293 " pdb=" C VALAa 293 " pdb=" N PROAa 294 " pdb=" CA PROAa 294 " ideal model delta harmonic sigma weight residual 180.00 133.18 46.82 0 5.00e+00 4.00e-02 8.77e+01 dihedral pdb=" CA VALAb 293 " pdb=" C VALAb 293 " pdb=" N PROAb 294 " pdb=" CA PROAb 294 " ideal model delta harmonic sigma weight residual 180.00 133.19 46.81 0 5.00e+00 4.00e-02 8.76e+01 ... (remaining 12060 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 2581 0.078 - 0.157: 433 0.157 - 0.235: 95 0.235 - 0.313: 14 0.313 - 0.391: 9 Chirality restraints: 3132 Sorted by residual: chirality pdb=" CB ILEAc 211 " pdb=" CA ILEAc 211 " pdb=" CG1 ILEAc 211 " pdb=" CG2 ILEAc 211 " both_signs ideal model delta sigma weight residual False 2.64 2.25 0.39 2.00e-01 2.50e+01 3.83e+00 chirality pdb=" CB ILEAa 211 " pdb=" CA ILEAa 211 " pdb=" CG1 ILEAa 211 " pdb=" CG2 ILEAa 211 " both_signs ideal model delta sigma weight residual False 2.64 2.25 0.39 2.00e-01 2.50e+01 3.80e+00 chirality pdb=" CB ILEAb 211 " pdb=" CA ILEAb 211 " pdb=" CG1 ILEAb 211 " pdb=" CG2 ILEAb 211 " both_signs ideal model delta sigma weight residual False 2.64 2.26 0.39 2.00e-01 2.50e+01 3.79e+00 ... (remaining 3129 not shown) Planarity restraints: 3609 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARGCb 16 " -0.513 9.50e-02 1.11e+02 2.30e-01 3.24e+01 pdb=" NE ARGCb 16 " 0.030 2.00e-02 2.50e+03 pdb=" CZ ARGCb 16 " 0.008 2.00e-02 2.50e+03 pdb=" NH1 ARGCb 16 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARGCb 16 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARGCa 16 " -0.513 9.50e-02 1.11e+02 2.30e-01 3.23e+01 pdb=" NE ARGCa 16 " 0.030 2.00e-02 2.50e+03 pdb=" CZ ARGCa 16 " 0.008 2.00e-02 2.50e+03 pdb=" NH1 ARGCa 16 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARGCa 16 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARGCc 16 " -0.512 9.50e-02 1.11e+02 2.30e-01 3.23e+01 pdb=" NE ARGCc 16 " 0.030 2.00e-02 2.50e+03 pdb=" CZ ARGCc 16 " 0.008 2.00e-02 2.50e+03 pdb=" NH1 ARGCc 16 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARGCc 16 " -0.018 2.00e-02 2.50e+03 ... (remaining 3606 not shown) Histogram of nonbonded interaction distances: 1.90 - 2.50: 161 2.50 - 3.10: 14888 3.10 - 3.70: 32428 3.70 - 4.30: 48440 4.30 - 4.90: 82631 Nonbonded interactions: 178548 Sorted by model distance: nonbonded pdb=" ND1 HISAc 48 " pdb="CU CUAc 502 " model vdw 1.899 3.060 nonbonded pdb=" ND1 HISAa 48 " pdb="CU CUAa 502 " model vdw 1.899 3.060 nonbonded pdb=" ND1 HISAb 48 " pdb="CU CUAb 502 " model vdw 1.899 3.060 nonbonded pdb=" ND1 HISAa 72 " pdb="CU CUAa 502 " model vdw 1.964 3.060 nonbonded pdb=" ND1 HISAc 72 " pdb="CU CUAc 502 " model vdw 1.965 3.060 ... (remaining 178543 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: 0.06 Found NCS groups: ncs_group { reference = chain 'Aa' selection = chain 'Ab' selection = chain 'Ac' } ncs_group { reference = chain 'Ca' selection = chain 'Cb' selection = chain 'Cc' } ncs_group { reference = chain 'Ba' selection = chain 'Bb' selection = chain 'Bc' } 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: 1.180 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: 0.020 Extract box with map and model: 0.420 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 18.710 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5407 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 0.051 21303 Z= 0.435 Angle : 1.040 16.986 29088 Z= 0.692 Chirality : 0.065 0.391 3132 Planarity : 0.011 0.230 3609 Dihedral : 18.436 89.710 7365 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.59 % Allowed : 5.19 % Favored : 94.21 % Rotamer: Outliers : 6.95 % Allowed : 22.86 % Favored : 70.19 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.17 % Twisted General : 0.13 % 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: -0.46 (0.17), residues: 2523 helix: 0.67 (0.15), residues: 1161 sheet: -0.04 (0.27), residues: 381 loop : -1.56 (0.19), residues: 981 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARGAb 299 TYR 0.022 0.002 TYRBa 184 PHE 0.027 0.002 PHEAa 212 TRP 0.027 0.002 TRPCc 159 HIS 0.005 0.002 HISAb 33 Details of bonding type rmsd/Z covalent geometry : bond 0.00644 / 0.44 (21303) covalent geometry : angle 1.04028 / 0.69 (29088) hydrogen bonds : bond 0.14410 / 9.87 ( 1116) hydrogen bonds : angle 7.26145 / 5.10 ( 3240) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5046 Ramachandran restraints generated. 2523 Oldfield, 0 Emsley, 2523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5046 Ramachandran restraints generated. 2523 Oldfield, 0 Emsley, 2523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 572 residues out of total 2157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 150 poor density : 422 time to evaluate : 0.767 Fit side-chains REVERT: Aa 65 VAL cc_start: 0.7029 (OUTLIER) cc_final: 0.6714 (p) REVERT: Aa 103 SER cc_start: 0.8187 (t) cc_final: 0.7902 (t) REVERT: Aa 117 GLU cc_start: 0.7160 (mm-30) cc_final: 0.6876 (mp0) REVERT: Aa 141 MET cc_start: 0.8104 (OUTLIER) cc_final: 0.7724 (ptp) REVERT: Aa 160 GLU cc_start: 0.7119 (mt-10) cc_final: 0.6563 (pt0) REVERT: Aa 167 ARG cc_start: 0.6077 (mtp85) cc_final: 0.5856 (mmt-90) REVERT: Aa 211 ILE cc_start: 0.3519 (OUTLIER) cc_final: 0.2832 (tp) REVERT: Aa 249 MET cc_start: 0.5133 (mtm) cc_final: 0.4898 (tmm) REVERT: Aa 273 LYS cc_start: 0.7471 (mtpm) cc_final: 0.7085 (mptp) REVERT: Aa 283 SER cc_start: 0.6872 (t) cc_final: 0.6393 (p) REVERT: Aa 285 LYS cc_start: 0.6476 (tttt) cc_final: 0.6117 (tttp) REVERT: Aa 287 GLU cc_start: 0.7999 (mt-10) cc_final: 0.7707 (mt-10) REVERT: Aa 296 ARG cc_start: 0.6621 (mtm-85) cc_final: 0.6294 (ptp90) REVERT: Aa 375 ARG cc_start: 0.5896 (mtt180) cc_final: 0.5078 (mpt180) REVERT: Aa 382 ASP cc_start: 0.6757 (m-30) cc_final: 0.6393 (m-30) REVERT: Aa 414 MET cc_start: 0.6041 (mmt) cc_final: 0.5794 (mtp) REVERT: Ca 37 PHE cc_start: 0.3042 (t80) cc_final: 0.2796 (t80) REVERT: Ca 157 MET cc_start: 0.3301 (ttp) cc_final: 0.2899 (ttt) REVERT: Ca 213 ARG cc_start: 0.5565 (mtt180) cc_final: 0.4782 (mtm180) REVERT: Ca 237 MET cc_start: 0.6234 (ttm) cc_final: 0.5056 (mmt) REVERT: Ba 84 GLU cc_start: 0.5900 (mt-10) cc_final: 0.5604 (mt-10) REVERT: Ba 279 CYS cc_start: 0.3504 (OUTLIER) cc_final: 0.2747 (m) REVERT: Bb 84 GLU cc_start: 0.5839 (mt-10) cc_final: 0.5561 (tt0) REVERT: Bc 84 GLU cc_start: 0.6181 (mt-10) cc_final: 0.5849 (mt-10) REVERT: Bc 227 ASN cc_start: 0.4526 (OUTLIER) cc_final: 0.4210 (p0) REVERT: Bc 279 CYS cc_start: 0.3848 (OUTLIER) cc_final: 0.3440 (m) REVERT: Ab 65 VAL cc_start: 0.6898 (OUTLIER) cc_final: 0.6445 (p) REVERT: Ab 93 MET cc_start: 0.7609 (ptp) cc_final: 0.7349 (ptm) REVERT: Ab 103 SER cc_start: 0.7999 (t) cc_final: 0.7630 (t) REVERT: Ab 104 TYR cc_start: 0.7262 (m-80) cc_final: 0.6960 (m-80) REVERT: Ab 108 GLN cc_start: 0.6965 (OUTLIER) cc_final: 0.6545 (tm-30) REVERT: Ab 117 GLU cc_start: 0.7257 (mm-30) cc_final: 0.7009 (mp0) REVERT: Ab 165 GLU cc_start: 0.6145 (mm-30) cc_final: 0.5935 (mt-10) REVERT: Ab 167 ARG cc_start: 0.6096 (mtp85) cc_final: 0.5685 (mmt-90) REVERT: Ab 211 ILE cc_start: 0.3451 (OUTLIER) cc_final: 0.2801 (tp) REVERT: Ab 249 MET cc_start: 0.5468 (mtm) cc_final: 0.5169 (tmm) REVERT: Ab 273 LYS cc_start: 0.7356 (mtpm) cc_final: 0.7061 (mptp) REVERT: Ab 283 SER cc_start: 0.6931 (t) cc_final: 0.6588 (p) REVERT: Ab 292 ARG cc_start: 0.6244 (mtp85) cc_final: 0.5944 (mmt180) REVERT: Ab 323 ARG cc_start: 0.7460 (mtm180) cc_final: 0.7218 (mtp-110) REVERT: Ab 375 ARG cc_start: 0.5765 (mtt180) cc_final: 0.5469 (mtt90) REVERT: Ab 414 MET cc_start: 0.5713 (mmt) cc_final: 0.5481 (mtp) REVERT: Ac 50 TYR cc_start: 0.6142 (p90) cc_final: 0.5489 (p90) REVERT: Ac 70 LYS cc_start: 0.6984 (OUTLIER) cc_final: 0.6710 (ptpt) REVERT: Ac 103 SER cc_start: 0.8053 (t) cc_final: 0.7524 (t) REVERT: Ac 108 GLN cc_start: 0.7144 (OUTLIER) cc_final: 0.6835 (tp40) REVERT: Ac 117 GLU cc_start: 0.7155 (mm-30) cc_final: 0.6944 (mp0) REVERT: Ac 140 THR cc_start: 0.7777 (OUTLIER) cc_final: 0.7572 (p) REVERT: Ac 160 GLU cc_start: 0.6812 (mt-10) cc_final: 0.6581 (pt0) REVERT: Ac 165 GLU cc_start: 0.6212 (mm-30) cc_final: 0.5993 (mt-10) REVERT: Ac 211 ILE cc_start: 0.3621 (OUTLIER) cc_final: 0.2914 (tp) REVERT: Ac 249 MET cc_start: 0.5357 (mtm) cc_final: 0.4951 (tmm) REVERT: Ac 251 MET cc_start: 0.5450 (ttt) cc_final: 0.4943 (tpt) REVERT: Ac 272 MET cc_start: 0.6990 (mmp) cc_final: 0.6725 (mmt) REVERT: Ac 273 LYS cc_start: 0.7439 (mtpm) cc_final: 0.7002 (mptp) REVERT: Ac 283 SER cc_start: 0.6997 (t) cc_final: 0.6581 (p) REVERT: Ac 285 LYS cc_start: 0.6542 (tttt) cc_final: 0.6034 (tptp) REVERT: Ac 287 GLU cc_start: 0.8052 (mt-10) cc_final: 0.7837 (mt-10) REVERT: Ac 323 ARG cc_start: 0.7396 (mtm180) cc_final: 0.7145 (mtm180) REVERT: Ac 330 TYR cc_start: 0.6892 (t80) cc_final: 0.6598 (t80) REVERT: Ac 382 ASP cc_start: 0.6569 (m-30) cc_final: 0.6366 (m-30) REVERT: Cb 37 PHE cc_start: 0.3217 (t80) cc_final: 0.2954 (t80) REVERT: Cb 157 MET cc_start: 0.3373 (ttp) cc_final: 0.2897 (ttm) REVERT: Cb 183 MET cc_start: 0.7498 (ttp) cc_final: 0.7096 (mtp) REVERT: Cb 213 ARG cc_start: 0.5920 (mtt180) cc_final: 0.5048 (mtm180) REVERT: Cb 230 MET cc_start: 0.4789 (tpt) cc_final: 0.4563 (mmm) REVERT: Cb 237 MET cc_start: 0.6267 (ttm) cc_final: 0.5795 (ttt) REVERT: Cb 249 ARG cc_start: 0.4253 (OUTLIER) cc_final: 0.3916 (mtm110) REVERT: Cc 37 PHE cc_start: 0.3254 (t80) cc_final: 0.3032 (t80) REVERT: Cc 65 ARG cc_start: 0.5728 (OUTLIER) cc_final: 0.4389 (tmt170) REVERT: Cc 114 ASN cc_start: 0.6864 (m-40) cc_final: 0.6293 (m-40) REVERT: Cc 157 MET cc_start: 0.2919 (ttp) cc_final: 0.2577 (ttt) REVERT: Cc 179 GLU cc_start: 0.7534 (tm-30) cc_final: 0.7179 (tt0) REVERT: Cc 209 LYS cc_start: 0.6107 (mttt) cc_final: 0.5716 (mmtt) REVERT: Cc 213 ARG cc_start: 0.5919 (mtt180) cc_final: 0.4968 (mtm180) REVERT: Cc 237 MET cc_start: 0.6214 (ttm) cc_final: 0.5844 (ttt) REVERT: Cc 245 PHE cc_start: 0.6523 (m-80) cc_final: 0.6257 (m-80) REVERT: Cc 249 ARG cc_start: 0.5114 (OUTLIER) cc_final: 0.4710 (mtm110) outliers start: 150 outliers final: 10 residues processed: 539 average time/residue: 0.6020 time to fit residues: 367.9826 Evaluate side-chains 322 residues out of total 2157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 296 time to evaluate : 0.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 65 VAL Chi-restraints excluded: chain Aa residue 118 ILE Chi-restraints excluded: chain Aa residue 141 MET Chi-restraints excluded: chain Aa residue 211 ILE Chi-restraints excluded: chain Ca residue 76 VAL Chi-restraints excluded: chain Ba residue 279 CYS Chi-restraints excluded: chain Bc residue 132 PHE Chi-restraints excluded: chain Bc residue 227 ASN Chi-restraints excluded: chain Bc residue 279 CYS Chi-restraints excluded: chain Ab residue 46 THR Chi-restraints excluded: chain Ab residue 65 VAL Chi-restraints excluded: chain Ab residue 80 THR Chi-restraints excluded: chain Ab residue 108 GLN Chi-restraints excluded: chain Ab residue 140 THR Chi-restraints excluded: chain Ab residue 211 ILE Chi-restraints excluded: chain Ac residue 65 VAL Chi-restraints excluded: chain Ac residue 70 LYS Chi-restraints excluded: chain Ac residue 80 THR Chi-restraints excluded: chain Ac residue 108 GLN Chi-restraints excluded: chain Ac residue 140 THR Chi-restraints excluded: chain Ac residue 211 ILE Chi-restraints excluded: chain Cb residue 76 VAL Chi-restraints excluded: chain Cb residue 249 ARG Chi-restraints excluded: chain Cc residue 65 ARG Chi-restraints excluded: chain Cc residue 76 VAL Chi-restraints excluded: chain Cc residue 249 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 216 optimal weight: 0.8980 chunk 98 optimal weight: 0.6980 chunk 194 optimal weight: 3.9990 chunk 227 optimal weight: 5.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 0.3980 chunk 66 optimal weight: 1.9990 chunk 247 optimal weight: 4.9990 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Aa 33 HIS Aa 306 ASN Ca 23 GLN ** Ca 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ba 223 ASN Bb 223 ASN Bb 227 ASN Bc 223 ASN Ab 33 HIS Ab 143 ASN Ab 182 ASN Ac 33 HIS Ac 38 GLN Ac 143 ASN Cb 18 HIS Cb 23 GLN ** Cb 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Cb 175 HIS Cb 181 ASN Cb 252 GLN ** Cc 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Cc 181 ASN Cc 239 HIS Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.194797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.164965 restraints weight = 22713.903| |-----------------------------------------------------------------------------| r_work (start): 0.3771 rms_B_bonded: 1.31 r_work: 0.3640 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3533 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.2552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 21303 Z= 0.158 Angle : 0.674 8.723 29088 Z= 0.349 Chirality : 0.048 0.396 3132 Planarity : 0.006 0.104 3609 Dihedral : 6.702 60.728 2843 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.58 % Favored : 97.30 % Rotamer: Outliers : 5.80 % Allowed : 22.11 % Favored : 72.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.17 % Twisted General : 0.13 % 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: 0.63 (0.17), residues: 2523 helix: 1.45 (0.15), residues: 1179 sheet: 0.55 (0.27), residues: 351 loop : -0.88 (0.19), residues: 993 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARGCa 249 TYR 0.021 0.002 TYRBa 184 PHE 0.018 0.002 PHEBc 218 TRP 0.015 0.002 TRPCa 159 HIS 0.008 0.001 HISAb 33 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.16 (21303) covalent geometry : angle 0.67408 / 0.35 (29088) hydrogen bonds : bond 0.04785 / 3.14 ( 1116) hydrogen bonds : angle 5.09945 / 3.58 ( 3240) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5046 Ramachandran restraints generated. 2523 Oldfield, 0 Emsley, 2523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5046 Ramachandran restraints generated. 2523 Oldfield, 0 Emsley, 2523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 2157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 289 time to evaluate : 0.735 Fit side-chains revert: symmetry clash REVERT: Aa 93 MET cc_start: 0.8682 (ptp) cc_final: 0.8274 (ptm) REVERT: Aa 100 ARG cc_start: 0.9031 (OUTLIER) cc_final: 0.8731 (ttm110) REVERT: Ca 37 PHE cc_start: 0.5332 (t80) cc_final: 0.4883 (t80) REVERT: Ca 157 MET cc_start: 0.4464 (ttp) cc_final: 0.4098 (ttt) REVERT: Ca 202 GLU cc_start: 0.8639 (OUTLIER) cc_final: 0.8269 (tm-30) REVERT: Ca 213 ARG cc_start: 0.7686 (mtt180) cc_final: 0.6845 (mtm180) REVERT: Ca 219 VAL cc_start: 0.6832 (OUTLIER) cc_final: 0.6556 (t) REVERT: Ca 237 MET cc_start: 0.6912 (ttm) cc_final: 0.6226 (mmt) REVERT: Ba 219 MET cc_start: 0.7634 (mmm) cc_final: 0.7367 (mmt) REVERT: Bb 145 ILE cc_start: 0.6683 (OUTLIER) cc_final: 0.6461 (pp) REVERT: Bb 192 PHE cc_start: 0.6829 (t80) cc_final: 0.6541 (t80) REVERT: Bb 259 MET cc_start: 0.6204 (mtm) cc_final: 0.5244 (mmm) REVERT: Bc 69 GLU cc_start: 0.7442 (pt0) cc_final: 0.7211 (pt0) REVERT: Bc 145 ILE cc_start: 0.6629 (OUTLIER) cc_final: 0.6380 (pp) REVERT: Bc 259 MET cc_start: 0.4972 (OUTLIER) cc_final: 0.3764 (mtm) REVERT: Ab 93 MET cc_start: 0.8814 (ptp) cc_final: 0.8553 (ptm) REVERT: Ab 163 MET cc_start: 0.8628 (OUTLIER) cc_final: 0.8423 (ttt) REVERT: Ab 256 SER cc_start: 0.8073 (OUTLIER) cc_final: 0.7795 (p) REVERT: Ab 360 ARG cc_start: 0.8264 (OUTLIER) cc_final: 0.6540 (ptp90) REVERT: Ac 285 LYS cc_start: 0.8827 (tttt) cc_final: 0.8421 (tptp) REVERT: Ac 330 TYR cc_start: 0.8557 (t80) cc_final: 0.8342 (t80) REVERT: Ac 375 ARG cc_start: 0.8309 (mtp85) cc_final: 0.8060 (mtt-85) REVERT: Cb 31 MET cc_start: 0.4761 (OUTLIER) cc_final: 0.4302 (mtm) REVERT: Cb 37 PHE cc_start: 0.5260 (t80) cc_final: 0.4835 (t80) REVERT: Cb 157 MET cc_start: 0.4372 (ttp) cc_final: 0.4006 (ttt) REVERT: Cb 213 ARG cc_start: 0.7628 (mtt180) cc_final: 0.6942 (mtm180) REVERT: Cb 230 MET cc_start: 0.6885 (tpt) cc_final: 0.6628 (mmm) REVERT: Cb 237 MET cc_start: 0.6940 (ttm) cc_final: 0.6219 (mmt) REVERT: Cb 249 ARG cc_start: 0.5961 (mtm-85) cc_final: 0.5207 (mtt180) REVERT: Cc 20 GLU cc_start: 0.4770 (OUTLIER) cc_final: 0.4552 (mm-30) REVERT: Cc 37 PHE cc_start: 0.5461 (t80) cc_final: 0.5172 (t80) REVERT: Cc 157 MET cc_start: 0.4421 (ttp) cc_final: 0.4008 (ttt) REVERT: Cc 183 MET cc_start: 0.8810 (ttm) cc_final: 0.8419 (ttt) REVERT: Cc 202 GLU cc_start: 0.8578 (OUTLIER) cc_final: 0.8145 (tm-30) REVERT: Cc 213 ARG cc_start: 0.7684 (mtt180) cc_final: 0.6857 (mtt180) REVERT: Cc 237 MET cc_start: 0.7008 (ttm) cc_final: 0.6633 (ttt) REVERT: Cc 249 ARG cc_start: 0.6894 (mtm-85) cc_final: 0.6511 (mtm110) outliers start: 125 outliers final: 20 residues processed: 385 average time/residue: 0.6138 time to fit residues: 266.9991 Evaluate side-chains 282 residues out of total 2157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 250 time to evaluate : 0.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 100 ARG Chi-restraints excluded: chain Aa residue 344 ASP Chi-restraints excluded: chain Ca residue 76 VAL Chi-restraints excluded: chain Ca residue 202 GLU Chi-restraints excluded: chain Ca residue 219 VAL Chi-restraints excluded: chain Ca residue 246 SER Chi-restraints excluded: chain Ba residue 132 PHE Chi-restraints excluded: chain Bb residue 132 PHE Chi-restraints excluded: chain Bb residue 145 ILE Chi-restraints excluded: chain Bb residue 271 GLN Chi-restraints excluded: chain Bc residue 145 ILE Chi-restraints excluded: chain Bc residue 227 ASN Chi-restraints excluded: chain Bc residue 259 MET Chi-restraints excluded: chain Ab residue 47 ILE Chi-restraints excluded: chain Ab residue 110 VAL Chi-restraints excluded: chain Ab residue 162 SER Chi-restraints excluded: chain Ab residue 163 MET Chi-restraints excluded: chain Ab residue 252 SER Chi-restraints excluded: chain Ab residue 256 SER Chi-restraints excluded: chain Ab residue 334 THR Chi-restraints excluded: chain Ab residue 360 ARG Chi-restraints excluded: chain Ac residue 47 ILE Chi-restraints excluded: chain Ac residue 145 GLN Chi-restraints excluded: chain Ac residue 162 SER Chi-restraints excluded: chain Ac residue 252 SER Chi-restraints excluded: chain Ac residue 256 SER Chi-restraints excluded: chain Cb residue 31 MET Chi-restraints excluded: chain Cb residue 76 VAL Chi-restraints excluded: chain Cb residue 91 ARG Chi-restraints excluded: chain Cc residue 20 GLU Chi-restraints excluded: chain Cc residue 76 VAL Chi-restraints excluded: chain Cc residue 202 GLU 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: 71.3715 > 50: distance: 61 - 63: 25.595 distance: 63 - 64: 44.744 distance: 64 - 65: 15.896 distance: 64 - 67: 32.698 distance: 65 - 66: 33.115 distance: 65 - 71: 14.069 distance: 67 - 68: 6.204 distance: 68 - 69: 19.093 distance: 69 - 70: 10.588 distance: 71 - 72: 11.320 distance: 72 - 73: 29.816 distance: 72 - 75: 36.056 distance: 73 - 74: 36.957 distance: 73 - 80: 42.970 distance: 75 - 76: 26.847 distance: 76 - 77: 13.792 distance: 77 - 78: 9.192 distance: 78 - 79: 9.019 distance: 80 - 81: 37.718 distance: 81 - 82: 37.333 distance: 81 - 84: 39.396 distance: 82 - 83: 23.494 distance: 82 - 87: 32.228 distance: 84 - 85: 10.596 distance: 85 - 86: 29.024 distance: 87 - 88: 21.284 distance: 88 - 89: 53.575 distance: 88 - 91: 37.058 distance: 89 - 90: 14.670 distance: 89 - 95: 38.128 distance: 91 - 92: 26.304 distance: 92 - 93: 12.737 distance: 92 - 94: 25.582 distance: 95 - 96: 7.777 distance: 96 - 97: 48.876 distance: 96 - 99: 32.223 distance: 97 - 98: 47.473 distance: 97 - 104: 7.356 distance: 99 - 100: 14.900 distance: 100 - 101: 10.919 distance: 101 - 102: 23.064 distance: 101 - 103: 31.833 distance: 104 - 105: 22.819 distance: 105 - 106: 42.249 distance: 105 - 108: 3.344 distance: 106 - 107: 38.467 distance: 106 - 112: 23.529 distance: 108 - 109: 31.460 distance: 109 - 110: 29.547 distance: 109 - 111: 36.632 distance: 112 - 113: 15.523 distance: 112 - 118: 9.277 distance: 113 - 114: 40.183 distance: 113 - 116: 12.298 distance: 114 - 115: 11.827 distance: 114 - 119: 38.765 distance: 116 - 117: 36.023 distance: 117 - 118: 51.439 distance: 119 - 120: 35.150 distance: 120 - 121: 32.954 distance: 120 - 123: 16.551 distance: 121 - 122: 29.689 distance: 121 - 124: 36.468 distance: 124 - 125: 45.317 distance: 124 - 130: 43.047 distance: 125 - 126: 4.606 distance: 125 - 128: 19.273 distance: 126 - 127: 7.919 distance: 126 - 131: 23.999 distance: 128 - 129: 24.540 distance: 131 - 132: 34.579 distance: 132 - 133: 12.177 distance: 132 - 135: 20.952 distance: 133 - 134: 10.205 distance: 133 - 138: 26.373 distance: 135 - 136: 39.689 distance: 135 - 137: 52.563