Starting phenix.real_space_refine on Fri Jul 3 03:51:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6djm_7936/07_2026/6djm_7936.cif Found real_map, /net/cci-nas-00/data/ceres_data/6djm_7936/07_2026/6djm_7936.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6djm_7936/07_2026/6djm_7936.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6djm_7936/07_2026/6djm_7936.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6djm_7936/07_2026/6djm_7936.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6djm_7936/07_2026/6djm_7936.cif" model { file = "/net/cci-nas-00/data/ceres_data/6djm_7936/07_2026/6djm_7936.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6djm_7936/07_2026/6djm_7936.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 12 5.49 5 Mg 4 5.21 5 S 84 5.16 5 C 7408 2.51 5 N 1984 2.21 5 O 2276 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 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: 11768 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2909 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2909 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2909 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2909 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 2.27, per 1000 atoms: 0.19 Number of scatterers: 11768 At special positions: 0 Unit cell: (101.365, 78.375, 165.11, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 84 16.00 P 12 15.00 Mg 4 11.99 O 2276 8.00 N 1984 7.00 C 7408 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: 0.91 Conformation dependent library (CDL) restraints added in 419.1 milliseconds 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2752 Finding SS restraints... Secondary structure from input PDB file: 68 helices and 20 sheets defined 42.7% alpha, 14.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.45 Creating SS restraints... Processing helix chain 'A' and resid 55 through 61 Processing helix chain 'A' and resid 78 through 91 Processing helix chain 'A' and resid 112 through 126 removed outlier: 3.831A pdb=" N ARG A 116 " --> pdb=" O PRO A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 144 removed outlier: 4.065A pdb=" N LEU A 142 " --> pdb=" O ALA A 138 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N TYR A 143 " --> pdb=" O VAL A 139 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ALA A 144 " --> pdb=" O LEU A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 193 removed outlier: 3.580A pdb=" N LYS A 191 " --> pdb=" O ASP A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 217 removed outlier: 3.670A pdb=" N GLU A 207 " --> pdb=" O THR A 203 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ILE A 208 " --> pdb=" O ALA A 204 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ASP A 211 " --> pdb=" O GLU A 207 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LYS A 215 " --> pdb=" O ASP A 211 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N CYS A 217 " --> pdb=" O LYS A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 230 removed outlier: 3.865A pdb=" N ALA A 228 " --> pdb=" O GLU A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 257 removed outlier: 4.063A pdb=" N CYS A 257 " --> pdb=" O GLU A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 262 Processing helix chain 'A' and resid 263 through 268 Processing helix chain 'A' and resid 273 through 283 removed outlier: 3.504A pdb=" N TYR A 279 " --> pdb=" O HIS A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 295 removed outlier: 3.531A pdb=" N ALA A 295 " --> pdb=" O LYS A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 306 removed outlier: 3.527A pdb=" N THR A 304 " --> pdb=" O GLY A 301 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N TYR A 306 " --> pdb=" O THR A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 319 removed outlier: 3.505A pdb=" N ARG A 312 " --> pdb=" O GLY A 308 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N THR A 318 " --> pdb=" O GLN A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 347 Processing helix chain 'A' and resid 359 through 364 removed outlier: 3.655A pdb=" N GLU A 364 " --> pdb=" O GLN A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 371 removed outlier: 4.146A pdb=" N SER A 368 " --> pdb=" O ALA A 365 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ILE A 369 " --> pdb=" O GLY A 366 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N VAL A 370 " --> pdb=" O PRO A 367 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N HIS A 371 " --> pdb=" O SER A 368 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 365 through 371' Processing helix chain 'B' and resid 55 through 61 Processing helix chain 'B' and resid 78 through 91 Processing helix chain 'B' and resid 112 through 126 removed outlier: 3.832A pdb=" N ARG B 116 " --> pdb=" O PRO B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 144 removed outlier: 4.066A pdb=" N LEU B 142 " --> pdb=" O ALA B 138 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N TYR B 143 " --> pdb=" O VAL B 139 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ALA B 144 " --> pdb=" O LEU B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 193 removed outlier: 3.580A pdb=" N LYS B 191 " --> pdb=" O ASP B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 217 removed outlier: 3.670A pdb=" N GLU B 207 " --> pdb=" O THR B 203 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ILE B 208 " --> pdb=" O ALA B 204 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ASP B 211 " --> pdb=" O GLU B 207 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LYS B 215 " --> pdb=" O ASP B 211 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N CYS B 217 " --> pdb=" O LYS B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 230 removed outlier: 3.865A pdb=" N ALA B 228 " --> pdb=" O GLU B 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 257 removed outlier: 4.063A pdb=" N CYS B 257 " --> pdb=" O GLU B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 262 Processing helix chain 'B' and resid 263 through 268 Processing helix chain 'B' and resid 273 through 283 removed outlier: 3.504A pdb=" N TYR B 279 " --> pdb=" O HIS B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 289 through 295 removed outlier: 3.531A pdb=" N ALA B 295 " --> pdb=" O LYS B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 306 removed outlier: 3.526A pdb=" N THR B 304 " --> pdb=" O GLY B 301 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N TYR B 306 " --> pdb=" O THR B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 319 removed outlier: 3.505A pdb=" N ARG B 312 " --> pdb=" O GLY B 308 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N THR B 318 " --> pdb=" O GLN B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 347 Processing helix chain 'B' and resid 359 through 364 removed outlier: 3.656A pdb=" N GLU B 364 " --> pdb=" O GLN B 360 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 371 removed outlier: 4.146A pdb=" N SER B 368 " --> pdb=" O ALA B 365 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ILE B 369 " --> pdb=" O GLY B 366 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N VAL B 370 " --> pdb=" O PRO B 367 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N HIS B 371 " --> pdb=" O SER B 368 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 365 through 371' Processing helix chain 'C' and resid 55 through 61 Processing helix chain 'C' and resid 78 through 91 Processing helix chain 'C' and resid 112 through 126 removed outlier: 3.832A pdb=" N ARG C 116 " --> pdb=" O PRO C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 144 removed outlier: 4.065A pdb=" N LEU C 142 " --> pdb=" O ALA C 138 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N TYR C 143 " --> pdb=" O VAL C 139 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ALA C 144 " --> pdb=" O LEU C 140 " (cutoff:3.500A) Processing helix chain 'C' and resid 181 through 193 removed outlier: 3.581A pdb=" N LYS C 191 " --> pdb=" O ASP C 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 217 removed outlier: 3.670A pdb=" N GLU C 207 " --> pdb=" O THR C 203 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ILE C 208 " --> pdb=" O ALA C 204 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ASP C 211 " --> pdb=" O GLU C 207 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LYS C 215 " --> pdb=" O ASP C 211 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N CYS C 217 " --> pdb=" O LYS C 213 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 230 removed outlier: 3.865A pdb=" N ALA C 228 " --> pdb=" O GLU C 224 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 257 removed outlier: 4.063A pdb=" N CYS C 257 " --> pdb=" O GLU C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 258 through 262 Processing helix chain 'C' and resid 263 through 268 Processing helix chain 'C' and resid 273 through 283 removed outlier: 3.504A pdb=" N TYR C 279 " --> pdb=" O HIS C 275 " (cutoff:3.500A) Processing helix chain 'C' and resid 289 through 295 removed outlier: 3.532A pdb=" N ALA C 295 " --> pdb=" O LYS C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 306 removed outlier: 3.526A pdb=" N THR C 304 " --> pdb=" O GLY C 301 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N TYR C 306 " --> pdb=" O THR C 303 " (cutoff:3.500A) Processing helix chain 'C' and resid 308 through 319 removed outlier: 3.505A pdb=" N ARG C 312 " --> pdb=" O GLY C 308 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N THR C 318 " --> pdb=" O GLN C 314 " (cutoff:3.500A) Processing helix chain 'C' and resid 337 through 347 Processing helix chain 'C' and resid 359 through 364 removed outlier: 3.655A pdb=" N GLU C 364 " --> pdb=" O GLN C 360 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 371 removed outlier: 4.146A pdb=" N SER C 368 " --> pdb=" O ALA C 365 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ILE C 369 " --> pdb=" O GLY C 366 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N VAL C 370 " --> pdb=" O PRO C 367 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N HIS C 371 " --> pdb=" O SER C 368 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 365 through 371' Processing helix chain 'D' and resid 55 through 61 Processing helix chain 'D' and resid 78 through 91 Processing helix chain 'D' and resid 112 through 126 removed outlier: 3.832A pdb=" N ARG D 116 " --> pdb=" O PRO D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 144 removed outlier: 4.065A pdb=" N LEU D 142 " --> pdb=" O ALA D 138 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N TYR D 143 " --> pdb=" O VAL D 139 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ALA D 144 " --> pdb=" O LEU D 140 " (cutoff:3.500A) Processing helix chain 'D' and resid 181 through 193 removed outlier: 3.580A pdb=" N LYS D 191 " --> pdb=" O ASP D 187 " (cutoff:3.500A) Processing helix chain 'D' and resid 202 through 217 removed outlier: 3.670A pdb=" N GLU D 207 " --> pdb=" O THR D 203 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ILE D 208 " --> pdb=" O ALA D 204 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ASP D 211 " --> pdb=" O GLU D 207 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LYS D 215 " --> pdb=" O ASP D 211 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N CYS D 217 " --> pdb=" O LYS D 213 " (cutoff:3.500A) Processing helix chain 'D' and resid 222 through 230 removed outlier: 3.865A pdb=" N ALA D 228 " --> pdb=" O GLU D 224 " (cutoff:3.500A) Processing helix chain 'D' and resid 252 through 257 removed outlier: 4.063A pdb=" N CYS D 257 " --> pdb=" O GLU D 253 " (cutoff:3.500A) Processing helix chain 'D' and resid 258 through 262 Processing helix chain 'D' and resid 263 through 268 Processing helix chain 'D' and resid 273 through 283 removed outlier: 3.505A pdb=" N TYR D 279 " --> pdb=" O HIS D 275 " (cutoff:3.500A) Processing helix chain 'D' and resid 289 through 295 removed outlier: 3.531A pdb=" N ALA D 295 " --> pdb=" O LYS D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 301 through 306 removed outlier: 3.525A pdb=" N THR D 304 " --> pdb=" O GLY D 301 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N TYR D 306 " --> pdb=" O THR D 303 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 319 removed outlier: 3.505A pdb=" N ARG D 312 " --> pdb=" O GLY D 308 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N THR D 318 " --> pdb=" O GLN D 314 " (cutoff:3.500A) Processing helix chain 'D' and resid 337 through 347 Processing helix chain 'D' and resid 359 through 364 removed outlier: 3.655A pdb=" N GLU D 364 " --> pdb=" O GLN D 360 " (cutoff:3.500A) Processing helix chain 'D' and resid 365 through 371 removed outlier: 4.146A pdb=" N SER D 368 " --> pdb=" O ALA D 365 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ILE D 369 " --> pdb=" O GLY D 366 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N VAL D 370 " --> pdb=" O PRO D 367 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N HIS D 371 " --> pdb=" O SER D 368 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 365 through 371' Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 32 removed outlier: 3.550A pdb=" N PHE A 31 " --> pdb=" O VAL A 17 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N LEU A 8 " --> pdb=" O LEU A 104 " (cutoff:3.500A) removed outlier: 8.344A pdb=" N THR A 106 " --> pdb=" O LEU A 8 " (cutoff:3.500A) removed outlier: 8.113A pdb=" N CYS A 10 " --> pdb=" O THR A 106 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N THR A 103 " --> pdb=" O TYR A 133 " (cutoff:3.500A) removed outlier: 7.722A pdb=" N ALA A 135 " --> pdb=" O THR A 103 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N LEU A 105 " --> pdb=" O ALA A 135 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 54 removed outlier: 3.547A pdb=" N ARG A 37 " --> pdb=" O THR A 66 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 71 through 72 Processing sheet with id=AA4, first strand: chain 'A' and resid 176 through 178 removed outlier: 5.971A pdb=" N ASN A 297 " --> pdb=" O ILE A 330 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 238 through 241 Processing sheet with id=AA6, first strand: chain 'B' and resid 29 through 32 removed outlier: 3.550A pdb=" N PHE B 31 " --> pdb=" O VAL B 17 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N LEU B 8 " --> pdb=" O LEU B 104 " (cutoff:3.500A) removed outlier: 8.343A pdb=" N THR B 106 " --> pdb=" O LEU B 8 " (cutoff:3.500A) removed outlier: 8.112A pdb=" N CYS B 10 " --> pdb=" O THR B 106 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N THR B 103 " --> pdb=" O TYR B 133 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N ALA B 135 " --> pdb=" O THR B 103 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N LEU B 105 " --> pdb=" O ALA B 135 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 53 through 54 removed outlier: 3.547A pdb=" N ARG B 37 " --> pdb=" O THR B 66 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 71 through 72 Processing sheet with id=AA9, first strand: chain 'B' and resid 176 through 178 removed outlier: 5.971A pdb=" N ASN B 297 " --> pdb=" O ILE B 330 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 238 through 241 Processing sheet with id=AB2, first strand: chain 'C' and resid 29 through 32 removed outlier: 3.551A pdb=" N PHE C 31 " --> pdb=" O VAL C 17 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N LEU C 8 " --> pdb=" O LEU C 104 " (cutoff:3.500A) removed outlier: 8.343A pdb=" N THR C 106 " --> pdb=" O LEU C 8 " (cutoff:3.500A) removed outlier: 8.113A pdb=" N CYS C 10 " --> pdb=" O THR C 106 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N THR C 103 " --> pdb=" O TYR C 133 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N ALA C 135 " --> pdb=" O THR C 103 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N LEU C 105 " --> pdb=" O ALA C 135 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 53 through 54 removed outlier: 3.547A pdb=" N ARG C 37 " --> pdb=" O THR C 66 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 71 through 72 Processing sheet with id=AB5, first strand: chain 'C' and resid 176 through 178 removed outlier: 5.971A pdb=" N ASN C 297 " --> pdb=" O ILE C 330 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 238 through 241 Processing sheet with id=AB7, first strand: chain 'D' and resid 29 through 32 removed outlier: 3.551A pdb=" N PHE D 31 " --> pdb=" O VAL D 17 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N LEU D 8 " --> pdb=" O LEU D 104 " (cutoff:3.500A) removed outlier: 8.343A pdb=" N THR D 106 " --> pdb=" O LEU D 8 " (cutoff:3.500A) removed outlier: 8.113A pdb=" N CYS D 10 " --> pdb=" O THR D 106 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N THR D 103 " --> pdb=" O TYR D 133 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N ALA D 135 " --> pdb=" O THR D 103 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N LEU D 105 " --> pdb=" O ALA D 135 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 53 through 54 removed outlier: 3.547A pdb=" N ARG D 37 " --> pdb=" O THR D 66 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 71 through 72 Processing sheet with id=AC1, first strand: chain 'D' and resid 176 through 178 removed outlier: 5.970A pdb=" N ASN D 297 " --> pdb=" O ILE D 330 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 238 through 241 424 hydrogen bonds defined for protein. 1092 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: 2.33 Time building geometry restraints manager: 1.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 3633 1.33 - 1.45: 1729 1.45 - 1.57: 6494 1.57 - 1.68: 12 1.68 - 1.80: 152 Bond restraints: 12020 Sorted by residual: bond pdb=" O3A ANP C 802 " pdb=" PB ANP C 802 " ideal model delta sigma weight residual 1.700 1.538 0.162 2.00e-02 2.50e+03 6.59e+01 bond pdb=" O3A ANP A 802 " pdb=" PB ANP A 802 " ideal model delta sigma weight residual 1.700 1.539 0.161 2.00e-02 2.50e+03 6.51e+01 bond pdb=" O3A ANP B 802 " pdb=" PB ANP B 802 " ideal model delta sigma weight residual 1.700 1.539 0.161 2.00e-02 2.50e+03 6.51e+01 bond pdb=" O3A ANP D 802 " pdb=" PB ANP D 802 " ideal model delta sigma weight residual 1.700 1.541 0.159 2.00e-02 2.50e+03 6.33e+01 bond pdb=" O5' ANP C 802 " pdb=" PA ANP C 802 " ideal model delta sigma weight residual 1.655 1.549 0.106 2.00e-02 2.50e+03 2.81e+01 ... (remaining 12015 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.68: 16153 3.68 - 7.37: 149 7.37 - 11.05: 10 11.05 - 14.74: 4 14.74 - 18.42: 4 Bond angle restraints: 16320 Sorted by residual: angle pdb=" PB ANP A 802 " pdb=" N3B ANP A 802 " pdb=" PG ANP A 802 " ideal model delta sigma weight residual 126.95 108.53 18.42 3.00e+00 1.11e-01 3.77e+01 angle pdb=" PB ANP B 802 " pdb=" N3B ANP B 802 " pdb=" PG ANP B 802 " ideal model delta sigma weight residual 126.95 109.57 17.38 3.00e+00 1.11e-01 3.36e+01 angle pdb=" PB ANP D 802 " pdb=" N3B ANP D 802 " pdb=" PG ANP D 802 " ideal model delta sigma weight residual 126.95 110.79 16.16 3.00e+00 1.11e-01 2.90e+01 angle pdb=" PB ANP C 802 " pdb=" N3B ANP C 802 " pdb=" PG ANP C 802 " ideal model delta sigma weight residual 126.95 111.66 15.29 3.00e+00 1.11e-01 2.60e+01 angle pdb=" O1B ANP C 802 " pdb=" PB ANP C 802 " pdb=" O2B ANP C 802 " ideal model delta sigma weight residual 120.08 108.34 11.74 3.00e+00 1.11e-01 1.53e+01 ... (remaining 16315 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.13: 7090 30.13 - 60.26: 90 60.26 - 90.38: 8 90.38 - 120.51: 0 120.51 - 150.64: 4 Dihedral angle restraints: 7192 sinusoidal: 2892 harmonic: 4300 Sorted by residual: dihedral pdb=" CA TYR A 166 " pdb=" C TYR A 166 " pdb=" N GLU A 167 " pdb=" CA GLU A 167 " ideal model delta harmonic sigma weight residual -180.00 -155.05 -24.95 0 5.00e+00 4.00e-02 2.49e+01 dihedral pdb=" CA TYR C 166 " pdb=" C TYR C 166 " pdb=" N GLU C 167 " pdb=" CA GLU C 167 " ideal model delta harmonic sigma weight residual -180.00 -155.06 -24.94 0 5.00e+00 4.00e-02 2.49e+01 dihedral pdb=" CA TYR B 166 " pdb=" C TYR B 166 " pdb=" N GLU B 167 " pdb=" CA GLU B 167 " ideal model delta harmonic sigma weight residual -180.00 -155.08 -24.92 0 5.00e+00 4.00e-02 2.48e+01 ... (remaining 7189 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 1284 0.060 - 0.120: 470 0.120 - 0.179: 34 0.179 - 0.239: 17 0.239 - 0.299: 3 Chirality restraints: 1808 Sorted by residual: chirality pdb=" C3' ANP A 802 " pdb=" C2' ANP A 802 " pdb=" C4' ANP A 802 " pdb=" O3' ANP A 802 " both_signs ideal model delta sigma weight residual False -2.36 -2.66 0.30 2.00e-01 2.50e+01 2.23e+00 chirality pdb=" C3' ANP B 802 " pdb=" C2' ANP B 802 " pdb=" C4' ANP B 802 " pdb=" O3' ANP B 802 " both_signs ideal model delta sigma weight residual False -2.36 -2.65 0.30 2.00e-01 2.50e+01 2.19e+00 chirality pdb=" C3' ANP D 802 " pdb=" C2' ANP D 802 " pdb=" C4' ANP D 802 " pdb=" O3' ANP D 802 " both_signs ideal model delta sigma weight residual False -2.36 -2.65 0.29 2.00e-01 2.50e+01 2.14e+00 ... (remaining 1805 not shown) Planarity restraints: 2084 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU B 242 " 0.039 5.00e-02 4.00e+02 5.91e-02 5.59e+00 pdb=" N PRO B 243 " -0.102 5.00e-02 4.00e+02 pdb=" CA PRO B 243 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO B 243 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU D 242 " -0.039 5.00e-02 4.00e+02 5.89e-02 5.55e+00 pdb=" N PRO D 243 " 0.102 5.00e-02 4.00e+02 pdb=" CA PRO D 243 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO D 243 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU C 242 " 0.039 5.00e-02 4.00e+02 5.89e-02 5.55e+00 pdb=" N PRO C 243 " -0.102 5.00e-02 4.00e+02 pdb=" CA PRO C 243 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO C 243 " 0.033 5.00e-02 4.00e+02 ... (remaining 2081 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 146 2.64 - 3.20: 9964 3.20 - 3.77: 17846 3.77 - 4.33: 26546 4.33 - 4.90: 43172 Nonbonded interactions: 97674 Sorted by model distance: nonbonded pdb="MG MG B 801 " pdb=" O2G ANP B 802 " model vdw 2.069 2.170 nonbonded pdb="MG MG A 801 " pdb=" O3G ANP A 802 " model vdw 2.078 2.170 nonbonded pdb="MG MG D 801 " pdb=" O2G ANP D 802 " model vdw 2.078 2.170 nonbonded pdb="MG MG C 801 " pdb=" O2G ANP C 802 " model vdw 2.087 2.170 nonbonded pdb="MG MG C 801 " pdb=" O2B ANP C 802 " model vdw 2.093 2.170 ... (remaining 97669 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.390 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: 0.170 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 11.390 Find NCS groups from input model: 0.100 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:1.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 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 : 0.010 0.162 12020 Z= 0.430 Angle : 1.005 18.422 16320 Z= 0.505 Chirality : 0.060 0.299 1808 Planarity : 0.007 0.059 2084 Dihedral : 10.989 150.638 4440 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % 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: -4.16 (0.18), residues: 1468 helix: -4.37 (0.10), residues: 568 sheet: -1.57 (0.35), residues: 196 loop : -1.50 (0.21), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 335 TYR 0.012 0.002 TYR A 218 PHE 0.024 0.003 PHE A 124 TRP 0.034 0.005 TRP A 340 HIS 0.011 0.003 HIS A 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00984 / 0.43 (12020) covalent geometry : angle 1.00508 / 0.50 (16320) hydrogen bonds : bond 0.29843 / 20.33 ( 424) hydrogen bonds : angle 10.62089 / 7.35 ( 1092) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 303 time to evaluate : 0.426 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 24 ASP cc_start: 0.8090 (m-30) cc_final: 0.7877 (m-30) REVERT: B 227 MET cc_start: 0.8515 (mmm) cc_final: 0.8275 (mmm) REVERT: C 44 MET cc_start: 0.8306 (mmt) cc_final: 0.8038 (mmm) REVERT: C 305 MET cc_start: 0.8099 (mmm) cc_final: 0.7838 (mmt) REVERT: D 24 ASP cc_start: 0.7452 (m-30) cc_final: 0.7206 (m-30) outliers start: 0 outliers final: 0 residues processed: 303 average time/residue: 0.1198 time to fit residues: 49.2638 Evaluate side-chains 143 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 143 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.2980 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 0.6980 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 0.5980 chunk 55 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 128 ASN A 161 HIS A 162 ASN B 161 HIS B 162 ASN B 173 HIS C 49 GLN C 161 HIS C 263 GLN D 49 GLN D 161 HIS D 353 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.103605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.089624 restraints weight = 18530.370| |-----------------------------------------------------------------------------| r_work (start): 0.3155 rms_B_bonded: 1.95 r_work: 0.3044 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2901 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8600 moved from start: 0.2426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 12020 Z= 0.133 Angle : 0.579 7.256 16320 Z= 0.301 Chirality : 0.044 0.142 1808 Planarity : 0.005 0.045 2084 Dihedral : 9.365 155.448 1644 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 1.04 % Allowed : 8.44 % Favored : 90.53 % 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: -2.70 (0.20), residues: 1468 helix: -2.73 (0.16), residues: 580 sheet: -1.44 (0.32), residues: 236 loop : -0.74 (0.25), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 37 TYR 0.010 0.001 TYR A 143 PHE 0.009 0.001 PHE A 255 TRP 0.015 0.002 TRP C 340 HIS 0.004 0.001 HIS C 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.13 (12020) covalent geometry : angle 0.57890 / 0.30 (16320) hydrogen bonds : bond 0.03908 / 2.65 ( 424) hydrogen bonds : angle 5.53802 / 3.87 ( 1092) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 170 time to evaluate : 0.350 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 41 GLN cc_start: 0.8103 (tp-100) cc_final: 0.7859 (pm20) REVERT: A 227 MET cc_start: 0.8752 (mmt) cc_final: 0.8434 (mmt) REVERT: A 286 ASP cc_start: 0.7361 (t0) cc_final: 0.7127 (t0) REVERT: B 176 MET cc_start: 0.8481 (mmm) cc_final: 0.8045 (mmt) REVERT: B 227 MET cc_start: 0.8837 (mmm) cc_final: 0.8609 (mmm) REVERT: B 316 GLU cc_start: 0.8153 (OUTLIER) cc_final: 0.7922 (mt-10) REVERT: C 44 MET cc_start: 0.8509 (mmt) cc_final: 0.8219 (mmm) REVERT: C 305 MET cc_start: 0.8787 (mmm) cc_final: 0.8519 (mmt) REVERT: C 324 THR cc_start: 0.8756 (t) cc_final: 0.8526 (p) REVERT: C 372 ARG cc_start: 0.7913 (ptt-90) cc_final: 0.7664 (ptt90) REVERT: D 47 MET cc_start: 0.7613 (ppp) cc_final: 0.7247 (ppp) REVERT: D 81 ASP cc_start: 0.8624 (m-30) cc_final: 0.8308 (m-30) REVERT: D 167 GLU cc_start: 0.7992 (OUTLIER) cc_final: 0.7713 (pt0) outliers start: 13 outliers final: 5 residues processed: 181 average time/residue: 0.0829 time to fit residues: 22.9320 Evaluate side-chains 139 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 132 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 316 GLU Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain D residue 167 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 44 optimal weight: 2.9990 chunk 82 optimal weight: 0.0970 chunk 56 optimal weight: 0.9990 chunk 130 optimal weight: 0.1980 chunk 15 optimal weight: 2.9990 chunk 93 optimal weight: 0.0870 chunk 102 optimal weight: 1.9990 chunk 105 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 60 optimal weight: 5.9990 chunk 18 optimal weight: 1.9990 overall best weight: 0.6760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 115 ASN B 115 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.102974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.089386 restraints weight = 18463.036| |-----------------------------------------------------------------------------| r_work (start): 0.3148 rms_B_bonded: 1.88 r_work: 0.3039 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2897 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 0.2771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 12020 Z= 0.127 Angle : 0.522 6.955 16320 Z= 0.268 Chirality : 0.044 0.133 1808 Planarity : 0.004 0.034 2084 Dihedral : 9.300 159.434 1644 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 1.11 % Allowed : 9.95 % Favored : 88.93 % 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: -1.81 (0.21), residues: 1468 helix: -1.77 (0.19), residues: 580 sheet: -1.13 (0.32), residues: 236 loop : -0.42 (0.25), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 28 TYR 0.012 0.001 TYR B 279 PHE 0.007 0.001 PHE D 262 TRP 0.011 0.002 TRP B 79 HIS 0.006 0.001 HIS C 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 (12020) covalent geometry : angle 0.52239 / 0.27 (16320) hydrogen bonds : bond 0.03093 / 2.09 ( 424) hydrogen bonds : angle 4.96301 / 3.47 ( 1092) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 141 time to evaluate : 0.288 Fit side-chains revert: symmetry clash REVERT: A 41 GLN cc_start: 0.8115 (tp-100) cc_final: 0.7879 (pm20) REVERT: A 227 MET cc_start: 0.8708 (mmt) cc_final: 0.8414 (mmt) REVERT: B 305 MET cc_start: 0.8505 (mmt) cc_final: 0.8092 (mmt) REVERT: C 6 THR cc_start: 0.7697 (t) cc_final: 0.7479 (m) REVERT: C 47 MET cc_start: 0.7058 (ppp) cc_final: 0.6795 (ppp) REVERT: C 123 MET cc_start: 0.9306 (tpp) cc_final: 0.9078 (mmp) REVERT: D 47 MET cc_start: 0.7675 (ppp) cc_final: 0.7106 (ppp) REVERT: D 81 ASP cc_start: 0.8602 (m-30) cc_final: 0.8264 (m-30) REVERT: D 167 GLU cc_start: 0.7897 (OUTLIER) cc_final: 0.7665 (pt0) REVERT: D 355 MET cc_start: 0.8795 (mmm) cc_final: 0.8548 (mmm) outliers start: 14 outliers final: 7 residues processed: 153 average time/residue: 0.0787 time to fit residues: 18.8528 Evaluate side-chains 138 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 130 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 115 ASN Chi-restraints excluded: chain B residue 316 GLU Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 167 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 108 optimal weight: 4.9990 chunk 97 optimal weight: 5.9990 chunk 37 optimal weight: 5.9990 chunk 9 optimal weight: 5.9990 chunk 85 optimal weight: 4.9990 chunk 43 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 142 optimal weight: 0.7980 chunk 48 optimal weight: 4.9990 chunk 88 optimal weight: 0.9980 chunk 92 optimal weight: 1.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 115 ASN A 173 HIS B 115 ASN C 41 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.098599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.084690 restraints weight = 18792.965| |-----------------------------------------------------------------------------| r_work (start): 0.3073 rms_B_bonded: 1.93 r_work: 0.2963 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2819 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8683 moved from start: 0.3033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.047 12020 Z= 0.291 Angle : 0.647 8.315 16320 Z= 0.329 Chirality : 0.049 0.144 1808 Planarity : 0.005 0.040 2084 Dihedral : 9.490 161.527 1644 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 2.15 % Allowed : 9.08 % Favored : 88.77 % 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: -1.49 (0.22), residues: 1468 helix: -1.46 (0.20), residues: 584 sheet: -0.83 (0.34), residues: 236 loop : -0.34 (0.25), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 116 TYR 0.015 0.002 TYR A 143 PHE 0.011 0.002 PHE D 262 TRP 0.018 0.003 TRP C 79 HIS 0.009 0.002 HIS A 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00682 / 0.29 (12020) covalent geometry : angle 0.64726 / 0.33 (16320) hydrogen bonds : bond 0.03509 / 2.38 ( 424) hydrogen bonds : angle 4.94773 / 3.47 ( 1092) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 127 time to evaluate : 0.501 Fit side-chains REVERT: A 41 GLN cc_start: 0.8173 (tp-100) cc_final: 0.7771 (pm20) REVERT: A 246 GLN cc_start: 0.8042 (mt0) cc_final: 0.7695 (mt0) REVERT: B 180 LEU cc_start: 0.9036 (OUTLIER) cc_final: 0.8829 (tp) REVERT: B 305 MET cc_start: 0.8650 (mmt) cc_final: 0.8379 (mmt) REVERT: C 47 MET cc_start: 0.7212 (ppp) cc_final: 0.6720 (ppp) REVERT: C 123 MET cc_start: 0.9315 (tpp) cc_final: 0.9104 (mmp) REVERT: C 241 GLU cc_start: 0.7776 (OUTLIER) cc_final: 0.7517 (tm-30) REVERT: D 47 MET cc_start: 0.7733 (ppp) cc_final: 0.7367 (ppp) REVERT: D 81 ASP cc_start: 0.8705 (m-30) cc_final: 0.8365 (m-30) REVERT: D 355 MET cc_start: 0.9010 (mmm) cc_final: 0.8757 (mmm) outliers start: 27 outliers final: 13 residues processed: 149 average time/residue: 0.0828 time to fit residues: 18.9788 Evaluate side-chains 135 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 120 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 ASN Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 83 GLU Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 288 ASP Chi-restraints excluded: chain B residue 292 ASP Chi-restraints excluded: chain B residue 316 GLU Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 363 ASP Chi-restraints excluded: chain C residue 41 GLN Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 241 GLU Chi-restraints excluded: chain D residue 51 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 78 optimal weight: 1.9990 chunk 135 optimal weight: 0.6980 chunk 53 optimal weight: 0.7980 chunk 88 optimal weight: 3.9990 chunk 137 optimal weight: 1.9990 chunk 103 optimal weight: 0.8980 chunk 63 optimal weight: 3.9990 chunk 56 optimal weight: 0.9980 chunk 116 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 136 optimal weight: 0.5980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 115 ASN B 115 ASN C 41 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.100499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.086818 restraints weight = 18493.820| |-----------------------------------------------------------------------------| r_work (start): 0.3111 rms_B_bonded: 1.88 r_work: 0.3002 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2859 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8645 moved from start: 0.3173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 12020 Z= 0.138 Angle : 0.526 7.364 16320 Z= 0.268 Chirality : 0.044 0.134 1808 Planarity : 0.004 0.032 2084 Dihedral : 9.233 158.722 1644 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 1.75 % Allowed : 10.91 % Favored : 87.34 % 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: -1.05 (0.22), residues: 1468 helix: -1.02 (0.21), residues: 584 sheet: -0.70 (0.35), residues: 236 loop : -0.12 (0.25), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 147 TYR 0.008 0.001 TYR D 143 PHE 0.007 0.001 PHE C 223 TRP 0.013 0.002 TRP B 79 HIS 0.004 0.001 HIS A 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.14 (12020) covalent geometry : angle 0.52563 / 0.27 (16320) hydrogen bonds : bond 0.02729 / 1.84 ( 424) hydrogen bonds : angle 4.73216 / 3.31 ( 1092) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 130 time to evaluate : 0.407 Fit side-chains revert: symmetry clash REVERT: A 41 GLN cc_start: 0.8273 (tp-100) cc_final: 0.7912 (pm20) REVERT: C 6 THR cc_start: 0.7713 (t) cc_final: 0.7462 (m) REVERT: C 47 MET cc_start: 0.7105 (ppp) cc_final: 0.6538 (ppp) REVERT: C 241 GLU cc_start: 0.7734 (OUTLIER) cc_final: 0.7470 (tm-30) REVERT: D 47 MET cc_start: 0.7693 (ppp) cc_final: 0.7369 (ppp) REVERT: D 81 ASP cc_start: 0.8671 (m-30) cc_final: 0.8331 (m-30) REVERT: D 176 MET cc_start: 0.8942 (mmm) cc_final: 0.8741 (mtp) outliers start: 22 outliers final: 13 residues processed: 147 average time/residue: 0.0750 time to fit residues: 17.0841 Evaluate side-chains 135 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 121 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 288 ASP Chi-restraints excluded: chain B residue 316 GLU Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain C residue 41 GLN Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 241 GLU Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 84 LYS Chi-restraints excluded: chain D residue 233 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 26 optimal weight: 0.9980 chunk 78 optimal weight: 5.9990 chunk 2 optimal weight: 1.9990 chunk 35 optimal weight: 0.1980 chunk 85 optimal weight: 0.6980 chunk 56 optimal weight: 0.0980 chunk 84 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 126 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 133 optimal weight: 0.7980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 115 ASN B 115 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.101649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.087897 restraints weight = 18551.298| |-----------------------------------------------------------------------------| r_work (start): 0.3129 rms_B_bonded: 1.90 r_work: 0.3018 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2876 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8630 moved from start: 0.3293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 12020 Z= 0.108 Angle : 0.496 6.827 16320 Z= 0.252 Chirality : 0.044 0.129 1808 Planarity : 0.003 0.031 2084 Dihedral : 9.052 157.882 1644 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 1.51 % Allowed : 11.07 % Favored : 87.42 % 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: -0.66 (0.22), residues: 1468 helix: -0.56 (0.22), residues: 564 sheet: -0.63 (0.35), residues: 236 loop : -0.02 (0.25), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 147 TYR 0.007 0.001 TYR D 143 PHE 0.005 0.001 PHE C 223 TRP 0.010 0.002 TRP B 79 HIS 0.004 0.001 HIS C 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.11 (12020) covalent geometry : angle 0.49610 / 0.25 (16320) hydrogen bonds : bond 0.02500 / 1.68 ( 424) hydrogen bonds : angle 4.56967 / 3.19 ( 1092) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 129 time to evaluate : 0.388 Fit side-chains revert: symmetry clash REVERT: A 41 GLN cc_start: 0.8270 (tp-100) cc_final: 0.7932 (pm20) REVERT: A 47 MET cc_start: 0.7348 (ppp) cc_final: 0.6976 (ppp) REVERT: C 6 THR cc_start: 0.7677 (t) cc_final: 0.7435 (m) REVERT: C 47 MET cc_start: 0.7011 (ppp) cc_final: 0.6377 (ppp) REVERT: C 241 GLU cc_start: 0.7723 (OUTLIER) cc_final: 0.7482 (tm-30) REVERT: D 47 MET cc_start: 0.7655 (ppp) cc_final: 0.7341 (ppp) REVERT: D 81 ASP cc_start: 0.8670 (m-30) cc_final: 0.8329 (m-30) REVERT: D 107 GLU cc_start: 0.7964 (pt0) cc_final: 0.7645 (pt0) REVERT: D 355 MET cc_start: 0.8918 (mmm) cc_final: 0.8716 (mmm) outliers start: 19 outliers final: 13 residues processed: 144 average time/residue: 0.0798 time to fit residues: 17.9769 Evaluate side-chains 144 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 130 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain B residue 83 GLU Chi-restraints excluded: chain B residue 115 ASN Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 288 ASP Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 241 GLU Chi-restraints excluded: chain C residue 288 ASP Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 233 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 83 optimal weight: 2.9990 chunk 84 optimal weight: 0.6980 chunk 64 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 98 optimal weight: 0.2980 chunk 112 optimal weight: 0.9980 chunk 123 optimal weight: 1.9990 chunk 97 optimal weight: 0.9980 chunk 0 optimal weight: 5.9990 chunk 86 optimal weight: 0.3980 chunk 120 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 12 ASN A 59 GLN A 115 ASN B 115 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.101697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.087761 restraints weight = 18444.036| |-----------------------------------------------------------------------------| r_work (start): 0.3128 rms_B_bonded: 1.92 r_work: 0.3018 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2874 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8632 moved from start: 0.3387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 12020 Z= 0.119 Angle : 0.494 6.702 16320 Z= 0.250 Chirality : 0.044 0.128 1808 Planarity : 0.003 0.031 2084 Dihedral : 8.960 157.835 1644 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 1.51 % Allowed : 10.83 % Favored : 87.66 % 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: -0.43 (0.22), residues: 1468 helix: -0.31 (0.22), residues: 564 sheet: -0.52 (0.35), residues: 236 loop : 0.05 (0.25), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 116 TYR 0.007 0.001 TYR A 143 PHE 0.006 0.001 PHE B 127 TRP 0.010 0.002 TRP D 79 HIS 0.004 0.001 HIS C 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.12 (12020) covalent geometry : angle 0.49368 / 0.25 (16320) hydrogen bonds : bond 0.02449 / 1.66 ( 424) hydrogen bonds : angle 4.46767 / 3.13 ( 1092) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 134 time to evaluate : 0.380 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 47 MET cc_start: 0.7327 (ppp) cc_final: 0.7011 (ppp) REVERT: B 107 GLU cc_start: 0.8422 (pt0) cc_final: 0.8148 (pt0) REVERT: C 6 THR cc_start: 0.7694 (t) cc_final: 0.7433 (m) REVERT: C 47 MET cc_start: 0.6981 (ppp) cc_final: 0.6270 (ppp) REVERT: C 313 MET cc_start: 0.8857 (mmm) cc_final: 0.8590 (mmm) REVERT: D 47 MET cc_start: 0.7607 (ppp) cc_final: 0.7224 (ppp) REVERT: D 81 ASP cc_start: 0.8704 (m-30) cc_final: 0.8358 (m-30) REVERT: D 107 GLU cc_start: 0.8003 (pt0) cc_final: 0.7633 (pt0) REVERT: D 283 MET cc_start: 0.9016 (mmm) cc_final: 0.8804 (mmm) REVERT: D 355 MET cc_start: 0.8943 (mmm) cc_final: 0.8715 (mmm) outliers start: 19 outliers final: 13 residues processed: 148 average time/residue: 0.0809 time to fit residues: 18.5771 Evaluate side-chains 138 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 125 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain B residue 115 ASN Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 288 ASP Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 363 ASP Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 288 ASP Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 84 LYS Chi-restraints excluded: chain D residue 233 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 76 optimal weight: 4.9990 chunk 35 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 chunk 26 optimal weight: 0.0970 chunk 120 optimal weight: 0.0970 chunk 50 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 85 optimal weight: 3.9990 chunk 4 optimal weight: 0.0050 chunk 110 optimal weight: 2.9990 chunk 90 optimal weight: 0.9990 overall best weight: 0.8394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 115 ASN B 115 ASN B 162 ASN C 49 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.101382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.087558 restraints weight = 18396.488| |-----------------------------------------------------------------------------| r_work (start): 0.3121 rms_B_bonded: 1.91 r_work: 0.3012 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2869 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8635 moved from start: 0.3464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12020 Z= 0.138 Angle : 0.506 6.202 16320 Z= 0.258 Chirality : 0.044 0.128 1808 Planarity : 0.004 0.031 2084 Dihedral : 8.939 158.951 1644 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 1.43 % Allowed : 11.15 % Favored : 87.42 % 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: -0.32 (0.22), residues: 1468 helix: -0.17 (0.23), residues: 564 sheet: -0.42 (0.35), residues: 236 loop : 0.06 (0.25), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 147 TYR 0.008 0.001 TYR A 143 PHE 0.006 0.001 PHE B 127 TRP 0.010 0.002 TRP B 79 HIS 0.004 0.001 HIS D 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.14 (12020) covalent geometry : angle 0.50588 / 0.26 (16320) hydrogen bonds : bond 0.02499 / 1.69 ( 424) hydrogen bonds : angle 4.43166 / 3.10 ( 1092) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 127 time to evaluate : 0.351 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 47 MET cc_start: 0.7324 (ppp) cc_final: 0.7016 (ppp) REVERT: B 107 GLU cc_start: 0.8435 (pt0) cc_final: 0.8172 (pt0) REVERT: B 176 MET cc_start: 0.8559 (mmm) cc_final: 0.8245 (mmt) REVERT: C 6 THR cc_start: 0.7689 (t) cc_final: 0.7425 (m) REVERT: C 47 MET cc_start: 0.6977 (ppp) cc_final: 0.6271 (ppp) REVERT: C 241 GLU cc_start: 0.7699 (OUTLIER) cc_final: 0.7462 (tm-30) REVERT: C 313 MET cc_start: 0.8854 (mmm) cc_final: 0.8596 (mmm) REVERT: D 47 MET cc_start: 0.7582 (ppp) cc_final: 0.7136 (ppp) REVERT: D 81 ASP cc_start: 0.8682 (m-30) cc_final: 0.8336 (m-30) REVERT: D 107 GLU cc_start: 0.8013 (pt0) cc_final: 0.7689 (pt0) REVERT: D 355 MET cc_start: 0.8953 (mmm) cc_final: 0.8734 (mmm) outliers start: 18 outliers final: 13 residues processed: 140 average time/residue: 0.0804 time to fit residues: 17.8706 Evaluate side-chains 136 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 122 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain B residue 115 ASN Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 288 ASP Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 363 ASP Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 241 GLU Chi-restraints excluded: chain C residue 288 ASP Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 84 LYS Chi-restraints excluded: chain D residue 233 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 124 optimal weight: 0.9990 chunk 69 optimal weight: 0.7980 chunk 36 optimal weight: 0.3980 chunk 33 optimal weight: 0.8980 chunk 15 optimal weight: 4.9990 chunk 29 optimal weight: 1.9990 chunk 47 optimal weight: 0.5980 chunk 57 optimal weight: 0.6980 chunk 70 optimal weight: 0.7980 chunk 56 optimal weight: 0.5980 chunk 131 optimal weight: 3.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 59 GLN A 115 ASN B 87 HIS B 115 ASN B 162 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.102033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.088334 restraints weight = 18183.079| |-----------------------------------------------------------------------------| r_work (start): 0.3135 rms_B_bonded: 1.89 r_work: 0.3026 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2883 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8623 moved from start: 0.3520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12020 Z= 0.113 Angle : 0.490 7.942 16320 Z= 0.248 Chirality : 0.044 0.127 1808 Planarity : 0.003 0.030 2084 Dihedral : 8.866 158.038 1644 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 1.35 % Allowed : 11.70 % Favored : 86.94 % 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: -0.17 (0.23), residues: 1468 helix: -0.03 (0.23), residues: 564 sheet: -0.35 (0.35), residues: 236 loop : 0.12 (0.25), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 147 TYR 0.007 0.001 TYR D 143 PHE 0.005 0.001 PHE B 127 TRP 0.010 0.002 TRP A 340 HIS 0.006 0.001 HIS B 87 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.11 (12020) covalent geometry : angle 0.49033 / 0.25 (16320) hydrogen bonds : bond 0.02386 / 1.62 ( 424) hydrogen bonds : angle 4.38083 / 3.06 ( 1092) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 126 time to evaluate : 0.444 Fit side-chains revert: symmetry clash REVERT: A 47 MET cc_start: 0.7331 (ppp) cc_final: 0.7025 (ppp) REVERT: B 107 GLU cc_start: 0.8427 (pt0) cc_final: 0.8165 (pt0) REVERT: C 6 THR cc_start: 0.7681 (t) cc_final: 0.7424 (m) REVERT: C 47 MET cc_start: 0.6980 (ppp) cc_final: 0.6204 (ppp) REVERT: C 207 GLU cc_start: 0.8487 (mm-30) cc_final: 0.8145 (mm-30) REVERT: C 241 GLU cc_start: 0.7694 (OUTLIER) cc_final: 0.7444 (tm-30) REVERT: C 313 MET cc_start: 0.8843 (mmm) cc_final: 0.8595 (mmm) REVERT: D 47 MET cc_start: 0.7569 (ppp) cc_final: 0.7112 (ppp) REVERT: D 81 ASP cc_start: 0.8668 (m-30) cc_final: 0.8318 (m-30) REVERT: D 107 GLU cc_start: 0.8007 (pt0) cc_final: 0.7688 (pt0) REVERT: D 355 MET cc_start: 0.8972 (mmm) cc_final: 0.8750 (mmm) outliers start: 17 outliers final: 12 residues processed: 138 average time/residue: 0.0737 time to fit residues: 16.0848 Evaluate side-chains 137 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 124 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain B residue 115 ASN Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 288 ASP Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 363 ASP Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 241 GLU Chi-restraints excluded: chain C residue 257 CYS Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 84 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/iotbx/cli_parser.py", line 987, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( ^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( ^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( ^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( ^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1602, in energies_sites pair_proxies = self.pair_proxies( ^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1505, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1386, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 55.5426 > 50: distance: 10 - 104: 21.935 distance: 24 - 92: 5.334 distance: 27 - 89: 17.408 distance: 43 - 46: 5.581 distance: 46 - 47: 3.956 distance: 47 - 48: 12.367 distance: 48 - 49: 6.720 distance: 48 - 50: 7.628 distance: 50 - 51: 4.296 distance: 51 - 52: 7.729 distance: 51 - 54: 5.247 distance: 52 - 53: 13.830 distance: 52 - 58: 9.687 distance: 54 - 55: 5.683 distance: 55 - 56: 4.929 distance: 58 - 59: 4.031 distance: 59 - 60: 14.777 distance: 59 - 62: 7.284 distance: 60 - 61: 6.465 distance: 60 - 66: 9.377 distance: 62 - 63: 12.631 distance: 63 - 64: 7.759 distance: 63 - 65: 3.725 distance: 66 - 67: 11.276 distance: 67 - 68: 12.640 distance: 67 - 70: 30.584 distance: 68 - 69: 28.066 distance: 68 - 71: 12.192 distance: 71 - 72: 7.430 distance: 71 - 77: 10.893 distance: 72 - 73: 14.637 distance: 72 - 75: 32.525 distance: 73 - 74: 24.796 distance: 73 - 78: 8.413 distance: 75 - 76: 16.544 distance: 76 - 77: 16.524 distance: 78 - 79: 6.192 distance: 79 - 80: 10.718 distance: 79 - 82: 15.524 distance: 80 - 81: 21.338 distance: 80 - 89: 3.671 distance: 82 - 83: 10.806 distance: 83 - 84: 19.870 distance: 84 - 85: 8.565 distance: 85 - 86: 6.006 distance: 86 - 87: 15.104 distance: 89 - 90: 13.302 distance: 90 - 91: 11.699 distance: 90 - 93: 8.286 distance: 91 - 92: 18.605 distance: 91 - 94: 27.277 distance: 94 - 95: 11.864 distance: 95 - 96: 30.327 distance: 95 - 98: 13.623 distance: 96 - 97: 19.512 distance: 96 - 101: 18.936 distance: 98 - 99: 22.627 distance: 98 - 100: 5.859 distance: 101 - 102: 12.739 distance: 102 - 103: 4.378 distance: 102 - 105: 15.559 distance: 103 - 104: 23.107 distance: 103 - 112: 10.340 distance: 105 - 106: 24.263 distance: 106 - 107: 8.471 distance: 106 - 108: 5.970 distance: 107 - 109: 11.200 distance: 108 - 110: 12.315 distance: 109 - 111: 12.530 distance: 110 - 111: 9.122 distance: 112 - 113: 8.855 distance: 112 - 118: 15.967 distance: 113 - 114: 7.711 distance: 113 - 116: 20.059 distance: 114 - 115: 6.816 distance: 114 - 119: 7.817 distance: 116 - 117: 6.042 distance: 117 - 118: 16.198