Starting phenix.real_space_refine on Sat Jun 14 12:35:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xc6_33113/06_2025/7xc6_33113.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xc6_33113/06_2025/7xc6_33113.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.79 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7xc6_33113/06_2025/7xc6_33113.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xc6_33113/06_2025/7xc6_33113.map" model { file = "/net/cci-nas-00/data/ceres_data/7xc6_33113/06_2025/7xc6_33113.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xc6_33113/06_2025/7xc6_33113.cif" } resolution = 2.79 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 68 5.16 5 C 10316 2.51 5 N 2691 2.21 5 O 3101 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 75 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 16176 Number of models: 1 Model: "" Number of chains: 2 Chain: "E" Number of atoms: 956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 956 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 7, 'TRANS': 110} Chain breaks: 2 Chain: "A" Number of atoms: 3805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 477, 3805 Classifications: {'peptide': 477} Link IDs: {'PTRANS': 20, 'TRANS': 456} Restraints were copied for chains: B, C, D Time building chain proxies: 8.60, per 1000 atoms: 0.53 Number of scatterers: 16176 At special positions: 0 Unit cell: (120.785, 128.282, 157.437, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 68 16.00 O 3101 8.00 N 2691 7.00 C 10316 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: 4.11 Conformation dependent library (CDL) restraints added in 2.3 seconds 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3860 Finding SS restraints... Secondary structure from input PDB file: 79 helices and 19 sheets defined 45.7% alpha, 11.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.81 Creating SS restraints... Processing helix chain 'E' and resid 33 through 54 Processing helix chain 'E' and resid 54 through 63 Processing helix chain 'E' and resid 82 through 87 removed outlier: 3.811A pdb=" N TYR E 86 " --> pdb=" O SER E 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 56 Processing helix chain 'A' and resid 64 through 81 removed outlier: 3.779A pdb=" N SER A 81 " --> pdb=" O GLN A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 98 Processing helix chain 'A' and resid 101 through 118 Processing helix chain 'A' and resid 118 through 131 Processing helix chain 'A' and resid 163 through 177 removed outlier: 3.939A pdb=" N GLY A 167 " --> pdb=" O VAL A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 204 Processing helix chain 'A' and resid 209 through 211 No H-bonds generated for 'chain 'A' and resid 209 through 211' Processing helix chain 'A' and resid 224 through 233 removed outlier: 3.850A pdb=" N CYS A 233 " --> pdb=" O GLN A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 252 Processing helix chain 'A' and resid 276 through 290 removed outlier: 3.588A pdb=" N SER A 280 " --> pdb=" O ASP A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 294 Processing helix chain 'A' and resid 308 through 327 removed outlier: 3.683A pdb=" N ASP A 325 " --> pdb=" O ASN A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 333 through 349 Processing helix chain 'A' and resid 388 through 396 removed outlier: 4.070A pdb=" N THR A 393 " --> pdb=" O SER A 390 " (cutoff:3.500A) Proline residue: A 394 - end of helix Processing helix chain 'A' and resid 408 through 414 Processing helix chain 'A' and resid 415 through 422 Processing helix chain 'A' and resid 446 through 450 Processing helix chain 'A' and resid 473 through 481 Processing helix chain 'B' and resid 47 through 56 Processing helix chain 'B' and resid 64 through 81 removed outlier: 3.778A pdb=" N SER B 81 " --> pdb=" O GLN B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 84 through 98 Processing helix chain 'B' and resid 101 through 118 Processing helix chain 'B' and resid 118 through 131 Processing helix chain 'B' and resid 163 through 177 removed outlier: 3.940A pdb=" N GLY B 167 " --> pdb=" O VAL B 163 " (cutoff:3.500A) Processing helix chain 'B' and resid 191 through 204 Processing helix chain 'B' and resid 209 through 211 No H-bonds generated for 'chain 'B' and resid 209 through 211' Processing helix chain 'B' and resid 224 through 233 removed outlier: 3.850A pdb=" N CYS B 233 " --> pdb=" O GLN B 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 252 Processing helix chain 'B' and resid 276 through 290 removed outlier: 3.588A pdb=" N SER B 280 " --> pdb=" O ASP B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 294 Processing helix chain 'B' and resid 308 through 327 removed outlier: 3.683A pdb=" N ASP B 325 " --> pdb=" O ASN B 321 " (cutoff:3.500A) Processing helix chain 'B' and resid 333 through 349 Processing helix chain 'B' and resid 388 through 396 removed outlier: 4.069A pdb=" N THR B 393 " --> pdb=" O SER B 390 " (cutoff:3.500A) Proline residue: B 394 - end of helix Processing helix chain 'B' and resid 408 through 414 Processing helix chain 'B' and resid 415 through 422 Processing helix chain 'B' and resid 446 through 450 Processing helix chain 'B' and resid 473 through 481 Processing helix chain 'C' and resid 47 through 56 Processing helix chain 'C' and resid 64 through 81 removed outlier: 3.778A pdb=" N SER C 81 " --> pdb=" O GLN C 77 " (cutoff:3.500A) Processing helix chain 'C' and resid 84 through 98 Processing helix chain 'C' and resid 101 through 118 Processing helix chain 'C' and resid 118 through 131 Processing helix chain 'C' and resid 163 through 177 removed outlier: 3.939A pdb=" N GLY C 167 " --> pdb=" O VAL C 163 " (cutoff:3.500A) Processing helix chain 'C' and resid 191 through 204 Processing helix chain 'C' and resid 209 through 211 No H-bonds generated for 'chain 'C' and resid 209 through 211' Processing helix chain 'C' and resid 224 through 233 removed outlier: 3.850A pdb=" N CYS C 233 " --> pdb=" O GLN C 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 242 through 252 Processing helix chain 'C' and resid 276 through 290 removed outlier: 3.588A pdb=" N SER C 280 " --> pdb=" O ASP C 276 " (cutoff:3.500A) Processing helix chain 'C' and resid 291 through 294 Processing helix chain 'C' and resid 308 through 327 removed outlier: 3.683A pdb=" N ASP C 325 " --> pdb=" O ASN C 321 " (cutoff:3.500A) Processing helix chain 'C' and resid 333 through 349 Processing helix chain 'C' and resid 388 through 396 removed outlier: 4.069A pdb=" N THR C 393 " --> pdb=" O SER C 390 " (cutoff:3.500A) Proline residue: C 394 - end of helix Processing helix chain 'C' and resid 408 through 414 Processing helix chain 'C' and resid 415 through 422 Processing helix chain 'C' and resid 446 through 450 Processing helix chain 'C' and resid 473 through 481 Processing helix chain 'D' and resid 47 through 56 Processing helix chain 'D' and resid 64 through 81 removed outlier: 3.778A pdb=" N SER D 81 " --> pdb=" O GLN D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 84 through 98 Processing helix chain 'D' and resid 101 through 118 Processing helix chain 'D' and resid 118 through 131 Processing helix chain 'D' and resid 163 through 177 removed outlier: 3.940A pdb=" N GLY D 167 " --> pdb=" O VAL D 163 " (cutoff:3.500A) Processing helix chain 'D' and resid 191 through 204 Processing helix chain 'D' and resid 209 through 211 No H-bonds generated for 'chain 'D' and resid 209 through 211' Processing helix chain 'D' and resid 224 through 233 removed outlier: 3.851A pdb=" N CYS D 233 " --> pdb=" O GLN D 229 " (cutoff:3.500A) Processing helix chain 'D' and resid 242 through 252 Processing helix chain 'D' and resid 276 through 290 removed outlier: 3.588A pdb=" N SER D 280 " --> pdb=" O ASP D 276 " (cutoff:3.500A) Processing helix chain 'D' and resid 291 through 294 Processing helix chain 'D' and resid 308 through 327 removed outlier: 3.683A pdb=" N ASP D 325 " --> pdb=" O ASN D 321 " (cutoff:3.500A) Processing helix chain 'D' and resid 333 through 349 Processing helix chain 'D' and resid 388 through 396 removed outlier: 4.070A pdb=" N THR D 393 " --> pdb=" O SER D 390 " (cutoff:3.500A) Proline residue: D 394 - end of helix Processing helix chain 'D' and resid 408 through 414 Processing helix chain 'D' and resid 415 through 422 Processing helix chain 'D' and resid 446 through 450 Processing helix chain 'D' and resid 473 through 481 Processing sheet with id=AA1, first strand: chain 'E' and resid 79 through 80 removed outlier: 6.944A pdb=" N PHE E 79 " --> pdb=" O VAL E 329 " (cutoff:3.500A) removed outlier: 8.769A pdb=" N ASP E 331 " --> pdb=" O PHE E 79 " (cutoff:3.500A) removed outlier: 5.496A pdb=" N ILE E 314 " --> pdb=" O THR E 330 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 79 through 80 removed outlier: 6.944A pdb=" N PHE E 79 " --> pdb=" O VAL E 329 " (cutoff:3.500A) removed outlier: 8.769A pdb=" N ASP E 331 " --> pdb=" O PHE E 79 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ARG E 354 " --> pdb=" O ILE E 333 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 336 through 337 Processing sheet with id=AA4, first strand: chain 'A' and resid 13 through 14 removed outlier: 6.354A pdb=" N LYS A 13 " --> pdb=" O SER A 42 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 145 through 151 Processing sheet with id=AA6, first strand: chain 'A' and resid 213 through 216 removed outlier: 6.617A pdb=" N CYS A 181 " --> pdb=" O SER A 214 " (cutoff:3.500A) removed outlier: 7.780A pdb=" N MET A 216 " --> pdb=" O CYS A 181 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N ILE A 183 " --> pdb=" O MET A 216 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N SER A 155 " --> pdb=" O ILE A 182 " (cutoff:3.500A) removed outlier: 7.537A pdb=" N LYS A 184 " --> pdb=" O SER A 155 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N HIS A 157 " --> pdb=" O LYS A 184 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N VAL A 156 " --> pdb=" O VAL A 238 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N VAL A 237 " --> pdb=" O LEU A 260 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 356 removed outlier: 6.422A pdb=" N LEU A 363 " --> pdb=" O ALA A 381 " (cutoff:3.500A) removed outlier: 7.455A pdb=" N ILE A 383 " --> pdb=" O LEU A 363 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N VAL A 365 " --> pdb=" O ILE A 383 " (cutoff:3.500A) removed outlier: 8.151A pdb=" N HIS A 385 " --> pdb=" O VAL A 365 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N GLN A 300 " --> pdb=" O SER A 380 " (cutoff:3.500A) removed outlier: 8.041A pdb=" N SER A 267 " --> pdb=" O GLN A 300 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N ILE A 302 " --> pdb=" O SER A 267 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N ALA A 269 " --> pdb=" O ILE A 302 " (cutoff:3.500A) removed outlier: 5.460A pdb=" N TYR A 304 " --> pdb=" O ALA A 269 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N VAL A 271 " --> pdb=" O TYR A 304 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 426 through 427 removed outlier: 6.322A pdb=" N ILE A 427 " --> pdb=" O GLU B 458 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 13 through 14 removed outlier: 6.354A pdb=" N LYS B 13 " --> pdb=" O SER B 42 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 213 through 216 removed outlier: 6.617A pdb=" N CYS B 181 " --> pdb=" O SER B 214 " (cutoff:3.500A) removed outlier: 7.779A pdb=" N MET B 216 " --> pdb=" O CYS B 181 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N ILE B 183 " --> pdb=" O MET B 216 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N SER B 155 " --> pdb=" O ILE B 182 " (cutoff:3.500A) removed outlier: 7.538A pdb=" N LYS B 184 " --> pdb=" O SER B 155 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N HIS B 157 " --> pdb=" O LYS B 184 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N VAL B 156 " --> pdb=" O VAL B 238 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N VAL B 237 " --> pdb=" O LEU B 260 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'B' and resid 354 through 356 removed outlier: 6.421A pdb=" N LEU B 363 " --> pdb=" O ALA B 381 " (cutoff:3.500A) removed outlier: 7.455A pdb=" N ILE B 383 " --> pdb=" O LEU B 363 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N VAL B 365 " --> pdb=" O ILE B 383 " (cutoff:3.500A) removed outlier: 8.151A pdb=" N HIS B 385 " --> pdb=" O VAL B 365 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N GLN B 300 " --> pdb=" O SER B 380 " (cutoff:3.500A) removed outlier: 8.041A pdb=" N SER B 267 " --> pdb=" O GLN B 300 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N ILE B 302 " --> pdb=" O SER B 267 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N ALA B 269 " --> pdb=" O ILE B 302 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N TYR B 304 " --> pdb=" O ALA B 269 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N VAL B 271 " --> pdb=" O TYR B 304 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 13 through 14 removed outlier: 6.354A pdb=" N LYS C 13 " --> pdb=" O SER C 42 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 145 through 151 Processing sheet with id=AB5, first strand: chain 'C' and resid 213 through 216 removed outlier: 6.617A pdb=" N CYS C 181 " --> pdb=" O SER C 214 " (cutoff:3.500A) removed outlier: 7.780A pdb=" N MET C 216 " --> pdb=" O CYS C 181 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N ILE C 183 " --> pdb=" O MET C 216 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N SER C 155 " --> pdb=" O ILE C 182 " (cutoff:3.500A) removed outlier: 7.538A pdb=" N LYS C 184 " --> pdb=" O SER C 155 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N HIS C 157 " --> pdb=" O LYS C 184 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N VAL C 156 " --> pdb=" O VAL C 238 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N VAL C 237 " --> pdb=" O LEU C 260 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'C' and resid 354 through 356 removed outlier: 6.422A pdb=" N LEU C 363 " --> pdb=" O ALA C 381 " (cutoff:3.500A) removed outlier: 7.455A pdb=" N ILE C 383 " --> pdb=" O LEU C 363 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N VAL C 365 " --> pdb=" O ILE C 383 " (cutoff:3.500A) removed outlier: 8.151A pdb=" N HIS C 385 " --> pdb=" O VAL C 365 " (cutoff:3.500A) removed outlier: 5.606A pdb=" N GLN C 300 " --> pdb=" O SER C 380 " (cutoff:3.500A) removed outlier: 8.041A pdb=" N SER C 267 " --> pdb=" O GLN C 300 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N ILE C 302 " --> pdb=" O SER C 267 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N ALA C 269 " --> pdb=" O ILE C 302 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N TYR C 304 " --> pdb=" O ALA C 269 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N VAL C 271 " --> pdb=" O TYR C 304 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 426 through 427 removed outlier: 6.423A pdb=" N ILE C 427 " --> pdb=" O GLU D 458 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 13 through 14 removed outlier: 6.354A pdb=" N LYS D 13 " --> pdb=" O SER D 42 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 213 through 216 removed outlier: 6.618A pdb=" N CYS D 181 " --> pdb=" O SER D 214 " (cutoff:3.500A) removed outlier: 7.779A pdb=" N MET D 216 " --> pdb=" O CYS D 181 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N ILE D 183 " --> pdb=" O MET D 216 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N SER D 155 " --> pdb=" O ILE D 182 " (cutoff:3.500A) removed outlier: 7.538A pdb=" N LYS D 184 " --> pdb=" O SER D 155 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N HIS D 157 " --> pdb=" O LYS D 184 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N VAL D 156 " --> pdb=" O VAL D 238 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N VAL D 237 " --> pdb=" O LEU D 260 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'D' and resid 354 through 356 removed outlier: 6.422A pdb=" N LEU D 363 " --> pdb=" O ALA D 381 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N ILE D 383 " --> pdb=" O LEU D 363 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N VAL D 365 " --> pdb=" O ILE D 383 " (cutoff:3.500A) removed outlier: 8.150A pdb=" N HIS D 385 " --> pdb=" O VAL D 365 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N GLN D 300 " --> pdb=" O SER D 380 " (cutoff:3.500A) removed outlier: 8.040A pdb=" N SER D 267 " --> pdb=" O GLN D 300 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N ILE D 302 " --> pdb=" O SER D 267 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N ALA D 269 " --> pdb=" O ILE D 302 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N TYR D 304 " --> pdb=" O ALA D 269 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N VAL D 271 " --> pdb=" O TYR D 304 " (cutoff:3.500A) 669 hydrogen bonds defined for protein. 1890 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: 5.89 Time building geometry restraints manager: 4.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5197 1.34 - 1.45: 2407 1.45 - 1.57: 8831 1.57 - 1.69: 0 1.69 - 1.81: 110 Bond restraints: 16545 Sorted by residual: bond pdb=" CB THR A 407 " pdb=" CG2 THR A 407 " ideal model delta sigma weight residual 1.521 1.467 0.054 3.30e-02 9.18e+02 2.66e+00 bond pdb=" CB THR D 407 " pdb=" CG2 THR D 407 " ideal model delta sigma weight residual 1.521 1.468 0.053 3.30e-02 9.18e+02 2.60e+00 bond pdb=" CB THR C 407 " pdb=" CG2 THR C 407 " ideal model delta sigma weight residual 1.521 1.468 0.053 3.30e-02 9.18e+02 2.59e+00 bond pdb=" CB GLU C 28 " pdb=" CG GLU C 28 " ideal model delta sigma weight residual 1.520 1.568 -0.048 3.00e-02 1.11e+03 2.54e+00 bond pdb=" CB THR B 407 " pdb=" CG2 THR B 407 " ideal model delta sigma weight residual 1.521 1.469 0.052 3.30e-02 9.18e+02 2.51e+00 ... (remaining 16540 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.23: 22063 2.23 - 4.47: 345 4.47 - 6.70: 33 6.70 - 8.93: 12 8.93 - 11.17: 9 Bond angle restraints: 22462 Sorted by residual: angle pdb=" CA LYS B 351 " pdb=" CB LYS B 351 " pdb=" CG LYS B 351 " ideal model delta sigma weight residual 114.10 125.27 -11.17 2.00e+00 2.50e-01 3.12e+01 angle pdb=" CA LYS A 351 " pdb=" CB LYS A 351 " pdb=" CG LYS A 351 " ideal model delta sigma weight residual 114.10 125.26 -11.16 2.00e+00 2.50e-01 3.11e+01 angle pdb=" CA LYS C 351 " pdb=" CB LYS C 351 " pdb=" CG LYS C 351 " ideal model delta sigma weight residual 114.10 125.24 -11.14 2.00e+00 2.50e-01 3.10e+01 angle pdb=" CA LYS D 351 " pdb=" CB LYS D 351 " pdb=" CG LYS D 351 " ideal model delta sigma weight residual 114.10 125.21 -11.11 2.00e+00 2.50e-01 3.09e+01 angle pdb=" N GLY D 431 " pdb=" CA GLY D 431 " pdb=" C GLY D 431 " ideal model delta sigma weight residual 115.80 107.39 8.41 1.74e+00 3.30e-01 2.34e+01 ... (remaining 22457 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.82: 8560 17.82 - 35.64: 1011 35.64 - 53.46: 267 53.46 - 71.28: 66 71.28 - 89.10: 40 Dihedral angle restraints: 9944 sinusoidal: 3970 harmonic: 5974 Sorted by residual: dihedral pdb=" CA ALA C 378 " pdb=" C ALA C 378 " pdb=" N ARG C 379 " pdb=" CA ARG C 379 " ideal model delta harmonic sigma weight residual 180.00 157.25 22.75 0 5.00e+00 4.00e-02 2.07e+01 dihedral pdb=" CA ALA B 378 " pdb=" C ALA B 378 " pdb=" N ARG B 379 " pdb=" CA ARG B 379 " ideal model delta harmonic sigma weight residual 180.00 157.25 22.75 0 5.00e+00 4.00e-02 2.07e+01 dihedral pdb=" CA ALA D 378 " pdb=" C ALA D 378 " pdb=" N ARG D 379 " pdb=" CA ARG D 379 " ideal model delta harmonic sigma weight residual 180.00 157.30 22.70 0 5.00e+00 4.00e-02 2.06e+01 ... (remaining 9941 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 1482 0.038 - 0.076: 700 0.076 - 0.114: 254 0.114 - 0.152: 68 0.152 - 0.190: 10 Chirality restraints: 2514 Sorted by residual: chirality pdb=" CA THR B 407 " pdb=" N THR B 407 " pdb=" C THR B 407 " pdb=" CB THR B 407 " both_signs ideal model delta sigma weight residual False 2.53 2.34 0.19 2.00e-01 2.50e+01 9.04e-01 chirality pdb=" CA THR D 407 " pdb=" N THR D 407 " pdb=" C THR D 407 " pdb=" CB THR D 407 " both_signs ideal model delta sigma weight residual False 2.53 2.34 0.19 2.00e-01 2.50e+01 9.01e-01 chirality pdb=" CA THR A 407 " pdb=" N THR A 407 " pdb=" C THR A 407 " pdb=" CB THR A 407 " both_signs ideal model delta sigma weight residual False 2.53 2.34 0.19 2.00e-01 2.50e+01 8.83e-01 ... (remaining 2511 not shown) Planarity restraints: 2873 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP E 299 " 0.038 5.00e-02 4.00e+02 5.72e-02 5.24e+00 pdb=" N PRO E 300 " -0.099 5.00e-02 4.00e+02 pdb=" CA PRO E 300 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO E 300 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CG GLU A 28 " 0.009 2.00e-02 2.50e+03 1.85e-02 3.42e+00 pdb=" CD GLU A 28 " -0.032 2.00e-02 2.50e+03 pdb=" OE1 GLU A 28 " 0.012 2.00e-02 2.50e+03 pdb=" OE2 GLU A 28 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU B 28 " -0.009 2.00e-02 2.50e+03 1.84e-02 3.38e+00 pdb=" CD GLU B 28 " 0.032 2.00e-02 2.50e+03 pdb=" OE1 GLU B 28 " -0.012 2.00e-02 2.50e+03 pdb=" OE2 GLU B 28 " -0.011 2.00e-02 2.50e+03 ... (remaining 2870 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 189 2.58 - 3.16: 13325 3.16 - 3.74: 26027 3.74 - 4.32: 38918 4.32 - 4.90: 62508 Nonbonded interactions: 140967 Sorted by model distance: nonbonded pdb=" O PRO E 300 " pdb=" OG SER C 341 " model vdw 2.003 3.040 nonbonded pdb=" O TRP D 409 " pdb=" OG SER D 412 " model vdw 2.030 3.040 nonbonded pdb=" O TRP A 409 " pdb=" OG SER A 412 " model vdw 2.030 3.040 nonbonded pdb=" O TRP B 409 " pdb=" OG SER B 412 " model vdw 2.030 3.040 nonbonded pdb=" O TRP C 409 " pdb=" OG SER C 412 " model vdw 2.030 3.040 ... (remaining 140962 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.580 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: 0.690 Check model and map are aligned: 0.120 Set scattering table: 0.160 Process input model: 38.130 Find NCS groups from input model: 0.500 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6467 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 0.054 16545 Z= 0.244 Angle : 0.717 11.169 22462 Z= 0.405 Chirality : 0.050 0.190 2514 Planarity : 0.004 0.057 2873 Dihedral : 17.666 89.098 6084 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.11 % Favored : 92.89 % Rotamer: Outliers : 7.75 % Allowed : 12.96 % Favored : 79.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.40 (0.17), residues: 2012 helix: -0.71 (0.15), residues: 814 sheet: -1.87 (0.27), residues: 296 loop : -2.30 (0.19), residues: 902 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 292 HIS 0.003 0.001 HIS C 220 PHE 0.013 0.002 PHE B 372 TYR 0.021 0.001 TYR E 86 ARG 0.003 0.000 ARG D 437 Details of bonding type rmsd hydrogen bonds : bond 0.13152 ( 669) hydrogen bonds : angle 6.17289 ( 1890) covalent geometry : bond 0.00565 (16545) covalent geometry : angle 0.71704 (22462) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 596 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 456 time to evaluate : 1.690 Fit side-chains revert: symmetry clash REVERT: E 85 LYS cc_start: 0.5792 (OUTLIER) cc_final: 0.5437 (mmtt) REVERT: E 299 ASP cc_start: 0.7491 (t70) cc_final: 0.7206 (t0) REVERT: A 310 ASP cc_start: 0.7136 (m-30) cc_final: 0.6553 (p0) REVERT: A 351 LYS cc_start: 0.8109 (OUTLIER) cc_final: 0.7781 (mtmm) REVERT: A 388 ASP cc_start: 0.7017 (OUTLIER) cc_final: 0.6559 (t0) REVERT: D 351 LYS cc_start: 0.6578 (OUTLIER) cc_final: 0.6308 (mmpt) REVERT: D 361 SER cc_start: 0.5197 (OUTLIER) cc_final: 0.4990 (m) outliers start: 140 outliers final: 14 residues processed: 561 average time/residue: 1.1925 time to fit residues: 760.0034 Evaluate side-chains 259 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 240 time to evaluate : 2.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 85 LYS Chi-restraints excluded: chain A residue 162 ASN Chi-restraints excluded: chain A residue 351 LYS Chi-restraints excluded: chain A residue 361 SER Chi-restraints excluded: chain A residue 388 ASP Chi-restraints excluded: chain A residue 390 SER Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 456 SER Chi-restraints excluded: chain B residue 221 ASN Chi-restraints excluded: chain B residue 405 THR Chi-restraints excluded: chain C residue 28 GLU Chi-restraints excluded: chain C residue 372 PHE Chi-restraints excluded: chain D residue 101 SER Chi-restraints excluded: chain D residue 118 SER Chi-restraints excluded: chain D residue 333 THR Chi-restraints excluded: chain D residue 351 LYS Chi-restraints excluded: chain D residue 361 SER Chi-restraints excluded: chain D residue 380 SER Chi-restraints excluded: chain D residue 452 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 168 optimal weight: 1.9990 chunk 150 optimal weight: 0.0170 chunk 83 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 101 optimal weight: 0.9980 chunk 80 optimal weight: 1.9990 chunk 155 optimal weight: 0.6980 chunk 60 optimal weight: 3.9990 chunk 94 optimal weight: 5.9990 chunk 116 optimal weight: 0.9980 chunk 180 optimal weight: 7.9990 overall best weight: 0.7418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 64 GLN A 67 GLN A 134 HIS A 252 HIS A 434 ASN B 48 GLN B 67 GLN B 319 GLN C 29 HIS C 67 GLN C 162 ASN C 332 GLN C 360 GLN C 385 HIS D 67 GLN D 83 ASN D 228 GLN D 252 HIS D 385 HIS D 402 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.124387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.105873 restraints weight = 23797.540| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 1.61 r_work: 0.3213 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3108 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.5130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 16545 Z= 0.161 Angle : 0.635 8.126 22462 Z= 0.338 Chirality : 0.049 0.214 2514 Planarity : 0.005 0.037 2873 Dihedral : 6.574 115.869 2225 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 4.98 % Allowed : 21.04 % Favored : 73.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.11 (0.18), residues: 2012 helix: 0.68 (0.17), residues: 810 sheet: -1.42 (0.26), residues: 354 loop : -1.80 (0.21), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 218 HIS 0.006 0.001 HIS E 40 PHE 0.013 0.002 PHE C 313 TYR 0.019 0.001 TYR A 382 ARG 0.005 0.001 ARG B 96 Details of bonding type rmsd hydrogen bonds : bond 0.03884 ( 669) hydrogen bonds : angle 4.75821 ( 1890) covalent geometry : bond 0.00362 (16545) covalent geometry : angle 0.63513 (22462) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 278 time to evaluate : 2.141 Fit side-chains revert: symmetry clash REVERT: E 299 ASP cc_start: 0.7648 (t70) cc_final: 0.7374 (t0) REVERT: A 310 ASP cc_start: 0.7643 (m-30) cc_final: 0.7149 (p0) REVERT: A 345 LYS cc_start: 0.7720 (mmpt) cc_final: 0.7279 (pptt) REVERT: C 339 SER cc_start: 0.8125 (t) cc_final: 0.7923 (t) REVERT: D 196 LEU cc_start: 0.9209 (OUTLIER) cc_final: 0.8813 (tp) REVERT: D 250 THR cc_start: 0.8627 (OUTLIER) cc_final: 0.8360 (m) REVERT: D 308 ASN cc_start: 0.7610 (p0) cc_final: 0.7343 (p0) REVERT: D 397 GLU cc_start: 0.7376 (mt-10) cc_final: 0.7126 (mm-30) outliers start: 90 outliers final: 24 residues processed: 338 average time/residue: 1.1693 time to fit residues: 451.6801 Evaluate side-chains 208 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 182 time to evaluate : 1.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 322 THR Chi-restraints excluded: chain E residue 357 ASN Chi-restraints excluded: chain A residue 118 SER Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 186 SER Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 456 SER Chi-restraints excluded: chain B residue 118 SER Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 137 ASP Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 259 ILE Chi-restraints excluded: chain B residue 405 THR Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 405 THR Chi-restraints excluded: chain C residue 438 VAL Chi-restraints excluded: chain C residue 456 SER Chi-restraints excluded: chain C residue 470 VAL Chi-restraints excluded: chain D residue 165 LEU Chi-restraints excluded: chain D residue 196 LEU Chi-restraints excluded: chain D residue 250 THR Chi-restraints excluded: chain D residue 452 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 65 optimal weight: 4.9990 chunk 122 optimal weight: 4.9990 chunk 156 optimal weight: 3.9990 chunk 169 optimal weight: 0.9990 chunk 163 optimal weight: 0.8980 chunk 43 optimal weight: 0.9980 chunk 136 optimal weight: 2.9990 chunk 114 optimal weight: 3.9990 chunk 88 optimal weight: 0.9990 chunk 171 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 GLN A 360 GLN A 434 ASN A 442 HIS B 385 HIS C 29 HIS C 319 GLN C 332 GLN C 374 ASN C 385 HIS D 67 GLN D 319 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.116657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.097364 restraints weight = 23899.358| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 1.58 r_work: 0.3081 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2973 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8681 moved from start: 0.7387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16545 Z= 0.148 Angle : 0.573 9.687 22462 Z= 0.305 Chirality : 0.047 0.203 2514 Planarity : 0.004 0.047 2873 Dihedral : 4.971 47.256 2195 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.76 % Favored : 93.24 % Rotamer: Outliers : 4.04 % Allowed : 23.59 % Favored : 72.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.18), residues: 2012 helix: 1.15 (0.18), residues: 842 sheet: -1.11 (0.26), residues: 328 loop : -1.65 (0.21), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 240 HIS 0.005 0.001 HIS E 40 PHE 0.014 0.001 PHE B 483 TYR 0.018 0.001 TYR A 243 ARG 0.005 0.000 ARG B 446 Details of bonding type rmsd hydrogen bonds : bond 0.04325 ( 669) hydrogen bonds : angle 4.55832 ( 1890) covalent geometry : bond 0.00334 (16545) covalent geometry : angle 0.57316 (22462) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 219 time to evaluate : 1.736 Fit side-chains REVERT: E 299 ASP cc_start: 0.7996 (t70) cc_final: 0.7784 (t0) REVERT: A 106 LYS cc_start: 0.8743 (OUTLIER) cc_final: 0.8520 (ttpp) REVERT: A 310 ASP cc_start: 0.8173 (m-30) cc_final: 0.7501 (p0) REVERT: A 319 GLN cc_start: 0.8835 (OUTLIER) cc_final: 0.7377 (mp10) REVERT: A 480 GLU cc_start: 0.7297 (OUTLIER) cc_final: 0.7074 (mt-10) REVERT: B 30 GLU cc_start: 0.8027 (OUTLIER) cc_final: 0.7552 (mp0) REVERT: B 62 ASN cc_start: 0.8403 (m-40) cc_final: 0.8171 (m-40) REVERT: B 224 ILE cc_start: 0.8204 (OUTLIER) cc_final: 0.7931 (tp) REVERT: B 259 ILE cc_start: 0.8923 (OUTLIER) cc_final: 0.8607 (mt) REVERT: C 339 SER cc_start: 0.8782 (t) cc_final: 0.8523 (t) REVERT: D 17 MET cc_start: 0.9075 (OUTLIER) cc_final: 0.8843 (ptp) REVERT: D 23 GLU cc_start: 0.7891 (OUTLIER) cc_final: 0.7631 (mt-10) REVERT: D 397 GLU cc_start: 0.8000 (mt-10) cc_final: 0.7700 (mm-30) outliers start: 73 outliers final: 19 residues processed: 274 average time/residue: 1.4264 time to fit residues: 440.6909 Evaluate side-chains 187 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 160 time to evaluate : 1.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 LYS Chi-restraints excluded: chain A residue 118 SER Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 186 SER Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 308 ASN Chi-restraints excluded: chain A residue 319 GLN Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 456 SER Chi-restraints excluded: chain A residue 480 GLU Chi-restraints excluded: chain B residue 30 GLU Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 224 ILE Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 259 ILE Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain C residue 405 THR Chi-restraints excluded: chain C residue 470 VAL Chi-restraints excluded: chain D residue 17 MET Chi-restraints excluded: chain D residue 23 GLU Chi-restraints excluded: chain D residue 38 SER Chi-restraints excluded: chain D residue 165 LEU Chi-restraints excluded: chain D residue 177 THR Chi-restraints excluded: chain D residue 452 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 128 optimal weight: 5.9990 chunk 48 optimal weight: 8.9990 chunk 109 optimal weight: 4.9990 chunk 166 optimal weight: 4.9990 chunk 33 optimal weight: 5.9990 chunk 96 optimal weight: 0.9990 chunk 141 optimal weight: 0.4980 chunk 42 optimal weight: 6.9990 chunk 173 optimal weight: 0.5980 chunk 108 optimal weight: 2.9990 chunk 160 optimal weight: 2.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 402 GLN C 29 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.111470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.091920 restraints weight = 23926.892| |-----------------------------------------------------------------------------| r_work (start): 0.3078 rms_B_bonded: 1.60 r_work: 0.2991 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2882 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8849 moved from start: 0.8779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 16545 Z= 0.163 Angle : 0.576 8.479 22462 Z= 0.308 Chirality : 0.048 0.185 2514 Planarity : 0.004 0.058 2873 Dihedral : 5.022 47.128 2194 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.21 % Favored : 92.79 % Rotamer: Outliers : 3.82 % Allowed : 23.92 % Favored : 72.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.19), residues: 2012 helix: 1.29 (0.18), residues: 834 sheet: -1.20 (0.26), residues: 354 loop : -1.56 (0.21), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 218 HIS 0.006 0.001 HIS C 286 PHE 0.015 0.001 PHE C 334 TYR 0.018 0.001 TYR D 243 ARG 0.003 0.000 ARG D 86 Details of bonding type rmsd hydrogen bonds : bond 0.04395 ( 669) hydrogen bonds : angle 4.54762 ( 1890) covalent geometry : bond 0.00386 (16545) covalent geometry : angle 0.57557 (22462) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 192 time to evaluate : 1.735 Fit side-chains REVERT: E 53 ASN cc_start: 0.7486 (OUTLIER) cc_final: 0.7094 (t0) REVERT: E 70 ILE cc_start: 0.6545 (OUTLIER) cc_final: 0.6149 (pp) REVERT: E 71 SER cc_start: 0.5774 (OUTLIER) cc_final: 0.5070 (p) REVERT: E 299 ASP cc_start: 0.8222 (t70) cc_final: 0.8016 (t0) REVERT: A 213 MET cc_start: 0.9154 (mmp) cc_final: 0.8951 (mmt) REVERT: A 290 PHE cc_start: 0.8579 (OUTLIER) cc_final: 0.8201 (t80) REVERT: A 308 ASN cc_start: 0.8093 (OUTLIER) cc_final: 0.7137 (m-40) REVERT: A 310 ASP cc_start: 0.8398 (m-30) cc_final: 0.7633 (p0) REVERT: A 319 GLN cc_start: 0.8961 (OUTLIER) cc_final: 0.7574 (mp10) REVERT: A 345 LYS cc_start: 0.7973 (mmpt) cc_final: 0.7469 (pptt) REVERT: B 30 GLU cc_start: 0.7939 (OUTLIER) cc_final: 0.7550 (mp0) REVERT: B 127 GLU cc_start: 0.8880 (tt0) cc_final: 0.8438 (tt0) REVERT: B 224 ILE cc_start: 0.8309 (OUTLIER) cc_final: 0.8107 (tp) REVERT: B 334 PHE cc_start: 0.8059 (t80) cc_final: 0.7835 (t80) REVERT: B 346 GLU cc_start: 0.7912 (tt0) cc_final: 0.7680 (tt0) REVERT: C 127 GLU cc_start: 0.8869 (tp30) cc_final: 0.8560 (tt0) REVERT: C 162 ASN cc_start: 0.8397 (m-40) cc_final: 0.8176 (m110) REVERT: D 23 GLU cc_start: 0.8134 (OUTLIER) cc_final: 0.7887 (mt-10) REVERT: D 50 ASP cc_start: 0.8662 (m-30) cc_final: 0.8424 (m-30) REVERT: D 397 GLU cc_start: 0.8232 (mt-10) cc_final: 0.7901 (mp0) outliers start: 69 outliers final: 25 residues processed: 246 average time/residue: 0.9899 time to fit residues: 276.7970 Evaluate side-chains 188 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 154 time to evaluate : 1.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 53 ASN Chi-restraints excluded: chain E residue 70 ILE Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 322 THR Chi-restraints excluded: chain E residue 323 SER Chi-restraints excluded: chain A residue 118 SER Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 290 PHE Chi-restraints excluded: chain A residue 308 ASN Chi-restraints excluded: chain A residue 319 GLN Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 445 MET Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain B residue 30 GLU Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 224 ILE Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 290 PHE Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain B residue 380 SER Chi-restraints excluded: chain C residue 30 GLU Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 290 PHE Chi-restraints excluded: chain C residue 390 SER Chi-restraints excluded: chain C residue 405 THR Chi-restraints excluded: chain C residue 438 VAL Chi-restraints excluded: chain C residue 470 VAL Chi-restraints excluded: chain D residue 23 GLU Chi-restraints excluded: chain D residue 38 SER Chi-restraints excluded: chain D residue 165 LEU Chi-restraints excluded: chain D residue 239 SER Chi-restraints excluded: chain D residue 452 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 76 optimal weight: 0.8980 chunk 79 optimal weight: 2.9990 chunk 2 optimal weight: 9.9990 chunk 91 optimal weight: 2.9990 chunk 92 optimal weight: 3.9990 chunk 83 optimal weight: 3.9990 chunk 175 optimal weight: 6.9990 chunk 177 optimal weight: 5.9990 chunk 154 optimal weight: 6.9990 chunk 127 optimal weight: 5.9990 chunk 137 optimal weight: 1.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 273 ASN C 29 HIS C 308 ASN D 64 ASN D 67 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.106856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.087634 restraints weight = 24516.847| |-----------------------------------------------------------------------------| r_work (start): 0.3012 rms_B_bonded: 1.58 r_work: 0.2924 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.2815 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.2815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8920 moved from start: 0.9371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 16545 Z= 0.225 Angle : 0.628 9.754 22462 Z= 0.334 Chirality : 0.050 0.187 2514 Planarity : 0.004 0.053 2873 Dihedral : 5.278 46.934 2193 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.41 % Favored : 92.59 % Rotamer: Outliers : 4.32 % Allowed : 23.81 % Favored : 71.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.19), residues: 2012 helix: 1.20 (0.17), residues: 834 sheet: -1.35 (0.25), residues: 374 loop : -1.49 (0.22), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 409 HIS 0.005 0.001 HIS C 157 PHE 0.021 0.002 PHE A 334 TYR 0.015 0.002 TYR A 323 ARG 0.004 0.001 ARG D 446 Details of bonding type rmsd hydrogen bonds : bond 0.05082 ( 669) hydrogen bonds : angle 4.65713 ( 1890) covalent geometry : bond 0.00542 (16545) covalent geometry : angle 0.62759 (22462) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 172 time to evaluate : 2.036 Fit side-chains REVERT: E 58 LYS cc_start: 0.7647 (tttt) cc_final: 0.7242 (tmmm) REVERT: E 70 ILE cc_start: 0.6874 (OUTLIER) cc_final: 0.6584 (pp) REVERT: E 71 SER cc_start: 0.6002 (OUTLIER) cc_final: 0.5235 (p) REVERT: A 290 PHE cc_start: 0.8726 (OUTLIER) cc_final: 0.8513 (t80) REVERT: A 308 ASN cc_start: 0.8074 (OUTLIER) cc_final: 0.7292 (m-40) REVERT: A 309 ILE cc_start: 0.8707 (OUTLIER) cc_final: 0.7952 (tp) REVERT: A 310 ASP cc_start: 0.8516 (m-30) cc_final: 0.7749 (p0) REVERT: A 319 GLN cc_start: 0.9047 (OUTLIER) cc_final: 0.7648 (mp10) REVERT: A 345 LYS cc_start: 0.8023 (mmpt) cc_final: 0.7523 (pptt) REVERT: A 359 ASN cc_start: 0.8619 (m110) cc_final: 0.8414 (m-40) REVERT: B 30 GLU cc_start: 0.8007 (OUTLIER) cc_final: 0.7632 (mp0) REVERT: B 127 GLU cc_start: 0.8896 (tt0) cc_final: 0.8470 (tt0) REVERT: B 291 TYR cc_start: 0.8764 (m-80) cc_final: 0.8544 (m-80) REVERT: B 334 PHE cc_start: 0.8088 (t80) cc_final: 0.7878 (t80) REVERT: B 397 GLU cc_start: 0.7497 (OUTLIER) cc_final: 0.6919 (mp0) REVERT: B 458 GLU cc_start: 0.8937 (OUTLIER) cc_final: 0.8337 (mt-10) REVERT: C 127 GLU cc_start: 0.8985 (tp30) cc_final: 0.8639 (tt0) REVERT: C 258 ASP cc_start: 0.8006 (t0) cc_final: 0.7748 (t0) REVERT: D 23 GLU cc_start: 0.8170 (OUTLIER) cc_final: 0.7876 (mt-10) REVERT: D 397 GLU cc_start: 0.8349 (mt-10) cc_final: 0.8116 (mp0) outliers start: 78 outliers final: 33 residues processed: 234 average time/residue: 0.9946 time to fit residues: 266.5465 Evaluate side-chains 194 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 151 time to evaluate : 1.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 46 SER Chi-restraints excluded: chain E residue 70 ILE Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 322 THR Chi-restraints excluded: chain E residue 323 SER Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 290 PHE Chi-restraints excluded: chain A residue 308 ASN Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 319 GLN Chi-restraints excluded: chain A residue 374 ASN Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 445 MET Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain B residue 30 GLU Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 187 SER Chi-restraints excluded: chain B residue 210 SER Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 290 PHE Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain B residue 364 LEU Chi-restraints excluded: chain B residue 380 SER Chi-restraints excluded: chain B residue 388 ASP Chi-restraints excluded: chain B residue 397 GLU Chi-restraints excluded: chain B residue 405 THR Chi-restraints excluded: chain B residue 458 GLU Chi-restraints excluded: chain C residue 30 GLU Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 290 PHE Chi-restraints excluded: chain C residue 372 PHE Chi-restraints excluded: chain C residue 390 SER Chi-restraints excluded: chain C residue 438 VAL Chi-restraints excluded: chain C residue 470 VAL Chi-restraints excluded: chain D residue 23 GLU Chi-restraints excluded: chain D residue 38 SER Chi-restraints excluded: chain D residue 165 LEU Chi-restraints excluded: chain D residue 177 THR Chi-restraints excluded: chain D residue 369 LEU Chi-restraints excluded: chain D residue 405 THR Chi-restraints excluded: chain D residue 452 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 63.4122 > 50: distance: 152 - 154: 8.788 distance: 154 - 155: 13.331 distance: 155 - 156: 4.529 distance: 155 - 158: 16.095 distance: 156 - 157: 13.808 distance: 156 - 159: 6.814 distance: 159 - 160: 8.264 distance: 160 - 161: 7.427 distance: 160 - 163: 20.557 distance: 161 - 162: 7.092 distance: 161 - 169: 9.194 distance: 163 - 164: 16.745 distance: 164 - 165: 24.876 distance: 164 - 166: 29.554 distance: 165 - 167: 21.588 distance: 166 - 168: 13.417 distance: 167 - 168: 23.140 distance: 169 - 170: 5.643 distance: 170 - 171: 11.965 distance: 170 - 173: 15.712 distance: 171 - 172: 37.256 distance: 171 - 177: 18.476 distance: 173 - 174: 14.679 distance: 174 - 175: 12.088 distance: 174 - 176: 10.740 distance: 177 - 178: 14.452 distance: 178 - 179: 18.315 distance: 179 - 180: 31.531 distance: 179 - 181: 31.473 distance: 181 - 182: 16.543 distance: 182 - 183: 19.172 distance: 182 - 185: 8.753 distance: 183 - 184: 16.128 distance: 183 - 189: 32.502 distance: 185 - 186: 9.962 distance: 186 - 187: 3.540 distance: 187 - 188: 18.151 distance: 189 - 190: 16.781 distance: 190 - 191: 24.580 distance: 190 - 193: 10.507 distance: 191 - 192: 9.212 distance: 191 - 200: 19.516 distance: 192 - 215: 18.211 distance: 193 - 194: 19.672 distance: 194 - 195: 40.374 distance: 195 - 196: 18.745 distance: 196 - 197: 6.808 distance: 197 - 198: 22.283 distance: 197 - 199: 16.240 distance: 200 - 201: 4.965 distance: 200 - 206: 19.038 distance: 201 - 202: 19.152 distance: 201 - 204: 20.627 distance: 202 - 203: 16.417 distance: 203 - 224: 13.859 distance: 204 - 205: 15.785 distance: 205 - 206: 11.551 distance: 207 - 208: 7.936 distance: 208 - 209: 5.690 distance: 208 - 211: 13.906 distance: 209 - 210: 8.760 distance: 209 - 215: 13.113 distance: 211 - 212: 7.529 distance: 212 - 213: 13.365 distance: 212 - 214: 13.319 distance: 215 - 216: 14.406 distance: 216 - 217: 18.404 distance: 216 - 219: 11.826 distance: 217 - 218: 11.788 distance: 219 - 220: 4.262 distance: 220 - 221: 9.182 distance: 221 - 222: 10.991 distance: 221 - 223: 6.316 distance: 224 - 225: 8.215 distance: 225 - 226: 15.406 distance: 225 - 228: 13.812 distance: 226 - 227: 9.249 distance: 226 - 235: 16.120 distance: 228 - 229: 3.805 distance: 229 - 230: 21.151 distance: 230 - 231: 5.135 distance: 231 - 232: 11.518 distance: 232 - 233: 13.339 distance: 232 - 234: 13.620