Starting phenix.real_space_refine on Wed Mar 4 20:17:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xc6_33113/03_2026/7xc6_33113.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xc6_33113/03_2026/7xc6_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 { model { file = "/net/cci-nas-00/data/ceres_data/7xc6_33113/03_2026/7xc6_33113.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xc6_33113/03_2026/7xc6_33113.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7xc6_33113/03_2026/7xc6_33113.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xc6_33113/03_2026/7xc6_33113.map" } resolution = 2.79 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= 0.004 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: 2.93, per 1000 atoms: 0.18 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: 1.37 Conformation dependent library (CDL) restraints added in 651.8 milliseconds 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: 0.57 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: 2.83 Time building geometry restraints manager: 1.85 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: 3.560 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: 0.320 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 14.310 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.230 ------------------------------------------------------------------------------- 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 : 7.04 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 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: -2.40 (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 ARG 0.003 0.000 ARG D 437 TYR 0.021 0.001 TYR E 86 PHE 0.013 0.002 PHE B 372 TRP 0.010 0.001 TRP E 292 HIS 0.003 0.001 HIS C 220 Details of bonding type rmsd covalent geometry : bond 0.00565 (16545) covalent geometry : angle 0.71704 (22462) hydrogen bonds : bond 0.13152 ( 669) hydrogen bonds : angle 6.17289 ( 1890) *********************** 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 : 0.596 Fit side-chains revert: symmetry clash 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: 0.7137 (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: 0.4992 (m) outliers start: 140 outliers final: 14 residues processed: 561 average time/residue: 0.4678 time to fit residues: 297.7405 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 : 0.583 ------------------------------------------------------------------------------- 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 98 optimal weight: 0.9990 chunk 194 optimal weight: 3.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 7.9990 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 0.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- 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 77 GLN A 134 HIS A 252 HIS A 360 GLN A 434 ASN B 67 GLN B 179 ASN C 29 HIS C 67 GLN C 162 ASN C 360 GLN C 385 HIS D 83 ASN D 228 GLN D 252 HIS D 385 HIS D 402 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.122523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.103820 restraints weight = 24029.767| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 1.60 r_work: 0.3185 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3080 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 moved from start: 0.7143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 16545 Z= 0.200 Angle : 0.690 10.609 22462 Z= 0.368 Chirality : 0.050 0.199 2514 Planarity : 0.005 0.046 2873 Dihedral : 6.952 130.259 2225 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.01 % Favored : 92.99 % Rotamer: Outliers : 5.48 % Allowed : 20.71 % Favored : 73.81 % 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: -1.29 (0.18), residues: 2012 helix: 0.51 (0.17), residues: 802 sheet: -1.45 (0.25), residues: 338 loop : -1.89 (0.20), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 446 TYR 0.014 0.002 TYR D 323 PHE 0.017 0.002 PHE D 290 TRP 0.017 0.002 TRP B 218 HIS 0.006 0.001 HIS D 385 Details of bonding type rmsd covalent geometry : bond 0.00449 (16545) covalent geometry : angle 0.68974 (22462) hydrogen bonds : bond 0.04500 ( 669) hydrogen bonds : angle 4.95985 ( 1890) *********************** 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 360 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 261 time to evaluate : 0.657 Fit side-chains REVERT: E 299 ASP cc_start: 0.7951 (t70) cc_final: 0.7739 (t0) REVERT: E 330 THR cc_start: 0.7465 (OUTLIER) cc_final: 0.7254 (p) REVERT: A 64 ASN cc_start: 0.8568 (OUTLIER) cc_final: 0.8029 (m110) REVERT: A 290 PHE cc_start: 0.8232 (OUTLIER) cc_final: 0.7763 (t80) REVERT: A 310 ASP cc_start: 0.7966 (m-30) cc_final: 0.7415 (p0) REVERT: A 333 THR cc_start: 0.6849 (OUTLIER) cc_final: 0.6548 (t) REVERT: A 345 LYS cc_start: 0.7836 (mmpt) cc_final: 0.7443 (pptt) REVERT: A 480 GLU cc_start: 0.7185 (OUTLIER) cc_final: 0.6849 (mt-10) REVERT: B 30 GLU cc_start: 0.7994 (OUTLIER) cc_final: 0.7434 (mp0) REVERT: B 62 ASN cc_start: 0.8213 (m-40) cc_final: 0.7998 (m110) REVERT: B 127 GLU cc_start: 0.8568 (tt0) cc_final: 0.8338 (tt0) REVERT: B 224 ILE cc_start: 0.8192 (mm) cc_final: 0.7919 (tp) REVERT: C 125 ILE cc_start: 0.8716 (mt) cc_final: 0.8345 (mt) REVERT: C 339 SER cc_start: 0.8777 (t) cc_final: 0.8508 (t) REVERT: C 358 ASP cc_start: 0.8515 (m-30) cc_final: 0.8156 (m-30) REVERT: D 23 GLU cc_start: 0.8109 (OUTLIER) cc_final: 0.7793 (mt-10) REVERT: D 196 LEU cc_start: 0.9287 (OUTLIER) cc_final: 0.8938 (tp) REVERT: D 250 THR cc_start: 0.9060 (OUTLIER) cc_final: 0.8783 (m) REVERT: D 292 ASP cc_start: 0.8750 (m-30) cc_final: 0.8451 (m-30) REVERT: D 397 GLU cc_start: 0.7942 (mt-10) cc_final: 0.7644 (mm-30) outliers start: 99 outliers final: 29 residues processed: 331 average time/residue: 0.5269 time to fit residues: 196.4161 Evaluate side-chains 194 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 156 time to evaluate : 0.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 322 THR Chi-restraints excluded: chain E residue 330 THR Chi-restraints excluded: chain E residue 357 ASN Chi-restraints excluded: chain A residue 64 ASN Chi-restraints excluded: chain A residue 106 LYS Chi-restraints excluded: chain A residue 118 SER Chi-restraints excluded: chain A residue 127 GLU Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 186 SER Chi-restraints excluded: chain A residue 210 SER Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 277 ILE 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 326 ILE Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 451 LEU 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 29 HIS Chi-restraints excluded: chain B residue 30 GLU Chi-restraints excluded: chain B residue 118 SER 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 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 D residue 23 GLU 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 157 optimal weight: 0.8980 chunk 127 optimal weight: 6.9990 chunk 28 optimal weight: 1.9990 chunk 143 optimal weight: 0.0670 chunk 119 optimal weight: 5.9990 chunk 71 optimal weight: 8.9990 chunk 188 optimal weight: 0.8980 chunk 160 optimal weight: 3.9990 chunk 137 optimal weight: 0.9980 chunk 166 optimal weight: 4.9990 chunk 83 optimal weight: 4.9990 overall best weight: 0.9720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 293 GLN A 434 ASN B 48 GLN B 179 ASN B 385 HIS C 29 HIS C 157 HIS C 374 ASN D 48 GLN D 67 GLN D 229 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.115121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.095646 restraints weight = 24309.944| |-----------------------------------------------------------------------------| r_work (start): 0.3141 rms_B_bonded: 1.61 r_work: 0.3057 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2949 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8749 moved from start: 0.7854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 16545 Z= 0.131 Angle : 0.538 7.647 22462 Z= 0.288 Chirality : 0.046 0.177 2514 Planarity : 0.004 0.046 2873 Dihedral : 4.945 44.771 2195 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.56 % Favored : 93.44 % Rotamer: Outliers : 4.26 % Allowed : 23.09 % Favored : 72.65 % 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: -0.74 (0.18), residues: 2012 helix: 0.95 (0.17), residues: 858 sheet: -1.23 (0.26), residues: 334 loop : -1.70 (0.21), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 379 TYR 0.012 0.001 TYR D 323 PHE 0.017 0.001 PHE C 334 TRP 0.009 0.001 TRP D 409 HIS 0.006 0.001 HIS E 40 Details of bonding type rmsd covalent geometry : bond 0.00302 (16545) covalent geometry : angle 0.53807 (22462) hydrogen bonds : bond 0.04104 ( 669) hydrogen bonds : angle 4.53241 ( 1890) *********************** 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 270 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 193 time to evaluate : 0.561 Fit side-chains REVERT: E 299 ASP cc_start: 0.8093 (t70) cc_final: 0.7874 (t0) REVERT: A 310 ASP cc_start: 0.8273 (m-30) cc_final: 0.7561 (p0) REVERT: A 319 GLN cc_start: 0.8865 (OUTLIER) cc_final: 0.7484 (mp10) REVERT: A 324 MET cc_start: 0.8489 (ttp) cc_final: 0.8187 (ttm) REVERT: A 345 LYS cc_start: 0.7991 (mmpt) cc_final: 0.7462 (pptt) REVERT: B 124 ASP cc_start: 0.8501 (m-30) cc_final: 0.8216 (m-30) REVERT: B 127 GLU cc_start: 0.8701 (tt0) cc_final: 0.8447 (tt0) REVERT: B 224 ILE cc_start: 0.8205 (mm) cc_final: 0.7952 (tp) REVERT: B 397 GLU cc_start: 0.7485 (OUTLIER) cc_final: 0.7034 (mp0) REVERT: C 339 SER cc_start: 0.8923 (t) cc_final: 0.8668 (t) REVERT: D 23 GLU cc_start: 0.7966 (OUTLIER) cc_final: 0.7763 (mt-10) REVERT: D 397 GLU cc_start: 0.8066 (mt-10) cc_final: 0.7742 (mm-30) outliers start: 77 outliers final: 19 residues processed: 252 average time/residue: 0.4771 time to fit residues: 136.2879 Evaluate side-chains 174 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 152 time to evaluate : 0.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ASN 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 326 ILE Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain B residue 397 GLU Chi-restraints excluded: chain B residue 405 THR Chi-restraints excluded: chain C residue 405 THR 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 39 optimal weight: 0.8980 chunk 99 optimal weight: 0.5980 chunk 93 optimal weight: 7.9990 chunk 195 optimal weight: 0.8980 chunk 79 optimal weight: 4.9990 chunk 72 optimal weight: 8.9990 chunk 197 optimal weight: 0.8980 chunk 156 optimal weight: 5.9990 chunk 174 optimal weight: 0.1980 chunk 193 optimal weight: 0.5980 chunk 90 optimal weight: 0.0970 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 385 HIS C 29 HIS C 162 ASN C 308 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.117741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.098634 restraints weight = 23953.299| |-----------------------------------------------------------------------------| r_work (start): 0.3187 rms_B_bonded: 1.60 r_work: 0.3104 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.2997 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8725 moved from start: 0.8214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 16545 Z= 0.101 Angle : 0.493 6.081 22462 Z= 0.265 Chirality : 0.045 0.133 2514 Planarity : 0.004 0.042 2873 Dihedral : 4.538 36.001 2194 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 2.71 % Allowed : 24.75 % Favored : 72.54 % 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: -0.34 (0.19), residues: 2012 helix: 1.40 (0.18), residues: 858 sheet: -1.10 (0.26), residues: 352 loop : -1.61 (0.22), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 96 TYR 0.020 0.001 TYR D 243 PHE 0.014 0.001 PHE C 334 TRP 0.008 0.001 TRP B 218 HIS 0.007 0.001 HIS E 40 Details of bonding type rmsd covalent geometry : bond 0.00224 (16545) covalent geometry : angle 0.49318 (22462) hydrogen bonds : bond 0.03404 ( 669) hydrogen bonds : angle 4.30374 ( 1890) *********************** 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 233 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 184 time to evaluate : 0.502 Fit side-chains REVERT: E 70 ILE cc_start: 0.6554 (OUTLIER) cc_final: 0.6196 (pp) REVERT: E 307 GLU cc_start: 0.7219 (OUTLIER) cc_final: 0.6942 (pt0) REVERT: A 310 ASP cc_start: 0.8214 (m-30) cc_final: 0.7540 (OUTLIER) REVERT: A 319 GLN cc_start: 0.8834 (OUTLIER) cc_final: 0.7483 (mp10) REVERT: A 345 LYS cc_start: 0.7955 (mmpt) cc_final: 0.7449 (pptt) REVERT: B 124 ASP cc_start: 0.8408 (m-30) cc_final: 0.8144 (m-30) REVERT: B 127 GLU cc_start: 0.8711 (tt0) cc_final: 0.8485 (tt0) REVERT: B 224 ILE cc_start: 0.8192 (mm) cc_final: 0.7966 (tp) REVERT: B 334 PHE cc_start: 0.8094 (t80) cc_final: 0.7869 (t80) REVERT: C 124 ASP cc_start: 0.8524 (m-30) cc_final: 0.8318 (m-30) REVERT: C 125 ILE cc_start: 0.8534 (mt) cc_final: 0.8160 (mt) REVERT: C 339 SER cc_start: 0.8904 (t) cc_final: 0.8639 (t) REVERT: D 397 GLU cc_start: 0.8085 (mt-10) cc_final: 0.7787 (mm-30) outliers start: 49 outliers final: 24 residues processed: 220 average time/residue: 0.4807 time to fit residues: 120.9144 Evaluate side-chains 186 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 160 time to evaluate : 0.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 70 ILE Chi-restraints excluded: chain E residue 307 GLU Chi-restraints excluded: chain A residue 17 MET Chi-restraints excluded: chain A residue 64 ASN 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 326 ILE Chi-restraints excluded: chain A residue 407 THR Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain B residue 30 GLU Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 354 VAL 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 459 ARG Chi-restraints excluded: chain C residue 470 VAL 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 20 optimal weight: 0.2980 chunk 191 optimal weight: 2.9990 chunk 182 optimal weight: 7.9990 chunk 150 optimal weight: 2.9990 chunk 6 optimal weight: 3.9990 chunk 173 optimal weight: 7.9990 chunk 25 optimal weight: 6.9990 chunk 145 optimal weight: 2.9990 chunk 126 optimal weight: 0.0020 chunk 171 optimal weight: 0.9980 chunk 12 optimal weight: 10.0000 overall best weight: 1.4592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 442 HIS C 29 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.110236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.090805 restraints weight = 24086.656| |-----------------------------------------------------------------------------| r_work (start): 0.3061 rms_B_bonded: 1.59 r_work: 0.2973 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2866 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.2866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8869 moved from start: 0.9019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 16545 Z= 0.153 Angle : 0.556 7.554 22462 Z= 0.298 Chirality : 0.047 0.155 2514 Planarity : 0.004 0.039 2873 Dihedral : 4.888 43.786 2193 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.76 % Favored : 93.24 % Rotamer: Outliers : 3.43 % Allowed : 24.03 % Favored : 72.54 % 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: -0.38 (0.19), residues: 2012 helix: 1.34 (0.18), residues: 858 sheet: -1.12 (0.26), residues: 352 loop : -1.59 (0.22), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 86 TYR 0.011 0.001 TYR D 323 PHE 0.013 0.001 PHE C 334 TRP 0.008 0.001 TRP D 240 HIS 0.005 0.001 HIS E 40 Details of bonding type rmsd covalent geometry : bond 0.00358 (16545) covalent geometry : angle 0.55587 (22462) hydrogen bonds : bond 0.04497 ( 669) hydrogen bonds : angle 4.48813 ( 1890) *********************** 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 233 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 171 time to evaluate : 0.549 Fit side-chains REVERT: E 58 LYS cc_start: 0.7594 (tttt) cc_final: 0.7179 (tmmm) REVERT: E 70 ILE cc_start: 0.6793 (OUTLIER) cc_final: 0.6492 (pp) REVERT: A 309 ILE cc_start: 0.8735 (OUTLIER) cc_final: 0.7999 (tp) REVERT: A 310 ASP cc_start: 0.8416 (m-30) cc_final: 0.7674 (p0) REVERT: A 319 GLN cc_start: 0.8976 (OUTLIER) cc_final: 0.7606 (mp10) REVERT: A 345 LYS cc_start: 0.8022 (mmpt) cc_final: 0.7577 (pptt) REVERT: B 124 ASP cc_start: 0.8496 (m-30) cc_final: 0.8189 (m-30) REVERT: B 458 GLU cc_start: 0.8849 (OUTLIER) cc_final: 0.8073 (mt-10) REVERT: C 162 ASN cc_start: 0.8550 (m-40) cc_final: 0.8269 (m110) REVERT: C 258 ASP cc_start: 0.7953 (t0) cc_final: 0.7738 (t0) REVERT: C 359 ASN cc_start: 0.9029 (m110) cc_final: 0.8812 (m110) REVERT: D 397 GLU cc_start: 0.8265 (mt-10) cc_final: 0.8007 (mp0) outliers start: 62 outliers final: 26 residues processed: 217 average time/residue: 0.5036 time to fit residues: 124.3226 Evaluate side-chains 178 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 148 time to evaluate : 0.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 70 ILE Chi-restraints excluded: chain E residue 322 THR 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 309 ILE Chi-restraints excluded: chain A residue 319 GLN Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 438 VAL 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 255 VAL Chi-restraints excluded: chain B residue 290 PHE Chi-restraints excluded: chain B residue 354 VAL 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 273 ASN 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 38 SER Chi-restraints excluded: chain D residue 58 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 196 optimal weight: 0.8980 chunk 50 optimal weight: 3.9990 chunk 11 optimal weight: 3.9990 chunk 115 optimal weight: 1.9990 chunk 26 optimal weight: 7.9990 chunk 12 optimal weight: 6.9990 chunk 18 optimal weight: 0.8980 chunk 38 optimal weight: 0.9990 chunk 57 optimal weight: 7.9990 chunk 73 optimal weight: 5.9990 chunk 63 optimal weight: 3.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 162 ASN C 29 HIS ** C 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 308 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.108946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.089709 restraints weight = 24315.960| |-----------------------------------------------------------------------------| r_work (start): 0.3046 rms_B_bonded: 1.59 r_work: 0.2960 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2853 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8885 moved from start: 0.9324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 16545 Z= 0.165 Angle : 0.556 7.978 22462 Z= 0.297 Chirality : 0.047 0.158 2514 Planarity : 0.004 0.038 2873 Dihedral : 4.894 42.060 2193 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.56 % Favored : 93.44 % Rotamer: Outliers : 3.32 % Allowed : 23.92 % Favored : 72.76 % 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: -0.38 (0.19), residues: 2012 helix: 1.33 (0.18), residues: 858 sheet: -1.23 (0.25), residues: 373 loop : -1.53 (0.22), residues: 781 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 86 TYR 0.021 0.001 TYR D 243 PHE 0.023 0.001 PHE A 334 TRP 0.009 0.001 TRP D 409 HIS 0.005 0.001 HIS E 40 Details of bonding type rmsd covalent geometry : bond 0.00396 (16545) covalent geometry : angle 0.55570 (22462) hydrogen bonds : bond 0.04325 ( 669) hydrogen bonds : angle 4.44089 ( 1890) *********************** REFINEMENT MACRO_CYCLE 6 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 229 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 169 time to evaluate : 0.663 Fit side-chains REVERT: E 58 LYS cc_start: 0.7716 (tttt) cc_final: 0.7305 (tmmm) REVERT: E 70 ILE cc_start: 0.6781 (OUTLIER) cc_final: 0.6579 (pp) REVERT: E 323 SER cc_start: 0.6212 (OUTLIER) cc_final: 0.5925 (p) REVERT: E 332 ASP cc_start: 0.6186 (m-30) cc_final: 0.5753 (p0) REVERT: A 290 PHE cc_start: 0.8647 (OUTLIER) cc_final: 0.8286 (t80) REVERT: A 310 ASP cc_start: 0.8435 (m-30) cc_final: 0.7716 (p0) REVERT: A 345 LYS cc_start: 0.8053 (mmpt) cc_final: 0.7618 (pptt) REVERT: B 124 ASP cc_start: 0.8527 (m-30) cc_final: 0.8225 (m-30) REVERT: B 458 GLU cc_start: 0.8886 (OUTLIER) cc_final: 0.8118 (mt-10) REVERT: C 162 ASN cc_start: 0.8548 (m-40) cc_final: 0.8245 (m110) REVERT: C 258 ASP cc_start: 0.7952 (t0) cc_final: 0.7685 (t0) REVERT: C 359 ASN cc_start: 0.9052 (m110) cc_final: 0.8846 (m110) REVERT: D 346 GLU cc_start: 0.7939 (mt-10) cc_final: 0.7553 (tp30) REVERT: D 397 GLU cc_start: 0.8325 (mt-10) cc_final: 0.8091 (mp0) outliers start: 60 outliers final: 30 residues processed: 217 average time/residue: 0.4522 time to fit residues: 112.8693 Evaluate side-chains 191 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 157 time to evaluate : 0.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 33 ASP Chi-restraints excluded: chain E residue 70 ILE 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 326 ILE Chi-restraints excluded: chain A residue 374 ASN Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 438 VAL 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 137 ASP Chi-restraints excluded: chain B residue 187 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 405 THR Chi-restraints excluded: chain B residue 458 GLU Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 165 LEU 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 405 THR Chi-restraints excluded: chain C residue 438 VAL Chi-restraints excluded: chain C residue 470 VAL 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 63 optimal weight: 0.9990 chunk 49 optimal weight: 2.9990 chunk 52 optimal weight: 0.3980 chunk 71 optimal weight: 0.7980 chunk 145 optimal weight: 0.8980 chunk 106 optimal weight: 10.0000 chunk 111 optimal weight: 3.9990 chunk 83 optimal weight: 2.9990 chunk 115 optimal weight: 0.9980 chunk 130 optimal weight: 1.9990 chunk 116 optimal weight: 2.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 162 ASN C 29 HIS ** C 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.111659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.092648 restraints weight = 24058.413| |-----------------------------------------------------------------------------| r_work (start): 0.3090 rms_B_bonded: 1.59 r_work: 0.3005 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2898 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8847 moved from start: 0.9415 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= 0.116 Angle : 0.519 9.197 22462 Z= 0.278 Chirality : 0.046 0.261 2514 Planarity : 0.004 0.038 2873 Dihedral : 4.627 37.510 2193 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 1.88 % Allowed : 25.42 % Favored : 72.70 % 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: -0.07 (0.19), residues: 2012 helix: 1.66 (0.18), residues: 834 sheet: -1.21 (0.26), residues: 368 loop : -1.28 (0.22), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 96 TYR 0.007 0.001 TYR C 31 PHE 0.013 0.001 PHE C 334 TRP 0.008 0.001 TRP D 409 HIS 0.006 0.001 HIS E 40 Details of bonding type rmsd covalent geometry : bond 0.00266 (16545) covalent geometry : angle 0.51934 (22462) hydrogen bonds : bond 0.03754 ( 669) hydrogen bonds : angle 4.29539 ( 1890) *********************** REFINEMENT MACRO_CYCLE 7 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 196 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 162 time to evaluate : 0.471 Fit side-chains REVERT: E 58 LYS cc_start: 0.7803 (tttt) cc_final: 0.7373 (tmmm) REVERT: E 350 ILE cc_start: 0.8218 (mp) cc_final: 0.7989 (tt) REVERT: A 310 ASP cc_start: 0.8410 (m-30) cc_final: 0.7678 (p0) REVERT: A 345 LYS cc_start: 0.8018 (mmpt) cc_final: 0.7618 (pptt) REVERT: B 124 ASP cc_start: 0.8471 (m-30) cc_final: 0.8169 (m-30) REVERT: C 127 GLU cc_start: 0.8843 (tp30) cc_final: 0.8529 (tt0) REVERT: C 162 ASN cc_start: 0.8503 (m-40) cc_final: 0.8209 (m110) REVERT: C 165 LEU cc_start: 0.8569 (OUTLIER) cc_final: 0.8357 (tp) REVERT: C 258 ASP cc_start: 0.7852 (t0) cc_final: 0.7649 (t0) REVERT: C 359 ASN cc_start: 0.9055 (m110) cc_final: 0.8820 (m110) REVERT: D 346 GLU cc_start: 0.7871 (mt-10) cc_final: 0.7570 (tp30) outliers start: 34 outliers final: 20 residues processed: 186 average time/residue: 0.4633 time to fit residues: 98.3847 Evaluate side-chains 169 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 148 time to evaluate : 0.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 322 THR 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 326 ILE Chi-restraints excluded: chain A residue 374 ASN Chi-restraints excluded: chain A residue 452 VAL 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 C residue 85 SER Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 290 PHE Chi-restraints excluded: chain C residue 372 PHE 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 17 optimal weight: 3.9990 chunk 98 optimal weight: 0.9990 chunk 46 optimal weight: 2.9990 chunk 38 optimal weight: 4.9990 chunk 170 optimal weight: 0.9990 chunk 145 optimal weight: 0.7980 chunk 166 optimal weight: 2.9990 chunk 161 optimal weight: 2.9990 chunk 154 optimal weight: 7.9990 chunk 184 optimal weight: 5.9990 chunk 11 optimal weight: 3.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 162 ASN A 474 GLN ** C 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 308 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.108407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.089279 restraints weight = 24090.977| |-----------------------------------------------------------------------------| r_work (start): 0.3036 rms_B_bonded: 1.58 r_work: 0.2951 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.2843 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8893 moved from start: 0.9504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 16545 Z= 0.166 Angle : 0.563 10.390 22462 Z= 0.299 Chirality : 0.048 0.227 2514 Planarity : 0.004 0.038 2873 Dihedral : 4.881 42.125 2193 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.66 % Favored : 93.34 % Rotamer: Outliers : 2.10 % Allowed : 25.47 % Favored : 72.43 % 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: -0.18 (0.19), residues: 2012 helix: 1.49 (0.18), residues: 842 sheet: -1.20 (0.26), residues: 364 loop : -1.30 (0.22), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 86 TYR 0.010 0.001 TYR D 323 PHE 0.026 0.001 PHE A 334 TRP 0.008 0.001 TRP D 409 HIS 0.004 0.001 HIS E 40 Details of bonding type rmsd covalent geometry : bond 0.00396 (16545) covalent geometry : angle 0.56290 (22462) hydrogen bonds : bond 0.04421 ( 669) hydrogen bonds : angle 4.40995 ( 1890) *********************** REFINEMENT MACRO_CYCLE 8 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 192 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 154 time to evaluate : 0.589 Fit side-chains REVERT: E 58 LYS cc_start: 0.7840 (tttt) cc_final: 0.7376 (tmmm) REVERT: E 323 SER cc_start: 0.6146 (OUTLIER) cc_final: 0.5890 (p) REVERT: E 350 ILE cc_start: 0.8169 (mp) cc_final: 0.7938 (tt) REVERT: A 310 ASP cc_start: 0.8416 (m-30) cc_final: 0.7662 (p0) REVERT: A 345 LYS cc_start: 0.7967 (mmpt) cc_final: 0.7566 (pptt) REVERT: A 432 MET cc_start: 0.8223 (OUTLIER) cc_final: 0.6862 (mmm) REVERT: B 124 ASP cc_start: 0.8527 (m-30) cc_final: 0.8225 (m-30) REVERT: C 162 ASN cc_start: 0.8533 (m-40) cc_final: 0.8253 (m110) REVERT: C 258 ASP cc_start: 0.7920 (t0) cc_final: 0.7681 (t0) REVERT: C 359 ASN cc_start: 0.9088 (m110) cc_final: 0.8846 (m110) REVERT: D 346 GLU cc_start: 0.7941 (mt-10) cc_final: 0.7624 (tp30) outliers start: 38 outliers final: 27 residues processed: 181 average time/residue: 0.4359 time to fit residues: 90.2963 Evaluate side-chains 170 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 141 time to evaluate : 0.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 326 ILE Chi-restraints excluded: chain A residue 374 ASN Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 432 MET Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 137 ASP Chi-restraints excluded: chain B residue 187 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 405 THR Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 290 PHE Chi-restraints excluded: chain C residue 372 PHE 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 38 SER Chi-restraints excluded: chain D residue 165 LEU Chi-restraints excluded: chain D residue 239 SER Chi-restraints excluded: chain D residue 369 LEU Chi-restraints excluded: chain D residue 452 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 133 optimal weight: 3.9990 chunk 1 optimal weight: 9.9990 chunk 82 optimal weight: 9.9990 chunk 13 optimal weight: 7.9990 chunk 21 optimal weight: 0.8980 chunk 55 optimal weight: 1.9990 chunk 171 optimal weight: 1.9990 chunk 151 optimal weight: 2.9990 chunk 100 optimal weight: 0.8980 chunk 56 optimal weight: 1.9990 chunk 166 optimal weight: 0.9980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 162 ASN ** C 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.109665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.090676 restraints weight = 24145.327| |-----------------------------------------------------------------------------| r_work (start): 0.3062 rms_B_bonded: 1.58 r_work: 0.2976 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.2868 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8876 moved from start: 0.9571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 16545 Z= 0.142 Angle : 0.542 9.944 22462 Z= 0.289 Chirality : 0.047 0.206 2514 Planarity : 0.004 0.038 2873 Dihedral : 4.768 39.307 2193 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 1.94 % Allowed : 25.69 % 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 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: -0.10 (0.19), residues: 2012 helix: 1.59 (0.18), residues: 834 sheet: -1.21 (0.26), residues: 364 loop : -1.25 (0.22), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 86 TYR 0.008 0.001 TYR D 323 PHE 0.013 0.001 PHE C 334 TRP 0.009 0.001 TRP D 409 HIS 0.006 0.001 HIS E 40 Details of bonding type rmsd covalent geometry : bond 0.00336 (16545) covalent geometry : angle 0.54233 (22462) hydrogen bonds : bond 0.04048 ( 669) hydrogen bonds : angle 4.32957 ( 1890) *********************** REFINEMENT MACRO_CYCLE 9 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 188 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 153 time to evaluate : 0.668 Fit side-chains REVERT: E 58 LYS cc_start: 0.7894 (tttt) cc_final: 0.7415 (tmmm) REVERT: E 323 SER cc_start: 0.6221 (OUTLIER) cc_final: 0.5969 (p) REVERT: E 350 ILE cc_start: 0.8025 (mp) cc_final: 0.7821 (tt) REVERT: A 310 ASP cc_start: 0.8415 (m-30) cc_final: 0.7641 (p0) REVERT: A 345 LYS cc_start: 0.7926 (mmpt) cc_final: 0.7533 (pptt) REVERT: A 432 MET cc_start: 0.8100 (OUTLIER) cc_final: 0.6602 (mmm) REVERT: B 124 ASP cc_start: 0.8475 (m-30) cc_final: 0.8213 (m-30) REVERT: B 351 LYS cc_start: 0.8711 (mmtp) cc_final: 0.8351 (mmmt) REVERT: C 162 ASN cc_start: 0.8539 (m-40) cc_final: 0.8277 (m110) REVERT: C 258 ASP cc_start: 0.7886 (t0) cc_final: 0.7661 (t0) REVERT: C 359 ASN cc_start: 0.9064 (m110) cc_final: 0.8818 (m110) REVERT: D 28 GLU cc_start: 0.8404 (mm-30) cc_final: 0.8192 (mp0) REVERT: D 346 GLU cc_start: 0.7926 (mt-10) cc_final: 0.7625 (tp30) outliers start: 35 outliers final: 27 residues processed: 178 average time/residue: 0.4632 time to fit residues: 94.1410 Evaluate side-chains 181 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 152 time to evaluate : 0.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 326 ILE Chi-restraints excluded: chain A residue 374 ASN Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 432 MET Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 137 ASP Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 290 PHE Chi-restraints excluded: chain B residue 341 SER Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain B residue 405 THR 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 405 THR Chi-restraints excluded: chain C residue 438 VAL Chi-restraints excluded: chain C residue 470 VAL 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 369 LEU Chi-restraints excluded: chain D residue 452 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 155 optimal weight: 4.9990 chunk 128 optimal weight: 3.9990 chunk 0 optimal weight: 20.0000 chunk 73 optimal weight: 0.1980 chunk 74 optimal weight: 0.8980 chunk 178 optimal weight: 0.9980 chunk 51 optimal weight: 0.9980 chunk 8 optimal weight: 10.0000 chunk 100 optimal weight: 3.9990 chunk 195 optimal weight: 3.9990 chunk 110 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 162 ASN ** C 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 308 ASN C 374 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.112064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.093241 restraints weight = 24155.731| |-----------------------------------------------------------------------------| r_work (start): 0.3108 rms_B_bonded: 1.59 r_work: 0.3024 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2917 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8836 moved from start: 0.9632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 16545 Z= 0.111 Angle : 0.513 9.129 22462 Z= 0.274 Chirality : 0.045 0.212 2514 Planarity : 0.004 0.038 2873 Dihedral : 4.530 35.063 2193 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 1.61 % Allowed : 26.14 % 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 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: 0.05 (0.19), residues: 2012 helix: 1.71 (0.18), residues: 842 sheet: -1.19 (0.26), residues: 368 loop : -1.16 (0.23), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 96 TYR 0.007 0.001 TYR A 291 PHE 0.030 0.001 PHE A 334 TRP 0.009 0.001 TRP B 409 HIS 0.006 0.001 HIS E 40 Details of bonding type rmsd covalent geometry : bond 0.00256 (16545) covalent geometry : angle 0.51290 (22462) hydrogen bonds : bond 0.03575 ( 669) hydrogen bonds : angle 4.22672 ( 1890) ********************** REFINEMENT MACRO_CYCLE 10 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 197 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 168 time to evaluate : 0.498 Fit side-chains REVERT: E 58 LYS cc_start: 0.7862 (tttt) cc_final: 0.7312 (tmmm) REVERT: A 310 ASP cc_start: 0.8368 (m-30) cc_final: 0.7582 (p0) REVERT: A 345 LYS cc_start: 0.7938 (mmpt) cc_final: 0.7569 (pptt) REVERT: B 124 ASP cc_start: 0.8401 (m-30) cc_final: 0.8097 (m-30) REVERT: B 315 GLU cc_start: 0.8556 (mm-30) cc_final: 0.8300 (mm-30) REVERT: B 351 LYS cc_start: 0.8678 (mmtp) cc_final: 0.8336 (mmmt) REVERT: C 127 GLU cc_start: 0.8843 (tp30) cc_final: 0.8549 (tt0) REVERT: C 162 ASN cc_start: 0.8510 (m-40) cc_final: 0.8268 (m110) REVERT: C 359 ASN cc_start: 0.9060 (m110) cc_final: 0.8828 (m110) REVERT: C 432 MET cc_start: 0.7745 (mtm) cc_final: 0.7490 (mtp) REVERT: D 28 GLU cc_start: 0.8422 (mm-30) cc_final: 0.8065 (pm20) REVERT: D 346 GLU cc_start: 0.7813 (mt-10) cc_final: 0.7580 (tp30) outliers start: 29 outliers final: 22 residues processed: 186 average time/residue: 0.4588 time to fit residues: 97.7265 Evaluate side-chains 176 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 154 time to evaluate : 0.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 46 SER Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 322 THR 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 326 ILE Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain B residue 85 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 C residue 85 SER Chi-restraints excluded: chain C residue 290 PHE Chi-restraints excluded: chain C residue 403 THR 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 83 optimal weight: 4.9990 chunk 110 optimal weight: 0.8980 chunk 165 optimal weight: 0.6980 chunk 34 optimal weight: 4.9990 chunk 61 optimal weight: 1.9990 chunk 31 optimal weight: 4.9990 chunk 96 optimal weight: 5.9990 chunk 162 optimal weight: 2.9990 chunk 149 optimal weight: 3.9990 chunk 86 optimal weight: 0.7980 chunk 50 optimal weight: 5.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 162 ASN B 348 GLN ** C 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.109593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.090709 restraints weight = 24143.512| |-----------------------------------------------------------------------------| r_work (start): 0.3064 rms_B_bonded: 1.58 r_work: 0.2979 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.2871 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8875 moved from start: 0.9644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 16545 Z= 0.148 Angle : 0.549 9.696 22462 Z= 0.292 Chirality : 0.047 0.198 2514 Planarity : 0.004 0.039 2873 Dihedral : 4.705 39.173 2193 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Rotamer: Outliers : 1.50 % Allowed : 26.52 % Favored : 71.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.03 (0.19), residues: 2012 helix: 1.62 (0.18), residues: 842 sheet: -1.18 (0.26), residues: 364 loop : -1.18 (0.23), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 48 TYR 0.022 0.001 TYR D 243 PHE 0.012 0.001 PHE C 334 TRP 0.008 0.001 TRP C 218 HIS 0.006 0.001 HIS E 40 Details of bonding type rmsd covalent geometry : bond 0.00353 (16545) covalent geometry : angle 0.54918 (22462) hydrogen bonds : bond 0.04082 ( 669) hydrogen bonds : angle 4.32620 ( 1890) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5003.01 seconds wall clock time: 86 minutes 15.73 seconds (5175.73 seconds total)